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Sample records for all-atom energy function

  1. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-01

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  2. Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.

    PubMed

    Genheden, Samuel; Cabedo Martinez, Ana I; Criddle, Michael P; Essex, Jonathan W

    2014-03-01

    We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's τ of 0.65 compared with experiment. PMID:24488307

  3. Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

    SciTech Connect

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2015-12-15

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.

  4. Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

    DOE PAGES

    Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

    2015-12-15

    All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H2ase shows that these fusion complexes approach stable equilibrium conformations during the MD simulations. Investigatingmore » protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

  5. In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

    NASA Astrophysics Data System (ADS)

    Herges, T.; Wenzel, W.

    2005-01-01

    We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

  6. Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

    NASA Astrophysics Data System (ADS)

    Verma, Abhinav; Wenzel, Wolfgang

    2008-03-01

    Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500cycles corresponding to 7.4×107 energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04Å to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5Å bRMSD from native.

  7. Large-scale relativistic calculations of ionization energies and total binding energies of all atoms and positive atomic ions with nuclear charge Z = 1-110

    NASA Astrophysics Data System (ADS)

    Kramida, Alexander; Froese Fischer, Charlotte; Reader, Joseph; Indelicato, Paul

    2015-05-01

    The latest versions of advanced multiconfiguration Dirac-Fock atomic codes, MCDFGME and Grasp2K, are used to calculate ionization energies (IE) and total binding energies of all atomic systems. Comparison with experiment and other benchmark data shows an excellent accuracy achieved in these calculations for H-, He-, and Li-like ions. In particular, our results for H-like ions with Z >2, obtained with the MCDFGME code, are the most accurate available today. For multi-electron ions, we combine the accurate single-configuration MCDFGME calculations with the correlation-difference energy (difference between the multiconfiguration and single-configuration total energies) calculated with Grasp2K. This approach results in a dramatically improved agreement of calculated IEs with experiment (less than 0.7 eV on average) for all systems, excluding those involving open f-shells. The most probable ground states are found for most systems, leaving questionable only about 100 out of total 6105 considered systems.

  8. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  9. Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom.

    PubMed

    Mishra, Avdesh; Iqbal, Sumaiya; Hoque, Md Tamjidul

    2016-06-01

    The success of solving the protein folding and structure prediction problems in molecular and structural biology relies on an accurate energy function. With the rapid advancement in the computational biology and bioinformatics fields, there is a growing need of solving unknown fold and structure faster and thus an accurate energy function is indispensable. To address this need, we develop a new potential function, namely 3DIGARS3.0, which is a linearly weighted combination of 3DIGARS, mined accessible surface area (ASA) and ubiquitously computed Phi (uPhi) and Psi (uPsi) energies - optimized by a Genetic Algorithm (GA). We use a dataset of 4332 protein-structures to generate uPhi and uPsi based score libraries to be used within the core 3DIGARS method. The optimized weight of each component is obtained by applying Genetic Algorithm based optimization on three challenging decoy sets. The improved 3DIGARS3.0 outperformed state-of-the-art methods significantly based on a set of independent test datasets.

  10. A coarse-grained protein-protein potential derived from an all-atom force field.

    PubMed

    Basdevant, Nathalie; Borgis, Daniel; Ha-Duong, Tap

    2007-08-01

    In order to study protein-protein nonbonded interactions, we present the development of a new reduced protein model that represents each amino acid residue with one to three coarse grains, whose physical properties are derived in a consistent bottom-up procedure from the higher-resolution all-atom AMBER force field. The resulting potential energy function is pairwise additive and includes distinct van-der-Waals and Coulombic terms. The van-der-Waals effective interactions are deduced from preliminary molecular dynamics simulations of all possible amino acid homodimers. They are best represented by a soft 1/r6 repulsion and a Gaussian attraction, with parameters obeying Lorentz-Berthelot mixing rules. For the Coulombic interaction, coarse grain charges are optimized for each separate protein in order to best represent the all-atom electrostatic potential outside the protein core. This approach leaves the possibility of using any implicit solvent model to describe solvation effects and electrostatic screening. The coarse-grained force field is tested carefully for a small homodimeric complex, the magainin. It is shown to reproduce satisfactorily the specificity of the all-atom underlying potential, in particular within a PB/SA solvation model. The coarse-grained potential is applied to the redocking prediction of three different protein-protein complexes: the magainin dimer, the barnase-barstar, and the trypsin-BPTI complexes. It is shown to provide per se an efficient and discriminating scoring energy function for the protein-protein docking problem that remains pertinent at both the global and refinement stage. PMID:17616119

  11. A coarse-grained protein-protein potential derived from an all-atom force field.

    PubMed

    Basdevant, Nathalie; Borgis, Daniel; Ha-Duong, Tap

    2007-08-01

    In order to study protein-protein nonbonded interactions, we present the development of a new reduced protein model that represents each amino acid residue with one to three coarse grains, whose physical properties are derived in a consistent bottom-up procedure from the higher-resolution all-atom AMBER force field. The resulting potential energy function is pairwise additive and includes distinct van-der-Waals and Coulombic terms. The van-der-Waals effective interactions are deduced from preliminary molecular dynamics simulations of all possible amino acid homodimers. They are best represented by a soft 1/r6 repulsion and a Gaussian attraction, with parameters obeying Lorentz-Berthelot mixing rules. For the Coulombic interaction, coarse grain charges are optimized for each separate protein in order to best represent the all-atom electrostatic potential outside the protein core. This approach leaves the possibility of using any implicit solvent model to describe solvation effects and electrostatic screening. The coarse-grained force field is tested carefully for a small homodimeric complex, the magainin. It is shown to reproduce satisfactorily the specificity of the all-atom underlying potential, in particular within a PB/SA solvation model. The coarse-grained potential is applied to the redocking prediction of three different protein-protein complexes: the magainin dimer, the barnase-barstar, and the trypsin-BPTI complexes. It is shown to provide per se an efficient and discriminating scoring energy function for the protein-protein docking problem that remains pertinent at both the global and refinement stage.

  12. An effective all-atom potential for proteins

    PubMed Central

    Irbäck, Anders; Mitternacht, Simon; Mohanty, Sandipan

    2009-01-01

    We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed α/β protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49–67-residue systems with high statistical accuracy, using only modest computational resources by today's standards. PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc PMID:19356242

  13. Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.

    PubMed

    McCullagh, Peter; Lake, Peter T; McCullagh, Martin

    2016-09-13

    An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.

  14. Microtubule Elasticity: Connecting All-Atom Simulations with Continuum Mechanics

    NASA Astrophysics Data System (ADS)

    Sept, David; Mackintosh, Fred C.

    2010-01-01

    The mechanical properties of microtubules have been extensively studied using a wide range of biophysical techniques, seeking to understand the mechanics of these cylindrical polymers. Here we develop a method for connecting all-atom molecular dynamics simulations with continuum mechanics and show how this can be applied to understand microtubule mechanics. Our coarse-graining technique applied to the microscopic simulation system yields consistent predictions for the Young’s modulus and persistence length of microtubules, while clearly demonstrating how binding of the drug Taxol decreases the stiffness of microtubules. The techniques we develop should be widely applicable to other macromolecular systems.

  15. All-atom simulations of crowding effects on ubiquitin dynamics

    NASA Astrophysics Data System (ADS)

    Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo

    2013-08-01

    It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.

  16. An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.

    PubMed

    Sun, Yingxin; Sun, Huai

    2014-03-01

    An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858

  17. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  18. Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2001-08-01

    Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).

  19. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    NASA Astrophysics Data System (ADS)

    Kim, Seung-Yeon; Kwak, Wooseop

    2014-12-01

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z( T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z( T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T 1 and the lower transition temperature T 2 of PTH(1-34) can be interpreted as the collapse temperature T θ and the folding temperature T f , respectively.

  20. Predicting transcription factor specificity with all-atom models.

    PubMed

    Jamal Rahi, Sahand; Virnau, Peter; Mirny, Leonid A; Kardar, Mehran

    2008-11-01

    The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR Escherichia coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and noncognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and sites of homologous TFs. We also examine a set of experimental mutations in both DNA and the protein. Using our explicit estimates of energy, we show that the specificity for PurR is dominated by direct protein-DNA interactions, and weakly influenced by bending of DNA.

  1. Benchmarking all-atom simulations using hydrogen exchange

    PubMed Central

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413

  2. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

    PubMed Central

    2016-01-01

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  3. An Evolutionary Strategy for All-Atom Folding of the 60-Amino-Acid Bacterial Ribosomal Protein L20

    PubMed Central

    Schug, A.; Wenzel, W.

    2006-01-01

    We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of “native content” in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence. PMID:16565067

  4. Folding peptides and proteins with all-atom physics: methods and applications

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2008-03-01

    Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re

  5. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

  6. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

    PubMed Central

    Na, Hyuntae; Jernigan, Robert L.; Song, Guang

    2015-01-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491

  7. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    PubMed

    Na, Hyuntae; Jernigan, Robert L; Song, Guang

    2015-10-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  8. Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.

    PubMed

    Zheng, Wenwei; Best, Robert B

    2015-12-10

    Theoretical models have often modeled protein folding dynamics as diffusion on a low-dimensional free energy surface, a remarkable simplification. However, the accuracy of such an approximation and the number of dimensions required were not clear. For all-atom folding simulations of ten small proteins in explicit solvent we show that the folding dynamics can indeed be accurately described as diffusion on just a single coordinate, the fraction of native contacts (Q). The diffusion models reproduce both folding rates, and finer details such as transition-path durations and diffusive propagators. The Q-averaged diffusion coefficients decrease with chain length, as anticipated from energy landscape theory. Although the Q-diffusion model does not capture transition-path durations for the protein NuG2, we show that this can be accomplished by designing an improved coordinate Qopt. Overall, one-dimensional diffusion on a suitable coordinate turns out to be a remarkably faithful model for the dynamics of the proteins considered.

  9. Examining the origins of the hydration force between lipid bilayers using all-atom simulations.

    PubMed

    Gentilcore, Anastasia N; Michaud-Agrawal, Naveen; Crozier, Paul S; Stevens, Mark J; Woolf, Thomas B

    2010-05-01

    Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

  10. All-atom molecular dynamics simulation of a photosystem i/detergent complex.

    PubMed

    Harris, Bradley J; Cheng, Xiaolin; Frymier, Paul

    2014-10-01

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  11. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    SciTech Connect

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  12. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

  13. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    NASA Astrophysics Data System (ADS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  14. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

  15. All-atom semiclassical dynamics study of quantum coherence in photosynthetic Fenna-Matthews-Olson complex.

    PubMed

    Kim, Hyun Woo; Kelly, Aaron; Park, Jae Woo; Rhee, Young Min

    2012-07-18

    Although photosynthetic pigment-protein complexes are in noisy environments, recent experimental and theoretical results indicate that their excitation energy transfer (EET) can exhibit coherent characteristics for over hundreds of femtoseconds. Despite the almost universal observations of the coherence to some degree, questions still remain regarding the detailed role of the protein and the extent of high-temperature coherence. Here we adopt a theoretical method that incorporates an all-atom description of the photosynthetic complex within a semiclassical framework in order to study EET in the Fenna-Matthews-Olson complex. We observe that the vibrational modes of the chromophore tend to diminish the coherence at the ensemble level, yet much longer-lived coherences may be observed at the single-complex level. We also observe that coherent oscillations in the site populations also commence within tens of femtoseconds even when the system is initially prepared in a non-oscillatory stationary state. We show that the protein acts to maintain the electronic couplings among the system of embedded chromophores. We also investigate the extent to which the protein's electrostatic modulation that disperses the chromophore electronic energies may affect the coherence lifetime. Further, we observe that even though mutation-induced disruptions in the protein structure may change the coupling pattern, a relatively strong level of coupling and associated coherence in the dynamics still remain. Finally, we demonstrate that thermal fluctuations in the chromophore couplings induce some redundancy in the coherent energy-transfer pathway. Our results indicate that a description of both chromophore coupling strengths and their fluctuations is crucial to better understand coherent EET processes in photosynthetic systems. PMID:22708971

  16. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

    PubMed

    Wang, Xueyi; Kapral, Gary; Murray, Laura; Richardson, David; Richardson, Jane; Snoeyink, Jack

    2008-01-01

    Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (>or= 0.4 A overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is

  17. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  18. Folding of proteins with an all-atom Go-model.

    PubMed

    Wu, L; Zhang, J; Qin, M; Liu, F; Wang, W

    2008-06-21

    The Go-like potential at a residual level has been successfully applied to the folding of proteins in many previous works. However, taking into consideration more detailed structural information in the atomic level, the definition of contacts used in these traditional Go-models may not be suitable for all-atom simulations. Here, in this work, we develop a rational definition of contacts considering the screening effect in the crowded intramolecular environment. In such a scheme, a large amount of screened atom pairs are excluded and the number of contacts is decreased compared to the case of the traditional definition. These contacts defined by such a new definition are compatible with the all-atom representation of protein structures. To verify the rationality of the new definition of contacts, the folding of proteins CI2 and SH3 is simulated by all-atom molecular dynamics simulations. A high folding cooperativity and good correlation of the simulated Phi-values with those obtained experimentally, especially for CI2, are found. This suggests that the all-atom Go-model is improved compared to the traditional Go-model. Based on the comparison of the Phi-values, the roles of side chains in the folding are discussed, and it is concluded that the side-chain structures are more important for local contacts in determining the transition state structures. Moreover, the relations between side chain and backbone orderings are also discussed.

  19. The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.

    PubMed

    Linhananta, Apichart; Boer, Jesse; MacKay, Ian

    2005-03-15

    The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

  20. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

    PubMed Central

    2016-01-01

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran–cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1–12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide–monosaccharide and protein–glycan linkages are derived

  1. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  2. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    PubMed

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  3. Simulation of lipid bilayer self-assembly using all-atom lipid force fields.

    PubMed

    Skjevik, Åge A; Madej, Benjamin D; Dickson, Callum J; Lin, Charles; Teigen, Knut; Walker, Ross C; Gould, Ian R

    2016-04-21

    In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.

  4. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  5. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

    PubMed

    Zhang, Chi; Liu, Song; Zhou, Yaoqi

    2004-02-01

    The conformations of loops are determined by the water-mediated interactions between amino acid residues. Energy functions that describe the interactions can be derived either from physical principles (physical-based energy function) or statistical analysis of known protein structures (knowledge-based statistical potentials). It is commonly believed that statistical potentials are appropriate for coarse-grained representation of proteins but are not as accurate as physical-based potentials when atomic resolution is required. Several recent applications of physical-based energy functions to loop selections appear to support this view. In this article, we apply a recently developed DFIRE-based statistical potential to three different loop decoy sets (RAPPER, Jacobson, and Forrest-Woolf sets). Together with a rotamer library for side-chain optimization, the performance of DFIRE-based potential in the RAPPER decoy set (385 loop targets) is comparable to that of AMBER/GBSA for short loops (two to eight residues). The DFIRE is more accurate for longer loops (9 to 12 residues). Similar trend is observed when comparing DFIRE with another physical-based OPLS/SGB-NP energy function in the large Jacobson decoy set (788 loop targets). In the Forrest-Woolf decoy set for the loops of membrane proteins, the DFIRE potential performs substantially better than the combination of the CHARMM force field with several solvation models. The results suggest that a single-term DFIRE-statistical energy function can provide an accurate loop prediction at a fraction of computing cost required for more complicate physical-based energy functions. A Web server for academic users is established for loop selection at the softwares/services section of the Web site http://theory.med.buffalo.edu/.

  6. An all-atom simulation study of the ordering of liquid squalane near a solid surface

    NASA Astrophysics Data System (ADS)

    Tsige, Mesfin; Patnaik, Soumya S.

    2008-05-01

    An all-atom molecular dynamics study using the OPLS force field has been carried out to obtain new insights in to the orientation and ordering of liquid squalane near a solid surface. As observed in previous experiments, the squalane molecules closest to a SiO 2 substrate are found to be tightly bound with their molecular axis preferentially parallel to the interface. Unlike linear alkanes, the squalane molecules are also found to lie preferentially parallel to the liquid/vapor interface. The simulation results predict that the molecular plane orientation of the squalane molecules changes from mainly parallel to perpendicular to the substrate in going further away from the substrate.

  7. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    PubMed

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  8. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264

  9. An All-Atom Model of the Structure of Human Copper Transporter 1

    PubMed Central

    Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.

    2013-01-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840

  10. Phenomenological Relativistic Energy Density Functionals

    SciTech Connect

    Lalazissis, G. A.; Kartzikos, S.; Niksic, T.; Paar, N.; Vretenar, D.; Ring, P.

    2009-08-26

    The framework of relativistic nuclear energy density functionals is applied to the description of a variety of nuclear structure phenomena, not only in spherical and deformed nuclei along the valley of beta-stability, but also in exotic systems with extreme isospin values and close to the particle drip-lines. Dynamical aspects of exotic nuclear structure is explored using the fully consistent quasiparticle random-phase approximation based on the relativistic Hartree-Bogoliubov model. Recent applications of energy density functionals with explicit density dependence of the meson-nucleon couplings are presented.

  11. Reproducible In-Silico Folding of a Four Helix 60 Amino Acid Protein in a Transferable All-Atom Forcefield

    NASA Astrophysics Data System (ADS)

    Schug, Alexander

    2005-03-01

    For predicting the protein tertiary structure one approach describes the native state of a protein as the global minimum of an appropiate free-energy forcefield. We have recently developed such a all-atom protein forcefield (PFF01). As major challenge remains the search for the global minimum for which we developed efficient methods. Using these we were able to predict the structure of helical proteins from different families ranging in size from 20 to 60 amino acids starting with random configurations. For the four helix 60 amino acid protein Bacterial Ribosomal Protein L20 (pdb code: 1GYZ) we used a simple client-master model for distributed computing. Starting from a set of random structures three phases of different folding simulations refined this set to a final one with 50 configurations. During this process the amount of native-like structures increased strongly. Six out of the ten structures best in energy approached the native structure within 5 åbackbone rmsd. The conformation with the lowest energy had a backbone rmsd value of 4.6 åtherefore correctly predicting the tertiary structure of 1GYZ.ReferencesA. Schug et al, Phys. Rev. Letters, 91:158102, 2003A. Schug et al, J. Am. Chem. Soc. (in press), 2004

  12. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  13. Learning Protein Folding Energy Functions

    PubMed Central

    Guan, Wei; Ozakin, Arkadas; Gray, Alexander; Borreguero, Jose; Pandit, Shashi; Jagielska, Anna; Wroblewska, Liliana; Skolnick, Jeffrey

    2014-01-01

    A critical open problem in ab initio protein folding is protein energy function design, which pertains to defining the energy of protein conformations in a way that makes folding most efficient and reliable. In this paper, we address this issue as a weight optimization problem and utilize a machine learning approach, learning-to-rank, to solve this problem. We investigate the ranking-via-classification approach, especially the RankingSVM method and compare it with the state-of-the-art approach to the problem using the MINUIT optimization package. To maintain the physicality of the results, we impose non-negativity constraints on the weights. For this we develop two efficient non-negative support vector machine (NNSVM) methods, derived from L2-norm SVM and L1-norm SVMs, respectively. We demonstrate an energy function which maintains the correct ordering with respect to structure dissimilarity to the native state more often, is more efficient and reliable for learning on large protein sets, and is qualitatively superior to the current state-of-the-art energy function. PMID:25311546

  14. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling

    PubMed Central

    Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu; Hatcher, Elizabeth; Vanommeslaeghe, Kenno; Foster, Theresa J.; Jamison, Francis W.; MacKerell, Alexander D.

    2011-01-01

    Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model. PMID:22125473

  15. A hierarchical coarse-grained (all-atom to all residue) approach to peptides (P1, P2) binding with a graphene sheet

    NASA Astrophysics Data System (ADS)

    Pandey, Ras; Kuang, Zhifeng; Farmer, Barry; Kim, Sang; Naik, Rajesh

    2012-02-01

    Recently, Kim et al. [1] have found that peptides P1: HSSYWYAFNNKT and P2: EPLQLKM bind selectively to graphene surfaces and edges respectively which are critical in modulating both the mechanical as well as electronic transport properties of graphene. Such distinctions in binding sites (edge versus surface) observed in electron micrographs were verified by computer simulation by an all-atomic model that captures the pi-pi bonding. We propose a hierarchical approach that involves input from the all-atom Molecular Dynamics (MD) study (with atomistic detail) into a coarse-grained Monte Carlo simulation to extend this study further to a larger scale. The binding energy of a free amino acid with the graphene sheet from all-atom simulation is used in the interaction parameter for the coarse-grained approach. Peptide chain executes its stochastic motion with the Metropolis algorithm. We investigate a number of local and global physical quantities and find that peptide P1 is likely to bind more strongly to graphene sheet than P2 and that it is anchored by three residues ^4Y^5W^6Y. [1] S.N. Kim et al J. Am. Chem. Soc. 133, 14480 (2011).

  16. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-10-01

    It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments. PMID:24187527

  17. Investigating a link between all-atom model simulation and the Ising-based theory on the helix-coil transition. II. Nonstationary properties

    NASA Astrophysics Data System (ADS)

    Takano, Mitsunori; Nakamura, Hironori K.; Nagayama, Kuniaki; Suyama, Akira

    2003-06-01

    The all-atom and the Ising-based models have both played their own roles to help our understanding of helix-coil transition. In this study, we address to what degree these two theoretical models can be consistent with each other in the nonstationary regime, complementing the preceding equilibrium study. We conducted molecular dynamics simulations of an all-atom model polyalanine chain and Monte Carlo simulations of a corresponding kinetic Ising chain. Nonstationary properties of each model were characterized through power spectrum, Allan variance, and autocorrelation analyses regarding the time course of a system order parameter. A clear difference was indicated between the two models: the Ising-based model showed a Lorentzian spectrum in the frequency domain and a single exponential form in the time domain, whereas the all-atom model showed a 1/f spectrum and a stretched exponential form. The observed stretched exponential form is in agreement with a very recent T-jump experiment. The effect of viscous damping on helix-coil dynamics was also studied. A possible source of the observed difference between the two models is discussed by considering the potential energy landscape, and the idea of dynamical disorder was introduced into the original Glauber model in the hope of bridging the gap between the two models. Other possible sources, e.g., the limitations of the Ising framework and the validity of the Markovian dynamics assumption, are also discussed.

  18. Energy functions for regularization algorithms

    NASA Technical Reports Server (NTRS)

    Delingette, H.; Hebert, M.; Ikeuchi, K.

    1991-01-01

    Regularization techniques are widely used for inverse problem solving in computer vision such as surface reconstruction, edge detection, or optical flow estimation. Energy functions used for regularization algorithms measure how smooth a curve or surface is, and to render acceptable solutions these energies must verify certain properties such as invariance with Euclidean transformations or invariance with parameterization. The notion of smoothness energy is extended here to the notion of a differential stabilizer, and it is shown that to void the systematic underestimation of undercurvature for planar curve fitting, it is necessary that circles be the curves of maximum smoothness. A set of stabilizers is proposed that meet this condition as well as invariance with rotation and parameterization.

  19. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

    PubMed Central

    2015-01-01

    We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically

  20. All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

    PubMed Central

    Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto

    2016-01-01

    In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 106 Å3 cubic boxes containing ~3 × 104 water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any “artificial” hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations. PMID:26817663

  1. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore.

    PubMed

    Di Marino, Daniele; Bonome, Emma Letizia; Tramontano, Anna; Chinappi, Mauro

    2015-08-01

    Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  2. Accelerating All-Atom MD Simulations of Lipids Using a Modified Virtual-Sites Technique.

    PubMed

    Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

    2014-12-01

    We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 Å(2) without virtual sites and 67.6 ± 0.3 Å(2) with virtual sites. In conclusion the virtual-sites technique on lipid membranes is a powerful simulation tool, but it should be used with care. The procedure can be applied to other force fields and lipids in a straightforward manner.

  3. A real-time all-atom structural search engine for proteins.

    PubMed

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

    2014-07-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

  4. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  5. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

  6. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    PubMed

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  7. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations*

    PubMed Central

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-01-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  8. Effect of calcium and magnesium on phosphatidylserine membranes: experiments and all-atomic simulations.

    PubMed

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-05-01

    It is known that phosphatidylserine (PS(-)) lipids have a very similar affinity for Ca(2+) and Mg(2+) cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca(2+) or Mg(2+) induces very different aggregation behavior for PS(-) liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca(2+) or Mg(2+) cations. These puzzling results suggest that although these two cations have a similar affinity for PS(-) lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS(-) membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca(2+) and Mg(2+) cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca(2+) cations present a peak at a distance ~2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg(2+) cations has two different peaks, located a few angstroms before and after the Ca(2+) peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca(2+) and Mg(2

  9. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    NASA Astrophysics Data System (ADS)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan

    2015-04-01

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  10. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    SciTech Connect

    Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  11. MolProbity: all-atom structure validation for macromolecular crystallography

    SciTech Connect

    Chen, Vincent B.; Arendall, W. Bryan III; Headd, Jeffrey J.; Keedy, Daniel A.; Immormino, Robert M.; Kapral, Gary J.; Murray, Laura W.; Richardson, Jane S.; Richardson, David C.

    2010-01-01

    MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

  12. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

    PubMed

    Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

    2016-02-23

    The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in

  13. All-atom molecular dynamics studies of the full-length β-amyloid peptides

    NASA Astrophysics Data System (ADS)

    Luttmann, Edgar; Fels, Gregor

    2006-03-01

    β-Amyloid peptides are believed to play an essential role in Alzheimer's disease (AD), due to their sedimentation in the form of β-amyloid aggregates in the brain of AD-patients, and the in vitro neurotoxicity of oligomeric aggregates. The monomeric peptides come in different lengths of 39-43 residues, of which the 42 alloform seems to be most strongly associated with AD-symptoms. Structural information on these peptides to date comes from NMR studies in acidic solutions, organic solvents, or on shorter fragments of the peptide. In addition X-ray and solid-state NMR investigations of amyloid fibrils yield insight into the structure of the final aggregate and therefore define the endpoint of any conformational change of an Aβ-monomer along the aggregation process. The conformational changes necessary to connect the experimentally known conformations are not yet understood and this process is an active field of research. In this paper, we report results from all-atom molecular dynamics simulations based on experimental data from four different peptides of 40 amino acids and two peptides consisting of 42 amino acids. The simulations allow for the analysis of intramolecular interactions and the role of structural features. In particular, they show the appearance of β-turn in the region between amino acid 21 and 33, forming a hook-like shape as it is known to exist in the fibrillar Aβ-structures. This folding does not depend on the formation of a salt bridge between Asp-23 and Lys-28 but requires the Aβ(1-42) as such structure was not observed in the shorter system Aβ(1-40).

  14. Effect of calcium and magnesium on phosphatidylserine membranes: experiments and all-atomic simulations.

    PubMed

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-05-01

    It is known that phosphatidylserine (PS(-)) lipids have a very similar affinity for Ca(2+) and Mg(2+) cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca(2+) or Mg(2+) induces very different aggregation behavior for PS(-) liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca(2+) or Mg(2+) cations. These puzzling results suggest that although these two cations have a similar affinity for PS(-) lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS(-) membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca(2+) and Mg(2+) cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca(2+) cations present a peak at a distance ~2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg(2+) cations has two different peaks, located a few angstroms before and after the Ca(2+) peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca(2+) and Mg(2

  15. Effect of Calcium and Magnesium on Phosphatidylserine Membranes: Experiments and All-Atomic Simulations

    PubMed Central

    Martín-Molina, Alberto; Rodríguez-Beas, César; Faraudo, Jordi

    2012-01-01

    It is known that phosphatidylserine (PS−) lipids have a very similar affinity for Ca2+ and Mg2+ cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca2+ or Mg2+ induces very different aggregation behavior for PS− liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca2+ or Mg2+ cations. These puzzling results suggest that although these two cations have a similar affinity for PS− lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS− membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca2+ and Mg2+ cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca2+ cations present a peak at a distance ∼2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg2+ cations has two different peaks, located a few angstroms before and after the Ca2+ peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca2+ and Mg2+, respectively. PMID:22824273

  16. Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations

    PubMed Central

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S.; Bechinger, Burkhard; Mousseau, Normand

    2015-01-01

    Mislocalization and aggregation of the huntingtin protein are related to Huntington’s disease. Its first exon—more specifically the first 17 amino acids (Htt17)—is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin’s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties—order parameter, thickness, and area per lipid—of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions. PMID:25762330

  17. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

    PubMed

    Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

    2016-02-23

    The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in

  18. Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations.

    PubMed

    Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma

    2008-06-01

    Tryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all-atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP-RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA-binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic-scale insights into the processes. PMID:18186477

  19. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

    PubMed Central

    Qin, Feng

    2015-01-01

    The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

  20. Hierarchical atom type definitions and extensible all-atom force fields.

    PubMed

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc.

  1. The equilibrium properties and folding kinetics of an all-atom Go xAF model of the Trp-cage

    NASA Astrophysics Data System (ADS)

    Linhananta, Apichart; Boer, Jesse; MacKay, Ian

    2005-03-01

    The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go ¯ model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial α-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

  2. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    PubMed

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-24

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.

  3. Weak Energy: Form and Function

    NASA Astrophysics Data System (ADS)

    Parks, Allen D.

    The equation of motion for a time-dependent weak value of a quantum mechanical observable contains a complex valued energy factor—the weak energy of evolution. This quantity is defined by the dynamics of the pre-selected and post-selected states which specify the observable's weak value. It is shown that this energy: (i) is manifested as dynamical and geometric phases that govern the evolution of the weak value during the measurement process; (ii) satisfies the Euler-Lagrange equations when expressed in terms of Pancharatnam (P) phase and Fubini-Study (FS) metric distance; (iii) provides for a PFS stationary action principle for quantum state evolution; (iv) time translates correlation amplitudes; (v) generalizes the temporal persistence of state normalization; and (vi) obeys a time-energy uncertainty relation. A similar complex valued quantity—the pointed weak energy of an evolving quantum state—is also defined and several of its properties in PFS coordinates are discussed. It is shown that the imaginary part of the pointed weak energy governs the state's survival probability and its real part is—to within a sign—the Mukunda-Simon geometric phase for arbitrary evolutions or the Aharonov-Anandan (AA) geometric phase for cyclic evolutions. Pointed weak energy gauge transformations and the PFS 1-form are defined and discussed and the relationship between the PFS 1-form and the AA connection 1-form is established. [Editors note: for a video of the talk given by Prof. Parks at the Aharonov-80 conference in 2012 at Chapman University, see http://quantum.chapman.edu/talk-25.

  4. Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics.

    PubMed

    Ding, Wei; Palaiokostas, Michail; Wang, Wen; Orsi, Mario

    2015-12-10

    Biological bilayer membranes typically contain varying amounts of lamellar and nonlamellar lipids. Lamellar lipids, such as dioleoylphosphatidylcholine (DOPC), are defined by their tendency to form the lamellar phase, ubiquitous in biology. Nonlamellar lipids, such as dioleoylphosphatidylethanolamine (DOPE), prefer instead to form nonlamellar phases, which are mostly nonbiological. However, nonlamellar lipids mix with lamellar lipids in biomembrane structures that remain overall lamellar. Importantly, changes in the lamellar vs nonlamellar lipid composition are believed to affect membrane function and modulate membrane proteins. In this work, we employ atomistic molecular dynamics simulations to quantify how a range of bilayer properties are altered by variations in the lamellar vs nonlamellar lipid composition. Specifically, we simulate five DOPC/DOPE bilayers at mixing ratios of 1/0, 3/1, 1/1, 1/3, and 0/1. We examine properties including lipid area and bilayer thickness, as well as the transmembrane profiles of electron density, lateral pressure, electric field, and dipole potential. While the bilayer structure is only marginally altered by lipid composition changes, dramatic effects are observed for the lateral pressure, electric field, and dipole potential profiles. Possible implications for membrane function are discussed.

  5. All-atom molecular dynamics simulations of actin-myosin interactions: a comparative study of cardiac α myosin, β myosin, and fast skeletal muscle myosin.

    PubMed

    Li, Minghui; Zheng, Wenjun

    2013-11-26

    Myosins are a superfamily of actin-binding motor proteins with significant variations in kinetic properties (such as actin binding affinity) between different isoforms. It remains unknown how such kinetic variations arise from the structural and dynamic tuning of the actin-myosin interface at the amino acid residue level. To address this key issue, we have employed molecular modeling and simulations to investigate, with atomistic details, the isoform dependence of actin-myosin interactions in the rigor state. By combining electron microscopy-based docking with homology modeling, we have constructed three all-atom models for human cardiac α and β and rabbit fast skeletal muscle myosin in complex with three actin subunits in the rigor state. Starting from these models, we have performed extensive all-atom molecular dynamics (MD) simulations (total of 100 ns per system) and then used the MD trajectories to calculate actin-myosin binding free energies with contributions from both electrostatic and nonpolar forces. Our binding calculations are in good agreement with the experimental finding of isoform-dependent differences in actin binding affinity between these myosin isoforms. Such differences are traced to changes in actin-myosin electrostatic interactions (i.e., hydrogen bonds and salt bridges) that are highly dynamic and involve several flexible actin-binding loops. By partitioning the actin-myosin binding free energy to individual myosin residues, we have also identified key myosin residues involved in the actin-myosin interactions, some of which were previously validated experimentally or implicated in cardiomyopathy mutations, and the rest make promising targets for future mutational experiments. PMID:24224850

  6. Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations

    PubMed Central

    Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki

    2016-01-01

    Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA+ ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named ‘the ADP model’ and ‘the ATP model’, where ADP and ATP are bound to AAA1 in the AAA+ ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455

  7. Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.

    PubMed

    Kamiya, Narutoshi; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki

    2016-08-01

    Dyneins are large microtubule motor proteins that convert ATP energy to mechanical power. High-resolution crystal structures of ADP-bound cytoplasmic dynein have revealed the organization of the motor domain, comprising the AAA(+) ring, the linker, the stalk/strut and the C sequence. Recently, the ADP.vanadate-bound structure, which is similar to the ATP hydrolysis transition state, revealed how the structure of dynein changes upon ATP binding. Although both the ADP- and ATP-bound state structures have been resolved, the dynamic properties at the atomic level remain unclear. In this work, we built two models named 'the ADP model' and 'the ATP model', where ADP and ATP are bound to AAA1 in the AAA(+) ring, respectively, to observe the initial procedure of the structural change from the unprimed to the primed state. We performed 200-ns molecular dynamics simulations for both models and compared their structures and dynamics. The motions of the stalk, consisting of a long coiled coil with a microtubule-binding domain, significantly differed between the two models. The elastic properties of the stalk were analyzed and compared with the experimental results. PMID:27334455

  8. A robust all-atom model for LCAT generated by homology modeling.

    PubMed

    Segrest, Jere P; Jones, Martin K; Catte, Andrea; Thirumuruganandham, Saravana P

    2015-03-01

    LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15-20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508

  9. A robust all-atom model for LCAT generated by homology modeling[S

    PubMed Central

    Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.

    2015-01-01

    LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15–20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508

  10. Adiabatic corrections to density functional theory energies and wave functions.

    PubMed

    Mohallem, José R; Coura, Thiago de O; Diniz, Leonardo G; de Castro, Gustavo; Assafrão, Denise; Heine, Thomas

    2008-09-25

    The adiabatic finite-nuclear-mass-correction (FNMC) to the electronic energies and wave functions of atoms and molecules is formulated for density-functional theory and implemented in the deMon code. The approach is tested for a series of local and gradient corrected density functionals, using MP2 results and diagonal-Born-Oppenheimer corrections from the literature for comparison. In the evaluation of absolute energy corrections of nonorganic molecules the LDA PZ81 functional works surprisingly better than the others. For organic molecules the GGA BLYP functional has the best performance. FNMC with GGA functionals, mainly BLYP, show a good performance in the evaluation of relative corrections, except for nonorganic molecules containing H atoms. The PW86 functional stands out with the best evaluation of the barrier of linearity of H2O and the isotopic dipole moment of HDO. In general, DFT functionals display an accuracy superior than the common belief and because the corrections are based on a change of the electronic kinetic energy they are here ranked in a new appropriate way. The approach is applied to obtain the adiabatic correction for full atomization of alcanes C(n)H(2n+2), n = 4-10. The barrier of 1 mHartree is approached for adiabatic corrections, justifying its insertion into DFT. PMID:18537228

  11. Universal Nuclear Energy Density Functional

    SciTech Connect

    Carlson, Joseph; Furnstahl, Richard; Horoi, Mihai; Lusk, Rusty; Nazarewicz, Witold; Ng, Esmond; Thompson, Ian; Vary, James

    2012-12-01

    An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. Until recently such an undertaking was hard to imagine, and even at the present time such an ambitious endeavor would be far beyond what a single researcher or a traditional research group could carry out.

  12. All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric C.; Twarock, Reidun

    2010-03-01

    Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.

  13. Nonlocal kinetic-energy-density functionals

    SciTech Connect

    Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |

    1996-04-01

    In this paper we present nonlocal kinetic-energy functionals {ital T}[{ital n}] within the average density approximation (ADA) framework, which do not require any extra input when applied to any electron system and recover the exact kinetic energy and the linear response function of a homogeneous system. In contrast with previous ADA functionals, these present good behavior of the long-range tail of the exact weight function. The averaging procedure for the kinetic functional (averaging the Fermi momentum of the electron gas, instead of averaging the electron density) leads to a functional without numerical difficulties in the calculation of extended systems, and it gives excellent results when applied to atoms and jellium surfaces. {copyright} {ital 1996 The American Physical Society.}

  14. Cable energy function of cortical axons.

    PubMed

    Ju, Huiwen; Hines, Michael L; Yu, Yuguo

    2016-01-01

    Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na(+)-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na(+)-counting method severely underestimates energy cost in the cable model by 20-70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship.

  15. Cable energy function of cortical axons

    PubMed Central

    Ju, Huiwen; Hines, Michael L.; Yu, Yuguo

    2016-01-01

    Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na+-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na+-counting method severely underestimates energy cost in the cable model by 20–70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship. PMID:27439954

  16. Cable energy function of cortical axons.

    PubMed

    Ju, Huiwen; Hines, Michael L; Yu, Yuguo

    2016-01-01

    Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na(+)-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na(+)-counting method severely underestimates energy cost in the cable model by 20-70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship. PMID:27439954

  17. Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions.

    PubMed

    Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-05-21

    Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system.

  18. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

    PubMed Central

    Nguyen, Trang Truc; Viet, Man Hoang

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM. PMID:24672329

  19. Solar wind-magnetosphere energy input functions

    SciTech Connect

    Bargatze, L.F.; McPherron, R.L.; Baker, D.N.

    1985-01-01

    A new formula for the solar wind-magnetosphere energy input parameter, P/sub i/, is sought by applying the constraints imposed by dimensional analysis. Applying these constraints yields a general equation for P/sub i/ which is equal to rho V/sup 3/l/sub CF//sup 2/F(M/sub A/,theta) where, rho V/sup 3/ is the solar wind kinetic energy density and l/sub CF//sup 2/ is the scale size of the magnetosphere's effective energy ''collection'' region. The function F which depends on M/sub A/, the Alfven Mach number, and on theta, the interplanetary magnetic field clock angle is included in the general equation for P/sub i/ in order to model the magnetohydrodynamic processes which are responsible for solar wind-magnetosphere energy transfer. By assuming the form of the function F, it is possible to further constrain the formula for P/sub i/. This is accomplished by using solar wind data, geomagnetic activity indices, and simple statistical methods. It is found that P/sub i/ is proportional to (rho V/sup 2/)/sup 1/6/VBG(theta) where, rho V/sup 2/ is the solar wind dynamic pressure and VBG(theta) is a rectified version of the solar wind motional electric field. Furthermore, it is found that G(theta), the gating function which modulates the energy input to the magnetosphere, is well represented by a ''leaky'' rectifier function such as sin/sup 4/(theta/2). This function allows for enhanced energy input when the interplanetary magnetic field is oriented southward. This function also allows for some energy input when the interplanetary magnetic field is oriented northward. 9 refs., 4 figs.

  20. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

    PubMed Central

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID

  1. Functional materials for energy-efficient buildings

    NASA Astrophysics Data System (ADS)

    Ebert, H.-P.

    2015-08-01

    The substantial improving of the energy efficiency is essential to meet the ambitious energy goals of the EU. About 40% of the European energy consumption belongs to the building sector. Therefore the reduction of the energy demand of the existing building stock is one of the key measures to deliver a substantial contribution to reduce CO2-emissions of our society. Buildings of the future have to be efficient in respect to energy consumption for construction and operation. Current research activities are focused on the development of functional materials with outstanding thermal and optical properties to provide, for example, slim thermally superinsulated facades, highly integrated heat storage systems or adaptive building components. In this context it is important to consider buildings as entities which fulfill energy and comfort claims as well as aesthetic aspects of a sustainable architecture.

  2. Harvesting Vibrational Energy Using Material Work Functions

    PubMed Central

    Varpula, Aapo; Laakso, Sampo J.; Havia, Tahvo; Kyynäräinen, Jukka; Prunnila, Mika

    2014-01-01

    Vibration energy harvesters scavenge energy from mechanical vibrations to energise low power electronic devices. In this work, we report on vibration energy harvesting scheme based on the charging phenomenon occurring naturally between two bodies with different work functions. Such work function energy harvester (WFEH) is similar to electrostatic energy harvester with the fundamental distinction that neither external power supplies nor electrets are needed. A theoretical model and description of different operation modes of WFEHs are presented. The WFEH concept is tested with macroscopic experiments, which agree well with the model. The feasibility of miniaturizing WFEHs is shown by simulating a realistic MEMS device. The WFEH can be operated as a charge pump that pushes charge and energy into an energy storage element. We show that such an operation mode is highly desirable for applications and that it can be realised with either a charge shuttle or with switches. The WFEH is shown to give equal or better output power in comparison to traditional electrostatic harvesters. Our findings indicate that WFEH has great potential in energy harvesting applications. PMID:25348004

  3. Harvesting vibrational energy using material work functions.

    PubMed

    Varpula, Aapo; Laakso, Sampo J; Havia, Tahvo; Kyynäräinen, Jukka; Prunnila, Mika

    2014-01-01

    Vibration energy harvesters scavenge energy from mechanical vibrations to energise low power electronic devices. In this work, we report on vibration energy harvesting scheme based on the charging phenomenon occurring naturally between two bodies with different work functions. Such work function energy harvester (WFEH) is similar to electrostatic energy harvester with the fundamental distinction that neither external power supplies nor electrets are needed. A theoretical model and description of different operation modes of WFEHs are presented. The WFEH concept is tested with macroscopic experiments, which agree well with the model. The feasibility of miniaturizing WFEHs is shown by simulating a realistic MEMS device. The WFEH can be operated as a charge pump that pushes charge and energy into an energy storage element. We show that such an operation mode is highly desirable for applications and that it can be realised with either a charge shuttle or with switches. The WFEH is shown to give equal or better output power in comparison to traditional electrostatic harvesters. Our findings indicate that WFEH has great potential in energy harvesting applications. PMID:25348004

  4. Harvesting vibrational energy using material work functions.

    PubMed

    Varpula, Aapo; Laakso, Sampo J; Havia, Tahvo; Kyynäräinen, Jukka; Prunnila, Mika

    2014-10-28

    Vibration energy harvesters scavenge energy from mechanical vibrations to energise low power electronic devices. In this work, we report on vibration energy harvesting scheme based on the charging phenomenon occurring naturally between two bodies with different work functions. Such work function energy harvester (WFEH) is similar to electrostatic energy harvester with the fundamental distinction that neither external power supplies nor electrets are needed. A theoretical model and description of different operation modes of WFEHs are presented. The WFEH concept is tested with macroscopic experiments, which agree well with the model. The feasibility of miniaturizing WFEHs is shown by simulating a realistic MEMS device. The WFEH can be operated as a charge pump that pushes charge and energy into an energy storage element. We show that such an operation mode is highly desirable for applications and that it can be realised with either a charge shuttle or with switches. The WFEH is shown to give equal or better output power in comparison to traditional electrostatic harvesters. Our findings indicate that WFEH has great potential in energy harvesting applications.

  5. Harvesting Vibrational Energy Using Material Work Functions

    NASA Astrophysics Data System (ADS)

    Varpula, Aapo; Laakso, Sampo J.; Havia, Tahvo; Kyynäräinen, Jukka; Prunnila, Mika

    2014-10-01

    Vibration energy harvesters scavenge energy from mechanical vibrations to energise low power electronic devices. In this work, we report on vibration energy harvesting scheme based on the charging phenomenon occurring naturally between two bodies with different work functions. Such work function energy harvester (WFEH) is similar to electrostatic energy harvester with the fundamental distinction that neither external power supplies nor electrets are needed. A theoretical model and description of different operation modes of WFEHs are presented. The WFEH concept is tested with macroscopic experiments, which agree well with the model. The feasibility of miniaturizing WFEHs is shown by simulating a realistic MEMS device. The WFEH can be operated as a charge pump that pushes charge and energy into an energy storage element. We show that such an operation mode is highly desirable for applications and that it can be realised with either a charge shuttle or with switches. The WFEH is shown to give equal or better output power in comparison to traditional electrostatic harvesters. Our findings indicate that WFEH has great potential in energy harvesting applications.

  6. Energy landscapes and functions of supramolecular systems

    NASA Astrophysics Data System (ADS)

    Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman V.; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H.; Newcomb, Christina J.; Palmer, Liam C.; Shekhawat, Gajendra S.; de La Cruz, Monica Olvera; Schatz, George C.; Stupp, Samuel I.

    2016-04-01

    By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps--we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.

  7. Energy landscapes and function of supramolecular systems

    PubMed Central

    Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H.; Newcomb, Christina J.; Palmer, Liam C.; Shekhawat, Gajendra S.; de la Cruz, Monica Olvera; Schatz, George C.; Stupp, Samuel I.

    2015-01-01

    By means of two supramolecular systems - peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps - we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, function and energy landscape are linked, superseding the more traditional connection between molecular design and function. PMID:26779883

  8. Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

    PubMed

    Denning, Elizabeth J; Priyakumar, U Deva; Nilsson, Lennart; Mackerell, Alexander D

    2011-07-15

    Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick base pair opening which is not consistent with experiment, whereas analysis of molecular dynamics (MD) simulations show the 2'-hydroxyl moiety to almost exclusively sample the O3' orientation. Quantum mechanical (QM) studies of RNA related model compounds indicate the energy minimum associated with the O3' orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2'-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3' orientations of the 2'-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and noncanonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2'-hydroxyl moiety and support a model whereby the 2'-hydroxyl can enhance the probability of conformational transitions in RNA.

  9. Density-dependent covariant energy density functionals

    SciTech Connect

    Lalazissis, G. A.

    2012-10-20

    Relativistic nuclear energy density functionals are applied to the description of a variety of nuclear structure phenomena at and away fromstability line. Isoscalar monopole, isovector dipole and isoscalar quadrupole giant resonances are calculated using fully self-consistent relativistic quasiparticle randomphase approximation, based on the relativistic Hartree-Bogoliubovmodel. The impact of pairing correlations on the fission barriers in heavy and superheavy nuclei is examined. The role of pion in constructing desnity functionals is also investigated.

  10. SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS

    SciTech Connect

    Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J

    2010-12-20

    We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.

  11. Electron energy-distribution functions in gases

    SciTech Connect

    Pitchford, L.C.

    1981-01-01

    Numerical calculation of the electron energy distribution functions in the regime of drift tube experiments is discussed. The discussion is limited to constant applied fields and values of E/N (ratio of electric field strength to neutral density) low enough that electron growth due to ionization can be neglected. (GHT)

  12. Towards the Universal Nuclear Energy Density Functional

    SciTech Connect

    Stoitsov, Mario; More, J.; Nazarewicz, Witold; Pei, Junchen; Sarich, J.; Schunck, Nicolas F; Staszczak, A.; Wild, S.

    2009-01-01

    The UNEDF SciDAC project to develop and optimize the energy density functional for atomic nuclei using state-of-the-art computational infrastructure is briefly described. The ultimate goal is to replace current phenomenological models of the nucleus with a well-founded microscopic theory with minimal uncertainties, capable of describing nuclear data and extrapolating to unknown regions.

  13. Editorial: Functional nanomaterials for energy applications

    SciTech Connect

    Devan, Rupesh S.; Ma, Yuan -Ron; Kim, Jin -Hyeok; Bhattacharya, Raghu N.; Ghosh, Kartik C.

    2015-02-16

    In order to leap forward from the energy crisis issues and improve lifestyle, we all are looking positively toward nanomaterials or nanostructures. Thus, the exploration of new features of both typical and novel materials at the nanoscale level is playing important role in the development of innovative and improved energy technologies that have the capability of conserve/convert energy at large extend. By tailoring the surface morphology of materials in its nanoforms, the functional properties can be significantly adapted and specifically combined to produce highly potent multifunctional materials for conversion, storage, and consumption of energy in various forms. The papers selected for this special issue represent a good panel for addressing various energy applications including solar cell, fuel cells, nanofluid twisters, and gas sensors. Of course, the selected topic and the papers are not an exhaustive representation of the utilization of functional nanomaterials for energy applications. Nevertheless, they represent the rich and many-facet knowledge, which we have the pleasure of sharing with the readers.

  14. Editorial: Functional nanomaterials for energy applications

    DOE PAGES

    Devan, Rupesh S.; Ma, Yuan -Ron; Kim, Jin -Hyeok; Bhattacharya, Raghu N.; Ghosh, Kartik C.

    2015-02-16

    In order to leap forward from the energy crisis issues and improve lifestyle, we all are looking positively toward nanomaterials or nanostructures. Thus, the exploration of new features of both typical and novel materials at the nanoscale level is playing important role in the development of innovative and improved energy technologies that have the capability of conserve/convert energy at large extend. By tailoring the surface morphology of materials in its nanoforms, the functional properties can be significantly adapted and specifically combined to produce highly potent multifunctional materials for conversion, storage, and consumption of energy in various forms. The papers selectedmore » for this special issue represent a good panel for addressing various energy applications including solar cell, fuel cells, nanofluid twisters, and gas sensors. Of course, the selected topic and the papers are not an exhaustive representation of the utilization of functional nanomaterials for energy applications. Nevertheless, they represent the rich and many-facet knowledge, which we have the pleasure of sharing with the readers.« less

  15. Dynamic performance of duolayers at the air/water interface. 2. Mechanistic insights from all-atom simulations.

    PubMed

    Christofferson, Andrew J; Yiapanis, George; Leung, Andy H M; Prime, Emma L; Tran, Diana N H; Qiao, Greg G; Solomon, David H; Yarovsky, Irene

    2014-09-18

    The novel duolayer system, comprising a monolayer of ethylene glycol monooctadecyl ether (C18E1) and the water-soluble polymer poly(vinylpyrrolidone) (PVP), has been shown to resist forces such as wind stress to a greater degree than the C18E1 monolayer alone. This paper reports all-atom molecular dynamics simulations comparing the monolayer (C18E1 alone) and duolayer systems under an applied force parallel to the air/water interface. The simulations show that, due to the presence of PVP at the interface, the duolayer film exhibits an increase in chain tilt, ordering, and density, as well as a lower lateral velocity compared to the monolayer. These results provide a molecular rationale for the improved performance of the duolayer system under wind conditions, as well as an atomic-level explanation for the observed efficacy of the duolayer system as an evaporation suppressant, which may serve as a useful guide for future development for thin films where resistance to external perturbation is desirable.

  16. Nonequilibrium self-energy functional theory

    NASA Astrophysics Data System (ADS)

    Hofmann, Felix; Eckstein, Martin; Arrigoni, Enrico; Potthoff, Michael

    2013-10-01

    The self-energy functional theory (SFT) is generalized to describe the real-time dynamics of correlated lattice-fermion models far from thermal equilibrium. This is achieved by starting from a reformulation of the original equilibrium theory in terms of double-time Green's functions on the Keldysh-Matsubara contour. With the help of a generalized Luttinger-Ward functional, we construct a functional Ω̂[Σ] which is stationary at the physical (nonequilibrium) self-energy Σ and which yields the grand potential of the initial thermal state Ω at the physical point. Nonperturbative approximations can be defined by specifying a reference system that serves to generate trial self-energies. These self-energies are varied by varying the reference system's one-particle parameters on the Keldysh-Matsubara contour. In the case of thermal equilibrium, this approach reduces to the conventional SFT. Contrary to the equilibrium theory, however, “unphysical” variations, i.e., variations that are different on the upper and the lower branches of the Keldysh contour, must be considered to fix the time dependence of the optimal physical parameters via the variational principle. Functional derivatives in the nonequilibrium SFT Euler equation are carried out analytically to derive conditional equations for the variational parameters that are accessible to a numerical evaluation via a time-propagation scheme. Approximations constructed by means of the nonequilibrium SFT are shown to be inherently causal, internally consistent, and to respect macroscopic conservation laws resulting from gauge symmetries of the Hamiltonian. This comprises the nonequilibrium dynamical mean-field theory but also dynamical-impurity and variational-cluster approximations that are specified by reference systems with a finite number of degrees of freedom. In this way, nonperturbative and consistent approximations can be set up, the numerical evaluation of which is accessible to an exact

  17. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    PubMed

    Gould, Tim; Bučko, Tomáš

    2016-08-01

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (<5% errors) in ∼80% of the cases, but can break down badly (>30% errors) in a small fraction of cases. PMID:27304856

  18. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    PubMed

    Gould, Tim; Bučko, Tomáš

    2016-08-01

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (<5% errors) in ∼80% of the cases, but can break down badly (>30% errors) in a small fraction of cases.

  19. CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

    PubMed Central

    Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D.

    2010-01-01

    The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids and carbohydrates. In the present paper an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present paper in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all-CHARMM” simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. PMID:19575467

  20. Potential energy function for the hydroperoxyl radical

    SciTech Connect

    Lemon, W.J.; Hase, W.L.

    1987-03-12

    A switching function formalism is used to derive an analytic potential energy surface for the O + OH in equilibrium HO/sub 2/ in equilibrium H + O/sub 2/ reactive system. Both experimental and ab initio data are used to derive parameters for the potential energy surface. Trajectory calculations for highly excited HO/sub 2/ are performed on this surface. From these trajectories quasi-periodic eigentrajectories are found for vibrational levels near the HO/sub 2/ dissociation threshold with small amounts of quanta in the OH stretch mode and large amounts of quanta in the OO stretch mode.

  1. Functional Carbon Materials for Electrochemical Energy Storage

    NASA Astrophysics Data System (ADS)

    Zhou, Huihui

    The ability to harvest and convert solar energy has been associated with the evolution of human civilization. The increasing consumption of fossil fuels since the industrial revolution, however, has brought to concerns in ecological deterioration and depletion of the fossil fuels. Facing these challenges, humankind is forced to seek for clean, sustainable and renewable energy resources, such as biofuels, hydraulic power, wind power, geothermal energy and other kinds of alternative energies. However, most alternative energy sources, generally in the form of electrical energy, could not be made available on a continuous basis. It is, therefore, essential to store such energy into chemical energy, which are portable and various applications. In this context, electrochemical energy-storage devices hold great promises towards this goal. The most common electrochemical energy-storage devices are electrochemical capacitors (ECs, also called supercapacitors) and batteries. In comparison to batteries, ECs posses high power density, high efficiency, long cycling life and low cost. ECs commonly utilize carbon as both (symmetric) or one of the electrodes (asymmetric), of which their performance is generally limited by the capacitance of the carbon electrodes. Therefore, developing better carbon materials with high energy density has been emerging as one the most essential challenges in the field. The primary objective of this dissertation is to design and synthesize functional carbon materials with high energy density at both aqueous and organic electrolyte systems. The energy density (E) of ECs are governed by E = CV 2/2, where C is the total capacitance and V is the voltage of the devices. Carbon electrodes with high capacitance and high working voltage should lead to high energy density. In the first part of this thesis, a new class of nanoporous carbons were synthesized for symmetric supercapacitors using aqueous Li2SO4 as the electrolyte. A unique precursor was adopted to

  2. Ischemia detection using Isoelectric Energy Function.

    PubMed

    Kumar, Amit; Singh, Mandeep

    2016-01-01

    A novel method has been proposed for the detection of ischemia using an isoelectric energy function (IEEF) resulting from ST segment deviations in ECG signals. The method consists of five stages: pre-processing, delineation, measurement of isoelectric energy, a beat characterization algorithm and detection of ischemia. The isoelectric energy threshold is used to differentiate ischemic beats from normal beats for ischemic episode detection. Then, ischemic episodes are classified as transmural or subendocardial. The method is validated for recordings of the annotated European ST-T database (EDB). The results show 98.12% average sensitivity (SE) and 98.16% average specificity (SP). These results are significantly better than those of existing methods cited in the literature. The advantage of the proposed method includes simplicity, ruggedness and automatic discarding of noisy beats. PMID:26623944

  3. Ischemia detection using Isoelectric Energy Function.

    PubMed

    Kumar, Amit; Singh, Mandeep

    2016-01-01

    A novel method has been proposed for the detection of ischemia using an isoelectric energy function (IEEF) resulting from ST segment deviations in ECG signals. The method consists of five stages: pre-processing, delineation, measurement of isoelectric energy, a beat characterization algorithm and detection of ischemia. The isoelectric energy threshold is used to differentiate ischemic beats from normal beats for ischemic episode detection. Then, ischemic episodes are classified as transmural or subendocardial. The method is validated for recordings of the annotated European ST-T database (EDB). The results show 98.12% average sensitivity (SE) and 98.16% average specificity (SP). These results are significantly better than those of existing methods cited in the literature. The advantage of the proposed method includes simplicity, ruggedness and automatic discarding of noisy beats.

  4. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

    PubMed

    Bottaro, Sandro; Lindorff-Larsen, Kresten; Best, Robert B

    2013-12-10

    The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an α-helical and a β-stranded peptide. The performance of the resulting effective energy function, termed EEF1-SB, is tested with respect to the properties of folded proteins, the folding of small peptides or fast-folding proteins, and NMR data for intrinsically disordered proteins. The results show that EEF1-SB provides a reasonable description of a wide range of systems, but its key advantage over other methods tested is that it captures very well the structure and dimension of disordered or weakly structured peptides. EEF1-SB is thus a computationally inexpensive (~ 10 times faster than Generalized-Born methods) and transferable approximation for treating solvent effects. PMID:24748852

  5. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    PubMed

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  6. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    PubMed

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  7. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations

    PubMed Central

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-01-01

    In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of

  8. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  9. Procurement function at Morgantown Energy Technology Center

    SciTech Connect

    Not Available

    1991-08-21

    The Morgantown Energy Technology Center (METC), is an US Department of Energy (DOE) facility in Morgantown, West Virginia. It is responsible for conducting research and managing research contracts dealing with coal and gas technology. The purpose of the audit was to evaluate the effectiveness of METC's internal control systems for major contracts and small purchases. Improved internal controls are needed over major contracts and small purchases. Specifically, METC's contracting officer's representatives were not formally approving invoices prior to payment to document that the contracted services or materials were received. Additionally, METC's systems of internal controls for small purchases was not effective in the areas of funding authorization, acquisition planning, and invoice processing. These internal control weaknesses precluded METC from assuring that (1) its small purchase needs were fully funded and satisfied requirements most effectively and economically, and (2) its major contracts and small purchases were received and correctly paid. The audit recommends improved internal controls over these functions.

  10. Casimir energies of cylinders: Universal function

    SciTech Connect

    Abalo, E. K.; Milton, K. A.; Kaplan, L.

    2010-12-15

    New exact results are given for the interior Casimir energies of infinitely long waveguides of triangular cross section (equilateral, hemiequilateral, and isosceles right triangles). Results for cylinders of rectangular cross section are rederived. In particular, results are obtained for interior modes belonging to Dirichlet and Neumann boundary conditions (TM and TE modes). These results are expressed in rapidly convergent series using the Chowla-Selberg formula, and in fact may be given in closed form, except for general rectangles. The energies are finite because only the first three heat-kernel coefficients can be nonzero for the case of polygonal boundaries. What appears to be a universal behavior of the Casimir energy as a function of the shape of the regular or quasiregular cross-sectional figure is presented. Furthermore, numerical calculations for arbitrary right triangular cross sections suggest that the universal behavior may be extended to waveguides of general polygonal cross sections. The new exact and numerical results are compared with the proximity force approximation (PFA).

  11. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  12. Building a Universal Nuclear Energy Density Functional

    SciTech Connect

    Carlson, Joe A.; Furnstahl, Dick; Horoi, Mihai; Lust, Rusty; Nazaewicc, Witek; Ng, Esmond; Thompson, Ian; Vary, James

    2012-12-30

    During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold:  First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties;  Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data;  Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

  13. Functional Mock-up Unit Export of EnergyPlus

    SciTech Connect

    2012-08-01

    The Functional Mock-up Unit Export of EnergyPlus is a software package that allows EnergyPlus to be exported as a Functional Mock-up Unit. This allows other software tools to run EnergyPlus as part of a larger simulation. To do so, the outside software needs to implement the Functional Mock-up interface standard (http://www.modelisar.com/), and be able to import Functional Mock-up Units for co-simulation.

  14. Functional derivative of the kinetic energy functional for spherically symmetric systems.

    PubMed

    Nagy, Á

    2011-07-28

    Ensemble non-interacting kinetic energy functional is constructed for spherically symmetric systems. The differential virial theorem is derived for the ensemble. A first-order differential equation for the functional derivative of the ensemble non-interacting kinetic energy functional and the ensemble Pauli potential is presented. This equation can be solved and a special case of the solution provides the original non-interacting kinetic energy of the density functional theory.

  15. Functional derivative of the kinetic energy functional for spherically symmetric systems.

    PubMed

    Nagy, Á

    2011-07-28

    Ensemble non-interacting kinetic energy functional is constructed for spherically symmetric systems. The differential virial theorem is derived for the ensemble. A first-order differential equation for the functional derivative of the ensemble non-interacting kinetic energy functional and the ensemble Pauli potential is presented. This equation can be solved and a special case of the solution provides the original non-interacting kinetic energy of the density functional theory. PMID:21806089

  16. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  17. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  18. Density functional theory for comprehensive orbital energy calculations.

    PubMed

    Nakata, Ayako; Tsuneda, Takao

    2013-08-14

    This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.

  19. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-01

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups.

  20. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-01

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups. PMID:26593668

  1. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

    NASA Astrophysics Data System (ADS)

    Wallace, Jason A.; Shen, Jana K.

    2012-11-01

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  2. Energy Transfer and a Recurring Mathematical Function

    ERIC Educational Resources Information Center

    Atkin, Keith

    2013-01-01

    This paper extends the interesting work of a previous contributor concerning the analogies between physical phenomena such as mechanical collisions and the transfer of power in an electric circuit. Emphasis is placed on a mathematical function linking these different areas of physics. This unifying principle is seen as an exciting opportunity to…

  3. Approach to kinetic energy density functionals: Nonlocal terms with the structure of the von Weizsaecker functional

    SciTech Connect

    Garcia-Aldea, David; Alvarellos, J. E.

    2008-02-15

    We propose a kinetic energy density functional scheme with nonlocal terms based on the von Weizsaecker functional, instead of the more traditional approach where the nonlocal terms have the structure of the Thomas-Fermi functional. The proposed functionals recover the exact kinetic energy and reproduce the linear response function of homogeneous electron systems. In order to assess their quality, we have tested the total kinetic energies as well as the kinetic energy density for atoms. The results show that these nonlocal functionals give as good results as the most sophisticated functionals in the literature. The proposed scheme for constructing the functionals means a step ahead in the field of fully nonlocal kinetic energy functionals, because they are capable of giving better local behavior than the semilocal functionals, yielding at the same time accurate results for total kinetic energies. Moreover, the functionals enjoy the possibility of being evaluated as a single integral in momentum space if an adequate reference density is defined, and then quasilinear scaling for the computational cost can be achieved.

  4. Advanced Functional Materials for Energy Related Applications

    NASA Astrophysics Data System (ADS)

    Sasan, Koroush

    The current global heavy dependency on fossil fuels gives rise to two critical problems: I) fossil fuels will be depleted in the near future; II) the release of green house gas CO2 generated by the combustion of fossil fuels contributes to global warming. To potentially address both problems, this dissertation documents three primary areas of investigation related to the development of alternative energy sources: electrocatalysts for fuel cells, photocatalysts for hydrogen generation, and photoreduction catalysts for converting CO2 to CH4. Fuel cells could be a promising source of alternative energy. Decreasing the cost and improving the durability and power density of Pt/C as a catalyst for reducing oxygen are major challenges for developing fuel cells. To address these concerns, we have synthesized a Nitrogen-Sulfur-Iron-doped porous carbon material. Our results indicate that the synthesized catalyst exhibits not only higher current density and stability but also higher tolerance to crossover chemicals than the commercial Pt/C catalyst. More importantly, the synthetic method is simple and inexpensive. Using photocatalysts and solar energy is another potential alternative solution for energy demand. We have synthesized a new biomimetic heterogeneous photocatalyst through the incorporation of homogeneous complex 1 [(i-SCH 2)2NC(O)C5H4N]-Fe2(CO) 6] into the highly robust zirconium-porphyrin based metal-organic framework (ZrPF). As photosensitizer ZrPF absorbs the visible light and produces photoexcited electrons that can be transferred through axial covalent bond to di-nuclear complex 1 for hydrogen generation. Additionally, we have studied the photoreduction of CO2 to CH4 using self-doped TiO2 (Ti+3@TiO 2) as photocatalytic materials. The incorporation of Ti3+ into TiO2 structures narrows the band gap, leading to significantly increased photocatalytic activity for the reduction of CO2 into renewable hydrocarbon fuel in the presence of water vapor under visible

  5. Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

    NASA Astrophysics Data System (ADS)

    Nam, Hoang Bao; Kouza, Maksim; Zung, Hoang; Li, Mai Suan

    2010-04-01

    Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

  6. Ionic velocities in an ionic liquid under high electric fields using all-atom and coarse-grained force field molecular dynamics

    NASA Astrophysics Data System (ADS)

    Daily, John W.; Micci, Michael M.

    2009-09-01

    Molecular dynamics has been used to estimate ionic velocities and electrical conductivity in the ionic liquid 1-ethyl-3-methylimidazolium/tetraflouroborate (EMIM-BF4). Both an all-atom and coarse grained force fields were explored. The simulations were carried out at high electric fields where one might expect the Wien effect to become important in conventional electrolytes and that effect is observed. While the original Wilson theory used to explain the Wien effect in conventional electrolytes does not work well for ionic liquids, a minor modification of the theory allowed it to be used to qualitatively describe the data. The two coarse-graining methods were noisier as expected, but result in a significant savings in computational cost.

  7. Photon Strength Function at Low Energies in 95Mo

    NASA Astrophysics Data System (ADS)

    Wiedeking, M.; Bernstein, L. A.; Allmond, J. M.; Basunia, M. S.; Bleuel, D. L.; Burke, J. T.; Fallon, P.; Firestone, R. B.; Goldblum, B. L.; Hatarik, R.; Krtička, M.; Lake, P. T.; Larsen, A. C.; Lee, I.-Y.; Lesher, S. R.; Paschalis, S.; Petri, M.; Phair, L.; Scielzo, N. D.

    2014-05-01

    A new and model-independent experimental method has been developed to determine the energy dependence of the photon strength function. It is designed to study statistical feeding from the quasi continuum to individual low-lying discrete levels. This new technique is presented and results for 95Mo are compared to data from the University of Oslo. In particular, questions regarding the existence of the low-energy enhancement in the photon strength function are addressed.

  8. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  9. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-01

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  10. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  11. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems. PMID:25612718

  12. Kinetic-energy density functional: Atoms and shell structure

    SciTech Connect

    Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |

    1996-09-01

    We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. {copyright} {ital 1996 The American Physical Society.}

  13. Functional materials for sustainable energy technologies: four case studies.

    PubMed

    Kuznetsov, V L; Edwards, P P

    2010-01-01

    The critical topic of energy and the environment has rarely had such a high profile, nor have the associated materials challenges been more exciting. The subject of functional materials for sustainable energy technologies is demanding and recognized as a top priority in providing many of the key underpinning technological solutions for a sustainable energy future. Energy generation, consumption, storage, and supply security will continue to be major drivers for this subject. There exists, in particular, an urgent need for new functional materials for next-generation energy conversion and storage systems. Many limitations on the performances and costs of these systems are mainly due to the materials' intrinsic performance. We highlight four areas of activity where functional materials are already a significant element of world-wide research efforts. These four areas are transparent conducting oxides, solar energy materials for converting solar radiation into electricity and chemical fuels, materials for thermoelectric energy conversion, and hydrogen storage materials. We outline recent advances in the development of these classes of energy materials, major factors limiting their intrinsic functional performance, and potential ways to overcome these limitations.

  14. An Atomistic Statistically Effective Energy Function for Computational Protein Design.

    PubMed

    Topham, Christopher M; Barbe, Sophie; André, Isabelle

    2016-08-01

    Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical

  15. An Atomistic Statistically Effective Energy Function for Computational Protein Design.

    PubMed

    Topham, Christopher M; Barbe, Sophie; André, Isabelle

    2016-08-01

    Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical

  16. Local Density Approximation Exchange-correlation Free-energy Functional

    NASA Astrophysics Data System (ADS)

    Karasiev, Valentin; Sjostrom, Travis; Dufty, James; Trickey, S. B.

    2014-03-01

    Restricted path integral Monte-Carlo (RPIMC) simulation data for the homogeneous electron gas at finite temperatures are used to fit the exchange-correlation free energy as a function of the density and temperature. Together with a new finite- T spin-polarization interpolation, this provides the local spin density approximation (LSDA) for the exchange-correlation free-energy functional required by finite- T density functional theory. We discuss and compare different methods of fitting to the RPIMC data. The new function reproduces the RPIMC data in the fitting range of Wigner-Seitz radius and temperature, satisfies correct high-density, low- and high- T asymptotic limits and is applicable beyond the range of fitting data. Work supported by U.S. Dept. of Energy, grant DE-SC0002139 and by the DOE Office of Fusion Sciences (FES).

  17. Functionalization of graphene for efficient energy conversion and storage.

    PubMed

    Dai, Liming

    2013-01-15

    As global energy consumption accelerates at an alarming rate, the development of clean and renewable energy conversion and storage systems has become more important than ever. Although the efficiency of energy conversion and storage devices depends on a variety of factors, their overall performance strongly relies on the structure and properties of the component materials. Nanotechnology has opened up new frontiers in materials science and engineering to meet this challenge by creating new materials, particularly carbon nanomaterials, for efficient energy conversion and storage. As a building block for carbon materials of all other dimensionalities (such as 0D buckyball, 1D nanotube, 3D graphite), the two-dimensional (2D) single atomic carbon sheet of graphene has emerged as an attractive candidate for energy applications due to its unique structure and properties. Like other materials, however, a graphene-based material that possesses desirable bulk properties rarely features the surface characteristics required for certain specific applications. Therefore, surface functionalization is essential, and researchers have devised various covalent and noncovalent chemistries for making graphene materials with the bulk and surface properties needed for efficient energy conversion and storage. In this Account, I summarize some of our new ideas and strategies for the controlled functionalization of graphene for the development of efficient energy conversion and storage devices, such as solar cells, fuel cells, supercapacitors, and batteries. The dangling bonds at the edge of graphene can be used for the covalent attachment of various chemical moieties while the graphene basal plane can be modified via either covalent or noncovalent functionalization. The asymmetric functionalization of the two opposite surfaces of individual graphene sheets with different moieties can lead to the self-assembly of graphene sheets into hierarchically structured materials. Judicious

  18. Core level binding energies of functionalized and defective graphene.

    PubMed

    Susi, Toma; Kaukonen, Markus; Havu, Paula; Ljungberg, Mathias P; Ayala, Paola; Kauppinen, Esko I

    2014-01-01

    X-ray photoelectron spectroscopy (XPS) is a widely used tool for studying the chemical composition of materials and it is a standard technique in surface science and technology. XPS is particularly useful for characterizing nanostructures such as carbon nanomaterials due to their reduced dimensionality. In order to assign the measured binding energies to specific bonding environments, reference energy values need to be known. Experimental measurements of the core level signals of the elements present in novel materials such as graphene have often been compared to values measured for molecules, or calculated for finite clusters. Here we have calculated core level binding energies for variously functionalized or defected graphene by delta Kohn-Sham total energy differences in the real-space grid-based projector-augmented wave density functional theory code (GPAW). To accurately model extended systems, we applied periodic boundary conditions in large unit cells to avoid computational artifacts. In select cases, we compared the results to all-electron calculations using an ab initio molecular simulations (FHI-aims) code. We calculated the carbon and oxygen 1s core level binding energies for oxygen and hydrogen functionalities such as graphane-like hydrogenation, and epoxide, hydroxide and carboxylic functional groups. In all cases, we considered binding energy contributions arising from carbon atoms up to the third nearest neighbor from the functional group, and plotted C 1s line shapes by using experimentally realistic broadenings. Furthermore, we simulated the simplest atomic defects, namely single and double vacancies and the Stone-Thrower-Wales defect. Finally, we studied modifications of a reactive single vacancy with O and H functionalities, and compared the calculated values to data found in the literature.

  19. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation.

    PubMed

    Sharma, Anirban; Ghorai, Pradip Kr

    2016-03-21

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  20. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    NASA Astrophysics Data System (ADS)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  1. Putative membrane lytic sites of P-type and S-type cardiotoxins from snake venoms as probed by all-atom molecular dynamics simulations.

    PubMed

    Gorai, Biswajit; Karthikeyan, Muthusamy; Sivaraman, Thirunavukkarasu

    2016-10-01

    Cardiotoxins (CTXs) belonging to the three-finger toxin superfamily of snake venoms are one of principal toxic components and the protein toxins exhibit membrane lytic activities when the venoms are injected into victims. In the present study, complex formations between CTX VI (a P-type CTX from Naja atra) and CTX1 (an S-type CTX from Naja naja) on zwitterionic POPC bilayers (a major lipid component of cell membranes) have been studied in near physiological conditions for a total dynamic time scale of 1.35 μs using all-atom molecular dynamics (MD) simulations. Comprehensive analyses of the MD data revealed that residues such as Leu1, Lys2, Tyr11, Lys31, Asp57 and Arg58 of CTX VI, and Ala16, Lys30 and Arg58 of CTX1 were crucial for establishing interactions with the POPC bilayer. Moreover, loop I, along with globular head and loop II of CTX VI, and loop II of CTX1 were found to be the structural regions chiefly governing complex formation of the respective proteins with POPC. Rationalizations for the differential binding modes of CTXs and implications of the findings for designing small molecular inhibitors to the toxins are also discussed. Graphical Abstract Binding modes of a P-type CTX and an S-type CTX towards the POPC bilayer. PMID:27628673

  2. Teaching Potential Energy Functions and Stability with Slap Bracelets

    NASA Astrophysics Data System (ADS)

    Van Hook, Stephen J.

    2005-10-01

    The slap bracelet, an inexpensive child's toy, makes it easy to engage students in hands-on exploration of potential energy curves as well as of stable, unstable, and meta-stable states. Rather than just observing the teacher performing a demonstration, the students can manipulate the equipment themselves and make their own observations, which are then pooled to focus a class discussion on potential energy functions and stability.

  3. Contacting mode operation of work function energy harvester

    NASA Astrophysics Data System (ADS)

    Varpula, A.; Laakso, S. J.; Havia, T.; Kyynäräinen, J.; Prunnila, M.

    2014-11-01

    The work function energy harvester (WFEH) is a variable capacitance vibration energy harvester where the charging of the capacitor electrodes is driven by the work function difference of the electrode materials. In this work, we investigate operation modes of the WFEH by utilizing a macroscopic parallel plate capacitor with Cu and Al electrodes and varying plate distance. We show that by charging the electrodes of the WFEH by letting the electrode plates touch during the operation a significant output power enhancement can be achieved in comparison to the case where the electrodes are charged and discharged only through a load resistor.

  4. On the accuracy of density functional theory and wave function methods for calculating vertical ionization energies

    SciTech Connect

    McKechnie, Scott; Booth, George H.; Cohen, Aron J.; Cole, Jacqueline M.

    2015-05-21

    The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.

  5. On the accuracy of density functional theory and wave function methods for calculating vertical ionization energies.

    PubMed

    McKechnie, Scott; Booth, George H; Cohen, Aron J; Cole, Jacqueline M

    2015-05-21

    The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.

  6. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  7. "Sloppy" nuclear energy density functionals: Effective model reduction

    NASA Astrophysics Data System (ADS)

    Nikšić, Tamara; Vretenar, Dario

    2016-08-01

    Concepts from information geometry are used to analyze parameter sensitivity for a nuclear energy density functional, representative of a class of semiempirical functionals that start from a microscopically motivated ansatz for the density dependence of the energy of a system of protons and neutrons. It is shown that such functionals are "sloppy," namely, characterized by an exponential range of sensitivity to parameter variations. Responsive to only a few stiff parameter combinations, sloppy functionals exhibit an exponential decrease of sensitivity to variations of the remaining soft parameters. By interpreting the space of model predictions as a manifold embedded in the data space, with the parameters of the functional as coordinates on the manifold, it is also shown that the exponential distribution of model manifold widths corresponds to the range of parameter sensitivity. Using the manifold boundary approximation method, we illustrate how to systematically construct effective nuclear density functionals of successively lower dimension in parameter space until sloppiness is eventually eliminated and the resulting functional contains only stiff combinations of parameters.

  8. Constrained Parmeterization of Reduced Density Approximation of Kinetic Energy Functionals

    NASA Astrophysics Data System (ADS)

    Chakraborty, Debajit; Trickey, Samuel; Karasiev, Valentin

    2014-03-01

    Evaluation of forces in ab initio MD is greatly accelerated by orbital-free DFT, especially at finite temperature. The recent achievement of a fully non-empirical constraint-based generalized gradient (GGA) functional for the Kohn-Sham KE Ts [ n ] brings to light the inherent limitations of GGAs. This motivates inclusion of higher-order derivatives in the form of reduced derivative approximation (RDA) functionals. That, in turn, requires new functional forms and design criteria. RDA functionals are constrained further to produce a positive-definite, non-singular Pauli potential. We focus on designing a non-empirical constraint-based meta-GGA functional with certain combinations of higher-order derivatives which avoid nuclear-site singularities to a specified order of gradient expansion. Here we report progress on this agenda. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.

  9. Towards the island of stability with relativistic energy density functionals

    SciTech Connect

    Prassa, V.; Niksic, T.; Lalazissis, G. A.; Vretenar, D.

    2012-10-20

    Relativistic energy density functionals (REDF) provide a complete and accurate, global description of nuclear structure phenomena. Modern semi-empirical functionals, adjusted to the nuclear matter equation of state and to empirical masses of deformed nuclei, are applied to studies of shapes of superheavy nuclei. The theoretical framework is tested in a comparison to empirical masses, quadrupole deformations, and energy barriers of actinide nuclei. The model is used in a self-consistent mean-field calculation of spherical, axial and triaxial shapes of superheavy nuclei, alpha-decay energies and lifetimes. The effect of explicit treatment of collective correlations is analyzed in calculations that consistently use a collective Hamiltonian model based on REDFs.

  10. Optimizing potential energy functions for maximal intrinsic hyperpolarizability

    SciTech Connect

    Zhou Juefei; Szafruga, Urszula B.; Kuzyk, Mark G.; Watkins, David S.

    2007-11-15

    We use numerical optimization to study the properties of (1) the class of one-dimensional potential energy functions and (2) systems of point nuclei in two dimensions that yield the largest intrinsic hyperpolarizabilities, which we find to be within 30% of the fundamental limit. In all cases, we use a one-electron model. It is found that a broad range of optimized potentials, each of very different character, yield the same intrinsic hyperpolarizability ceiling of 0.709. Furthermore, all optimized potential energy functions share common features such as (1) the value of the normalized transition dipole moment to the dominant state, which forces the hyperpolarizability to be dominated by only two excited states and (2) the energy ratio between the two dominant states. All optimized potentials are found to obey the three-level ansatz to within about 1%. Many of these potential energy functions may be implementable in multiple quantum well structures. The subset of potentials with undulations reaffirm that modulation of conjugation may be an approach for making better organic molecules, though there appear to be many others. Additionally, our results suggest that one-dimensional molecules may have larger diagonal intrinsic hyperpolarizability {beta}{sub xxx}{sup int} than higher-dimensional systems.

  11. A density functional for core-valence correlation energy.

    PubMed

    Ranasinghe, Duminda S; Frisch, Michael J; Petersson, George A

    2015-12-01

    A density functional, εCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of εLY P (corr)(ρc), εV WN5 (corr)(ρc, ρv), εPBE (corr)(ρc, ρv), εSlater (ex)(ρc, ρv), εHCTH (ex)(ρc, ρv), εHF (ex)(ρc, ρv), and FCV-DFTNi,Zi, a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from εCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the εCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory. PMID:26646873

  12. A density functional for core-valence correlation energy

    NASA Astrophysics Data System (ADS)

    Ranasinghe, Duminda S.; Frisch, Michael J.; Petersson, George A.

    2015-12-01

    A density functional, ɛCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of ɛLY Pcorr(ρc), ɛV WN5corr(ρc, ρv), ɛPBEcorr(ρc, ρv), ɛSlaterex(ρc, ρv), ɛHCTHex(ρc, ρv), ɛHFex(ρc, ρv), and F CV -DFT (" separators=" N i , Z i ) , a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from ɛCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the ɛCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory.

  13. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  14. Many-body theory and Energy Density Functionals

    NASA Astrophysics Data System (ADS)

    Baldo, M.

    2016-07-01

    In this paper a method is first presented to construct an Energy Density Functional on a microscopic basis. The approach is based on the Kohn-Sham method, where one introduces explicitly the Nuclear Matter Equation of State, which can be obtained by an accurate many-body calculation. In this way it connects the functional to the bare nucleon-nucleon interaction. It is shown that the resulting functional can be performing as the best Gogny force functional. In the second part of the paper it is shown how one can go beyond the mean-field level and the difficulty that can appear. The method is based on the particle-vibration coupling scheme and a formalism is presented that can handle the correct use of the vibrational degrees of freedom within a microscopic approach.

  15. Nitroborazines as potential high energy materials: density functional theoretical calculations.

    PubMed

    Janning, Jay D; Ball, David W

    2010-05-01

    As part of a search for new high energy density materials, we used density functional theoretical calculations to determine the thermochemical properties of various nitro-substituted borazine molecules. Optimized geometries, vibrational frequencies and spectra, and enthalpies of formation and combustion were determined for nitroborazine, dinitroborazine, trinitroborazine, and methyltrinitroborazine with substituents on either the boron atoms or the nitrogen atoms of the parent borazine ring. Our results indicate that the specific enthalpy of combustion ranged from 4 to 11 kJ g(-1), with increasing substitution of nitro groups lowering the energy of combustion per unit mass.

  16. Curvature and Frontier Orbital Energies in Density Functional Theory

    SciTech Connect

    Stein, Tamar; Autschbach, Jochen; Govind, Niranjan; Kronik, Leeor; Baer, Roi

    2012-12-20

    Perdew et al. [Phys. Rev. Lett 49, 1691 (1982)] discovered and proved two different properties that exact Kohn-Sham density functional theory (DFT) must obey: (i) The exact total energy versus particle number must be a series of linear segments between integer electron points; (ii) Across an integer number of electrons, the exchange-correlation potential may ``jump’’ by a constant, known as the derivative discontinuity (DD). Here, we show analytically that in both the original and the generalized Kohn-Sham formulation of DFT, the two are in fact two sides of the same coin. Absence of a derivative discontinuity necessitates deviation from piecewise linearity, and the latter can be used to correct for the former, thereby restoring the physical meaning of the orbital energies. Using selected small molecules, we show that this results in a simple correction scheme for any underlying functional, including semi-local and hybrid functionals as well as Hartree-Fock theory, suggesting a practical correction for the infamous gap problem of density functional theory. Moreover, we show that optimally-tuned range-separated hybrid functionals can inherently minimize both DD and curvature, thus requiring no correction, and show that this can be used as a sound theoretical basis for novel tuning strategies.

  17. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

    PubMed

    Noel, Jeffrey K; Whitford, Paul C; Onuchic, José N

    2012-07-26

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called "Shadow". The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.

  18. Extraction of electron plasma energy distribution function using distortion meters

    NASA Astrophysics Data System (ADS)

    Azooz, A. A.

    2006-06-01

    A new method for direct evaluation of the electron energy distribution function in plasmas is suggested, which involves the use of audio frequencies distortion factor meters. The amount of distortion suffered by a Langmuir probe AC current produced by superimposing a clean AC voltage on the DC probe voltage is measured. Although such distortions are proportional to the second derivative of the probe characteristic at any point when its neighborhood can be approximated by a second-degree polynomial, the instrument function is always sharper than that of harmonic differentiation. The method is analyzed theoretically, and tested experimentally. It is also shown that distortion additionally provides a direct measure of the electron temperature.

  19. Controlling the Electron Energy Distribution Function Using an Anode

    NASA Astrophysics Data System (ADS)

    Baalrud, Scott D.; Barnat, Edward V.; Hopkins, Mathew M.

    2014-10-01

    Positively biased electrodes inserted into plasmas influence the electron energy distribution function (EEDF) by providing a sink for low energy electrons that would otherwise be trapped by ion sheaths at the chamber walls. We develop a model for the EEDF in a hot filament generated discharge in the presence of positively biased electrodes of various surface areas, and compare the model results with experimental Langmuir probe measurements and particle-in-cell simulations. In the absence of an anode, the EEDF is characterized by a cool trapped population at energies below the sheath energy, and a comparatively warm tail population associated with the filament primaries. Anodes that are small enough to collect a negligible fraction of the electrons exiting the plasma have little affect on the EEDF, but as the anode area approaches √{me /mi }Aw , where Aw is the chamber wall area, the anode collects most of the electrons leaving the plasma. This drastically reduces the density of the otherwise trapped population, causing an effective heating of the electrons and a corresponding density decrease. A global model is developed based on the EEDF model and current balance, which shows the interconnected nature of the electron temperature, density and the plasma potential. This work was supported by the Office of Fusion Energy Science at the U.S. Department of Energy under Contract DE-AC04-94SL85000, and by the University of Iowa Old Gold Program.

  20. Finite-size instabilities in nuclear energy density functionals

    SciTech Connect

    Hellemans, V.; Heenen, P.-H.; Bender, M.

    2012-10-20

    The systematic lack of convergence of self-consistent mean-field calculations with certain parameterizations of the Skyrme energy density functional has been attributed to the appearance of finite-size instabilities. In this contribution, we investigate what happens at the instability associated with the C{sub 0}{sup {Delta}s}s{sub 0} Dot-Operator {Delta}s{sub 0} term in a high-spin state of the superdeformed band in {sup 194}Hg.

  1. Contrastive studies of potential energy functions of some diatomic molecules

    NASA Astrophysics Data System (ADS)

    Abdallah, Hassan H.; Abdullah, Hewa Y.

    2016-03-01

    It was proposed that iron hydride, FeH, would be formed only on grains at the clouds through the reaction of the adsorbed H atoms or H2 molecules with the adsorbed Fe atoms on the grains. The importance of FeH in Astrophysics presents an additional motivation to study its energetic, spectroscopic constants and Potential Energy Curves. The structural optimization for ground state of FeH was calculated by different theoretical methods, namely, Hartree-Fock (HF), the density functional theory (DFT), B3LYP, MP2 method and QCISD(T) methods and compared with available data from the literature. The single ionized forms, cation and anion, were also obtained at the same level of calculations. Charges, dipole moment, geometrical parameters, molecular orbital energies and spectroscopic parameters were calculated and reported. In addition, the molecular ionization potential, electron affinity and dissociation energy were investigated.

  2. Energy functionals for inhomogeneous many-electron systems

    SciTech Connect

    Geldart, D.J.W. . Dept. of Physics); Rasolt, M. )

    1991-10-01

    The primary purpose of these lectures is to provide a pedagogical introduction Density Functional Theory (DF). We begin with the very early picture of Thomas and Fermi for the ground state energy of a neutral atom and proceed to the highly successful method of Kohn and Sham (KS) which focuses attention on the exchange-correlation contribution E{sub XC}(n) to the energy functional. We stress the importance of a systematic approach to the study of the subtle nonlocal structure of E{sub XC}(n) in inhomogeneous systems. The local and global convergence properties of gradient expansions are examined in some detail for detail for both density and low density systems. The structure of E{sub XC}(n) in the low density regime is described. Aspects of energy functionals which are determined by global symmetries and boundary conditions (in contrast to largely local energetics) are illustrated by the examples of the structure factor in bounded geometry and band gap discontinuities in semiconductors. An illustrative application of DFT is made to the problem of instabilities of the strongly correlated low density electron liquid with respect to charge modulated ground states.

  3. Prediction of protein complexes using empirical free energy functions.

    PubMed Central

    Weng, Z.; Vajda, S.; Delisi, C.

    1996-01-01

    A long sought goal in the physical chemistry of macromolecular structure, and one directly relevant to understanding the molecular basis of biological recognition, is predicting the geometry of bimolecular complexes from the geometries of their free monomers. Even when the monomers remain relatively unchanged by complex formation, prediction has been difficult because the free energies of alternative conformations of the complex have been difficult to evaluate quickly and accurately. This has forced the use of incomplete target functions, which typically do no better than to provide tens of possible complexes with no way of choosing between them. Here we present a general framework for empirical free energy evaluation and report calculations, based on a relatively complete and easily executable free energy function, that indicate that the structures of complexes can be predicted accurately from the structures of monomers, including close sequence homologues. The calculations also suggest that the binding free energies themselves may be predicted with reasonable accuracy. The method is compared to an alternative formulation that has also been applied recently to the same data set. Both approaches promise to open new opportunities in macromolecular design and specificity modification. PMID:8845751

  4. All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. Application to M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) compounds.

    PubMed

    Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E

    2013-10-31

    A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row). PMID:24079472

  5. Descriptions of carbon isotopes within the energy density functional theory

    SciTech Connect

    Ismail, Atef; Cheong, Lee Yen; Yahya, Noorhana; Tammam, M.

    2014-10-24

    Within the energy density functional (EDF) theory, the structure properties of Carbon isotopes are systematically studied. The shell model calculations are done for both even-A and odd-A nuclei, to study the structure of rich-neutron Carbon isotopes. The EDF theory indicates the single-neutron halo structures in {sup 15}C, {sup 17}C and {sup 19}C, and the two-neutron halo structures in {sup 16}C and {sup 22}C nuclei. It is also found that close to the neutron drip-line, there exist amazing increase in the neutron radii and decrease on the binding energies BE, which are tightly related with the blocking effect and correspondingly the blocking effect plays a significant role in the shell model configurations.

  6. Free energy functional for nonequilibrium systems: an exactly solvable case.

    PubMed

    Derrida, B; Lebowitz, J L; Speer, E R

    2001-10-01

    We consider the steady state of an open system in which there is a flux of matter between two reservoirs at different chemical potentials. For a large system of size N, the probability of any macroscopic density profile rho(x) is exp[-NF([rho])]; F thus generalizes to nonequilibrium systems the notion of free energy density for equilibrium systems. Our exact expression for F is a nonlocal functional of rho, which yields the macroscopically long range correlations in the nonequilibrium steady state previously predicted by fluctuating hydrodynamics and observed experimentally. PMID:11580688

  7. Relativistic Energy Density Functionals: Exotic modes of excitation

    SciTech Connect

    Vretenar, D.; Paar, N.; Marketin, T.

    2008-11-11

    The framework of relativistic energy density functionals has been applied to the description of a variety of nuclear structure phenomena, not only in spherical and deformed nuclei along the valley of {beta}-stability, but also in exotic systems with extreme isospin values and close to the particle drip-lines. Dynamical aspects of exotic nuclear structure have been investigated with the relativistic quasiparticle random-phase approximation. We present results for the evolution of low-lying dipole (pygmy) strength in neutron-rich nuclei, and charged-current neutrino-nucleus cross sections.

  8. Nuclear clustering in the energy density functional approach

    SciTech Connect

    Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.

    2015-10-15

    Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.

  9. Physical invariant strain energy function for passive myocardium.

    PubMed

    Shariff, M H B M

    2013-04-01

    Principal axis formulations are regularly used in isotropic elasticity, but they are not often used in dealing with anisotropic problems. In this paper, based on a principal axis technique, we develop a physical invariant orthotropic constitutive equation for incompressible solids, where it contains only a one variable (general) function. The corresponding strain energy function depends on six invariants that have immediate physical interpretation. These invariants are useful in facilitating an experiment to obtain a specific constitutive equation for a particular type of materials. The explicit appearance of the classical ground-state constants in the constitutive equation simplifies the calculation for their admissible values. A specific constitutive model is proposed for passive myocardium, and the model fits reasonably well with existing simple shear and biaxial experimental data. It is also able to predict a set of data from a simple shear experiment.

  10. BUILDING A UNIVERSAL NUCLEAR ENERGY DENSITY FUNCTIONAL (UNEDF)

    SciTech Connect

    Nazarewicz, Witold

    2012-07-01

    The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties. Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data. Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

  11. Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations.

    PubMed

    Horn, Paul R; Head-Gordon, Martin

    2016-02-28

    In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.

  12. Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Horn, Paul R.; Head-Gordon, Martin

    2016-02-01

    In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.

  13. [THE ENERGY FUNCTION OF RAT CARDIAC MITOCHONDRIA UNDER ARTIFICIAL HYPOBIOSIS].

    PubMed

    Melnytchuk, S D; Khyzhnyak, S V; Morozova, V S; Stepanova, L I; Umanskaya, A A; Voitsitsky, V M

    2015-01-01

    We investigated the energy activity of mitochondria from rat cardiomyocytes under the artificial carbon dioxide hypobiosis, which led to physiological changes in the organism (the decrease of body temperature, the reduction of heart rate, etc.). The respiratory and phosphorylation activities in mitochondria of cardiomyocytes is reduced when using two oxidation substrates (succinate and malate), which characterize the rate of the oxygen consumption by the mitochondria. The partial uncoupling of the oxidation and phosphorylation processes when using the malate unlike succinate was established. The activity of NADH-KoQ-oxidoreductase (complex I of the respiratory chain) is inhibited, but the activities of succinate dehydrogenase and cytochrome oxidase don't change. Probably, the priority of the succinate use under the artificial hypobiosis provides the support of the mitochondria functional activity on a sufficient energy level. It is evidenced by the ATP-synthetase activity. The modifications of the structural and functional state of the inner mitochondria membrane of the cardiomyocytes are directed to the adaptation under the artificial carbon dioxide hypobiosis. PMID:26387156

  14. Interfacial properties and design of functional energy materials.

    PubMed

    Sumpter, Bobby G; Liang, Liangbo; Nicolaï, Adrien; Meunier, Vincent

    2014-11-18

    CONSPECTUS: The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality and performance. This demand can potentially be realized by harnessing the power of self-assembly, a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately noncovalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, for example, lithographic, approach. However, while function in simple systems such as single crystals can often be evaluated a priori, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various support substrates. Typical molecular self-assembly involves noncovalent intermolecular and substrate-molecule interactions. These interactions remain poorly understood, due to the combination of many-body interactions compounded by local or collective influences from the substrate atomic lattice and electronic structure. Progress toward unraveling the underlying physicochemical processes that control the structure and macroscopic physical, chemical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling, and simulation with precision synthesis, advanced experimental characterization, and device measurements. Theory, modeling, and simulation can accelerate the process of materials understanding and design

  15. Interfacial properties and design of functional energy materials.

    PubMed

    Sumpter, Bobby G; Liang, Liangbo; Nicolaï, Adrien; Meunier, Vincent

    2014-11-18

    CONSPECTUS: The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality and performance. This demand can potentially be realized by harnessing the power of self-assembly, a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately noncovalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, for example, lithographic, approach. However, while function in simple systems such as single crystals can often be evaluated a priori, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various support substrates. Typical molecular self-assembly involves noncovalent intermolecular and substrate-molecule interactions. These interactions remain poorly understood, due to the combination of many-body interactions compounded by local or collective influences from the substrate atomic lattice and electronic structure. Progress toward unraveling the underlying physicochemical processes that control the structure and macroscopic physical, chemical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling, and simulation with precision synthesis, advanced experimental characterization, and device measurements. Theory, modeling, and simulation can accelerate the process of materials understanding and design

  16. [High energy shockwave-induced acute changes in renal function].

    PubMed

    Li, B Y

    1992-09-01

    Attempting to understand the effects of HESW on renal function, we studied prospectively 40 patients with nephrolithiasis in 4 groups, using different number of pulsation and the same voltage to identify different effects. Stone burdens and position were similar in these groups. Each group received 1,500, 2,000, 2,500, or 3,000 pulses respectively at 12.5 kV from JT-3 lithotripter. In all groups, the levels of urinary NAG, beta 2MG, ALB and serum beta 2MG were significantly increased at day 1-3 after ESWL (P < 0.001), and then decreased to the levels of pre-ESWL except serum beta 2MG and urinary NAG levels of group C and D at day 7 after ESWL, which were significantly higher (P < 0.05) than those of pre-ESWL. There was significant correlation between either urinary NAG (r = 0.977, P < 0.05) or urinary beta 2MG (r = 0.933, P < 0.001) and the number of pulses at day 3 post-ESWL. In addition, there was a significant difference in urinary NAG levels between group D and group A, B or C at day 3 post-ESWL, and the same was true in urinary beta 2MG levels between group C or D and group A or B. These findings suggested that shock wave induced acute changes in renal function and transient renal tubular damages, and that the tubular damages might last longer more than 7 days, although these functional changes recovered within one week. The changes were related to the energy levels of shock wave, and the degree of renal damage would increase when the energy level was above 12.5 kV x 2,500 pulses.

  17. Building A Universal Nuclear Energy Density Functional (UNEDF)

    SciTech Connect

    Joe Carlson; Dick Furnstahl; Mihai Horoi; Rusty Lusk; Witek Nazarewicz; Esmond Ng; Ian Thompson; James Vary

    2012-09-30

    During the period of Dec. 1 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory. The main physics areas of UNEDF, defined at the beginning of the project, were: ab initio structure; ab initio functionals; DFT applications; DFT extensions; reactions.

  18. Protein side chain conformation predictions with an MMGBSA energy function.

    PubMed

    Gaillard, Thomas; Panel, Nicolas; Simonson, Thomas

    2016-06-01

    The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an "MMGBSA" energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803-819. © 2016 Wiley Periodicals, Inc.

  19. Imaging performance of annular apertures. IV - Apodization and point spread functions. V - Total and partial energy integral functions

    NASA Technical Reports Server (NTRS)

    Tschunko, H. F. A.

    1983-01-01

    Reference is made to a study by Tschunko (1979) in which it was discussed how apodization modifies the modulation transfer function for various central obstruction ratios. It is shown here how apodization, together with the central obstruction ratio, modifies the point spread function, which is the basic element for the comparison of imaging performance and for the derivation of energy integrals and other functions. At high apodization levels and lower central obstruction (less than 0.1), new extended radial zones are formed in the outer part of the central ring groups. These transmutation of the image functions are of more than theoretical interest, especially if the irradiance levels in the outer ring zones are to be compared to the background irradiance levels. Attention is then given to the energy distribution in point images generated by annular apertures apodized by various transmission functions. The total energy functions are derived; partial energy integrals are determined; and background irradiance functions are discussed.

  20. Interfacial Properties and Design of Functional Energy Materials

    SciTech Connect

    Sumpter, Bobby G; Liang, Liangbo; Nicolai, Adrien; Meunier, V.

    2014-01-01

    The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality, such as efficient energy conversion/storage/transmission, over multiple length scales. This demand can potentially be realized by harnessing the power of self-assembly a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately non-covalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, e.g., lithographic approach. However, while function (e.g., charge mobility) in simple systems such as single crystals can often be predicted, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale (long-range) order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various substrates. Typically molecular self-assembly involves poorly understood non-covalent intermolecular and substrate-molecule interactions compounded by local and/or collective influences from the substrate atomic lattice (symmetry and/or topological features) and electronic structure. Thus, progress towards unraveling the underlying physicochemical processes that control the structure and macroscopic physical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling and simulation with precision synthesis, advanced experimental characterization, and device measurements. In this mode, theory and simulation can greatly accelerate the

  1. Correlation functions in liquids and crystals: free-energy functional and liquid-to-crystal transition.

    PubMed

    Bharadwaj, Atul S; Singh, Swarn L; Singh, Yashwant

    2013-08-01

    A free-energy functional for a crystal that contains both the symmetry-conserved and symmetry-broken parts of the direct pair-correlation function has been used to investigate the crystallization of fluids in three dimensions. The symmetry-broken part of the direct pair-correlation function has been calculated using a series in ascending powers of the order parameters and which contains three- and higher-body direct correlation functions of the isotropic phase. It is shown that a very accurate description of freezing transitions for a wide class of potentials is found by considering the first two terms of this series. The results found for freezing parameters including the structure of the frozen phase for fluids interacting via the inverse power potential u(r)=ε(σ/r)(n) for n ranging from 4 to ∞ are in very good agreement with simulation results. It is found that for n>6.5 the fluid freezes into a face-centered cubic (fcc) structure while for n≤6 the body-centered cubic (bcc) structure is preferred. The fluid-bcc-fcc triple point is found to be at 1/n=0.158, which is in good agreement with simulation result. PMID:24032780

  2. Kinetic-energy density functionals with nonlocal terms with the structure of the Thomas-Fermi functional

    SciTech Connect

    Garcia-Aldea, David; Alvarellos, J. E.

    2007-11-15

    We study two families of approximate nonlocal kinetic-energy functionals that include a full von Weizsaecker functional, and that have nonlocal terms with the mathematical structure of the Thomas-Fermi functional. The functionals recover the exact kinetic energy and the linear response function of a homogeneous electron system. The first family is a generalization of a successful previous nonlocal functional. The second family is proposed in the paper, and is designed to obtain functionals suitable for use in both localized and extended systems. Furthermore, this family has been designed to be evaluated by a single integration in momentum space when a constant reference density is used. The atomic total kinetic energies are in good agreement with the exact calculations. The kinetic-energy density corresponding to each functional has been assessed to control its quality. The results show that, in general, these functionals behave better than both the Thomas-Fermi and all semilocal generalized gradient approximation functionals when describing the kinetic-energy density of atoms, providing a better description of the nonlocal effects of the kinetic energy of electron systems.

  3. Measurement of the nucleon structure function using high energy muons

    SciTech Connect

    Meyers, P.D.

    1983-12-01

    We have measured the inclusive deep inelastic scattering of muons on nucleons in iron using beams of 93 and 215 GeV muons. To perform this measurement, we have built and operated the Multimuon Spectrometer (MMS) in the muon beam at Fermilab. The MMS is a magnetized iron target/spectrometer/calorimeter which provides 5.61 kg/cm/sup 2/ of target, 9% momentum resolution on scattered muons, and a direct measure of total hadronic energy with resolution sigma/sub nu/ = 1.4..sqrt..nu(GeV). In the distributed target, the average beam energies at the interaction are 88.0 and 209 GeV. Using the known form of the radiatively-corrected electromagnetic cross section, we extract the structure function F/sub 2/(x,Q/sup 2/) with a typical precision of 2% over the range 5 < Q/sup 2/ < 200 GeV/sup 2//c/sup 2/. We compare our measurements to the predictions of lowest order quantum chromodynamics (QCD) and find a best fit value of the QCD scale parameter ..lambda../sub LO/ = 230 +- 40/sup stat/ +- 80/sup syst/ MeV/c, assuming R = 0 and without applying Fermi motion corrections. Comparing the cross sections at the two beam energies, we measure R = -0.06 +- 0.06/sup stat/ +- 0.11/sup syst/. Our measurements show qualitative agreement with QCD, but quantitative comparison is hampered by phenomenological uncertainties. The experimental situation is quite good, with substantial agreement between our measurements and those of others. 86 references.

  4. Accurate Zero Parameter Correlation Energy Functional Obtained from the Homogeneous Electron Gas with an Energy Gap

    NASA Astrophysics Data System (ADS)

    Krieger, J. B.; Chen, Jiqiang; Iafrate, G. J.; Savin, A.

    1998-03-01

    We have obtained an analytic approximation to E_c(r_g, ζ,G) where G is an energy gap separating the occupied and unoccupied states of a homogeneous electron gas for ζ=3D0 and ξ=3D1. When G=3D0, E_c(r_g, ζ) reduces to the usual LSD result. This functional is employed in calculating correlation energies for unpolarized atoms and ions for Z <= 18 by taking G[n]=3D1/8|nabla ln n|^2, which reduces to the ionization energy in the large r limit in an exact Kohn-Sham (KS) theory. The resulting functional is self-interaction-corrected employing a method which is invariant under a unitary transformation. We find that the application of this approach to the calculation of the Ec functional reduces the error in the LSD result by more than 95%. When the value of G is approximately corrected to include the effect of higher lying unoccupied localized states, the resulting values of Ec are within a few percent of the exact results.

  5. Does shallow geothermal energy use threaten groundwater ecosystem functions?

    NASA Astrophysics Data System (ADS)

    Brielmann, Heike; Schmidt, Susanne I.; Ferraro, Francesco; Schreglmann, Kathrin; Griebler, Christian; Lueders, Tillmann

    2010-05-01

    Today, the use of geothermal energy is strongly promoted as an alternative and sustainable source of energy. However, regarding the authorization, regulation and monitoring of such facilities with respect to possible environmental impacts, a severe lack of knowledge has been identified. Aquifers are not only abiotic reservoirs of water and sediment, but they are complex ecosystems harbouring an almost untapped diversity of microorganisms and fauna. Intrinsic groundwater organisms are highly adapted to extremely oligotrophic, but stable conditions including temperature. At the same time, groundwater biota are the key drivers of important ecosystem services, especially functions connected to water quality. So what happens if groundwater biota need to cope with sudden temperature dynamics caused by GSHP use? Potential effects of thermal use on pristine aquifers, and on groundwater systems already facing enhanced loads of nutrients or contamination require urgent scientific attention. Within this project, we have assessed - both in the field and in the laboratory - the impacts of temperature discharge and withdrawal on biotic parameters and functional characteristics of exemplary shallow groundwater systems. In the field, aquifer microbes did not show significant impacts under increased temperatures in terms of total cell numbers, selected enzyme activities and carbon production. However, bacterial diversity clearly increased with temperature, accompanied by the appearance of new bacterial lineages and the disappearance of others. On the contrary, faunal diversity decreased with temperature, highlighting the temperature sensitivity of groundwater invertebrates. These results demonstrate that aquifer thermal energy discharge can affect intrinsic aquifer biotic populations, while at the same time being only one of several drivers contributing to total variability connected to seasonal dynamics and spatial heterogeneity. In laboratory column experiments covering a larger

  6. Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials.

    PubMed

    Giridharagopal, Rajiv; Cox, Phillip A; Ginger, David S

    2016-09-20

    From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to study materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of

  7. Functional Scanning Probe Imaging of Nanostructured Solar Energy Materials.

    PubMed

    Giridharagopal, Rajiv; Cox, Phillip A; Ginger, David S

    2016-09-20

    From hybrid perovskites to semiconducting polymer/fullerene blends for organic photovoltaics, many new materials being explored for energy harvesting and storage exhibit performance characteristics that depend sensitively on their nanoscale morphology. At the same time, rapid advances in the capability and accessibility of scanning probe microscopy methods over the past decade have made it possible to study processing/structure/function relationships ranging from photocurrent collection to photocarrier lifetimes with resolutions on the scale of tens of nanometers or better. Importantly, such scanning probe methods offer the potential to combine measurements of local structure with local function, and they can be implemented to study materials in situ or devices in operando to better understand how materials evolve in time in response to an external stimulus or environmental perturbation. This Account highlights recent advances in the development and application of scanning probe microscopy methods that can help address such questions while filling key gaps between the capabilities of conventional electron microscopy and newer super-resolution optical methods. Focusing on semiconductor materials for solar energy applications, we highlight a range of electrical and optoelectronic scanning probe microscopy methods that exploit the local dynamics of an atomic force microscope tip to probe key properties of the solar cell material or device structure. We discuss how it is possible to extract relevant device properties using noncontact scanning probe methods as well as how these properties guide materials development. Specifically, we discuss intensity-modulated scanning Kelvin probe microscopy (IM-SKPM), time-resolved electrostatic force microscopy (trEFM), frequency-modulated electrostatic force microscopy (FM-EFM), and cantilever ringdown imaging. We explain these developments in the context of classic atomic force microscopy (AFM) methods that exploit the physics of

  8. Towards a Microscopic Reaction Description Based on Energy Density Functionals

    SciTech Connect

    Nobre, G A; DIetrich, F S; Escher, J E; Thompson, I J; Dupuis, M; Terasaki, J; Engel, J

    2011-09-26

    A microscopic calculation of reaction cross sections for nucleon-nucleus scattering has been performed by explicitly coupling the elastic channel to all particle-hole excitations in the target and one-nucleon pickup channels. The particle-hole states may be regarded as doorway states through which the flux flows to more complicated configurations, and subsequently to long-lived compound nucleus resonances. Target excitations for {sup 40,48}Ca, {sup 58}Ni, {sup 90}Zr and {sup 144}Sm were described in a random-phase framework using a Skyrme functional. Reaction cross sections obtained agree very well with experimental data and predictions of a state-of-the-art fitted optical potential. Couplings between inelastic states were found to be negligible, while the pickup channels contribute significantly. The effect of resonances from higher-order channels was assessed. Elastic angular distributions were also calculated within the same method, achieving good agreement with experimental data. For the first time observed absorptions are completely accounted for by explicit channel coupling, for incident energies between 10 and 70 MeV, with consistent angular distribution results.

  9. Multifragment azimuthal correlation functions: Probes for reaction dynamics in collisions of intermediate energy heavy ions

    SciTech Connect

    Lacey, R.A.; Elmaani, A.; Lauret, J.; Li, T.; Bauer, W.; Craig, D.; Cronqvist, M.; Gualtieri, E.; Hannuschke, S.; Reposeur, T.; Vander Molen, A.; Westfall, G.D.; Wilson, W.K.; Winfield, J.S.; Yee, J.; Yennello, S.; Nadasen, A.; Tickle, R.S.; Norbeck, E. National Superconducting Cyclotron Laboratory Department of Physics, Michigan State University, East Lansing, Michigan 48824-1321 Department of Physics, University of Michigan at Dearborn, Dearborn, Michigan 48128 Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1120 Department of Physics, University of Iowa, Iowa City, Iowa 52242 )

    1993-03-01

    Multifragment azimuthal correlation functions have been measured as a function of beam energy and impact parameter for the Ar+Sc system ([ital E]/[ital A]=35 to 115 MeV). The observed azimuthal correlation functions---which do not require corrections for dispersion of the reaction plane---exhibit strong asymmetries which are dependent on impact parameter and beam energy. Rotational collective motion and flow seem to dominate the correlation functions at low beam energies. It is proposed that multifragment azimuthal correlation functions can provide a useful probe for intermediate energy heavy ion reaction dynamics.

  10. Covariant energy density functionals: The assessment of global performance across the nuclear landscape

    SciTech Connect

    Afanasjev, A. V.

    2015-10-15

    The assessment of the global performance of the state-of-the-art covariant energy density functionals and related theoretical uncertainties in the description of ground state observables has recently been performed. Based on these results, the correlations between global description of binding energies and nuclear matter properties of covariant energy density functionals have been studied in this contribution.

  11. Is there a low-energy enhancement in the photon strength function in molybdenum?

    NASA Astrophysics Data System (ADS)

    Sheets, S. A.

    2008-04-01

    Recent claims of a low-energy enhancement in the photon strength function of 96Mo are investigated. Using the DANCE detector the gamma-ray spectra following resonance neutron capture was measured. The spectrum fitting method was used to indirectly extract a photon strength function from the gamma-ray spectra. No strong low energy enhancement in the photon strength function was found.

  12. Is there a low energy enhancement in the photon strength function in molybdenum?

    SciTech Connect

    Sheets, S A

    2008-01-30

    Recent claims of a low energy enhancement in the photon strength function of {sup 96}Mo are investigated. Using the DANCE detector the gamma-ray spectra following resonance neutron capture was measured. The spectrum fitting method was used to indirectly extract a photon strength function from the gamma-ray spectra. No strong low energy enhancement in the photon strength function was found.

  13. Changes in cotton gin energy consumption apportioned by ten functions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The public is concerned about air quality and sustainability. Cotton producers, gin owners and plant managers are concerned about rising energy prices. Both have an interest in cotton gin energy consumption trends. Changes in cotton gins’ energy consumption over the past fifty years, a period of ...

  14. Quasar Spectral Energy Distributions As A Function Of Physical Property

    NASA Astrophysics Data System (ADS)

    Townsend, Shonda; Ganguly, R.; Stark, M. A.; Derseweh, J. A.; Richmond, J. M.

    2012-05-01

    Galaxy evolution models have shown that quasars are a crucial ingredient in the evolution of massive galaxies. Outflows play a key role in the story of quasars and their host galaxies, by helping regulate the accretion process, the star-formation rate and mass of the host galaxy (i.e., feedback). The prescription for modeling outflows as a contributor to feedback requires knowledge of the outflow velocity, geometry, and column density. In particular, we need to understand how these depend on physical parameters and how much is determined stochastically (and with what distribution). In turn, models of outflows have shown particular sensitivity to the shape of the spectral energy distribution (SED), depending on the UV luminosity to transfer momentum to the gas, the X-ray luminosity to regulate how efficiently that transfer can be, etc. To investigate how SED changes with physical properties, we follow up on Richards et al. (2006), who constructed SEDs with varying luminosity. Here, we construct SEDs as a function of redshift, and physical property (black hole mass, bolometric luminosity, Eddington ratio) for volume limited samples drawn from the Sloan Digital Sky Survey, with photometry supplemented from 2MASS, WISE, GALEX, ROSAT, and Chandra. To estimate black hole masses, we adopt the scaling relations from Greene & Ho (2005) based on the H-alpha emission line FWHM. This requires redshifts less than 0.4. To construct volume-limited subsamples, we begin by adopting g=19.8 as a nominal limiting magnitude over which we are guaranteed to detect z<0.4 quasars. At redshift 0.4, we are complete down to Mg=-21.8, which yields 3300 objects from Data Release 7. At z=0.1, we are complete down to Mg=-18.5. This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. 09-ADP09-0016 issued through the Astrophysics Data Analysis Program.

  15. Protein-energy malnutrition impairs functional outcome in global ischemia.

    PubMed

    Bobyn, P Joan; Corbett, Dale; Saucier, Deborah M; Noyan-Ashraf, M Hossein; Juurlink, Bernhard H J; Paterson, Phyllis G

    2005-12-01

    We investigated whether protein-energy malnutrition (PEM) exacerbates brain injury in global ischemia. It was hypothesized that PEM would increase secondary brain damage by worsening ischemia-induced depletion of glutathione (GSH) and increasing oxidative stress. Adult male gerbils were fed an adequate protein (12.5%; C) or low protein (2%; PEM) diet for 4 weeks and subjected to 5 min of bilateral carotid artery occlusion (Ischemia) or sham surgery (Sham). At 12 h post-ischemia, GSH and markers of oxidative stress were measured in hippocampus and neocortex. The remaining gerbils were tested in the open field on days 3, 7, and 10, with viable hippocampal CA1 neurons assessed on day 10. Although the habituation of C-Ischemia gerbils in the open field was normal by day 7, PEM-Ischemia gerbils failed to habituate even by day 10 and spent greater time in the outer zone (P < 0.05). Mean (+/-SEM) total number of viable CA1 neurons at 10 days post-ischemia were C-Sham = 713 (13), C-Ischemia = 264 (48), PEM-Sham = 716 (12), and PEM-Ischemia = 286 (66). Although PEM did not increase CA1 neuron loss caused by ischemia, a subset (4/12) of PEM-Ischemia gerbils showed dramatic reactive gliosis accompanied by extensive neuronal loss. Hippocampal protein thiols were decreased by PEM and ischemia. Although the mechanism is yet to be established, the finding that PEM worsens functional outcome following global ischemia is clinically relevant since 16% of elderly are nutritionally compromised at the time of admission for stroke.

  16. Recycling Energy to Restore Impaired Ankle Function during Human Walking

    PubMed Central

    Collins, Steven H.; Kuo, Arthur D.

    2010-01-01

    Background Humans normally dissipate significant energy during walking, largely at the transitions between steps. The ankle then acts to restore energy during push-off, which may be the reason that ankle impairment nearly always leads to poorer walking economy. The replacement of lost energy is necessary for steady gait, in which mechanical energy is constant on average, external dissipation is negligible, and no net work is performed over a stride. However, dissipation and replacement by muscles might not be necessary if energy were instead captured and reused by an assistive device. Methodology/Principal Findings We developed a microprocessor-controlled artificial foot that captures some of the energy that is normally dissipated by the leg and “recycles” it as positive ankle work. In tests on subjects walking with an artificially-impaired ankle, a conventional prosthesis reduced ankle push-off work and increased net metabolic energy expenditure by 23% compared to normal walking. Energy recycling restored ankle push-off to normal and reduced the net metabolic energy penalty to 14%. Conclusions/Significance These results suggest that reduced ankle push-off contributes to the increased metabolic energy expenditure accompanying ankle impairments, and demonstrate that energy recycling can be used to reduce such cost. PMID:20174659

  17. Energy density functional analysis of shape coexistence in {sup 44}S

    SciTech Connect

    Li, Z. P.; Yao, J. M.; Vretenar, D.; Niksic, T.; Meng, J.

    2012-10-20

    The structure of low-energy collective states in the neutron-rich nucleus {sup 44}S is analyzed using a microscopic collective Hamiltonian model based on energy density functionals (EDFs). The calculated triaxial energy map, low-energy spectrum and corresponding probability distributions indicate a coexistence of prolate and oblate shapes in this nucleus.

  18. Symmetry Energy as a Function of Density and Mass

    SciTech Connect

    Danielewicz, Pawel; Lee, Jenny

    2007-10-26

    Energy in nuclear matter is, in practice, completely characterized at different densities and asymmetries, when the density dependencies of symmetry energy and of energy of symmetric matter are specified. The density dependence of the symmetry energy at subnormal densities produces mass dependence of nuclear symmetry coefficient and, thus, can be constrained by that latter dependence. We deduce values of the mass dependent symmetry coefficients, by using excitation energies to isobaric analog states. The coefficient systematic, for intermediate and high masses, is well described in terms of the symmetry coefficient values of a{sub a}{sup V} = (31.5-33.5) MeV for the volume coefficient and a{sub a}{sup S} = (9-12) MeV for the surface coefficient. These two further correspond to the parameter values describing density dependence of symmetry energy, of L{approx}95 MeV and K{sub sym}{approx}25 MeV.

  19. Energy-like Liapunov functionals for linear elastic systems on a Hilbert space.

    NASA Technical Reports Server (NTRS)

    Walker, J. A.

    1973-01-01

    An approach is presented for generating energy-like functionals for linear elastic dynamic systems on a Hilbert space. The objective is to obtain a family of functionals which may be used for stability analysis of the equilibrium, i.e., Liapunov functionals. Although the energy functional, when one exists, is always a member of this family, the family is shown to exist even when an energy functional does not. Several discrete and distributed-parameter examples are presented, as are certain specific techniques for utilizing this approach.

  20. All-atom Simulation of Amyloid Aggregates

    NASA Astrophysics Data System (ADS)

    Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.

    Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.

  1. Propagation of spectral functions and dilepton production at SIS energies

    SciTech Connect

    Wolf, Gy.; Kaempfer, B.; Zetenyi, M.

    2012-06-15

    The time evolution of vector meson spectral functions is studied within a BUU-type transport model. Applications focus on {rho} and {omega} mesons being important pieces for the interpretation of the dielectron invariant mass spectrum. Since the evolution of the spectral functions is driven by the local density, the inmedium modifications turn out to compete, in this approach, with the known vacuum contributions.

  2. Binding Energy of d¹º Transition Metals to Alkenes By Wave Function Theory and Density Functional Theory

    SciTech Connect

    Averkiev, Boris B; Zhao, Yan; Truhlar, Donald G

    2010-06-01

    The structures of Pd(PH₃)₂ and Pt(PH₃)₂ complexes with ethene and conjugated CnHn+2 systems (n=4, 6, 8, and 10) were studied. Their binding energies were calculated using both wave function theory (WFT) and density functional theory (DFT). Previously it was reported that the binding energy of the alkene to the transition metal does not depend strongly on the size of the conjugated CnHn+2 ligand, but that DFT methods systematically underestimate the binding energy more and more significantly as the size of the conjugated system is increased. Our results show that recently developed density functionals predict the binding energy for these systems much more accurately. New benchmark calculations carried out by the coupled cluster method based on Brueckner orbitals with double excitations and a quasiperturbative treatment of connected triple excitations (BCCD(T)) with a very large basis set agree even better with the DFT predictions than do the previous best estimates. The mean unsigned error in absolute and relative binding energies of the alkene ligands to Pd(PH₃)₂ is 2.5 kcal/mol for the ωB97 and M06 density functionals and 2.9 kcal/mol for the M06-L functional. Adding molecular mechanical damped dispersion yields even smaller mean unsigned errors: 1.3 kcal/mol for the M06-D functional, 1.5 kcal/mol for M06- L-D, and 1.8 kcal/mol for B97-D and ωB97X-D. The new functionals also lead to improved accuracy for the analogous Pt complexes. These results show that recently developed density functionals may be very useful for studying catalytic systems involving Pd d¹º centers and alkenes.

  3. The energy spectra of solar energetic protons in the large energy range: their functional form and parameters.

    NASA Astrophysics Data System (ADS)

    Nymmik, Rikho; Pervaia, Taisia

    2016-07-01

    Experimental data on the fluxes of protons of solar energetic particles (SEP) are analyzed. It is known that above energies of 2-45 MeV (averaging 27-30 MeV), the proton spectra are a power-law function of the energy (at relativistic energies - from the momentum) of the particles. At lower energies, the spectra become harder, with the high-energy part of the spectra forming the "knee". This report is devoted to the determination of the parameters of the SEP spectra, having the form of a "double power-law shape", to ascertain the reliability of the parameters of the approximations of the experimental data.

  4. The Changes of Energy Interactions between Nucleus Function and Mitochondria Functions Causing Transmutation of Chronic Inflammation into Cancer Metabolism.

    PubMed

    Ponizovskiy, Michail R

    2016-01-01

    Interactions between nucleus and mitochondria functions induce the mechanism of maintenance stability of cellular internal energy according to the first law of thermodynamics in able-bodied cells and changes the mechanisms of maintenance stability of cellular internal energy creating a transition stationary state of ablebodied cells into quasi-stationary pathologic states of acute inflammation transiting then into chronic inflammation and then transmuting into cancer metabolism. The mechanisms' influences of intruding etiologic pathologic agents (microbe, virus, etc.) lead to these changes of energy interactions between nucleus and mitochondria functions causing general acute inflammation, then passing into local chronic inflammation, and reversing into cancer metabolism transmutation. Interactions between biochemical processes and biophysical processes of cellular capacitors' operations create a supplementary mechanism of maintenance stability of cellular internal energy in the norm and in pathology. Discussion of some scientific works eliminates doubts of the authors of these works. PMID:27480780

  5. Energy level alignment and quantum conductance of functionalized metal-molecule junctions: Density functional theory versus GW calculations

    SciTech Connect

    Jin, Chengjun; Markussen, Troels; Thygesen, Kristian S.; Strange, Mikkel; Solomon, Gemma C.

    2013-11-14

    We study the effect of functional groups (CH{sub 3}*4, OCH{sub 3}, CH{sub 3}, Cl, CN, F*4) on the electronic transport properties of 1,4-benzenediamine molecular junctions using the non-equilibrium Green function method. Exchange and correlation effects are included at various levels of theory, namely density functional theory (DFT), energy level-corrected DFT (DFT+Σ), Hartree-Fock and the many-body GW approximation. All methods reproduce the expected trends for the energy of the frontier orbitals according to the electron donating or withdrawing character of the substituent group. However, only the GW method predicts the correct ordering of the conductance amongst the molecules. The absolute GW (DFT) conductance is within a factor of two (three) of the experimental values. Correcting the DFT orbital energies by a simple physically motivated scissors operator, Σ, can bring the DFT conductances close to experiments, but does not improve on the relative ordering. We ascribe this to a too strong pinning of the molecular energy levels to the metal Fermi level by DFT which suppresses the variation in orbital energy with functional group.

  6. Is there a low-energy enhancement in the photon strength function in molybdenum?

    SciTech Connect

    Sheets, S. A.

    2008-04-17

    Recent claims of a low-energy enhancement in the photon strength function of {sup 96}Mo are investigated. Using the DANCE detector the gamma-ray spectra following resonance neutron capture was measured. The spectrum fitting method was used to indirectly extract a photon strength function from the gamma-ray spectra. No strong low energy enhancement in the photon strength function was found.

  7. Expanded explorations into the optimization of an energy function for protein design

    PubMed Central

    Huang, Yao-ming; Bystroff, Christopher

    2014-01-01

    Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the existence of a general energy function for proteins is by no means guaranteed. Here we present new insights towards the application of machine learning to the problem of finding a general energy function for protein design. Machine learning requires the definition of an objective function, which carries with it the implied definition of success in protein design. We explored four functions, consisting of two functional forms, each with two criteria for success. Optimization was carried out by a Monte Carlo search through the space of all variable parameters. Cross-validation of the optimized energy function against a test set gave significantly different results depending on the choice of objective function, pointing to relative correctness of the built-in assumptions. Novel energy cross-terms correct for the observed non-additivity of energy terms and an imbalance in the distribution of predicted amino acids. This paper expands on the work presented at ACM-BCB, Orlando FL , October 2012. PMID:24384706

  8. Expanded explorations into the optimization of an energy function for protein design.

    PubMed

    Huang, Yao-Ming; Bystroff, Christopher

    2013-01-01

    Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the existence of a general energy function for proteins is by no means guaranteed. Here, we present new insights toward the application of machine learning to the problem of finding a general energy function for protein design. Machine learning requires the definition of an objective function, which carries with it the implied definition of success in protein design. We explored four functions, consisting of two functional forms, each with two criteria for success. Optimization was carried out by a Monte Carlo search through the space of all variable parameters. Cross-validation of the optimized energy function against a test set gave significantly different results depending on the choice of objective function, pointing to relative correctness of the built-in assumptions. Novel energy cross terms correct for the observed nonadditivity of energy terms and an imbalance in the distribution of predicted amino acids. This paper expands on the work presented at the 2012 ACM-BCB.

  9. Longitudinal trial functions and the cosmic ray energy scale

    NASA Technical Reports Server (NTRS)

    Linsley, J.

    1985-01-01

    Formulae which were proposed to represent the longitudinal profiles of cosmic ray air showers are compared, and the physical interpretation of their parameters is examined. Applications to the problem of energy calibration are pointed out. Adoption of a certain especially simple formula is recommended, and its use is illustrated.

  10. Visualization of Potential Energy Function Using an Isoenergy Approach and 3D Prototyping

    ERIC Educational Resources Information Center

    Teplukhin, Alexander; Babikov, Dmitri

    2015-01-01

    In our three-dimensional world, one can plot, see, and comprehend a function of two variables at most, V(x,y). One cannot plot a function of three or more variables. For this reason, visualization of the potential energy function in its full dimensionality is impossible even for the smallest polyatomic molecules, such as triatomics. This creates…

  11. The effect of bond functions on dissociation energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.

    1985-01-01

    The procedure employing bond functions recently suggested by Wright and Buenker has been applied to the N2 X 1 Sigma g + potential curve within the CAS SCF + MRSD CI treatment of electron correlation. The basis set used herein is identical to that employed by these authors in their SCF + CI calculations. The De and and the shape of the resulting potential curve, as judged by the computed vibrational levels, is not so accurate as would be expected from the results reported by Wright and Buenker (1984). The results indicate that using the CI superposition errors associated with bond functions to cancel basis set incompleteness depends on the treatment of the electron correlation.

  12. Functional zinc oxide nanostructures for electronic and energy applications

    NASA Astrophysics Data System (ADS)

    Prasad, Abhishek

    ZnO has proven to be a multifunctional material with important nanotechnological applications. ZnO nanostructures can be grown in various forms such as nanowires, nanorods, nanobelts, nanocombs etc. In this work, ZnO nanostructures are grown in a double quartz tube configuration thermal Chemical Vapor Deposition (CVD) system. We focus on functionalized ZnO Nanostructures by controlling their structures and tuning their properties for various applications. The following topics have been investigated: (1) We have fabricated various ZnO nanostructures using a thermal CVD technique. The growth parameters were optimized and studied for different nanostructures. (2) We have studied the application of ZnO nanowires (ZnONWs) for field effect transistors (FETs). Unintentional n-type conductivity was observed in our FETs based on as-grown ZnO NWs. We have then shown for the first time that controlled incorporation of hydrogen into ZnO NWs can introduce p-type characters to the nanowires. We further found that the n-type behaviors remained, leading to the ambipolar behaviors of hydrogen incorporated ZnO NWs. Importantly, the detected p- and n- type behaviors are stable for longer than two years when devices were kept in ambient conditions. All these can be explained by an ab initio model of Zn vacancy-Hydrogen complexes, which can serve as the donor, acceptors, or green photoluminescence quencher, depend on the number of hydrogen atoms involved. (3) Next ZnONWs were tested for electron field emission. We focus on reducing the threshold field (Eth) of field emission from non-aligned ZnO NWs. As encouraged by our results on enhancing the conductivity of ZnO NWs by hydrogen annealing described in Chapter 3, we have studied the effect of hydrogen annealing for improving field emission behavior of our ZnO NWs. We found that optimally annealed ZnO NWs offered much lower threshold electric field and improved emission stability. We also studied field emission from ZnO NWs at moderate

  13. AMPK: a master energy regulator for gonadal function.

    PubMed

    Bertoldo, Michael J; Faure, Melanie; Dupont, Joëlle; Froment, Pascal

    2015-01-01

    From C. elegans to mammals (including humans), nutrition and energy metabolism significantly influence reproduction. At the cellular level, some detectors of energy status indicate whether energy reserves are abundant (obesity), or poor (diet restriction). One of these detectors is AMPK (5' AMP-activated protein kinase), a protein kinase activated by ATP deficiency but also by several natural substances such as polyphenols or synthetic molecules like metformin, used in the treatment of insulin resistance. AMPK is expressed in muscle and liver, but also in the ovary and testis. This review focuses on the main effects of AMPK identified in gonadal cells. We describe the role of AMPK in gonadal steroidogenesis, in proliferation and survival of somatic gonadal cells and in the maturation of oocytes or spermatozoa. We discuss also the role of AMPK in germ and somatic cell interactions within the cumulus-oocyte complex and in the blood testis barrier. Finally, the interface in the gonad between AMPK and modification of metabolism is reported and discussion about the role of AMPK on fertility, in regards to the treatment of infertility associated with insulin resistance (male obesity, polycystic ovary syndrome). PMID:26236179

  14. AMPK: a master energy regulator for gonadal function

    PubMed Central

    Bertoldo, Michael J.; Faure, Melanie; Dupont, Joëlle; Froment, Pascal

    2015-01-01

    From C. elegans to mammals (including humans), nutrition and energy metabolism significantly influence reproduction. At the cellular level, some detectors of energy status indicate whether energy reserves are abundant (obesity), or poor (diet restriction). One of these detectors is AMPK (5′ AMP-activated protein kinase), a protein kinase activated by ATP deficiency but also by several natural substances such as polyphenols or synthetic molecules like metformin, used in the treatment of insulin resistance. AMPK is expressed in muscle and liver, but also in the ovary and testis. This review focuses on the main effects of AMPK identified in gonadal cells. We describe the role of AMPK in gonadal steroidogenesis, in proliferation and survival of somatic gonadal cells and in the maturation of oocytes or spermatozoa. We discuss also the role of AMPK in germ and somatic cell interactions within the cumulus-oocyte complex and in the blood testis barrier. Finally, the interface in the gonad between AMPK and modification of metabolism is reported and discussion about the role of AMPK on fertility, in regards to the treatment of infertility associated with insulin resistance (male obesity, polycystic ovary syndrome). PMID:26236179

  15. Evaluation of the Effects of Different Energy Drinks and Coffee on Endothelial Function.

    PubMed

    Molnar, Janos; Somberg, John C

    2015-11-01

    Endothelial function plays an important role in circulatory physiology. There has been differing reports on the effect of energy drink on endothelial function. We set out to evaluate the effect of 3 energy drinks and coffee on endothelial function. Endothelial function was evaluated in healthy volunteers using a device that uses digital peripheral arterial tonometry measuring endothelial function as the reactive hyperemia index (RHI). Six volunteers (25 ± 7 years) received energy drink in a random order at least 2 days apart. Drinks studied were 250 ml "Red Bull" containing 80 mg caffeine, 57 ml "5-hour Energy" containing 230 mg caffeine, and a can of 355 ml "NOS" energy drink containing 120 mg caffeine. Sixteen volunteers (25 ± 5 years) received a cup of 473 ml coffee containing 240 mg caffeine. Studies were performed before drink (baseline) at 1.5 and 4 hours after drink. Two of the energy drinks (Red Bull and 5-hour Energy) significantly improved endothelial function at 4 hours after drink, whereas 1 energy drink (NOS) and coffee did not change endothelial function significantly. RHI increased by 82 ± 129% (p = 0.028) and 63 ± 37% (p = 0.027) after 5-hour Energy and Red Bull, respectively. The RHI changed after NOS by 2 ± 30% (p = 1.000) and by 7 ± 30% (p = 1.000) after coffee. In conclusion, some energy drinks appear to significantly improve endothelial function. Caffeine does not appear to be the component responsible for these differences.

  16. Active electron energy distribution function control in direct current discharge using an auxiliary electrode

    SciTech Connect

    Schweigert, I. V.; Kaganovich, I. D.; Demidov, V. I.

    2013-10-15

    The electron energy distribution functions are studied in the low voltage dc discharge with a constriction, which is a diaphragm with an opening. The dc discharge glows in helium and is sustained by the electron current emitted from a heated cathode. We performed kinetic simulations of dc discharge characteristics and electron energy distribution functions for different gas pressures (0.8 Torr-4 Torr) and discharge current of 0.1 A. The results of these simulations indicate the ability to control the shape of the electron energy distribution functions by variation of the diaphragm opening radius.

  17. Functional determinants and Casimir energy in higher dimensional spherically symmetric background potentials

    NASA Astrophysics Data System (ADS)

    Fucci, Guglielmo; Kirsten, Klaus

    2016-07-01

    In this paper we analyze the spectral zeta function associated with a Laplace operator acting on scalar functions on an N-dimensional Euclidean space in the presence of a spherically symmetric background potential. The obtained analytic continuation of the spectral zeta function is then used to derive very simple results for the functional determinant of the operator and the Casimir energy of the scalar field.

  18. Phosphorylation Energy Hypothesis: Open Chemical Systems and Their Biological Functions

    NASA Astrophysics Data System (ADS)

    Qian, Hong

    2007-05-01

    Biochemical systems and processes in living cells generally operate far from equilibrium. This review presents an overview of a statistical thermodynamic treatment for such systems, with examples from several key components in cellular signal transduction. Open-system nonequilibrium steady-state (NESS) models are introduced. The models account quantitatively for the energetics and thermodynamics in phosphorylation-dephosphorylation switches, GTPase timers, and specificity amplification through kinetic proofreading. The chemical energy derived from ATP and GTP hydrolysis establishes the NESS of a cell and makes the cell—a mesoscopic-biochemical reaction system that consists of a collection of thermally driven fluctuating macromolecules—a genetically programmed chemical machine.

  19. Nanoscale friction as a function of activation energies

    NASA Astrophysics Data System (ADS)

    Chong, W. W. F.; Rahnejat, H.

    2015-12-01

    Understanding the scale-dependence of friction is increasingly viewed as a critical quest. With progressively thinner films, mixed and boundary regimes of lubrication have become commonplace. Therefore, at the micro-scale a greater need for mitigating friction is desired in order to improve operational efficiency of many machines and mechanisms. Furthermore, there is a growing tendency to use low friction hard wear-resistant advanced coatings to guard against wear. In parallel, there has been much attention paid to lubricant rheology and formulation. However, only in recent times there has been an emerging view of lubricant-surface combination as a system. In this perspective it is essential to relate the observed and measured friction at component level to the underlying interactions in micro/nano-scales. This is the approach in this paper. Observed phenomenon at micro-scale are related back to the activation energies of lubricant-surface system, providing in particular results for surface modified Ni-SiC coated specimen in combination with formulated lubricants, the combination of which represent the lubricant-surface system of choice in cylinders of high performance race engine. The nano-scale conjunction of an AFM tip with lubricated surface-engineered specimen, subjected to various conjunctional loading and sliding kinematics is investigated. It is shown that the measured frictional characteristics can be adequately described in terms of activation energies in line with the Eyring’s thermal activation model for cases of fairly smooth asperity tip contact conjunctions.

  20. Description of induced nuclear fission with Skyrme energy functionals. II. Finite temperature effects

    NASA Astrophysics Data System (ADS)

    Schunck, N.; Duke, D.; Carr, H.

    2015-03-01

    Understanding the mechanisms of induced nuclear fission for a broad range of neutron energies could help resolve fundamental science issues, such as the formation of elements in the universe, but could have also a large impact on societal applications in energy production or nuclear waste management. The goal of this paper is to set up the foundations of a microscopic theory to study the static aspects of induced fission as a function of the excitation energy of the incident neutron, from thermal to fast neutrons. To account for the high excitation energy of the compound nucleus, we employ a statistical approach based on finite temperature nuclear density functional theory with Skyrme energy densities, which we benchmark on the 239Pu(n ,f ) reaction. We compute the evolution of the least-energy fission pathway across multidimensional potential energy surfaces with up to five collective variables as a function of the nuclear temperature and predict the evolution of both the inner and the outer fission barriers as a function of the excitation energy of the compound nucleus. We show that the coupling to the continuum induced by the finite temperature is negligible in the range of neutron energies relevant for many applications of neutron-induced fission. We prove that the concept of quantum localization introduced recently can be extended to T >0 , and we apply the method to study the interaction energy and total kinetic energy of fission fragments as a function of the temperature for the most probable fission. While large uncertainties in theoretical modeling remain, we conclude that a finite temperature nuclear density functional may provide a useful framework to obtain accurate predictions of fission fragment properties.

  1. Linearity condition for orbital energies in density functional theory (V): Extension to excited state calculations

    NASA Astrophysics Data System (ADS)

    Imamura, Yutaka; Suzuki, Kensei; Iizuka, Takeshi; Nakai, Hiromi

    2015-01-01

    A new scheme is proposed for constructing an orbital-specific (OS) exchange-correlation functional that satisfies multiple linearity conditions for orbital energies (LCOEs). The Hartree-Fock exchange portions in the OS exchange-correlation functional, based on a multiply range-separated functional, are set so as to satisfy the multiple LCOEs. The current scheme has also been extended to calculations of core, valence, and Rydberg excitations. Numerical assessments on ionization potentials, electron affinities and excitation energies have confirmed accurate descriptions of core, valence, and Rydberg orbitals by the OS hybrid functional.

  2. Spectroscopic properties of nuclear skyrme energy density functionals.

    PubMed

    Tarpanov, D; Dobaczewski, J; Toivanen, J; Carlsson, B G

    2014-12-19

    We address the question of how to improve the agreement between theoretical nuclear single-particle energies (SPEs) and observations. Empirically, in doubly magic nuclei, the SPEs can be deduced from spectroscopic properties of odd nuclei that have one more or one less neutron or proton. Theoretically, bare SPEs, before being confronted with observations, must be corrected for the effects of the particle vibration coupling (PVC). In the present work, we determine the PVC corrections in a fully self-consistent way. Then, we adjust the SPEs, with PVC corrections included, to empirical data. In this way, the agreement with observations, on average, improves; nevertheless, large discrepancies still remain. We conclude that the main source of disagreement is still in the underlying mean fields, and not in including or neglecting the PVC corrections.

  3. The curvature elastic-energy function of the lipid-water cubic mesophase

    NASA Astrophysics Data System (ADS)

    Chung, Hesson; Caffrey, Martin

    1994-03-01

    CELL and lipid membranes are able to bend, as manifested during membrane fusion and the formation of non-lamellar lyotropic mesopbases in water. But there is an energy cost to bending of lipid layers, called the curvature elastic energy. Although the functional form of this energy is known1, a complete quantitative knowledge of the curvature elastic energy, which is central to predicting the relative stability of the large number of phases that lipid membranes can adopt, has been lacking. Here we use X-ray synchrotron diffraction measurements of the variation of lattice parameter with pressure and temperature for the periodic Ia3d (Q230) cubic phase of hydrated monoolein to calculate the complete curvature elastic-energy function for the lipid cubic mesophase. This allows us to predict the stabilities of different cubic and lamellar phases for this system as a function of composition.

  4. Towards improved local hybrid functionals by calibration of exchange-energy densities

    SciTech Connect

    Arbuznikov, Alexei V. E-mail: martin.kaupp@tu-berlin.de; Kaupp, Martin E-mail: martin.kaupp@tu-berlin.de

    2014-11-28

    A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.

  5. Spinless relativistic particle in energy-dependent potential and normalization of the wave function

    NASA Astrophysics Data System (ADS)

    Benchikha, Amar; Chetouani, Lyazid

    2014-06-01

    The problem of normalization related to a Klein-Gordon particle subjected to vector plus scalar energy-dependent potentials is clarified in the context of the path integral approach. In addition the correction relating to the normalizing constant of wave functions is exactly determined. As examples, the energy dependent linear and Coulomb potentials are considered. The wave functions obtained via spectral decomposition, were found exactly normalized.

  6. Towards improved local hybrid functionals by calibration of exchange-energy densities

    NASA Astrophysics Data System (ADS)

    Arbuznikov, Alexei V.; Kaupp, Martin

    2014-11-01

    A new approach for the calibration of (semi-)local and exact exchange-energy densities in the context of local hybrid functionals is reported. The calibration functions are derived from only the electron density and its spatial derivatives, avoiding spatial derivatives of the exact-exchange energy density or other computationally unfavorable contributions. The calibration functions fulfill the seven more important out of nine known exact constraints. It is shown that calibration improves substantially the definition of a non-dynamical correlation energy term for generalized gradient approximation (GGA)-based local hybrids. Moreover, gauge artifacts in the potential-energy curves of noble-gas dimers may be corrected by calibration. The developed calibration functions are then evaluated for a large range of energy-related properties (atomization energies, reaction barriers, ionization potentials, electron affinities, and total atomic energies) of three sets of local hybrids, using a simple one-parameter local-mixing. The functionals are based on (a) local spin-density approximation (LSDA) or (b) Perdew-Burke-Ernzerhof (PBE) exchange and correlation, and on (c) Becke-88 (B88) exchange and Lee-Yang-Parr (LYP) correlation. While the uncalibrated GGA-based functionals usually provide very poor thermochemical data, calibration allows a dramatic improvement, accompanied by only a small deterioration of reaction barriers. In particular, an optimized BLYP-based local-hybrid functional has been found that is a substantial improvement over the underlying global hybrids, as well as over previously reported LSDA-based local hybrids. It is expected that the present calibration approach will pave the way towards new generations of more accurate hyper-GGA functionals based on a local mixing of exchange-energy densities.

  7. Ab initio ground-state potential energy function and vibration-rotation energy levels of imidogen, NH.

    PubMed

    Koput, Jacek

    2015-06-30

    The accurate ground-state potential energy function of imidogen, NH, has been determined from ab initio calculations using the multireference averaged coupled-pair functional (MR-ACPF) method in conjunction with the correlation-consistent core-valence basis sets up to octuple-zeta quality. The importance of several effects, including electron correlation beyond the MR-ACPF level of approximation, the scalar relativistic, adiabatic, and nonadiabatic corrections were discussed. Along with the large one-particle basis set, all of these effects were found to be crucial to attain "spectroscopic" accuracy of the theoretical predictions of vibration-rotation energy levels of NH.

  8. Long-range correlation energy calculated from coupled atomic response functions

    SciTech Connect

    Ambrosetti, Alberto; Reilly, Anthony M.; Tkatchenko, Alexandre; DiStasio, Robert A.

    2014-05-14

    An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy.

  9. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics.

    PubMed

    Koretke, K K; Luthey-Schulten, Z; Wolynes, P G

    1998-03-17

    The protein energy landscape theory is used to obtain optimal energy functions for protein structure prediction via simulated annealing. The analysis here takes advantage of a more complete statistical characterization of the protein energy landscape and thereby improves on previous approximations. This schema partially takes into account correlations in the energy landscape. It also incorporates the relationships between folding dynamics and characteristic energy scales that control the collapse of the proteins and modulate rigidity of short-range interactions. Simulated annealing for the optimal energy functions, which are associative memory hamiltonians using a database of folding patterns, generally leads to quantitatively correct structures. In some cases the algorithm achieves "creativity," i.e., structures result that are better than any homolog in the database.

  10. Modeling the Transfer Function for the Dark Energy Survey

    DOE PAGES

    Chang, C.

    2015-03-04

    We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with themore » corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.« less

  11. Modeling the Transfer Function for the Dark Energy Survey

    SciTech Connect

    Chang, C.

    2015-03-04

    We present a forward-modeling simulation framework designed to model the data products from the Dark Energy Survey (DES). This forward-model process can be thought of as a transfer function—a mapping from cosmological/astronomical signals to the final data products used by the scientists. Using output from the cosmological simulations (the Blind Cosmology Challenge), we generate simulated images (the Ultra Fast Image Simulator) and catalogs representative of the DES data. In this work we demonstrate the framework by simulating the 244 deg2 coadd images and catalogs in five bands for the DES Science Verification data. The simulation output is compared with the corresponding data to show that major characteristics of the images and catalogs can be captured. We also point out several directions of future improvements. Two practical examples—star-galaxy classification and proximity effects on object detection—are then used to illustrate how one can use the simulations to address systematics issues in data analysis. With clear understanding of the simplifications in our model, we show that one can use the simulations side-by-side with data products to interpret the measurements. This forward modeling approach is generally applicable for other upcoming and future surveys. It provides a powerful tool for systematics studies that is sufficiently realistic and highly controllable.

  12. Energy distribution functions of kilovolt ions in a modified Penning discharge

    NASA Technical Reports Server (NTRS)

    Roth, J. R.

    1972-01-01

    The distribution function of ion energy parallel to the magnetic field of a Penning discharge was measured with a retarding potential energy analyzer. Simultaneous measurements of the ion energy distribution function perpendicular to the magnetic field were made with a charge-exchange neutral detector. The ion energy distribution functions are approximately Maxwellian, and their kinetic temperatures are equal within experimental error. This suggests that turbulent processes previously observed Maxwellianize the velocity distribution along a radius in velocity space, and result in an isotropic energy distribution. The kinetic temperatures are on the order of kilovolts, and the tails of the ion energy distribution functions are Maxwellian up to a factor of 7 e-folds in energy. When the distributions depart from Maxwellian, they are enhanced above the Maxwellian tail. Above densities of about 10 to the 10th power particles/cc, this enhancement appears to be the result of a second, higher temperature Maxwellian distribution. At these high particle energies, only the ions perpendicular to the magnetic field lines were investigated.

  13. Fully nonlocal kinetic energy density functionals: a proposal and a general assessment for atomic systems.

    PubMed

    García-Aldea, David; Alvarellos, J E

    2008-08-21

    Following some recent ideas on the construction of kinetic energy density functionals that reproduce the linear response function of the homogeneous electron gas, a family of them with a nonlocal term based on the von Weizsacker functional and with a dependence on the logarithm of the density is presented. As localized systems are the most difficult to study with explicit kinetic functionals, in this paper we apply to atomic systems a number of families of fully nonlocal kinetic functionals. We have put our attention in both the total kinetic energy and the local behavior of the kinetic energy density, and the results clearly show the quality of these fully nonlocal functionals. They make a good description of the local behavior of the kinetic energy density and maintain good results for the total kinetic energies. We must remark that almost all the functionals discussed in the paper, when using an adequate reference density, can be evaluated as a single integral in momentum space, with a quasilinear scaling for the computational cost.

  14. A twisted wire-shaped dual-function energy device for photoelectric conversion and electrochemical storage.

    PubMed

    Sun, Hao; You, Xiao; Deng, Jue; Chen, Xuli; Yang, Zhibin; Chen, Peining; Fang, Xin; Peng, Huisheng

    2014-06-23

    A wire-shaped energy device that can perform photoelectric conversion and electrochemical storage was developed through a simple but effective twisting process. The energy wire exhibited a high energy conversion efficiency of 6.58 % and specific capacitance of 85.03 μF cm(-1) or 2.13 mF cm(-2), and the two functions were alternately realized without sacrificing either performance.

  15. Atomic electron energies including relativistic effects and quantum electrodynamic corrections

    NASA Technical Reports Server (NTRS)

    Aoyagi, M.; Chen, M. H.; Crasemann, B.; Huang, K. N.; Mark, H.

    1977-01-01

    Atomic electron energies have been calculated relativistically. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all orbitals in all atoms with 2 less than or equal to Z less than or equal to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. These results will serve for detailed comparison of calculations based on other approaches. The magnitude of quantum electrodynamic corrections is exhibited quantitatively for each state.

  16. Functional Metal Oxide Nanostructures: Their Synthesis, Characterization, and Energy Applications

    NASA Astrophysics Data System (ADS)

    Iyer, Aparna

    This research focuses on studying metal oxides (MnO 2, Co3O4, MgO, Y2O3) for various applications including water oxidation and photocatalytic oxidation, developing different synthesis methodologies, and presenting detailed characterization studies of these metal oxides. This research consists of three major parts. The first part is studying novel applications and developing a synthesis method for manganese oxide nanomaterials. Manganese oxide materials were studied for renewable energy applications by using them as catalysts for water oxidation reactions. In this study, various crystallographic forms of manganese oxides (amorphous, 2D layered, 1D 2 x 2 tunnel structures) were evaluated for water oxidation catalysis. Amorphous manganese oxides (AMO) were found to be catalytically active for chemical and photochemical water oxidation compared to cryptomelane type tunnel manganese oxides (2 x 2 tunnels; OMS2) or layered birnessite (OL-1) materials. Detailed characterization was done to establish a correlation between the properties of the manganese oxide materials and their catalytic activities in water oxidation. The gas phase photocatalytic oxidation of 2-propanol under visible light was studied using manganese oxide 2 x 2 tunnel structures (OMS-2) as catalysts (Chapter 3). The reaction is 100% selective to acetone. As suggested by the photocatalytic and characterization data, important factors for the design of active OMS-2 photocatalysts are synthesis methodology, morphology, mixed valency and the release of oxygen from the OMS-2 structure. Manganese oxide octahedral molecular sieves (2 x 2 tunnels; OMS-2) with self-assembled dense or hollow sphere morphologies were fabricated via a room temperature ultrasonic atomization assisted synthesis (Chapter 4). The properties and catalytic activities of these newly developed materials were compared with that of OMS-2 synthesized by conventional reflux route. These materials exhibit exceptionally high catalytic activities

  17. Estimation of bone Calcium-to-Phosphorous mass ratio using dual-energy nonlinear polynomial functions

    NASA Astrophysics Data System (ADS)

    Sotiropoulou, P.; Koukou, V.; Martini, N.; Michail, C.; Kounadi, E.; Kandarakis, I.; Nikiforidis, G.; Fountos, G.

    2015-09-01

    In this study an analytical approximation of dual-energy inverse functions is presented for the estimation of the calcium-to-phosphorous (Ca/P) mass ratio, which is a crucial parameter in bone health. Bone quality could be examined by the X-ray dual-energy method (XDEM), in terms of bone tissue material properties. Low- and high-energy, log- intensity measurements were combined by using a nonlinear function, to cancel out the soft tissue structures and generate the dual energy bone Ca/P mass ratio. The dual-energy simulated data were obtained using variable Ca and PO4 thicknesses on a fixed total tissue thickness. The XDEM simulations were based on a bone phantom. Inverse fitting functions with least-squares estimation were used to obtain the fitting coefficients and to calculate the thickness of each material. The examined inverse mapping functions were linear, quadratic, and cubic. For every thickness, the nonlinear quadratic function provided the optimal fitting accuracy while requiring relative few terms. The dual-energy method, simulated in this work could be used to quantify bone Ca/P mass ratio with photon-counting detectors.

  18. An experimental method to obtain the elastic strain energy function from torsion-tension tests

    NASA Technical Reports Server (NTRS)

    Peng, S. T. J.; Landel, R. F.

    1976-01-01

    It is shown that by employing a torsion-tension test, it is possible to have a complete mapping near the origin of the two principal strain invariants associated with the rate of change of the strain energy function. However, the mathematical representation of the twist moment and normal forces vs strain and the strain energy function are complex. This problem is solved by using a set of solid cylindrical bars with different diameters such that the difference in diameter of two successive bars is small. The stress-strain equations can be grossly oversimplified by considering differences in twist moment and normal force as a function of difference in radius.

  19. Efficient Calculations of Dispersion Energies for Nanoscale Systems from Coupled Density Response Functions.

    PubMed

    Podeszwa, Rafał; Cencek, Wojciech; Szalewicz, Krzysztof

    2012-06-12

    Dispersion energies computed from coupled Kohn-Sham (CKS) dynamic density-density response functions are known to be highly accurate. At the same time, the computational algorithm is of only modest complexity compared to other accurate methods of dispersion energy calculation. We present a new implementation of this algorithm that removes several computational barriers present in current implementations and enables calculations of dispersion energies for systems with more than 200 atoms using more than 5000 basis functions. The improvements were mainly achieved by reorganizing the algorithm to minimize memory and disk usage. We present applications to two systems: the buckycatcher complex with fullerene and the vancomycin complex with a diacetyl-Lys-d-Ala-d-Ala bacterial wall precursor, both calculations performed with triple-ζ-quality basis sets. Our implementation makes it possible to use ab initio computed dispersion energies in popular "density functional theory plus dispersion" approaches.

  20. Adsorption on heterogeneous surfaces: site energy distribution functions from Fritz-Schlüender isotherms.

    PubMed

    Kumar, Kannuchamy Vasanth; Monteiro de Castro, Mateus Carvalho; Martinez-Escandell, Manuel; Molina-Sabio, Miguel; Rodriguez-Reinoso, Francisco

    2010-08-23

    Different site energy distribution functions based on the condensation approximation method are proposed for the liquid-phase or gas-phase adsorption equilibrium data following the Fritz-Schlüender isotherm. Energy distribution functions for the four limiting cases of the Fritz-Schlüender isotherm are also discussed. The proposed models are successfully applied to the experimental equilibrium data of nitrogen molecules at 77 K on a pitch-based activated carbon (PA) and a pitch-based activated carbon containing boron (PBA). An energy distribution function based on FS isotherm containing five parameters suggest a unimodal distribution of binding sites for carbon PA, the binding site energies being distributed as exponential or unimodal, depending on the pressure, in the case of carbon PBA. The advantages of the proposed models are discussed.

  1. Theory of Covalent Adsorbate Frontier Orbital Energies on Functionalized Light-Absorbing Semiconductor Surfaces.

    PubMed

    Yu, Min; Doak, Peter; Tamblyn, Isaac; Neaton, Jeffrey B

    2013-05-16

    Functional hybrid interfaces between organic molecules and semiconductors are central to many emerging information and solar energy conversion technologies. Here we demonstrate a general, empirical parameter-free approach for computing and understanding frontier orbital energies - or redox levels - of a broad class of covalently bonded organic-semiconductor surfaces. We develop this framework in the context of specific density functional theory (DFT) and many-body perturbation theory calculations, within the GW approximation, of an exemplar interface, thiophene-functionalized silicon (111). Through detailed calculations taking into account structural and binding energetics of mixed-monolayers consisting of both covalently attached thiophene and hydrogen, chlorine, methyl, and other passivating groups, we quantify the impact of coverage, nonlocal polarization, and interface dipole effects on the alignment of the thiophene frontier orbital energies with the silicon band edges. For thiophene adsorbate frontier orbital energies, we observe significant corrections to standard DFT (∼1 eV), including large nonlocal electrostatic polarization effects (∼1.6 eV). Importantly, both results can be rationalized from knowledge of the electronic structure of the isolated thiophene molecule and silicon substrate systems. Silicon band edge energies are predicted to vary by more than 2.5 eV, while molecular orbital energies stay similar, with the different functional groups studied, suggesting the prospect of tuning energy alignment over a wide range for photoelectrochemistry and other applications.

  2. Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

    PubMed Central

    Oferkin, Igor V.; Katkova, Ekaterina V.; Sulimov, Alexey V.; Kutov, Danil C.; Sobolev, Sergey I.; Voevodin, Vladimir V.; Sulimov, Vladimir B.

    2015-01-01

    The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method. PMID:26693223

  3. Dependence of Structural and Electronic Properties of Uranium Monochalcogenides on Exchange--Correlation Energy Functionals

    NASA Astrophysics Data System (ADS)

    Suzuki, Shugo; Ohta, Hidehisa; Komatsu, Takumi; Yasuda, Sho

    2011-08-01

    We study the dependence of the structural properties of uranium monochalcogenides, UX where X = S, Se, and Te, as well as their electronic ones on the exchange--correlation energy functionals within the spin density functional theory, carrying out all electron calculations by the fully relativistic full-potential linear-combination-of-atomic-orbitals method. We employ two functionals of the local spin density approximation (LSDA) and two functionals of the generalized gradient approximations (GGA); the former two are the Perdew--Zunger and Perdew--Wang functionals and the latter two are the Perdew--Burke--Ernzerhof (PBE) and PBEsol functionals. We also examine the effects of the relativistic correction to the LSDA exchange part of each functional. We find that, for lattice constants, bulk moduli, and cohesive energies, the results of the calculations using the PBE functional are in the best agreement with the experimental results. On the contrary, we find that calculated total magnetic moments and one-electron energies are almost the same for all the LSDA and GGA functionals employed in this work, failing to improve the agreement between the calculated and experimental results even if the gradient and relativistic corrections are included. We also find that the relativistic correction plays minor roles in both the structural and electronic properties.

  4. Kinetic Energy of Hydrocarbons as a Function of Electron Density and Convolutional Neural Networks.

    PubMed

    Yao, Kun; Parkhill, John

    2016-03-01

    We demonstrate a convolutional neural network trained to reproduce the Kohn-Sham kinetic energy of hydrocarbons from an input electron density. The output of the network is used as a nonlocal correction to conventional local and semilocal kinetic functionals. We show that this approximation qualitatively reproduces Kohn-Sham potential energy surfaces when used with conventional exchange correlation functionals. The density which minimizes the total energy given by the functional is examined in detail. We identify several avenues to improve on this exploratory work, by reducing numerical noise and changing the structure of our functional. Finally we examine the features in the density learned by the neural network to anticipate the prospects of generalizing these models.

  5. Glycolytic Enzymes Localize to Synapses under Energy Stress to Support Synaptic Function.

    PubMed

    Jang, SoRi; Nelson, Jessica C; Bend, Eric G; Rodríguez-Laureano, Lucelenie; Tueros, Felipe G; Cartagenova, Luis; Underwood, Katherine; Jorgensen, Erik M; Colón-Ramos, Daniel A

    2016-04-20

    Changes in neuronal activity create local and transient changes in energy demands at synapses. Here we discover a metabolic compartment that forms in vivo near synapses to meet local energy demands and support synaptic function in Caenorhabditis elegans neurons. Under conditions of energy stress, glycolytic enzymes redistribute from a diffuse localization in the cytoplasm to a punctate localization adjacent to synapses. Glycolytic enzymes colocalize, suggesting the ad hoc formation of a glycolysis compartment, or a "glycolytic metabolon," that can maintain local levels of ATP. Local formation of the glycolytic metabolon is dependent on presynaptic scaffolding proteins, and disruption of the glycolytic metabolon blocks the synaptic vesicle cycle, impairs synaptic recovery, and affects locomotion. Our studies indicate that under energy stress conditions, energy demands in C. elegans synapses are met locally through the assembly of a glycolytic metabolon to sustain synaptic function and behavior. VIDEO ABSTRACT.

  6. Detailed first-principles studies on surface energy and work function of hexagonal metals

    NASA Astrophysics Data System (ADS)

    Ji, De-Peng; Zhu, Quanxi; Wang, Shao-Qing

    2016-09-01

    The surface energies and work functions for ten kinds of Miller-indices surfaces of hexagonal metals, Be, Mg, Tc, Re, Ru, and Os are calculated by means of the density functional theory (DFT) method. The results show that the metals belonging to the same group have a very similar rule in work functions and surface energies. The work functions of (0001), (01 1 - 1)" separators=",, and (10 1 - 0)" separators=", surfaces are generally larger than the work functions of (11 2 - 1)" separators=",, (11 2 - 2)" separators=",, (11 2 - 3)" separators=",, and (31 4 - 0)" separators=", surfaces. In contrast to work functions, there is more regularity in the crystallographic orientation dependence of surface energies. However, for the metals belonging to different groups, there are always some differences in the exact order of orientation dependence. It is also shown that the work functions and surface energies of the main group metals decrease as they go from top to the bottom in the same group of periodic table, while for the transition metals, they do not always obey this rule.

  7. Reverse energy partitioning-An efficient algorithm for computing the density of states, partition functions, and free energy of solids.

    PubMed

    Do, Hainam; Wheatley, Richard J

    2016-08-28

    A robust and model free Monte Carlo simulation method is proposed to address the challenge in computing the classical density of states and partition function of solids. Starting from the minimum configurational energy, the algorithm partitions the entire energy range in the increasing energy direction ("upward") into subdivisions whose integrated density of states is known. When combined with the density of states computed from the "downward" energy partitioning approach [H. Do, J. D. Hirst, and R. J. Wheatley, J. Chem. Phys. 135, 174105 (2011)], the equilibrium thermodynamic properties can be evaluated at any temperature and in any phase. The method is illustrated in the context of the Lennard-Jones system and can readily be extended to other molecular systems and clusters for which the structures are known. PMID:27586913

  8. Reverse energy partitioning—An efficient algorithm for computing the density of states, partition functions, and free energy of solids

    NASA Astrophysics Data System (ADS)

    Do, Hainam; Wheatley, Richard J.

    2016-08-01

    A robust and model free Monte Carlo simulation method is proposed to address the challenge in computing the classical density of states and partition function of solids. Starting from the minimum configurational energy, the algorithm partitions the entire energy range in the increasing energy direction ("upward") into subdivisions whose integrated density of states is known. When combined with the density of states computed from the "downward" energy partitioning approach [H. Do, J. D. Hirst, and R. J. Wheatley, J. Chem. Phys. 135, 174105 (2011)], the equilibrium thermodynamic properties can be evaluated at any temperature and in any phase. The method is illustrated in the context of the Lennard-Jones system and can readily be extended to other molecular systems and clusters for which the structures are known.

  9. Generalized gradient approximation exchange energy functional with correct asymptotic behavior of the corresponding potential.

    PubMed

    Carmona-Espíndola, Javier; Gázquez, José L; Vela, Alberto; Trickey, S B

    2015-02-01

    A new non-empirical exchange energy functional of the generalized gradient approximation (GGA) type, which gives an exchange potential with the correct asymptotic behavior, is developed and explored. In combination with the Perdew-Burke-Ernzerhof (PBE) correlation energy functional, the new CAP-PBE (CAP stands for correct asymptotic potential) exchange-correlation functional gives heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies on standard test sets that are fully competitive with those obtained from other GGA-type functionals that do not have the correct asymptotic exchange potential behavior. Distinct from them, the new functional provides important improvements in quantities dependent upon response functions, e.g., static and dynamic polarizabilities and hyperpolarizabilities. CAP combined with the Lee-Yang-Parr correlation functional gives roughly equivalent results. Consideration of the computed dynamical polarizabilities in the context of the broad spectrum of other properties considered tips the balance to the non-empirical CAP-PBE combination. Intriguingly, these improvements arise primarily from improvements in the highest occupied and lowest unoccupied molecular orbitals, and not from shifts in the associated eigenvalues. Those eigenvalues do not change dramatically with respect to eigenvalues from other GGA-type functionals that do not provide the correct asymptotic behavior of the potential. Unexpected behavior of the potential at intermediate distances from the nucleus explains this unexpected result and indicates a clear route for improvement.

  10. Toward an energy function for the contact map representation of proteins.

    PubMed

    Park, K; Vendruscolo, M; Domany, E

    2000-08-01

    We analyzed several energy functions for predicting the native state of proteins from an energy minimization procedure. We derived the parameters of a given energy function by imposing the basic requirement that the energy of the native conformation of a protein is lower than that of any conformation chosen from a set of decoys. Our work is motivated by a recent result which proved that the simple pairwise contact approximation of the energy is insufficient to satisfy simultaneously such a basic requirement for all the proteins in a database. Here, we investigate the reasons of such negative results and show how to improve the predictive power of methods based on energy minimization. We generated decoys by gapless threading, and we derive energy parameters by perceptron learning. We first considered hydrophobic contributions to the energy, defined in several ways, and showed that the additional hydrophobic terms enlarge slightly the number of proteins that can be stabilized together. Next, we performed various modifications of the pairwise energy term. We introduced (1) a distinction between inter-residue contacts on the surface and in the core of a protein and (2) a simple distance-dependent pairwise interaction in which a two-tier definition of contact replaces the original (single-tier) one. Our results suggest that a detailed treatment of the pairwise potential is likely to be more relevant than the consideration of other forces. PMID:10842339

  11. Functional body composition: insights into the regulation of energy metabolism and some clinical applications.

    PubMed

    Müller, M J; Bosy-Westphal, A; Later, W; Haas, V; Heller, M

    2009-09-01

    The application of advanced methods and techniques and their continuous development enable detailed body composition analyses (BCAs) and modeling of body composition at different levels (e.g., at atomic, molecular, organ-tissue and whole body level). Functional body composition integrates body components into regulatory systems (e.g., on energy balance). Regulation of body weight is closely linked to the mass and function of individual body components. Fat mass is part of the energy intake regulatory feedback system. In addition, fat-free mass (FFM) and fat mass are both determinants of resting energy expenditure (REE). Up to 80% of the variance in energy intake and energy expenditure is explained by body composition. A deviation from normal associations between body components and function suggests a metabolic disequilibrium (e.g., in the REE-FFM relationship or in the plasma leptin-fat mass association) that may occur in response to weight changes and diseases. The concept of functional body composition adds to a more sophisticated view on nutritional status and diseases, as well as to a characterization of biomedical traits that will provide functional evidence relating genetic variants.

  12. Electron energy distribution function by using probe method in electron cyclotron resonance multicharged ion source

    SciTech Connect

    Kumakura, Sho Kurisu, Yosuke; Kimura, Daiju; Yano, Keisuke; Imai, Youta; Sato, Fuminobu; Kato, Yushi; Iida, Toshiyuki

    2014-02-15

    We are constructing a tandem type electron cyclotron resonance (ECR) ion source (ECRIS). High-energy electrons in ECRIS plasma affect electron energy distribution and generate multicharged ion. In this study, we measure electron energy distribution function (EEDF) of low energy region (≦100 eV) in ECRIS plasma at extremely low pressures (10{sup −3}–10{sup −5} Pa) by using cylindrical Langmuir probe. From the result, it is found that the EEDF correlates with the electron density and the temperature from the conventional probe analysis. In addition, we confirm that the tail of EEDF spreads to high energy region as the pressure rises and that there are electrons with high energy in ECR multicharged ion source plasma. The effective temperature estimated from the experimentally obtained EEDF is larger than the electron temperature obtained from the conventional method.

  13. Electron energy distribution function by using probe method in electron cyclotron resonance multicharged ion source.

    PubMed

    Kumakura, Sho; Kurisu, Yosuke; Kimura, Daiju; Yano, Keisuke; Imai, Youta; Sato, Fuminobu; Kato, Yushi; Iida, Toshiyuki

    2014-02-01

    We are constructing a tandem type electron cyclotron resonance (ECR) ion source (ECRIS). High-energy electrons in ECRIS plasma affect electron energy distribution and generate multicharged ion. In this study, we measure electron energy distribution function (EEDF) of low energy region (≦100 eV) in ECRIS plasma at extremely low pressures (10(-3)-10(-5) Pa) by using cylindrical Langmuir probe. From the result, it is found that the EEDF correlates with the electron density and the temperature from the conventional probe analysis. In addition, we confirm that the tail of EEDF spreads to high energy region as the pressure rises and that there are electrons with high energy in ECR multicharged ion source plasma. The effective temperature estimated from the experimentally obtained EEDF is larger than the electron temperature obtained from the conventional method.

  14. Validation of local hybrid functionals for TDDFT calculations of electronic excitation energies

    NASA Astrophysics Data System (ADS)

    Maier, Toni M.; Bahmann, Hilke; Arbuznikov, Alexei V.; Kaupp, Martin

    2016-02-01

    The first systematic evaluation of local hybrid functionals for the calculation of electronic excitation energies within linear-response time-dependent density functional theory (TDDFT) is reported. Using our recent efficient semi-numerical TDDFT implementation [T. M. Maier et al., J. Chem. Theory Comput. 11, 4226 (2015)], four simple, thermochemically optimized one-parameter local hybrid functionals based on local spin-density exchange are evaluated against a database of singlet and triplet valence excitations of organic molecules, and against a mixed database including also Rydberg, intramolecular charge-transfer (CT) and core excitations. The four local hybrids exhibit comparable performance to standard global or range-separated hybrid functionals for common singlet valence excitations, but several local hybrids outperform all other functionals tested for the triplet excitations of the first test set, as well as for relative energies of excited states. Evaluation for the combined second test set shows that local hybrids can also provide excellent Rydberg and core excitations, in the latter case rivaling specialized functionals optimized specifically for such excitations. This good performance of local hybrids for different excitation types could be traced to relatively large exact-exchange (EXX) admixtures in a spatial region intermediate between valence and asymptotics, as well as close to the nucleus, and lower EXX admixtures in the valence region. In contrast, the tested local hybrids cannot compete with the best range-separated hybrids for intra- and intermolecular CT excitation energies. Possible directions for improvement in the latter category are discussed. As the used efficient TDDFT implementation requires essentially the same computational effort for global and local hybrids, applications of local hybrid functionals to excited-state problems appear promising in a wide range of fields. Influences of current-density dependence of local kinetic-energy

  15. Molecular modeling of the binding modes of the Iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

    PubMed Central

    Mozolewska, Magdalena A.; Krupa, Paweł; Scheraga, Harold A.; Liwo, Adam

    2015-01-01

    The Iron sulfur protein 1 (Isu1) from yeast, and the J-type co-chaperone Jac1, are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the “Γ” shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105, L109, and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J. Mol. Biol. 2012, 417, 1–12). These residues were also found, by UNRES/MD simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N95, T98, P102, H112, V159, L167 and A170 of Jac1, not yet tested experimentally, were also found important in binding. PMID:25973573

  16. Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches.

    PubMed

    Mozolewska, Magdalena A; Krupa, Paweł; Scheraga, Harold A; Liwo, Adam

    2015-08-01

    The iron-sulfur protein 1 (Isu1) and the J-type co-chaperone Jac1 from yeast are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ-shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105 , L109 , and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1-12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N(95), T(98), P(102), H(112), V(159), L(167), and A(170) of Jac1, not yet tested experimentally, were also found to be important in binding.

  17. Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

    PubMed

    Guidez, Emilie B; Gordon, Mark S

    2015-03-12

    The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

  18. Using Density Functional Theory (DFT) for the Calculation of Atomization Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.

  19. Low-energy ion distribution functions on a magnetically quiet day at geostationary altitude /L = 7/

    NASA Technical Reports Server (NTRS)

    Singh, N.; Raitt, W. J.; Yasuhara, F.

    1982-01-01

    Ion energy and pitch angle distribution functions are examined for a magnetically quiet day using averaged data from ATS 6. For both field-aligned and perpendicular fluxes, the populations have a mixture of characteristic energies, and the distribution functions can be fairly well approximated by Maxwellian distributions over three different energy bands in the range 3-600 eV. Pitch angle distributions varying with local time, and energy distributions are used to compute total ion density. Pitch angle scattering mechanisms responsible for the observed transformation of pitch angle distribution are examined, and it is found that a magnetic noise of a certain power spectral density belonging to the electromagnetic ion cyclotron mode near the ion cyclotron frequency can be effective in trapping the field aligned fluxes by pitch angle scattering.

  20. Neutrophil function and energy status in Holstein cows with uterine health disorders.

    PubMed

    Hammon, D S; Evjen, I M; Dhiman, T R; Goff, J P; Walters, J L

    2006-09-15

    The objectives of this study were to investigate the associations between peripheral blood neutrophil (PMN) function, energy status, and uterine health in periparturient dairy cows. Data were collected from 83 multiparous Holstein cows. Blood samples for PMN function determination were collected weekly from 1 week prior to calving (week -1) through 4 weeks after calving and again at 8 weeks after calving. Energy metabolites were measured and dry matter intake (DMI) was determined from weeks -2 to 5 to evaluate energy status of cows during the periparturient period. All cows were examined for uterine health disorders. Blood PMN killing ability was evaluated by determining myeloperoxidase activity and cytochrome c reduction activity in isolated blood PMN's. For cows that were diagnosed with puerperal metritis and subclinical (SC) endometritis and puerperal metritis, blood PMN functions were significantly (P<0.05) impaired during the periparturient period, compared to cows with normal uterine health. Cows with subclinical endometritis and puerperal metritis or SC endometritis also had significantly (P<0.01) higher NEFA and significantly (P<0.001) lower DMI during the periparturient period, and significantly (P<0.05) higher BHBA during early lactation, compared to cows with normal uterine health. Neutrophil function was also significantly (P<0.01) impaired in cows with peripartum negative energy balance, which was characterized by elevated blood levels of NEFA and decreased DMI. Decreased PMN function and energy balance were associated with uterine health disorders and the decreases in PMN function and energy balance occurred prior to parturition and prior to the detection of these uterine disorders.

  1. A high time resolution study of the solar wind-magnetosphere energy coupling function

    NASA Technical Reports Server (NTRS)

    Akasofu, S.-I.; Carbary, J. F.; Meng, C.-I.; Sullivan, J. P.; Lepping, R. P.

    1982-01-01

    A high time resolution study of the relationships between the solar wind-magnetosphere energy coupling function and the total energy dissipation rate of the magnetosphere is made using 5-min average values of solar wind data and of the geomagnetic indices AE and Dst. All the results are essentially the same as those obtained by the earlier studies which were based on the hourly average data set. Therefore, it is confirmed that the magnetosphere is primarily a driven system

  2. Electron energy distribution function and electron characteristics of conventional and micro hollow cathode discharges

    NASA Astrophysics Data System (ADS)

    Petrov, G. M.; Zhechev, D.

    2002-05-01

    The conventional hollow cathode discharge, micro hollow cathode discharge, and the transition between them have been analyzed. The time independent and spatially averaged electron energy distribution function, electron density, mean electron energy, excitation, and ionization rates have been calculated and compared. The direct comparison showed substantial differences between the conventional and micro hollow cathode discharges, particularly in absorbed power per unit volume, degree of ionization, and excitation and ionization rates.

  3. Statistical Measurement of the Gamma-Ray Source-count Distribution as a Function of Energy

    NASA Astrophysics Data System (ADS)

    Zechlin, Hannes-S.; Cuoco, Alessandro; Donato, Fiorenza; Fornengo, Nicolao; Regis, Marco

    2016-08-01

    Statistical properties of photon count maps have recently been proven as a new tool to study the composition of the gamma-ray sky with high precision. We employ the 1-point probability distribution function of six years of Fermi-LAT data to measure the source-count distribution dN/dS and the diffuse components of the high-latitude gamma-ray sky as a function of energy. To that aim, we analyze the gamma-ray emission in five adjacent energy bands between 1 and 171 GeV. It is demonstrated that the source-count distribution as a function of flux is compatible with a broken power law up to energies of ˜50 GeV. The index below the break is between 1.95 and 2.0. For higher energies, a simple power-law fits the data, with an index of {2.2}-0.3+0.7 in the energy band between 50 and 171 GeV. Upper limits on further possible breaks as well as the angular power of unresolved sources are derived. We find that point-source populations probed by this method can explain {83}-13+7% ({81}-19+52%) of the extragalactic gamma-ray background between 1.04 and 1.99 GeV (50 and 171 GeV). The method has excellent capabilities for constraining the gamma-ray luminosity function and the spectra of unresolved blazars.

  4. Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory

    NASA Astrophysics Data System (ADS)

    Tait, E. W.; Ratcliff, L. E.; Payne, M. C.; Haynes, P. D.; Hine, N. D. M.

    2016-05-01

    Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable.

  5. Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory.

    PubMed

    Tait, E W; Ratcliff, L E; Payne, M C; Haynes, P D; Hine, N D M

    2016-05-18

    Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable. PMID:27094207

  6. Amino-functionalized green fluorescent carbon dots as surface energy transfer biosensors for hyaluronidase.

    PubMed

    Liu, Siyu; Zhao, Ning; Cheng, Zhen; Liu, Hongguang

    2015-04-21

    Amino-functionalized fluorescent carbon dots have been prepared by hydrothermal treatment of glucosamine with excess pyrophosphate. The produced carbon dots showed stabilized green emission fluorescence at various excitation wavelengths and pH environments. Herein, we demonstrate the surface energy transfer between the amino-functionalized carbon dots and negatively charged hyaluronate stabilized gold nanoparticles. Hyaluronidase can degrade hyaluronate and break down the hyaluronate stabilized gold nanoparticles to inhibit the surface energy transfer. The developed fluorescent carbon dot/gold nanoparticle system can be utilized as a biosensor for sensitive and selective detection of hyaluronidase by two modes which include fluorescence measurements and colorimetric analysis.

  7. End User Functional and Performance Requirements for HTGR Energy Supply to Industrial Processes

    SciTech Connect

    L.E. Demick

    2010-09-01

    This document specifies end user functional and performance requirements to be used in the development of the design of a high temperature gas-cooled reactor (HTGR) based plant supplying energy to industrial processes. These requirements were developed from collaboration with industry and HTGR suppliers and from detailed evaluation of integration of the HTGR technology in industrial processes. The functional and performance requirements specified herein are an effective representation of the industrial sector energy needs and an effective basis for developing a plant design that will serve the broadest range of industrial applications.

  8. The energy coupling function and the power generated by the solar wind-magnetosphere dynamo

    NASA Technical Reports Server (NTRS)

    Kan, J. R.; Lee, L. C.; Akasofu, S.-I.

    1980-01-01

    A solar wind parameter epsilon, known as the energy coupling function, has been shown to correlate with the power consumption in the magnetosphere. It is shown in the present paper that the parameter epsilon can be identified semi-quantitatively as the dynamo power delivered from the solar wind to an open magnetosphere. This identification not only provides a theoretical basis for the energy coupling function, but also constitutes an observational verification of the solar wind-magnetosphere dynamo along the magnetotail. Moreover, one can now conclude that a substorm results when the dynamo power exceeds 10 to the 18th erg/s.

  9. Relativistic Energy Density Functionals: beyond mean-field description of exotic structures

    SciTech Connect

    Vretenar, D.; Niksic, T.; Ring, P.; Lalazissis, G. A.

    2009-01-28

    The framework of relativistic energy density functionals is extended to include correlations related to the restoration of broken symmetries and to fluctuations of collective variables. The generator coordinate method is used to perform configuration mixing of angular-momentum and particle-number projected relativistic wave functions. This approach enables a quantitative description of the evolution of shell-structure, deformation and shape coexistence phenomena in nuclei with soft potential energy surfaces, and singular properties of excitation spectra and transition rates at critical points of quantum shape phase transitions.

  10. From dilute matter to the equilibrium point in the energy-density-functional theory

    NASA Astrophysics Data System (ADS)

    Yang, C. J.; Grasso, M.; Lacroix, D.

    2016-09-01

    Due to the large value of the scattering length in nuclear systems, standard density-functional theories based on effective interactions usually fail to reproduce the nuclear Fermi-liquid behavior both at very low densities and close to equilibrium. Guided on one side by the success of the Skyrme density functional and, on the other side, by resummation techniques used in effective field theories for systems with large scattering lengths, a new energy-density functional is proposed. This functional, adjusted on microscopic calculations, reproduces the nuclear equations of state of neutron and symmetric matter at various densities. Furthermore, it provides reasonable saturation properties as well as an appropriate density dependence for the symmetry energy.

  11. Covariant energy density functionals: Nuclear matter constraints and global ground state properties

    NASA Astrophysics Data System (ADS)

    Afanasjev, A. V.; Agbemava, S. E.

    2016-05-01

    The correlations between global description of the ground state properties (binding energies, charge radii) and nuclear matter properties of the state-of-the-art covariant energy density functionals have been studied. It was concluded that the strict enforcement of the constraints on the nuclear matter properties (NMP) defined in Dutra et al. [Phys. Rev. C 90, 055203 (2014), 10.1103/PhysRevC.90.055203] will not necessarily lead to the functionals with good description of the binding energies and other ground and excited state properties. In addition, it will not substantially reduce the uncertainties in the predictions of the binding energies in neutron-rich systems. It turns out that the functionals, which come close to satisfying these NMP constraints, have some problems in the description of existing data. On the other hand, these problems are either absent or much smaller in the functionals which are carefully fitted to finite nuclei but which violate some NMP constraints. This is a consequence of the fact that the properties of finite nuclei are defined not only by nuclear matter properties but also by underlying shell effects. The mismatch of phenomenological content, existing in all modern functionals, related to nuclear matter physics and the physics of finite nuclei could also be responsible.

  12. Energy of Cohesion, Compressibility, and the Potential Energy Functions of the Graphite System

    NASA Technical Reports Server (NTRS)

    Girifalco, L. A.; Lad, R. A.

    1956-01-01

    The lattice summations of the potential energy of importance in the graphite system have been computed by direct summation assuming a Lennard-Jones 6-12 potential between carbon atoms. From these summations, potential energy curves were constructed for interactions between a carbon atom and a graphite monolayer, between a carbon atom and a graphite surface, between a graphite monolayer and a semi-infinite graphite crystal and between two graphite semi-infinite crystals. Using these curves, the equilibrium distance between two isolated physically interacting carbon atoms was found to be 2.70 a, where a is the carbon-carbon distance in a graphite sheet. The distance between a surface plane and the rest of the crystal was found to be 1.7% greater than the interlayer spacing. Theoretical values of the energy of cohesion and the compressibility were calculated from the potential curve for the interaction between two semi-infinite crystals. They were (delta)E(sub c) = -330 ergs/sq cm and beta =3.18x10(exp -12)sq cm/dyne, respectively. These compared favorably with the experimental values of (delta)E(sub c) = -260 ergs/sq cm and beta = 2.97 X 10(exp -2) sq cm/dyne.

  13. Towards an Optimal Gradient-dependent Energy Functional of the PZ-SIC Form

    DOE PAGES

    Jónsson, Elvar Örn; Lehtola, Susi; Jónsson, Hannes

    2015-06-01

    Results of Perdew–Zunger self-interaction corrected (PZ-SIC) density functional theory calculations of the atomization energy of 35 molecules are compared to those of high-level quantum chemistry calculations. While the PBE functional, which is commonly used in calculations of condensed matter, is known to predict on average too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, wheremore » the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop in the exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F2 molecule being a notable outlier.« less

  14. Towards an Optimal Gradient-dependent Energy Functional of the PZ-SIC Form

    SciTech Connect

    Jónsson, Elvar Örn; Lehtola, Susi; Jónsson, Hannes

    2015-06-01

    Results of Perdew–Zunger self-interaction corrected (PZ-SIC) density functional theory calculations of the atomization energy of 35 molecules are compared to those of high-level quantum chemistry calculations. While the PBE functional, which is commonly used in calculations of condensed matter, is known to predict on average too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, where the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop in the exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F2 molecule being a notable outlier.

  15. Neutron-star matter within the energy-density functional theory and neutron-star structure

    SciTech Connect

    Fantina, A. F.; Chamel, N.; Goriely, S.; Pearson, J. M.

    2015-02-24

    In this lecture, we will present some nucleonic equations of state of neutron-star matter calculated within the nuclear energy-density functional theory using generalized Skyrme functionals developed by the Brussels-Montreal collaboration. These equations of state provide a consistent description of all regions of a neutron star. The global structure of neutron stars predicted by these equations of state will be discussed in connection with recent astrophysical observations.

  16. Complex-energy approach to sum rules within nuclear density functional theory

    NASA Astrophysics Data System (ADS)

    Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; Olsen, Erik

    2015-04-01

    Background: The linear response of the nucleus to an external field contains unique information about the effective interaction, the correlations governing the behavior of the many-body system, and the properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or the nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. Purpose: To establish an efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random-phase approximation (QRPA). Methods: To compute sum rules, we carry out contour integration of the response function in the complex-energy plane. We benchmark our results against the conventional matrix formulation of the QRPA theory, the Thouless theorem for the energy-weighted sum rule, and the dielectric theorem for the inverse-energy-weighted sum rule. Results: We derive the sum-rule expressions from the contour integration of the complex-energy FAM. We demonstrate that calculated sum-rule values agree with those obtained from the matrix formulation of the QRPA. We also discuss the applicability of both the Thouless theorem about the energy-weighted sum rule and the dielectric theorem for the inverse-energy-weighted sum rule to nuclear density functional theory in cases when the EDF is not based on a Hamiltonian. Conclusions: The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method

  17. Non-empirical pairing energy functional in nuclear matter and finite nuclei

    SciTech Connect

    Hebeler, K.; Duguet, T.; Lesinski, T.; Schwenk, A.

    2009-10-15

    We study {sup 1}S{sub 0} pairing gaps in neutron and nuclear matter as well as T=1 pairing in finite nuclei on the basis of microscopic two-nucleon interactions. Special attention is paid to the consistency of the pairing interaction and normal self-energy contributions. We find that pairing gaps obtained from low-momentum interactions depend only weakly on approximation schemes for the normal self-energy, required in present energy-density functional calculations, while pairing gaps from hard potentials are very sensitive to the effective-mass approximation scheme.

  18. Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions

    SciTech Connect

    Lin, Bin; Wong, Ka-Yiu; Hu, Char Y.; Kokubo, Hironori; Pettitt, Bernard M.

    2011-07-07

    Although detailed atomic models may be applied for a full description of solvation, simpler phenomenologicalmodels are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

  19. A site energy distribution function from Toth isotherm for adsorption of gases on heterogeneous surfaces.

    PubMed

    Kumar, K Vasanth; de Castro, M Monteiro; Martinez-Escandell, M; Molina-Sabio, M; Rodriguez-Reinoso, F

    2011-04-01

    A site energy distribution function based on a condensation approximation method is proposed for gas-phase adsorption systems following the Toth isotherm. The proposed model is successfully applied to estimate the site energy distribution of three pitch-based activated carbons (PA, PFeA and PBA) developed in our laboratory and also for other common adsorbent materials for different gas molecules. According to the proposed model the site energy distribution curves of the activated carbons are found to be exponential for hydrogen at 77 K. The site energy distribution of some of the activated carbon fibers, ambersorb, Dowex optipore, 13X Zeolite for different adsorbate molecules represents a quasi-Gaussian curve with a widened left hand side, indicating that most sites have adsorption energies lower than a statistical mean value.

  20. Fourfold Clusters of Rovibrational Energies in H2Te Studied With an Ab Initio Potential Energy Function

    NASA Technical Reports Server (NTRS)

    Jensen, Per; Li, Yan; Hirsch, Gerhard; Buenker, Robert J.; Lee, Timothy J.; Arnold, James O. (Technical Monitor)

    1994-01-01

    We report an ab initio investigation of the cluster effect (i.e., the formation of nearly degenerate, four member groups of rotation-vibration energy levels at higher J and K(sub a). values) in the H2Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD(T) method where the (1s-4f) core electrons of Te were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10,000/cm above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H2Te-130 and its deuterated isotopomers have been calculated with the MORBID (Morse Oscillator Rigid Bender Internal Dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J less than or = 40 in the vibrational ground state, the upsilon(sub 2) state, the "first triad" (the upsilon(sub l)/upsilon(sub 3)/2upsilon(sub 2) interacting vibrational states), and the "second triad" (the upsilon(sub 1) + upsilon(sub 2/upsilon(sub 2) + upsilon(sub 3)/3upsilon(sub 2) states) of H2Te-130. We find that the cluster formation in H2Te is very similar to those of of H2Se and H2S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H2Se. Hence the experimental observation of the cluster states in H2Te will be at least as difficult as in H2Se.

  1. Ion energy distribution functions of low energy beams formed by wire extraction electrodes

    SciTech Connect

    Tokumura, S.; Kasuya, T.; Vasquez, M. Jr.; Maeno, S.; Wada, M.

    2012-02-15

    The two-electrode extractor system made of 0.1 mm diameter tungsten wires separated by 0.7 mm has formed an argon ion beam with 50 V extraction potential. Energy spreads of the extracted beams were typically less than 2 eV when the beam current density was low. The beam intensity rapidly decreased as the distance between the extractor and the beam detector increased, indicating space charge limited transport of the beam. Problems associated with the emittance measurements are also discussed.

  2. Molecular density functional theory for water with liquid-gas coexistence and correct pressure

    SciTech Connect

    Jeanmairet, Guillaume Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  3. Molecular density functional theory for water with liquid-gas coexistence and correct pressure.

    PubMed

    Jeanmairet, Guillaume; Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  4. Structure-based prediction of transcription factor binding specificity using an integrative energy function

    PubMed Central

    Farrel, Alvin; Murphy, Jonathan; Guo, Jun-tao

    2016-01-01

    Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regulation networks. In this article, we present a structure-based method for computational prediction of TFBSs using a novel, integrative energy (IE) function. The new energy function combines a multibody (MB) knowledge-based potential and two atomic energy terms (hydrogen bond and π interaction) that might not be accurately captured by the knowledge-based potential owing to the mean force nature and low count problem. We applied the new energy function to the TFBS prediction using a non-redundant dataset that consists of TFs from 12 different families. Our results show that the new IE function improves the prediction accuracy over the knowledge-based, statistical potentials, especially for homeodomain TFs, the second largest TF family in mammals. Contact: jguo4@uncc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307632

  5. Functional unit, technological dynamics, and scaling properties for the life cycle energy of residences.

    PubMed

    Frijia, Stephane; Guhathakurta, Subhrajit; Williams, Eric

    2012-02-01

    Prior LCA studies take the operational phase to include all energy use within a residence, implying a functional unit of all household activities, but then exclude related supply chains such as production of food, appliances, and household chemicals. We argue that bounding the functional unit to provision of a climate controlled space better focuses the LCA on the building, rather than activities that occur within a building. The second issue explored in this article is how technological change in the operational phase affects life cycle energy. Heating and cooling equipment is replaced at least several times over the lifetime of a residence; improved efficiency of newer equipment affects life cycle energy use. The third objective is to construct parametric models to describe LCA results for a family of related products. We explore these three issues through a case study of energy use of residences: one-story and two-story detached homes, 1,500-3,500 square feet in area, located in Phoenix, Arizona, built in 2002 and retired in 2051. With a restricted functional unit and accounting for technological progress, approximately 30% of a building's life cycle energy can be attributed to materials and construction, compared to 0.4-11% in previous studies. PMID:22192002

  6. The roles of melanin-concentrating hormone in energy balance and reproductive function: Are they connected?

    PubMed

    Naufahu, Jane; Cunliffe, Adam D; Murray, Joanne F

    2013-01-01

    Melanin-concentrating hormone (MCH) is an anabolic neuropeptide with multiple and diverse physiological functions including a key role in energy homoeostasis. Rodent studies have shown that the ablation of functional MCH results in a lean phenotype, increased energy expenditure and resistance to diet-induced obesity. These findings have generated interest among pharmaceutical companies vigilant for potential anti-obesity agents. Nutritional status affects reproductive physiology and behaviours, thereby optimising reproductive success and the ability to meet energetic demands. This complex control system entails the integration of direct or indirect peripheral stimuli with central effector systems and involves numerous mediators. A role for MCH in the reproductive axis has emerged, giving rise to the premise that MCH may serve as an integratory mediator between those discrete systems that regulate energy balance and reproductive function. Hence, this review focuses on published evidence concerning i) the role of MCH in energy homoeostasis and ii) the regulatory role of MCH in the reproductive axis. The question as to whether the MCH system mediates the integration of energy homoeostasis with the neuroendocrine reproductive axis and, if so, by what means has received limited coverage in the literature; evidence to date and current theories are summarised herein.

  7. Comparing two Bayes methods based on the free energy functions in Bernoulli mixtures.

    PubMed

    Yamazaki, Keisuke; Kaji, Daisuke

    2013-08-01

    Hierarchical learning models are ubiquitously employed in information science and data engineering. The structure makes the posterior distribution complicated in the Bayes method. Then, the prediction including construction of the posterior is not tractable though advantages of the method are empirically well known. The variational Bayes method is widely used as an approximation method for application; it has the tractable posterior on the basis of the variational free energy function. The asymptotic behavior has been studied in many hierarchical models and a phase transition is observed. The exact form of the asymptotic variational Bayes energy is derived in Bernoulli mixture models and the phase diagram shows that there are three types of parameter learning. However, the approximation accuracy or interpretation of the transition point has not been clarified yet. The present paper precisely analyzes the Bayes free energy function of the Bernoulli mixtures. Comparing free energy functions in these two Bayes methods, we can determine the approximation accuracy and elucidate behavior of the parameter learning. Our results claim that the Bayes free energy has the same learning types while the transition points are different.

  8. Functional unit, technological dynamics, and scaling properties for the life cycle energy of residences.

    PubMed

    Frijia, Stephane; Guhathakurta, Subhrajit; Williams, Eric

    2012-02-01

    Prior LCA studies take the operational phase to include all energy use within a residence, implying a functional unit of all household activities, but then exclude related supply chains such as production of food, appliances, and household chemicals. We argue that bounding the functional unit to provision of a climate controlled space better focuses the LCA on the building, rather than activities that occur within a building. The second issue explored in this article is how technological change in the operational phase affects life cycle energy. Heating and cooling equipment is replaced at least several times over the lifetime of a residence; improved efficiency of newer equipment affects life cycle energy use. The third objective is to construct parametric models to describe LCA results for a family of related products. We explore these three issues through a case study of energy use of residences: one-story and two-story detached homes, 1,500-3,500 square feet in area, located in Phoenix, Arizona, built in 2002 and retired in 2051. With a restricted functional unit and accounting for technological progress, approximately 30% of a building's life cycle energy can be attributed to materials and construction, compared to 0.4-11% in previous studies.

  9. Physiological Interactions of Nanoparticles in Energy Metabolism, Immune Function and Their Biosafety: A Review.

    PubMed

    Gomes, Antony; Sengupta, Jayeeta; Datta, Poulami; Ghosh, Sourav; Gomes, Aparna

    2016-01-01

    Nanoparticles owing to their unique physico-chemical properties have found its application in various biological processes, including metabolic pathways taking place within the body. This review tried to focus the involvement of nanoparticles in metabolic pathways and its influence in the energy metabolism, a fundamental criteria for the survival and physiological activity of living beings. The human body utilizes energy derived from food resources through a series of biochemical reactions involving several enzymes, co-factors (metals, non-metals, vitamins etc.) through the metabolic pathways (glycolysis, tri carboxylic acid cycle, oxidative phosphorylation, electron transport chain, etc.) in cellular system. Energy metabolism is also involved in the immune networking of the body for self defence and against pathophysiology. The immune system comprises of different cells and tissues, bioactive molecules for self defence and to fight against diseases. In the recent times, it has been reported through in vivo and in vitro studies that nanoparticles have direct influence on body's immune functions, and can modulate immunity by either suppressing or enhancing it. A comprehensive overview of nanoparticles and its involvement in immune function of the body in normal and pathophysiological conditions has been discussed. Considering these perspectives on nanoparticle interaction another important area which has been highlighted is the biosafety issues which are necessary before therapeutic applications. It is expected that development of physiologically compatible nanoparticles controlling energy metabolic processes, immune functions may show new dimension in the pathophysiology linked with energy and immunity.

  10. Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.; Lomakina, Ekaterina I.

    2009-08-01

    Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

  11. Physiological Interactions of Nanoparticles in Energy Metabolism, Immune Function and Their Biosafety: A Review.

    PubMed

    Gomes, Antony; Sengupta, Jayeeta; Datta, Poulami; Ghosh, Sourav; Gomes, Aparna

    2016-01-01

    Nanoparticles owing to their unique physico-chemical properties have found its application in various biological processes, including metabolic pathways taking place within the body. This review tried to focus the involvement of nanoparticles in metabolic pathways and its influence in the energy metabolism, a fundamental criteria for the survival and physiological activity of living beings. The human body utilizes energy derived from food resources through a series of biochemical reactions involving several enzymes, co-factors (metals, non-metals, vitamins etc.) through the metabolic pathways (glycolysis, tri carboxylic acid cycle, oxidative phosphorylation, electron transport chain, etc.) in cellular system. Energy metabolism is also involved in the immune networking of the body for self defence and against pathophysiology. The immune system comprises of different cells and tissues, bioactive molecules for self defence and to fight against diseases. In the recent times, it has been reported through in vivo and in vitro studies that nanoparticles have direct influence on body's immune functions, and can modulate immunity by either suppressing or enhancing it. A comprehensive overview of nanoparticles and its involvement in immune function of the body in normal and pathophysiological conditions has been discussed. Considering these perspectives on nanoparticle interaction another important area which has been highlighted is the biosafety issues which are necessary before therapeutic applications. It is expected that development of physiologically compatible nanoparticles controlling energy metabolic processes, immune functions may show new dimension in the pathophysiology linked with energy and immunity. PMID:27398436

  12. First order variation of the dispersion function with particle energy deviation

    SciTech Connect

    Delahaye, J.P.; Jaeger, J.

    1984-12-01

    The variation of the dispersion function with the particle energy deviation can presently be calculated from second order transfer matrices; its periodic solution is determined numerically. The general differential equations for the dispersion function deduced from the complete equation of motion to second order are solved, using Green's function integral leading to an analytical expression of the periodic solution of the dispersion function D/sub 0/ and of the first order perturbation, D/sub 1/, with respect to energy deviation. The same method can be extended to higher order perturbations of the dispersion function. The determination of the periodic solution as well as the transportation of these two dispersion functions through any element depends only on two particular integrals. These integrals are derived for the general case of a combined function magnet, with up to second order components. The derivation includes the contribution from the edges. Chapter 2 and 3 deal with closed machines, chapter 4 applies these results to beam transport lines. These analytical expressions are then applied to a typical machine in order to illustrate the most important driving terms; the results do agree with those obtained by optics programs like MAD or DIMAT based on second order transfer matrices.

  13. Ab initio design of low work function complex oxides for thermionic energy conversion

    NASA Astrophysics Data System (ADS)

    Mack, Stephanie; Li, Guo; Neaton, Jeffrey

    Understanding and controlling work functions, or band edge energies, is of interest for a variety of applications in optoelectronics and energy conversion. In particular, while recent advances in device design have improved the feasibility of thermionic generators, new low work function materials are needed to enable their widespread use. Perovskite-based oxides (ABO3) are a diverse class of materials that, depending on the transition metal atoms on the A and B sites, can give rise to myriad emergent and collective phenomena. Here, we use density functional theory calculations to examine how the work function of one such oxide, SrRuO3 (SRO), can be tuned by monolayers of SrTiO3 (STO) and other polar or near-polar oxides. We find that SRO work functions can be tuned by over 1 eV with one layer of STO, although the calculated reduction in work function is an order of magnitude less than would be expected from the bulk polarization. We understand the variation in work function via a detailed analysis of Born effective charges at the surface, which are as small as 10% of their bulk values, and charge rearrangement at the STO surface and SRO/STO interface.

  14. Measurement of the electron structure function F2e at LEP energies

    NASA Astrophysics Data System (ADS)

    Abdallah, J.; Abreu, P.; Adam, W.; Adzic, P.; Albrecht, T.; Alemany-Fernandez, R.; Allmendinger, T.; Allport, P. P.; Amaldi, U.; Amapane, N.; Amato, S.; Anashkin, E.; Andreazza, A.; Andringa, S.; Anjos, N.; Antilogus, P.; Apel, W.-D.; Arnoud, Y.; Ask, S.; Asman, B.; Augustin, J. E.; Augustinus, A.; Baillon, P.; Ballestrero, A.; Bambade, P.; Barbier, R.; Bardin, D.; Barker, G. J.; Baroncelli, A.; Battaglia, M.; Baubillier, M.; Becks, K.-H.; Begalli, M.; Behrmann, A.; Belous, K.; Ben-Haim, E.; Benekos, N.; Benvenuti, A.; Berat, C.; Berggren, M.; Bertrand, D.; Besancon, M.; Besson, N.; Bloch, D.; Blom, M.; Bluj, M.; Bonesini, M.; Boonekamp, M.; Booth, P. S. L.; Borisov, G.; Botner, O.; Bouquet, B.; Bowcock, T. J. V.; Boyko, I.; Bracko, M.; Brenner, R.; Brodet, E.; Bruckman, P.; Brunet, J. M.; Buschbeck, B.; Buschmann, P.; Calvi, M.; Camporesi, T.; Canale, V.; Carena, F.; Castro, N.; Cavallo, F.; Chapkin, M.; Charpentier, Ph.; Checchia, P.; Chierici, R.; Chliapnikov, P.; Chudoba, J.; Chung, S. U.; Cieslik, K.; Collins, P.; Contri, R.; Cosme, G.; Cossutti, F.; Costa, M. J.; Crennell, D.; Cuevas, J.; D'Hondt, J.; da Silva, T.; Da Silva, W.; Della Ricca, G.; De Angelis, A.; De Boer, W.; De Clercq, C.; De Lotto, B.; De Maria, N.; De Min, A.; de Paula, L.; Di Ciaccio, L.; Di Simone, A.; Doroba, K.; Drees, J.; Eigen, G.; Ekelof, T.; Ellert, M.; Elsing, M.; Espirito Santo, M. C.; Fanourakis, G.; Fassouliotis, D.; Feindt, M.; Fernandez, J.; Ferrer, A.; Ferro, F.; Flagmeyer, U.; Foeth, H.; Fokitis, E.; Fulda-Quenzer, F.; Fuster, J.; Gandelman, M.; Garcia, C.; Gavillet, Ph.; Gazis, E.; Gokieli, R.; Golob, B.; Gomez-Ceballos, G.; Gonçalves, P.; Graziani, E.; Grosdidier, G.; Grzelak, K.; Guy, J.; Haag, C.; Hallgren, A.; Hamacher, K.; Hamilton, K.; Haug, S.; Hauler, F.; Hedberg, V.; Hennecke, M.; Hoffman, J.; Holmgren, S.-O.; Holt, P. J.; Houlden, M. A.; Jackson, J. N.; Jarlskog, G.; Jarry, P.; Jeans, D.; Johansson, E. K.; Jonsson, P.; Joram, C.; Jungermann, L.; Kapusta, F.; Katsanevas, S.; Katsoufis, E.; Kernel, G.; Kersevan, B. P.; Kerzel, U.; King, B. T.; Kjaer, N. J.; Kluit, P.; Kokkinias, P.; Kourkoumelis, C.; Kouznetsov, O.; Krumstein, Z.; Kucharczyk, M.; Lamsa, J.; Leder, G.; Ledroit, F.; Leinonen, L.; Leitner, R.; Lemonne, J.; Lepeltier, V.; Lesiak, T.; Liebig, W.; Liko, D.; Lipniacka, A.; Lopes, J. H.; Lopez, J. M.; Loukas, D.; Lutz, P.; Lyons, L.; MacNaughton, J.; Malek, A.; Maltezos, S.; Mandl, F.; Marco, J.; Marco, R.; Marechal, B.; Margoni, M.; Marin, J.-C.; Mariotti, C.; Markou, A.; Martinez-Rivero, C.; Masik, J.; Mastroyiannopoulos, N.; Matorras, F.; Matteuzzi, C.; Mazzucato, F.; Mazzucato, M.; Mc Nulty, R.; Meroni, C.; Migliore, E.; Mitaroff, W.; Mjoernmark, U.; Moa, T.; Moch, M.; Moenig, K.; Monge, R.; Montenegro, J.; Moraes, D.; Moreno, S.; Morettini, P.; Mueller, U.; Muenich, K.; Mulders, M.; Mundim, L.; Murray, W.; Muryn, B.; Myatt, G.; Myklebust, T.; Nassiakou, M.; Navarria, F.; Nawrocki, K.; Nemecek, S.; Nicolaidou, R.; Nikolenko, M.; Oblakowska-Mucha, A.; Obraztsov, V.; Olshevski, A.; Onofre, A.; Orava, R.; Osterberg, K.; Ouraou, A.; Oyanguren, A.; Paganoni, M.; Paiano, S.; Palacios, J. P.; Palka, H.; Papadopoulou, Th. D.; Pape, L.; Parkes, C.; Parodi, F.; Parzefall, U.; Passeri, A.; Passon, O.; Peralta, L.; Perepelitsa, V.; Perrotta, A.; Petrolini, A.; Piedra, J.; Pieri, L.; Pierre, F.; Pimenta, M.; Piotto, E.; Podobnik, T.; Poireau, V.; Pol, M. E.; Polok, G.; Pozdniakov, V.; Pukhaeva, N.; Pullia, A.; Radojicic, D.; Rebecchi, P.; Rehn, J.; Reid, D.; Reinhardt, R.; Renton, P.; Richard, F.; Ridky, J.; Rivero, M.; Rodriguez, D.; Romero, A.; Ronchese, P.; Roudeau, P.; Rovelli, T.; Ruhlmann-Kleider, V.; Ryabtchikov, D.; Sadovsky, A.; Salmi, L.; Salt, J.; Sander, C.; Savoy-Navarro, A.; Schwickerath, U.; Sekulin, R.; Siebel, M.; Sisakian, A.; Slominski, W.; Smadja, G.; Smirnova, O.; Sokolov, A.; Sopczak, A.; Sosnowski, R.; Spassov, T.; Stanitzki, M.; Stocchi, A.; Strauss, J.; Stugu, B.; Szczekowski, M.; Szeptycka, M.; Szumlak, T.; Szwed, J.; Tabarelli, T.; Tegenfeldt, F.; Timmermans, J.; Tkatchev, L.; Tobin, M.; Todorovova, S.; Tomé, B.; Tonazzo, A.; Tortosa, P.; Travnicek, P.; Treille, D.; Tristram, G.; Trochimczuk, M.; Troncon, C.; Turluer, M.-L.; Tyapkin, I. A.; Tyapkin, P.; Tzamarias, S.; Uvarov, V.; Valenti, G.; Van Dam, P.; Van Eldik, J.; van Remortel, N.; Van Vulpen, I.; Vegni, G.; Veloso, F.; Venus, W.; Verdier, P.; Verzi, V.; Vilanova, D.; Vitale, L.; Vrba, V.; Wahlen, H.; Washbrook, A. J.; Weiser, C.; Wicke, D.; Wickens, J.; Wilkinson, G.; Winter, M.; Witek, M.; Yushchenko, O.; Zalewska, A.; Zalewski, P.; Zavrtanik, D.; Zhuravlov, V.; Zimin, N. I.; Zintchenko, A.; Zupan, M.

    2014-10-01

    The hadronic part of the electron structure function F2e has been measured for the first time, using e+e- data collected by the DELPHI experiment at LEP, at centre-of-mass energies of √{ s} = 91.2- 209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F2e data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F2γ analyses and help in refining existing parameterisations.

  15. Advanced multiconfiguration methods for complex atoms: I. Energies and wave functions

    NASA Astrophysics Data System (ADS)

    Froese Fischer, Charlotte; Godefroid, Michel; Brage, Tomas; Jönsson, Per; Gaigalas, Gediminas

    2016-09-01

    Multiconfiguration wave function expansions combined with configuration interaction methods are a method of choice for complex atoms where atomic state functions are expanded in a basis of configuration state functions. Combined with a variational method such as the multiconfiguration Hartree-Fock (MCHF) or multiconfiguration Dirac-Hartree-Fock (MCDHF), the associated set of radial functions can be optimized for the levels of interest. The present review updates the variational MCHF theory to include MCDHF, describes the multireference single and double process for generating expansions and the systematic procedure of a computational scheme for monitoring convergence. It focuses on the calculations of energies and wave functions from which other atomic properties can be predicted such as transition rates, hyperfine structures and isotope shifts, for example.

  16. On universality of stress-energy tensor correlation functions in supergravity [rapid communication

    NASA Astrophysics Data System (ADS)

    Buchel, Alex

    2005-03-01

    Using the Minkowski space AdS/CFT prescription we explicitly compute in the low-energy limit the two-point correlation function of the boundary stress-energy tensor in a large class of type IIB supergravity backgrounds with a regular translationally invariant horizon. The relevant set of supergravity backgrounds includes all geometries which can be interpreted via gauge theory/string theory correspondence as being holographically dual to finite temperature gauge theories in Minkowski space-times. The fluctuation-dissipation theorem relates this correlation function computation to the previously established universality of the shear viscosity from supergravity duals, and to the universality of the low energy absorption cross section for minimally coupled massless scalars into a general spherically symmetric black hole. It further generalizes the latter results for the supergravity black brane geometries with non-spherical horizons.

  17. Constraints on the inner edge of neutron star crusts from relativistic nuclear energy density functionals

    SciTech Connect

    Moustakidis, Ch. C.; Lalazissis, G. A.; Niksic, T.; Vretenar, D.; Ring, P.

    2010-06-15

    The transition density n{sub t} and pressure P{sub t} at the inner edge between the liquid core and the solid crust of a neutron star are analyzed using the thermodynamical method and the framework of relativistic nuclear energy density functionals. Starting from a functional that has been carefully adjusted to experimental binding energies of finite nuclei, and varying the density dependence of the corresponding symmetry energy within the limits determined by isovector properties of finite nuclei, we estimate the constraints on the core-crust transition density and pressure of neutron stars: 0.086 fm{sup -3}<=n{sub t}<0.090 fm{sup -3} and 0.3 MeV fm{sup -3}

  18. Electromagnetic semitransparent δ-function plate: Casimir interaction energy between parallel infinitesimally thin plates

    NASA Astrophysics Data System (ADS)

    Parashar, Prachi; Milton, Kimball A.; Shajesh, K. V.; Schaden, M.

    2012-10-01

    We derive boundary conditions for electromagnetic fields on a δ-function plate. The optical properties of such a plate are shown to necessarily be anisotropic in that they only depend on the transverse properties of the plate. We unambiguously obtain the boundary conditions for a perfectly conducting δ-function plate in the limit of infinite dielectric response. We show that a material does not “optically vanish” in the thin-plate limit. The thin-plate limit of a plasma slab of thickness d with plasma frequency ωp2=ζp/d reduces to a δ-function plate for frequencies (ω=iζ) satisfying ζd≪ζpd≪1. We show that the Casimir interaction energy between two parallel perfectly conducting δ-function plates is the same as that for parallel perfectly conducting slabs. Similarly, we show that the interaction energy between an atom and a perfect electrically conducting δ-function plate is the usual Casimir-Polder energy, which is verified by considering the thin-plate limit of dielectric slabs. The “thick” and “thin” boundary conditions considered by Bordag are found to be identical in the sense that they lead to the same electromagnetic fields.

  19. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.

    PubMed

    Cheng, Gong; Qian, Bin; Samudrala, Ram; Baker, David

    2005-01-01

    The prediction of functional sites in newly solved protein structures is a challenge for computational structural biology. Most methods for approaching this problem use evolutionary conservation as the primary indicator of the location of functional sites. However, sequence conservation reflects not only evolutionary selection at functional sites to maintain protein function, but also selection throughout the protein to maintain the stability of the folded state. To disentangle sequence conservation due to protein functional constraints from sequence conservation due to protein structural constraints, we use all atom computational protein design methodology to predict sequence profiles expected under solely structural constraints, and to compute the free energy difference between the naturally occurring amino acid and the lowest free energy amino acid at each position. We show that functional sites are more likely than non-functional sites to have computed sequence profiles which differ significantly from the naturally occurring sequence profiles and to have residues with sub-optimal free energies, and that incorporation of these two measures improves sequence based prediction of protein functional sites. The combined sequence and structure based functional site prediction method has been implemented in a publicly available web server.

  20. Energy Optimization of Many-Body Wave Functions: Application to Silicon Interstitial Defects

    NASA Astrophysics Data System (ADS)

    Parker, W. D.; Driver, K. P.; Hennig, R. G.; Wilkins, J. W.; Umrigar, C. J.

    2006-03-01

    Energy minimization [1], as opposed to the standard variance minimization [2], of the Jastrow factor results not only in lower variational Monte Carlo (VMC) energies but also in lower diffusion Monte Carlo (DMC) energies for systems that employ a nonlocal pseudopotential. We apply this approach to solids: single-interstitials in silicon. Allowing the Jastrow for the defect atom(s) to differ from that for bulk atoms lowers the VMC energy but not the DMC energy, indicating the pseudopotential locality error is small. DMC energies from 8 and 64 atom cells (plus interstitial) computed with energy-optimized trial wave functions estimate a 0.2 eV finite-size error in the formation energy. Cubic spline and Lagrange polynomial representations of orbitals have comparable efficiency in memory usage, run time and accuracy. [1] C. J. Umrigar and C. Filippi, Phys. Rev. Lett. 94, 150201 (2005). [2] C. J. Umrigar, K. G. Wilson and J. W. Wilkins, Phys. Rev. Lett. 60, 1719 (1988).

  1. Development of an Enhanced Payback Function for the Superior Energy Performance Program

    SciTech Connect

    Therkelsen, Peter; Rao, Prakash; McKane, Aimee; Sabouni, Ridah; Sheihing, Paul

    2015-08-03

    The U.S. DOE Superior Energy Performance (SEP) program provides recognition to industrial and commercial facilities that achieve certification to the ISO 50001 energy management system standard and third party verification of energy performance improvements. Over 50 industrial facilities are participating and 28 facilities have been certified in the SEP program. These facilities find value in the robust, data driven energy performance improvement result that the SEP program delivers. Previous analysis of SEP certified facility data demonstrated the cost effectiveness of SEP and identified internal staff time to be the largest cost component related to SEP implementation and certification. This paper analyzes previously reported and newly collected data of costs and benefits associated with the implementation of an ISO 50001 and SEP certification. By disaggregating “sunk energy management system (EnMS) labor costs”, this analysis results in a more accurate and detailed understanding of the costs and benefits of SEP participation. SEP is shown to significantly improve and sustain energy performance and energy cost savings, resulting in a highly attractive return on investment. To illustrate these results, a payback function has been developed and is presented. On average facilities with annual energy spend greater than $2M can expect to implement SEP with a payback of less than 1.5 years. Finally, this paper also observes and details decreasing facility costs associated with implementing ISO 50001 and certifying to the SEP program, as the program has improved from pilot, to demonstration, to full launch.

  2. Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array

    SciTech Connect

    Van Essen, B; Panda, R; Wood, A; Ebeling, C; Hauck, S

    2010-12-01

    Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous

  3. Complex-energy approach to sum rules within nuclear density functional theory

    SciTech Connect

    Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; Olsen, Erik

    2015-04-27

    The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish an efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.

  4. Complex-energy approach to sum rules within nuclear density functional theory

    DOE PAGES

    Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; Olsen, Erik

    2015-04-27

    The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish anmore » efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.« less

  5. Time evolution of the electron energy distribution function in pulsed microwave magnetoplasma in H2

    NASA Astrophysics Data System (ADS)

    Jauberteau, J. L.; Jauberteau, I.; Cortázar, O. D.; Megía-Macías, A.

    2016-03-01

    Time evolution of the Electron Energy Distribution Function (EEDF) is measured in pulsed hydrogen microwave magnetoplasma working at 2.45 GHz. Analysis is performed both in resonance (B = 0.087 T) and off-resonance conditions (B = 0.120 T), at two pressures (0.38 Pa and 0.62 Pa), respectively, and for different incident microwave powers. The important effect of the magnetic field on the electron kinetic is discussed, and a critical analysis of Langmuir probe measurements is given. The Electron Energy Distribution Function is calculated using the Druyvesteyn theory (EEDF) and is corrected using the theory developed by Arslanbekov in the case of magnetized plasma. Three different components are observed in the EEDF, whatever the theory used. They are: (a) a low electron energy component at energy lower than 10 eV, which is ascribed to the electron having inelastic collisions with heavy species (H2, H, ions), (b) a high energy component with a mean energy ranging from 10 to 20 eV, which is generally ascribed to the heating of the plasma by the incident microwave power, and (c) a third component observed between the two other ones, mainly at low pressure and in resonance conditions, has been correlated to the electron rotation in the magnetic field.

  6. Accurate Diels-Alder reaction energies from efficient density functional calculations.

    PubMed

    Mezei, Pál D; Csonka, Gábor I; Kállay, Mihály

    2015-06-01

    We assess the performance of the semilocal PBE functional; its global hybrid variants; the highly parametrized empirical M06-2X and M08-SO; the range separated rCAM-B3LYP and MCY3; the atom-pairwise or nonlocal dispersion corrected semilocal PBE and TPSS; the dispersion corrected range-separated ωB97X-D; the dispersion corrected double hybrids such as PWPB95-D3; the direct random phase approximation, dRPA, with Hartree-Fock, Perdew-Burke-Ernzerhof, and Perdew-Burke-Ernzerhof hybrid reference orbitals and the RPAX2 method based on a Perdew-Burke-Ernzerhof exchange reference orbitals for the Diels-Alder, DARC; and self-interaction error sensitive, SIE11, reaction energy test sets with large, augmented correlation consistent valence basis sets. The dRPA energies for the DARC test set are extrapolated to the complete basis set limit. CCSD(T)/CBS energies were used as a reference. The standard global hybrid functionals show general improvements over the typical endothermic energy error of semilocal functionals, but despite the increased accuracy the precision of the methods increases only slightly, and thus all reaction energies are simply shifted into the exothermic direction. Dispersion corrections give mixed results for the DARC test set. Vydrov-Van Voorhis 10 correction to the reaction energies gives superior quality results compared to the too-small D3 correction. Functionals parametrized for energies of noncovalent interactions like M08-SO give reasonable results without any dispersion correction. The dRPA method that seamlessly and theoretically correctly includes noncovalent interaction energies gives excellent results with properly chosen reference orbitals. As the results for the SIE11 test set and H2(+) dissociation show that the dRPA methods suffer from delocalization error, good reaction energies for the DARC test set from a given method do not prove that the method is free from delocalization error. The RPAX2 method shows good performance for the DARC

  7. Structural and Functional Hierarchy in Photosynthetic Energy Conversion-from Molecules to Nanostructures.

    PubMed

    Szabó, Tibor; Magyar, Melinda; Hajdu, Kata; Dorogi, Márta; Nyerki, Emil; Tóth, Tünde; Lingvay, Mónika; Garab, Győző; Hernádi, Klára; Nagy, László

    2015-12-01

    Basic principles of structural and functional requirements of photosynthetic energy conversion in hierarchically organized machineries are reviewed. Blueprints of photosynthesis, the energetic basis of virtually all life on Earth, can serve the basis for constructing artificial light energy-converting molecular devices. In photosynthetic organisms, the conversion of light energy into chemical energy takes places in highly organized fine-tunable systems with structural and functional hierarchy. The incident photons are absorbed by light-harvesting complexes, which funnel the excitation energy into reaction centre (RC) protein complexes containing redox-active chlorophyll molecules; the primary charge separations in the RCs are followed by vectorial transport of charges (electrons and protons) in the photosynthetic membrane. RCs possess properties that make their use in solar energy-converting and integrated optoelectronic systems feasible. Therefore, there is a large interest in many laboratories and in the industry toward their use in molecular devices. RCs have been bound to different carrier matrices, with their photophysical and photochemical activities largely retained in the nano-systems and with electronic connection to conducting surfaces. We show examples of RCs bound to carbon-based materials (functionalized and non-functionalized single- and multiwalled carbon nanotubes), transitional metal oxides (ITO) and conducting polymers and porous silicon and characterize their photochemical activities. Recently, we adapted several physical and chemical methods for binding RCs to different nanomaterials. It is generally found that the P(+)(QAQB)(-) charge pair, which is formed after single saturating light excitation is stabilized after the attachment of the RCs to the nanostructures, which is followed by slow reorganization of the protein structure. Measuring the electric conductivity in a direct contact mode or in electrochemical cell indicates that there is an

  8. Structural and Functional Hierarchy in Photosynthetic Energy Conversion—from Molecules to Nanostructures

    NASA Astrophysics Data System (ADS)

    Szabó, Tibor; Magyar, Melinda; Hajdu, Kata; Dorogi, Márta; Nyerki, Emil; Tóth, Tünde; Lingvay, Mónika; Garab, Győző; Hernádi, Klára; Nagy, László

    2015-12-01

    Basic principles of structural and functional requirements of photosynthetic energy conversion in hierarchically organized machineries are reviewed. Blueprints of photosynthesis, the energetic basis of virtually all life on Earth, can serve the basis for constructing artificial light energy-converting molecular devices. In photosynthetic organisms, the conversion of light energy into chemical energy takes places in highly organized fine-tunable systems with structural and functional hierarchy. The incident photons are absorbed by light-harvesting complexes, which funnel the excitation energy into reaction centre (RC) protein complexes containing redox-active chlorophyll molecules; the primary charge separations in the RCs are followed by vectorial transport of charges (electrons and protons) in the photosynthetic membrane. RCs possess properties that make their use in solar energy-converting and integrated optoelectronic systems feasible. Therefore, there is a large interest in many laboratories and in the industry toward their use in molecular devices. RCs have been bound to different carrier matrices, with their photophysical and photochemical activities largely retained in the nano-systems and with electronic connection to conducting surfaces. We show examples of RCs bound to carbon-based materials (functionalized and non-functionalized single- and multiwalled carbon nanotubes), transitional metal oxides (ITO) and conducting polymers and porous silicon and characterize their photochemical activities. Recently, we adapted several physical and chemical methods for binding RCs to different nanomaterials. It is generally found that the P+(QAQB)- charge pair, which is formed after single saturating light excitation is stabilized after the attachment of the RCs to the nanostructures, which is followed by slow reorganization of the protein structure. Measuring the electric conductivity in a direct contact mode or in electrochemical cell indicates that there is an

  9. Effects of high-energy ultrasound on the functional properties of proteins.

    PubMed

    Higuera-Barraza, O A; Del Toro-Sanchez, C L; Ruiz-Cruz, S; Márquez-Ríos, E

    2016-07-01

    In recent years, high-energy ultrasound has been used as an alternative to improve the functional properties of various proteins, such as from milk, eggs, soy and poultry. The benefits of implementing this technology depend on the inherent characteristics of the protein source and the intensity and amplitude of the ultrasound, as well as on the pH, temperature, ionic strength, time, and all of the variables that have an effect on the physicochemical properties of proteins. Therefore, it is necessary to establish the optimal conditions for each type of food. The use of ultrasound is a promising technique in food technology with a low impact on the environment, and it has thus become known as a green technology. Therefore, this review focuses on the application of high-energy ultrasound to food; its effects on the functional properties of proteins; and how different conditions such as the frequency, time, amplitude, temperature, and protein concentration affect the functional properties.

  10. Neutral-atom electron binding energies from relaxed-orbital relativistic Hartree-Fock-Slater calculations for Z between 2 and 106

    NASA Technical Reports Server (NTRS)

    Huang, K.-N.; Aoyagi, M.; Mark, H.; Chen, M. H.; Crasemann, B.

    1976-01-01

    Electron binding energies in neutral atoms have been calculated relativistically, with the requirement of complete relaxation. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first-order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all elements with atomic numbers ranging from 2 to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. Binding energies including relaxation are listed for all electrons in all atoms over the indicated range of atomic numbers. A self-energy correction is included for the 1s, 2s, and 2p(1/2) levels. Results for selected atoms are compared with energies calculated by other methods and with experimental values.

  11. Energy trapping of thickness-shear vibration modes of elastic plates with functionally graded materials.

    PubMed

    Wang, Ji; Yang, Jiashi; Li, Jiangyu

    2007-03-01

    Energy trapping has important applications in the design of thickness-shear resonators. Considerable efforts have been made for the effective utilization and improvement of energy trapping with variations of plate configurations, such as adding electrodes and contouring. As a new approach in seeking improved energy trapping feature, we analyze thickness-shear vibrations in an elastic plate with functionally graded material (FGM) of in-plane variation of mechanical properties, such as elastic constants and density. A simple and general equation governing the thickness-shear modes is derived from a variational analysis. A plate with piecewise constant material properties is analyzed as an example. It is shown that such a plate can support thickness-shear vibration modes with obvious energy trapping. Bechmann's number for the existence of only one trapped mode also can be determined accordingly.

  12. Region Graph Partition Function Expansion and Approximate Free Energy Landscapes: Theory and Some Numerical Results

    NASA Astrophysics Data System (ADS)

    Zhou, Haijun; Wang, Chuang

    2012-08-01

    Graphical models for finite-dimensional spin glasses and real-world combinatorial optimization and satisfaction problems usually have an abundant number of short loops. The cluster variation method and its extension, the region graph method, are theoretical approaches for treating the complicated short-loop-induced local correlations. For graphical models represented by non-redundant or redundant region graphs, approximate free energy landscapes are constructed in this paper through the mathematical framework of region graph partition function expansion. Several free energy functionals are obtained, each of which use a set of probability distribution functions or functionals as order parameters. These probability distribution function/functionals are required to satisfy the region graph belief-propagation equation or the region graph survey-propagation equation to ensure vanishing correction contributions of region subgraphs with dangling edges. As a simple application of the general theory, we perform region graph belief-propagation simulations on the square-lattice ferromagnetic Ising model and the Edwards-Anderson model. Considerable improvements over the conventional Bethe-Peierls approximation are achieved. Collective domains of different sizes in the disordered and frustrated square lattice are identified by the message-passing procedure. Such collective domains and the frustrations among them are responsible for the low-temperature glass-like dynamical behaviors of the system.

  13. Surface Studies with Combined Free Energy Functionals of Electronic and Liquid Densities

    NASA Astrophysics Data System (ADS)

    Letchworth Weaver, Kendra; Sundararaman, Ravishankar; Arias, Tomás

    2012-02-01

    The microscopic structure of both a solid surface and a contacting liquid can be dramatically affected by the interaction between the two systems, particularly at the interface between a polar surface and a polar liquid. We present a study of oxide and metallic surfaces in an aqueous electrolyte environment with Joint Density Functional Theory (JDFT), a computationally efficient alternative to molecular dynamics simulations which replaces thermal sampling with a single variational principle for the free energy of the full system. Within the rigorous framework of JDFT, we introduce classical density-functionals for ionic species and describe how to couple them with existing functionals for liquid water and traditional electronic density-functionals. Calculations employ a liquid water functional, which captures bulk properties and microscopic structure over the entire phase diagram of the liquid, and a density-only coupling functional between the electronic and liquid systems, which can reproduce solvation free energies of small molecules to within chemical accuracy. With this microscopically accurate description of the liquid-solid interface structure, we gain physical insight which could direct future studies of catalysis and electrode stability in electrochemical systems.

  14. Universal features of the free-energy functional at the freezing transition for repulsive potentials.

    PubMed

    Verma, Anurag; Ford, David M

    2011-05-01

    The free-energy difference between coexisting solid and liquid phases is studied in the context of classical density functional theory (DFT). A bridge function is used to represent the higher-order (n>2) terms in the perturbative expansion of the excess Helmholtz free energy, and the values of this bridge function within the solid lattice are determined by inversion using literature Monte Carlo simulation results. Four potential models, specifically hard-sphere and inverse twelfth-, sixth-, and fourth-power repulsive, are studied. The face-centered cubic (fcc) solid is considered for the hard-sphere and inverse twelfth- and sixth-power potentials, while the body-centered cubic (bcc) solid is considered for the inverse sixth- and fourth-power potentials. For a given solid structure there is a remarkable similarity among the bridge functions for different potentials that is analogous to the universality in the sum of elementary diagrams, or bridge functions, of liquid-state theory as originally observed by Rosenfeld and Ashcroft [Phys. Rev. A 20, 1208 (1979)]. In further analogy with liquid-state theory, the bridge functions in the present problem are plotted as functionals of the second-order convolution term in the perturbative expansion. In each case, the plot indicates a unique functionality in the dense regions of the solid near the lattice sites but a scattered and nonunique behavior in the void regions. Interestingly, knowledge of the functional relationship in the unique region near the lattice sites seems to be sufficient to quantitatively model the solid-fluid phase transition. These qualitative observations are true for both fcc and bcc solid phases, although there are some quantitative differences between them. The findings suggest that pursuit of a closure-based DFT of solid-fluid transitions may be profitable. PMID:21728493

  15. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

    PubMed

    Cisneros, Gerardo Andrés; Wikfeldt, Kjartan Thor; Ojamäe, Lars; Lu, Jibao; Xu, Yao; Torabifard, Hedieh; Bartók, Albert P; Csányi, Gábor; Molinero, Valeria; Paesani, Francesco

    2016-07-13

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

  16. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

    PubMed

    Cisneros, Gerardo Andrés; Wikfeldt, Kjartan Thor; Ojamäe, Lars; Lu, Jibao; Xu, Yao; Torabifard, Hedieh; Bartók, Albert P; Csányi, Gábor; Molinero, Valeria; Paesani, Francesco

    2016-07-13

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments. PMID:27186804

  17. Aromatic Lateral Substituents Influence the Excitation Energies of Hexaaza Lanthanide Macrocyclic Complexes: A Wave Function Theory and Density Functional Study.

    PubMed

    Rabanal-León, Walter A; Murillo-López, Juliana A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

    2015-09-24

    The high interest in lanthanide chemistry, and particularly in their luminescence, has been encouraged by the need of understanding the lanthanide chemical coordination and how the design of new luminescent materials can be affected by this. This work is focused on the understanding of the electronic structure, bonding nature, and optical properties of a set of lanthanide hexaaza macrocyclic complexes, which can lead to potential optical applications. Here we found that the DFT ground state of the open-shell complexes are mainly characterized by the manifold of low lying f states, having small HOMO-LUMO energy gaps. The results obtained from the wave function theory calculations (SO-RASSI) put on evidence the multiconfigurational character of their ground state and it is observed that the large spin-orbit coupling and the weak crystal field produce a strong mix of the ground and the excited states. The electron localization function (ELF) and the energy decomposition analysis (EDA) support the idea of a dative interaction between the macrocyclic ligand and the lanthanide center for all the studied systems; noting that, this interaction has a covalent character, where the d-orbital participation is evidenced from NBO analysis, leaving the f shell completely noninteracting in the chemical bonding. From the optical part we observed in all cases the characteristic intraligand (IL) (π-π*) and ligand to metal charge-transfer (LMCT) bands that are present in the ultraviolet and visible regions, and for the open-shell complexes we found the inherent f-f electronic transitions on the visible and near-infrared region. PMID:26325624

  18. Observations of the directional distribution of the wind energy input function over swell waves

    NASA Astrophysics Data System (ADS)

    Shabani, Behnam; Babanin, Alex V.; Baldock, Tom E.

    2016-02-01

    Field measurements of wind stress over shallow water swell traveling in different directions relative to the wind are presented. The directional distribution of the measured stresses is used to confirm the previously proposed but unverified directional distribution of the wind energy input function. The observed wind energy input function is found to follow a much narrower distribution (β∝cos⁡3.6θ) than the Plant (1982) cosine distribution. The observation of negative stress angles at large wind-wave angles, however, indicates that the onset of negative wind shearing occurs at about θ≈ 50°, and supports the use of the Snyder et al. (1981) directional distribution. Taking into account the reverse momentum transfer from swell to the wind, Snyder's proposed parameterization is found to perform exceptionally well in explaining the observed narrow directional distribution of the wind energy input function, and predicting the wind drag coefficients. The empirical coefficient (ɛ) in Snyder's parameterization is hypothesised to be a function of the wave shape parameter, with ɛ value increasing as the wave shape changes between sinusoidal, sawtooth, and sharp-crested shoaling waves.

  19. An Energy-Based Limit State Function for Estimation of Structural Reliability in Shock Environments

    DOE PAGES

    Guthrie, Michael A.

    2013-01-01

    limit state function is developed for the estimation of structural reliability in shock environments. This limit state function uses peak modal strain energies to characterize environmental severity and modal strain energies at failure to characterize the structural capacity. The Hasofer-Lind reliability index is briefly reviewed and its computation for the energy-based limit state function is discussed. Applications to two degree of freedom mass-spring systems and to a simple finite element model are considered. For these examples, computation of the reliability index requires little effort beyond a modal analysis, but still accounts for relevant uncertainties in both the structure and environment.more » For both examples, the reliability index is observed to agree well with the results of Monte Carlo analysis. In situations where fast, qualitative comparison of several candidate designs is required, the reliability index based on the proposed limit state function provides an attractive metric which can be used to compare and control reliability.« less

  20. Energy flow and functional compensation in Great Basin small mammals under natural and anthropogenic environmental change

    PubMed Central

    Terry, Rebecca C.; Rowe, Rebecca J.

    2015-01-01

    Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities—particularly the spread of nonnative annual grasslands—has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management. PMID:26170294

  1. Energy flow and functional compensation in Great Basin small mammals under natural and anthropogenic environmental change.

    PubMed

    Terry, Rebecca C; Rowe, Rebecca J

    2015-08-01

    Research on the ecological impacts of environmental change has primarily focused at the species level, leaving the responses of ecosystem-level properties like energy flow poorly understood. This is especially so over millennial timescales inaccessible to direct observation. Here we examine how energy flow within a Great Basin small mammal community responded to climate-driven environmental change during the past 12,800 y, and use this baseline to evaluate responses observed during the past century. Our analyses reveal marked stability in energy flow during rapid climatic warming at the terminal Pleistocene despite dramatic turnover in the distribution of mammalian body sizes and habitat-associated functional groups. Functional group turnover was strongly correlated with climate-driven changes in regional vegetation, with climate and vegetation change preceding energetic shifts in the small mammal community. In contrast, the past century has witnessed a substantial reduction in energy flow caused by an increase in energetic dominance of small-bodied species with an affinity for closed grass habitats. This suggests that modern changes in land cover caused by anthropogenic activities--particularly the spread of nonnative annual grasslands--has led to a breakdown in the compensatory dynamics of energy flow. Human activities are thus modifying the small mammal community in ways that differ from climate-driven expectations, resulting in an energetically novel ecosystem. Our study illustrates the need to integrate across ecological and temporal scales to provide robust insights for long-term conservation and management. PMID:26170294

  2. Comment on "Single-point kinetic energy density functionals: A pointwise kinetic energy density analysis and numerical convergence investigation"

    NASA Astrophysics Data System (ADS)

    Trickey, S. B.; Karasiev, Valentin V.; Chakraborty, Debajit

    2015-09-01

    We suggest a more nuanced view of the merit and utility of generalized gradient approximations (GGAs) for the noninteracting kinetic energy (KE) than the critique of Xia and Carter (XC) [Phys. Rev. B 91, 045124 (2015), 10.1103/PhysRevB.91.045124]. Specifically, the multiple valuedness of the Pauli term enhancement factor (denoted G [n ] by XC) with respect to the inhomogeneity variable s can be excluded by enforcement of a bound on the Kohn-Sham KE to achieve universality of the functional along with enforcement of proper large-s behavior. This is physically sensible in that the excluded G values occur for s values that correspond to low densities. The behavior is exacerbated by peculiarities of pseudodensities. The VT84F KE GGA, constructed with these constraints, does not have the numerical instability in our older PBE2 functional analyzed by XC.

  3. Stringent test for non-additive, non-interacting, kinetic energy functionals

    NASA Astrophysics Data System (ADS)

    Jiang, Kaili; Nafziger, Jonathan; Wasserman, Adam

    Partition Density Functional Theory (PDFT) provides an ideal framework for testing and developing new approximations to the non-additive and non-interacting kinetic energy functional (Tsnadd [ {nα } ]), understood as a functional of the set of fragment ground-state densities. We present our progress on both of these fronts: (1) Systematic comparison of the performance of various existing approximations to Tsnadd [ {nα } ] ; and (2) Development of new approximations. We find that a re-parametrization of the GGA enhancement factor employed for the construction of Tsnadd [ {nα } ] through the conjointness conjecture captures essential features of the functional derivatives of Tsnadd [ {nα } ] . A physically-motivated two-orbital approximation for Tsnadd [ {nα } ] is shown to outperform most other approximations for the case of He2, and an intriguing one-parameter formula makes this approximation accurate for all noble-gas diatomics.

  4. Free-energy functional method for inverse problem of self assembly

    NASA Astrophysics Data System (ADS)

    Torikai, Masashi

    2015-04-01

    A new theoretical approach is described for the inverse self-assembly problem, i.e., the reconstruction of the interparticle interaction from a given structure. This theory is based on the variational principle for the functional that is constructed from a free energy functional in combination with Percus's approach [J. Percus, Phys. Rev. Lett. 8, 462 (1962)]. In this theory, the interparticle interaction potential for the given structure is obtained as the function that maximizes the functional. As test cases, the interparticle potentials for two-dimensional crystals, such as square, honeycomb, and kagome lattices, are predicted by this theory. The formation of each target lattice from an initial random particle configuration in Monte Carlo simulations with the predicted interparticle interaction indicates that the theory is successfully applied to the test cases.

  5. Free-energy functional method for inverse problem of self assembly.

    PubMed

    Torikai, Masashi

    2015-04-14

    A new theoretical approach is described for the inverse self-assembly problem, i.e., the reconstruction of the interparticle interaction from a given structure. This theory is based on the variational principle for the functional that is constructed from a free energy functional in combination with Percus's approach [J. Percus, Phys. Rev. Lett. 8, 462 (1962)]. In this theory, the interparticle interaction potential for the given structure is obtained as the function that maximizes the functional. As test cases, the interparticle potentials for two-dimensional crystals, such as square, honeycomb, and kagome lattices, are predicted by this theory. The formation of each target lattice from an initial random particle configuration in Monte Carlo simulations with the predicted interparticle interaction indicates that the theory is successfully applied to the test cases.

  6. Functions of a new photoreceptor membrane. [energy conversion via halobacteria rhodopsin changes

    NASA Technical Reports Server (NTRS)

    Oesterhelt, D.; Stoeckenius, W.

    1973-01-01

    In the investigation of light responses on halobacteria phototaxis; ATP synthesis; and changes in O2 consumption, purple membrane biosynthesis, and proton translocation were found. The last three effects are discussed, which suggest that the purple membrane may function as an energy-coupling membrane for light. It is also suggested that purple membrane, through cyclic light-induced conformational changes of its bacteriorhodopsin, directly converts absorbed light energy into a proton gradient and presumably also an electric potential difference across the membrane analogous to observations in other prokaryotic cells, mitochondria, and chloroplasts.

  7. Interacting boson model from energy density functionals: {gamma}-softness and the related topics

    SciTech Connect

    Nomura, K.

    2012-10-20

    A comprehensive way of deriving the Hamiltonian of the interacting boson model (IBM) is described. Based on the fact that the multi-nucleon induced surface deformation in finite nucleus is simulated by effective boson degrees of freedom, the potential energy surface calculated with self-consistent mean-field method employing a given energy density functional (EDF) is mapped onto the IBM analog, and thereby the excitation spectra and transition rates with good symmetry quantum numbers are calculated. Recent applications of the proposed approach are reported: (i) an alternative robust interpretation of the {gamma}-soft nuclei and (ii) shape coexistence in lead isotopes.

  8. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

    PubMed

    Jorgensen, William L; Tirado-Rives, Julian

    2005-05-10

    An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

  9. A priori classical density functionals of water: toward first principles exploration of aqueous based energy systems

    NASA Astrophysics Data System (ADS)

    Sundararaman, Ravishankar; Letchworth Weaver, Kendra; Arias, Tomas

    2011-03-01

    We present a novel description of water which will allow the first a priori studies of catalysis of biofuels in aqueous electrochemical environments. Our method offers a computationally efficient alternative to the thermal sampling required by molecular dynamics yet provides a more realistic description of bulk water than including explicit frozen water or traditional continuum solvation models. Into Joint Density Functional Theory (JDFT), which joins an electron density-functional for the solute with classical density-functional theories for liquid water into a single variational principle for the free energy of the combined system, we introduce the innovation of an a priori form of the coupling functional between the quantum-mechanical system and liquid water based on a local density approximation to the Hohenberg-Kohn density-only functional. Without any fits to solvation data whatsoever, this new method predicts solvation energies of small organic molecules well compared to state-of-the art empirical quantum-chemical cavity approaches. The site interaction potentials produced closely resemble the widely used TIP3P site potentials for water without requiring any empirical parameters. R. Sundararaman et al, unpublished, to be presented at the APS March Meeting (2011)

  10. Density-Functional Theory Studies of Correlation Energy Effects at Metallic Surfaces.

    NASA Astrophysics Data System (ADS)

    Mohammed, Abdel-Raouf Eid

    In this thesis we study the effects of correlation in the inhomogeneous electron gas at metallic surfaces. These studies are performed within the context of density-functional theory (DFT). Using accurate representations of the electronic density profile, we have estimated variationally the surface correlation energy of jellium metal. The accuracy of these estimates is founded in the assumption that the exchange -correlation energy functional of the density is approximated accurately by the wave-vector analysis method, and by the fact that the non-local exchange energy contributions are treated exactly. In contrast to the previously accepted conclusion that for surfaces correlation effects are as significant as exchange, our results indicate the ratio of these energies to lie between 34% - 97% over the metallic density range, the smaller ratios corresponding to the higher density metals. In this work we have also examined the local density (LDA) and gradient expansion approximations (GEA) (to O((DEL)('2))) for the correlation energy. We have demonstrated for realistic metal surface densities the cancellation of the errors in the LDA for exchange and correlation, and shown that the density profiles at surfaces would have to be unphysically slowly varying for the correlation energy GEA to converge. We have also studied the effects of correlation at surfaces by screening the exchange, and observe that the surface exchange energy for screened-Coulomb interaction decreases as the screening length is reduced. Thus, the more short-ranged the interaction, the easier it is to split the crystal in two. In addition we have derived the DFT first gradient correction coefficient in the GEA for the screened-Coulomb exchange energy, and shown it to be the same as that obtained within Hartree -Fock theory (HFT) for finite screening. This coefficient reduces to the DFT bare-Coulomb interaction value in the limit of no screening in which limit the HFT coefficient is singular. The GEA

  11. Functional block copolymers for applications in advanced materials, energy storage, and lithography

    NASA Astrophysics Data System (ADS)

    Hardy, Christopher George

    Block copolymers spontaneously self-assembly into a wide variety of ordered nanostructures on the length scale of 5 - 100 nm due to the thermodynamic immiscibility between the covalently linked, chemically distinct polymer chains. Incorporating desirable functional groups into block copolymer systems can lead to confinement of the functional group to a specific domain upon microphase separation of the block copolymer. The resulting materials display desirable characteristics of the functional group in a well-ordered nanostructure. Such systems have been utilized in a wide variety of applications including catalysis, ceramic materials, and membranes. This dissertation is focused on the synthesis, characterization, self-assembly and materials processing of various functionalized block copolymer systems. An assortment of monomers functionalized with specific groups were prepared and polymerized by a variety of polymerization techniques including atom transfer radical polymerization, reversible addition-fragmentation chain transfer polymerization, and ring-opening metathesis polymerization. Self-assembly of the functionalized block copolymers led to well defined nanostructures in bulk and thin films. Depending upon the functional group incorporated, the ordered materials were utilized in various applications including ordered catalysts, energy storage, and templates for nanolithography..

  12. Free energy from stationary implementation of the DFT+EDMFT functional

    NASA Astrophysics Data System (ADS)

    Birol, Turan; Haule, Kristjan

    The workhorse of first principles calculations on crystalline solids is the Density Functional Theory at the level of Local Density Approximation (LDA). Despite its various successes, LDA is prone to an overbinding problem, which introduces an error in optimized lattice constants and other structural parameters. Various Generalized Gradient Approximations are introduced to correct for this problem, but they often fail to systematically correct it, in particular in correlated electron materials. We developed a stationary and functional derivable Embedded Dynamical Mean Field Theory combined with the DFT (EDMFT+DFT) to calculate the free energy and to optimize the structural parameters in correlated electron compounds. In our stationary formalism, the first order error in the density leads to a much smaller, second order error in the free energy. We consider the correlated metal SrVO3, Mott insulating FeO, elemental Ce, and iron chalcogenide FeSe as examples to show that EDMFT predicts the lattice constants with high accuracy.

  13. Evolution of the electron energy distribution function during genesis of breakdown plasma

    SciTech Connect

    Bhattacharjee, Sudeep; Paul, Samit; Ghosh, Sayandip

    2014-08-15

    During the process of plasma initiation by an electromagnetic wave, it is found that the electron energy distribution function (EEDF) that is initially Maxwellian with the most probable energy at room temperature, evolves with time and tends toward a Bi-Maxwellian – indicating attainment of thermodynamic equilibrium in the individual electron populations prior to breakdown, with a significant increase in hot electron density. In the intermediate states during the evolution, however, non-equilibrium processes are prevalent under fast pulse excitation and the EEDF initially exhibits substantial deviation from a Maxwellian. An analysis of the deviation has been carried out by optimizing the residual sum of squares of the probabilities obtained from the simulation and a fitted Maxwellian curve. The equilibrium regain time defined as the time required to attain thermodynamic equilibrium again, is investigated as a function of neutral pressure, wave electric, and external magnetostatic fields.

  14. Functional integration of vertical flight path and speed control using energy principles

    NASA Technical Reports Server (NTRS)

    Lambregts, A. A.

    1984-01-01

    A generalized automatic flight control system was developed which integrates all longitudinal flight path and speed control functions previously provided by a pitch autopilot and autothrottle. In this design, a net thrust command is computed based on total energy demand arising from both flight path and speed targets. The elevator command is computed based on the energy distribution error between flight path and speed. The engine control is configured to produce the commanded net thrust. The design incorporates control strategies and hierarchy to deal systematically and effectively with all aircraft operational requirements, control nonlinearities, and performance limits. Consistent decoupled maneuver control is achieved for all modes and flight conditions without outer loop gain schedules, control law submodes, or control function duplication.

  15. Simulation of Charged Systems in Heterogeneous Dielectric Media via a True Energy Functional

    NASA Astrophysics Data System (ADS)

    Jadhao, Vikram; Solis, Francisco J.; de la Cruz, Monica Olvera

    2012-11-01

    For charged systems in heterogeneous dielectric media, a key obstacle for molecular dynamics (MD) simulations is the need to solve the Poisson equation in the media. This obstacle can be bypassed using MD methods that treat the local polarization charge density as a dynamic variable, but such approaches require access to a true free energy functional, one that evaluates to the equilibrium electrostatic energy at its minimum. In this Letter, we derive the needed functional. As an application, we develop a Car-Parrinello MD method for the simulation of free charges present near a spherical emulsion droplet separating two immiscible liquids with different dielectric constants. Our results show the presence of nonmonotonic ionic profiles in the dielectric with a lower dielectric constant.

  16. Nonlinear vibration energy harvesting based on variable double well potential function

    NASA Astrophysics Data System (ADS)

    Yang, Wei; Towfighian, Shahrzad

    2016-04-01

    Converting ambient mechanical energy to electricity, vibration energy harvesting, enables powering of the low-power remote sensors. Nonlinear energy harvesters have the advantage of a wider frequency spectrum compared to linear resonators making them more efficient in scavenging the broadband frequency of ambient vibrations. To increase the output power of the nonlinear resonators, we propose an energy harvester composed of a cantilever piezoelectric beam carrying a movable magnet facing a fixed magnet at a distance. The movable magnet on the beam is attached to a spring at the base of the beam. The spring-magnet system on the cantilever beam creates the variable double well potential function. The spring attached to the magnet is in its compressed position when the beam is not deflected, as the beam oscillates, the spring energy gradually releases and further increases the amplitude of vibration. To describe the motion of the cantilever beam, we obtained two coupled partial differential equations by assuming the cantilever beam as Euler-Bernoulli beam considering the effect of the moving magnet. Method of multiple scales is used to solve the coupled equations. The cantilever beam with the two magnets is a bi-stable system. Making one magnet movable can create internal resonance that is explored as a mechanism to increase the frequency bandwidth. The effect of system parameters on the frequency bandwidth of the resonator is investigated through numerical solutions. This study benefits vibration energy harvesting to achieve a higher performance when excited by the wideband ambient vibrations.

  17. Study of the Dielectric Function of Graphene from Spectroscopic Ellipsometry and Electron Energy Loss Spectroscopy

    NASA Astrophysics Data System (ADS)

    Nelson, Florence

    For more than 60 years, semiconductor research has been advancing up the periodic table. The first transistor was made from germanium. This later gave way to silicon-based devices due to the latter's ability to form an excellent interface with thermally-grown oxide. Now for the last ˜8 years, the focus has moved up one more row to carbon for post-CMOS devices in order to comply with the scaling limitations of Moore's law. However, for each of these, the measurements of film properties and dimensions have always been required for technological applications. These measurement methods often incorporate the use of light or electrons in order to take advantage of a wavelength that is on the order of, or smaller than, the feature sizes of interest. This thesis compares the dielectric function of graphene measured by an optical method to that obtained from an electron energy loss method in order to observe the effect of contamination and substrate on the optical properties of graphene exposed to the environment. Whether viewed in terms of how light affects a material (dielectric function) or how a material affects light (refractive index), the optical response is a quantity that may be used to obtain information about a film's thickness, energy structure, and the types of excitations that are responsible for energy loss. The three main experimental methods used in this thesis work are spectroscopic ellipsometry (SE), scanning transmission electron microscopy (STEM), and electron energy loss spectroscopy (EELS). SE is commonly used in clean-room environments for optical measurement over the energy range of ˜0-5 eV. This method is used to study graphene's dielectric function from the ultraviolet (UV) through infrared (IR) regions through use of an oscillator dispersion model. A nearly constant absorbance over the IR and into the visible region is observed due to vertical transitions between graphene's linearly dispersed pi-bands at the Dirac points. An exciton

  18. Applications of Skyrme energy-density functional to fusion reactions for synthesis of superheavy nuclei

    SciTech Connect

    Wang Ning; Scheid, Werner; Wu Xizhen; Liu Min; Li Zhuxia

    2006-10-15

    The Skyrme energy-density functional approach has been extended to study massive heavy-ion fusion reactions. Based on the potential barrier obtained and the parametrized barrier distribution the fusion (capture) excitation functions of a lot of heavy-ion fusion reactions are studied systematically. The average deviations of fusion cross sections at energies near and above the barriers from experimental data are less than 0.05 for 92% of 76 fusion reactions with Z{sub 1}Z{sub 2}<1200. For the massive fusion reactions, for example, the {sup 238}U-induced reactions and {sup 48}Ca+{sup 208}Pb, the capture excitation functions have been reproduced remarkably well. The influence of structure effects in the reaction partners on the capture cross sections is studied with our parametrized barrier distribution. By comparing the reactions induced by double-magic nucleus {sup 48}Ca and by {sup 32}S and {sup 35}Cl, the ''threshold-like'' behavior in the capture excitation function for {sup 48}Ca-induced reactions is explored and an optimal balance between the capture cross section and the excitation energy of the compound nucleus is studied. Finally, the fusion reactions with {sup 36}S, {sup 37}Cl, {sup 48}Ca, and {sup 50}Ti bombarding {sup 248}Cm, {sup 247,249}Bk, {sup 250,252,254}Cf, and {sup 252,254}Es, as well as the reactions leading to the same compound nucleus with Z=120 and N=182, are studied further. The calculation results for these reactions are useful for searching for the optimal fusion configuration and suitable incident energy in the synthesis of superheavy nuclei.

  19. Mathematical representation of the incident solar energy as a function of latitude and time

    SciTech Connect

    Simmons, P.A.

    1988-07-01

    A simple mathematical representation of the incoming solar radiation as a function of latitude and time is introduced. The expression approximates the total zonally and daily averaged solar energy incident on the earth's surface before any is absorbed. It includes dependence on both the obliquity and the precession of the equinoxes and, with its accuracy limits, the representation is convenient for use in long-term climate modelling. 7 references.

  20. Radial profile of the electron energy distribution function in RF capacitive gas-discharge plasma

    NASA Astrophysics Data System (ADS)

    Dimitrova, M.; Popov, Tsv; Puac, N.; Skoro, N.; Spasic, K.; Malovic, G.; Dias, F. M.; Petrovic, Z. Lj

    2016-03-01

    This paper reports experimental results on low-pressure argon capacitive RF discharge (parallel-plate capacitively-coupled plasma - CCP) under different conditions, namely, gas pressure in the range 3 -r- 30 Pa and RF power in the range 10 - 100 W. The IV characteristics measured were processed by two different second-derivative probe techniques for determination of the plasma parameters and the electron energy distribution function. The radial profiles of the main plasma parameters are presented.

  1. Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling

    PubMed Central

    MacDonald, James T.; Kelley, Lawrence A.; Freemont, Paul S.

    2013-01-01

    Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http

  2. Blind test of density-functional-based methods on intermolecular interaction energies

    NASA Astrophysics Data System (ADS)

    Taylor, DeCarlos E.; Ángyán, János G.; Galli, Giulia; Zhang, Cui; Gygi, Francois; Hirao, Kimihiko; Song, Jong Won; Rahul, Kar; Anatole von Lilienfeld, O.; Podeszwa, Rafał; Bulik, Ireneusz W.; Henderson, Thomas M.; Scuseria, Gustavo E.; Toulouse, Julien; Peverati, Roberto; Truhlar, Donald G.; Szalewicz, Krzysztof

    2016-09-01

    In the past decade, a number of approaches have been developed to fix the failure of (semi)local density-functional theory (DFT) in describing intermolecular interactions. The performance of several such approaches with respect to highly accurate benchmarks is compared here on a set of separation-dependent interaction energies for ten dimers. Since the benchmarks were unknown before the DFT-based results were collected, this comparison constitutes a blind test of these methods.

  3. Horizon News Function and Quasi-Local Energy-Momentum Flux Near Black Hole

    NASA Astrophysics Data System (ADS)

    Wu, Yu-Huei

    2008-09-01

    From the 'quasi-local' definition of horizons, e.g. isolated horizon and dynamical horizon, the consequence quasi-local energy-momentum near horizons can be observed by using the idea of frame alignment. In particular, we find the horizon news function from the asymptotic expansion near horizons and use this to describe the gravitational flux and change of mass of a black hole.

  4. On the form of the strain energy function for a family of SBR materials. [Styrene-Butadiene Rubber

    NASA Technical Reports Server (NTRS)

    Arenz, R. J.

    1977-01-01

    Styrene-butadiene materials with varying crosslink densities are analyzed through use of a strain energy function of the type introduced by Valanis and Landel (1967). A form of the strain energy function derived from strip biaxial tests proves to be accurate when checked against uniaxial and other biaxial test results.

  5. Global study of beyond-mean-field correlation energies in covariant energy density functional theory using a collective Hamiltonian method

    NASA Astrophysics Data System (ADS)

    Lu, K. Q.; Li, Z. X.; Li, Z. P.; Yao, J. M.; Meng, J.

    2015-02-01

    We report the first global study of dynamic correlation energies (DCEs) associated with rotational motion and quadrupole shape vibrational motion in a covariant energy density functional (CEDF) for 575 even-even nuclei with proton numbers ranging from Z =8 to Z =108 by solving a five-dimensional collective Hamiltonian, the collective parameters of which are determined from triaxial relativistic mean field plus BCS calculation using the PC-PK1 force. After taking into account these beyond mean-field DCEs, the root-mean-square (rms) deviation with respect to nuclear masses is reduced significantly down to 1.14 MeV, which is smaller than those of other successful CEDFs: NL3* (2.96 MeV), DD-ME2 (2.39 MeV), DD -ME δ (2.29 MeV), and DD-PC1 (2.01 MeV). Moreover, the rms deviation for two-nucleon separation energies is reduced by ˜34 % in comparison with the cranking prescription.

  6. Improved Potential Energy Surface of Ozone Constructed Using the Fitting by Permutationally Invariant Polynomial Function

    DOE PAGES

    Ayouz, Mehdi; Babikov, Dmitri

    2012-01-01

    New global potential energy surface for the ground electronic state of ozone is constructed at the complete basis set level of the multireference configuration interaction theory. A method of fitting the data points by analytical permutationally invariant polynomial function is adopted. A small set of 500 points is preoptimized using the old surface of ozone. In this procedure the positions of points in the configuration space are chosen such that the RMS deviation of the fit is minimized. New ab initio calculations are carried out at these points and are used to build new surface. Additional points are addedmore » to the vicinity of the minimum energy path in order to improve accuracy of the fit, particularly in the region where the surface of ozone exhibits a shallow van der Waals well. New surface can be used to study formation of ozone at thermal energies and its spectroscopy near the dissociation threshold.« less

  7. Local electrochemical functionality in energy storage materials and devices by scanning probe microscopies: status and perspectives.

    PubMed

    Kalinin, Sergei V; Balke, Nina

    2010-09-15

    Energy storage and conversion systems are an integral component of emerging green technologies, including mobile electronic devices, automotive, and storage components of solar and wind energy economics. Despite the rapidly expanding manufacturing capabilities and wealth of phenomenological information on the macroscopic device behaviors, the microscopic mechanisms underpinning battery and fuel cell operations in the nanometer-micrometer range are virtually unknown. This lack of information is due to the dearth of experimental techniques capable of addressing elementary mechanisms involved in battery operation, including electronic and ion transport, vacancy injection, and interfacial reactions, on the nanometer scale. In this article, a brief overview of scanning probe microscopy (SPM) methods addressing nanoscale electrochemical functionalities is provided and compared with macroscopic electrochemical methods. Future applications of emergent SPM methods, including near field optical, electromechanical, microwave, and thermal probes and combined SPM-(S)TEM (scanning transmission electron microscopy) methods in energy storage and conversion materials are discussed.

  8. Local electrochemical functionality in energy storage materials and devices by scanning probe microscopies: Status and perspectives

    SciTech Connect

    Kalinin, S. V.; Balke, N.

    2010-01-01

    Energy storage and conversion systems are an integral component of emerging green technologies, including mobile electronic devices, automotive, and storage components of solar and wind energy economics. Despite the rapidly expanding manufacturing capabilities and wealth of phenomenological information on the macroscopic device behaviors, the microscopic mechanisms underpinning battery and fuel cell operations in the nanometer–micrometer range are virtually unknown. This lack of information is due to the dearth of experimental techniques capable of addressing elementary mechanisms involved in battery operation, including electronic and ion transport, vacancy injection, and interfacial reactions, on the nanometer scale. In this article, a brief overview of scanning probe microscopy (SPM) methods addressing nanoscale electrochemical functionalities is provided and compared with macroscopic electrochemical methods. Future applications of emergent SPM methods, including near field optical, electromechanical, microwave, and thermal probes and combined SPM-(S)TEM (scanning transmission electron microscopy) methods in energy storage and conversion materials are discussed.

  9. Local electrochemical functionality in energy storage materials and devices by scanning probe microscopies: status and perspectives

    SciTech Connect

    Kalinin, Sergei V; Balke, Nina

    2010-01-01

    Energy storage and conversion systems are an integral component of emerging green technologies, including mobile electronic devices, automotive, and storage components of solar and wind energy economics. Despite the rapidly expanding manufacturing capabilities and wealth of phenomenological information on the macroscopic device behaviors, the microscopic mechanisms underpinning battery and fuel cell operations in the nanometer-micrometer range are virtually unknown. This lack of information is due to the dearth of experimental techniques capable of addressing elementary mechanisms involved in battery operation, including electronic and ion transport, vacancy injection, and interfacial reactions, on the nanometer scale. In this article, a brief overview of scanning probe microscopy (SPM) methods addressing nanoscale electrochemical functionalities is provided and compared with macroscopic electrochemical methods. Future applications of emergent SPM methods, including near field optical, electromechanical, microwave, and thermal probes and combined SPM-(S)TEM (scanning transmission electron microscopy) methods in energy storage and conversion materials are discussed.

  10. Analysis of electron energy distribution function in the Linac4 H⁻ source.

    PubMed

    Mochizuki, S; Mattei, S; Nishida, K; Hatayama, A; Lettry, J

    2016-02-01

    To understand the Electron Energy Distribution Function (EEDF) in the Radio Frequency Inductively Coupled Plasmas (RF-ICPs) in hydrogen negative ion sources, the detailed analysis of the EEDFs using numerical simulation and the theoretical approach based on Boltzmann equation has been performed. It is shown that the EEDF of RF-ICPs consists of two parts, one is the low energy part which obeys Maxwellian distribution and the other is high energy part deviated from Maxwellian distribution. These simulation results have been confirmed to be reasonable by the analytical approach. The results suggest that it is possible to enhance the dissociation of molecules and the resultant H(-) negative ion production by reducing the gas pressure. PMID:26931990

  11. Analysis of electron energy distribution function in the Linac4 H⁻ source.

    PubMed

    Mochizuki, S; Mattei, S; Nishida, K; Hatayama, A; Lettry, J

    2016-02-01

    To understand the Electron Energy Distribution Function (EEDF) in the Radio Frequency Inductively Coupled Plasmas (RF-ICPs) in hydrogen negative ion sources, the detailed analysis of the EEDFs using numerical simulation and the theoretical approach based on Boltzmann equation has been performed. It is shown that the EEDF of RF-ICPs consists of two parts, one is the low energy part which obeys Maxwellian distribution and the other is high energy part deviated from Maxwellian distribution. These simulation results have been confirmed to be reasonable by the analytical approach. The results suggest that it is possible to enhance the dissociation of molecules and the resultant H(-) negative ion production by reducing the gas pressure.

  12. A numerical method for determining highly precise electron energy distribution functions from Langmuir probe characteristics

    SciTech Connect

    Bang, Jin-Young; Chung, Chin-Wook

    2010-12-15

    Electron energy distribution functions (EEDFs) were determined from probe characteristics using a numerical ac superimposed method with a distortion correction of high derivative terms by varying amplitude of a sinusoidal perturbation voltage superimposed onto the dc sweep voltage, depending on the related electron energy. Low amplitude perturbation applied around the plasma potential represented the low energy peak of the EEDF exactly, and high amplitude perturbation applied around the floating potential was effective to suppress noise or distortion of the probe characteristic, which is fatal to the tail electron distribution. When a small random noise was imposed over the stabilized prove characteristic, the numerical differentiation method was not suitable to determine the EEDF, while the numerical ac superimposed method was able to obtain a highly precise EEDF.

  13. Nanocluster ionization energies and work function of aluminum, and their temperature dependence

    SciTech Connect

    Halder, Avik; Kresin, Vitaly V.

    2015-10-28

    Ionization threshold energies of Al{sub n} (n = 32-95) nanoclusters are determined by laser ionization of free neutral metal clusters thermalized to several temperatures in the range from 65 K to 230 K. The photoion yield curves of cold clusters follow a quadratic energy dependence above threshold, in agreement with the Fowler law of surface photoemission. Accurate data collection and analysis procedures make it possible to resolve very small (few parts in a thousand) temperature-induced shifts in the ionization energies. Extrapolation of the data to the bulk limit enables a determination of the thermal shift of the polycrystalline metal work function, found to be in excellent agreement with theoretical prediction based on the influence of thermal expansion. Small clusters display somewhat larger thermal shifts, reflecting their greater susceptibility to thermal expansion. Ionization studies of free size-resolved nanoclusters facilitate understanding of the interplay of surface, electronic, and lattice properties under contamination-free conditions.

  14. Online platform for simulations of ion energy distribution functions behind a plasma boundary sheath

    NASA Astrophysics Data System (ADS)

    Wollny, Alexander; Shihab, Mohammed; Brinkmann, Ralf Peter

    2012-10-01

    Plasma processes, particularly plasma etching and plasma deposition are crucial for a large variety of industrial manufacturing purposes. For these processes the knowledge of the ion energy distribution function plays a key role. Measurements of the ion energy and ion angular distribution functions (IEDF, IADF) are at least challenging and often impossible in industrial processes. An alternative to measurements of the IEDF are simulations. With this contribution we present a self-consistent model available online for everyone. The simulation of ion energy and ion angular distribution functions involves the well known plasma boundary sheath model by Brinkmann [1-4], which is controlled via a web interface (http://sheath.tet.rub.de). After a successful simulation run all results are evaluable within the browser and ready for download for further analysis.[4pt] [1] R.P. Brinkmann, J. Phys. D: Appl. Phys. 44, 042002 (2011)[0pt] [2] R.P. Brinkmann, J. Phys. D: Appl. Phys. 42, 194009 (2009)[0pt] [3] R.P. Brinkmann, J. App. Phys. 102, 093303 (2007)[0pt] [4] M. Kratzer et al., J. Appl. Phys. 90, 2169 (2001)

  15. Smart Polyacrylonitrile (PAN) Nanofibers with Thermal Energy Storage and Retrieval Functionality

    NASA Astrophysics Data System (ADS)

    Cherry, De'Andre James

    Phase change materials (PCMs) are generally substances with a high heat of fusion in the process of solid to liquid phase change. The nature of PCMs make them efficient materials to store and retrieve large amounts of thermal energy. Presently, high efficiency thermal energy storage/retrieval in applications where flexibility and space saving are required, such as smart textiles, still remains as a challenge. In this study, lauric acid (LA) and myristic acid (MA) were combined to prepare a specific binary fatty acid eutectic (LA-MA) with a melting point near the operating body temperature of a human being and then encapsulated in polyacrylonitrile (PAN) nanofibers through the electrospinning technique. Functionalized PCM-enhanced PAN nanofibers containing LA-MA at 30%, 50%, 70% and 100% of the weight of the PAN were successfully synthesized. The morphological structures and thermal energy storage capacity of the PCM-enhanced PAN nanofibers were characterized by electron microscopy (EM) and differential scanning calorimetry (DSC). The novel PCM-enhanced PAN nanofibers maintained their cylindrical fiber morphology after multiple heating-cooling cycles and retained their latent heat storage functionality. Thus, it is envisioned that the prepared PCM-enhanced PAN nanofibers will find use in applications such as smart textiles where temperature regulation functionality is required.

  16. Do Bond Functions Help for the Calculation of Accurate Bond Energies?

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

    1998-01-01

    The bond energies of 8 chemically bound diatomics are computed using several basis sets with and without bond functions (BF). The bond energies obtained using the aug-pVnZ+BF basis sets (with a correction for basis set superposition error, BSSE) tend to be slightly smaller that the results obtained using the aug-pV(n+I)Z basis sets, but slightly larger than the BSSE corrected aug-pV(n+I)Z results. The aug-cc-pVDZ+BF and aug-cc-pVTZ+BF basis sets yield reasonable estimates of bond energies, but, in most cases, these results cannot be considered highly accurate. Extrapolation of the results obtained with basis sets including bond functions appears to be inferior to the results obtained by extrapolation using atom-centered basis sets. Therefore bond functions do not appear to offer a path for obtaining highly accurate results for chemically bound systems at a lower computational cost than atom centered basis sets.

  17. Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors

    NASA Astrophysics Data System (ADS)

    Shin, Ilgyou; Carter, Emily A.

    2014-05-01

    We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect and (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.

  18. Stochastic averaging based on generalized harmonic functions for energy harvesting systems

    NASA Astrophysics Data System (ADS)

    Jiang, Wen-An; Chen, Li-Qun

    2016-09-01

    A stochastic averaging method is proposed for nonlinear vibration energy harvesters subject to Gaussian white noise excitation. The generalized harmonic transformation scheme is applied to decouple the electromechanical equations, and then obtained an equivalent nonlinear system which is uncoupled to an electric circuit. The frequency function is given through the equivalent potential energy which is independent of the total energy. The stochastic averaging method is developed by using the generalized harmonic functions. The averaged Itô equations are derived via the proposed procedure, and the Fokker-Planck-Kolmogorov (FPK) equations of the decoupled system are established. The exact stationary solution of the averaged FPK equation is used to determine the probability densities of the amplitude and the power of the stationary response. The procedure is applied to three different type Duffing vibration energy harvesters under Gaussian white excitations. The effects of the system parameters on the mean-square voltage and the output power are examined. It is demonstrated that quadratic nonlinearity only and quadratic combined with properly cubic nonlinearities can increase the mean-square voltage and the output power, respectively. The approximate analytical outcomes are qualitatively and quantitatively supported by the Monte Carlo simulations.

  19. Density Functional Theory Calculations of Activation Energies for Carrier Capture by Defects in Semiconductors

    NASA Astrophysics Data System (ADS)

    Modine, N. A.; Wright, A. F.; Lee, S. R.

    The rate of defect-induced carrier recombination is determined by both defect levels and carrier capture cross-sections. Density functional theory (DFT) has been widely and successfully used to predict defect levels, but only recently has work begun to focus on using DFT to determine carrier capture cross-sections. Lang and Henry developed the theory of carrier-capture by multiphonon emission in the 1970s and showed that carrier-capture cross-sections differ between defects primarily due to differences in their carrier capture activation energies. We present an approach to using DFT to calculate carrier capture activation energies that does not depend on an assumed configuration coordinate and that fully accounts for anharmonic effects, which can substantially modify carrier activation energies. We demonstrate our approach for intrinisic defects in GaAs and GaN and discuss how our results depend on the choice of exchange-correlation functional and the treatment of spin polarization. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  20. Dietary Energy Density, Renal Function, and Progression of Chronic Kidney Disease

    PubMed Central

    Rouhani, Mohammad Hossein; Najafabadi, Mojgan Mortazavi; Esmaillzadeh, Ahmad; Feizi, Awat

    2016-01-01

    Background. There is evidence of the association between dietary energy density and chronic diseases. However, no report exists regarding the relation between DED and chronic kidney disease (CKD). Objective. To examine the association between dietary energy density (DED), renal function, and progression of chronic kidney disease (CKD). Design. Cross-sectional. Setting. Three nephrology clinics. Subjects. Two hundred twenty-one subjects with diagnosed CKD. Main Outcome Measure. Dietary intake of patients was assessed by a validated food frequency questionnaire. DED (in kcal/g) was calculated with the use of energy content and weight of solid foods and energy yielding beverages. Renal function was measured by blood urea nitrogen (BUN), serum creatinine (Cr), and estimated glomerular filtration rate (eGFR). Results. Patients in the first tertile of DED consumed more amounts of carbohydrate, dietary fiber, potassium, phosphorus, zinc, magnesium, calcium, folate, vitamin C, and vitamin B2. After adjusting for confounders, we could not find any significant trend for BUN and Cr across tertiles of DED. In multivariate model, an increased risk of being in the higher stage of CKD was found among those in the last tertile of DED (OR: 3.15; 95% CI: 1.30, 7.63; P = 0.01). Conclusion. We observed that lower DED was associated with better nutrient intake and lower risk of CKD progression.

  1. Self-energy-corrected electronic energy level alignment in molecular junctions and at interfaces with hybrid functionals

    NASA Astrophysics Data System (ADS)

    Kotiuga, Michele; Egger, David; Kronik, Leeor; Neaton, Jeffrey B.

    2015-03-01

    Accurate calculations of energy level alignment at complex interfaces are imperative for understanding a variety of transport and spectroscopy measurements, as well as for elucidating new interfacial electronic structure phenomena. However, standard approaches to such calculations, based on density functional theory (DFT), are well known to be deficient. In prior work on molecular junctions and physisorbed molecules on surfaces, an approximate GW approach, DFT+ Σ, has been successful in describing the conductance and level alignment of amine and pyridine terminated molecules on gold surfaces and in junctions. Here, via the use of hybrid functionals, we preform quantitative studies of the level alignment of thiol- and carbon-terminated phenyls on gold, where the formation of a strong chemical bond and presence of gateway states limit the validity of the DFT+ Σ approximation as currently formulated. We contrast these systems to prior work on weakly-coupled molecules, including bipyridine or phenyl-diamines. Additionally, we compute transmission functions using both DFT-PBE and DFT-HSE starting points and predict conductance and thermopower with these methods, comparing to experiments where possible. We acknowledge DOE, DOD, NERSC, ERC, ISF, and FWF.

  2. Tensor polarization dependent fragmentation functions and e+e-→V π X at high energies

    NASA Astrophysics Data System (ADS)

    Chen, Kai-bao; Yang, Wei-hua; Wei, Shu-yi; Liang, Zuo-tang

    2016-08-01

    We present the systematic results for three-dimensional fragmentation functions of spin-1 hadrons defined via the quark-quark correlator. There are totally 72 such fragmentation functions, among them 18 are twist-2, 36 are twist-3 and 18 are twist-4. We also present the relationships between the twist-3 parts and those defined via the quark-gluon-quark correlator obtained from the QCD equation of motion. We show that the two particle semi-inclusive hadron production process e+e-→V π X at high energies is one of the best places to study the three-dimensional tensor polarization dependent fragmentation functions. We present the general kinematic analysis of this process and show that the cross section should be expressed in terms of 81 independent structure functions. After that we present parton model results for the hadronic tensor, the structure functions, and the azimuthal and spin asymmetries in terms of these gauge invariant fragmentation functions at the leading order perturbative quantum chromodynamics up to twist-3.

  3. An Energy-Independent Pro-longevity Function of Triacylglycerol in Yeast

    PubMed Central

    Hall, Kevin W.; Deng, Xiexiong; Li, Pan; Benning, Christoph; Williams, Barry L.; Kuo, Min-Hao

    2016-01-01

    Intracellular triacylglycerol (TAG) is a ubiquitous energy storage lipid also involved in lipid homeostasis and signaling. Comparatively, little is known about TAG’s role in other cellular functions. Here we show a pro-longevity function of TAG in the budding yeast Saccharomyces cerevisiae. In yeast strains derived from natural and laboratory environments a correlation between high levels of TAG and longer chronological lifespan was observed. Increased TAG abundance through the deletion of TAG lipases prolonged chronological lifespan of laboratory strains, while diminishing TAG biosynthesis shortened lifespan without apparently affecting vegetative growth. TAG-mediated lifespan extension was independent of several other known stress response factors involved in chronological aging. Because both lifespan regulation and TAG metabolism are conserved, this cellular pro-longevity function of TAG may extend to other organisms. PMID:26907989

  4. Generating and analyzing constrained dark energy equations of state and systematics functions

    SciTech Connect

    Samsing, Johan; Linder, Eric V.

    2010-02-15

    Some functions entering cosmological analysis, such as the dark energy equation of state or systematic uncertainties, are unknown functions of redshift. To include them without assuming a particular form, we derive an efficient method for generating realizations of all possible functions subject to certain bounds or physical conditions, e.g. w is an element of [-1,+1] as for quintessence. The method is optimal in the sense that it is both pure and complete in filling the allowed space of principal components. The technique is applied to propagation of systematic uncertainties in supernova population drift and dust corrections and calibration through to cosmology parameter estimation and bias in the magnitude-redshift Hubble diagram. We identify specific ranges of redshift and wavelength bands where the greatest improvements in supernova systematics due to population evolution and dust correction can be achieved.

  5. An Energy-Independent Pro-longevity Function of Triacylglycerol in Yeast.

    PubMed

    Handee, Witawas; Li, Xiaobo; Hall, Kevin W; Deng, Xiexiong; Li, Pan; Benning, Christoph; Williams, Barry L; Kuo, Min-Hao

    2016-02-01

    Intracellular triacylglycerol (TAG) is a ubiquitous energy storage lipid also involved in lipid homeostasis and signaling. Comparatively, little is known about TAG's role in other cellular functions. Here we show a pro-longevity function of TAG in the budding yeast Saccharomyces cerevisiae. In yeast strains derived from natural and laboratory environments a correlation between high levels of TAG and longer chronological lifespan was observed. Increased TAG abundance through the deletion of TAG lipases prolonged chronological lifespan of laboratory strains, while diminishing TAG biosynthesis shortened lifespan without apparently affecting vegetative growth. TAG-mediated lifespan extension was independent of several other known stress response factors involved in chronological aging. Because both lifespan regulation and TAG metabolism are conserved, this cellular pro-longevity function of TAG may extend to other organisms. PMID:26907989

  6. Guaiacol hydrodeoxygenation mechanism on Pt(111): insights from density functional theory and linear free energy relations.

    PubMed

    Lee, Kyungtae; Gu, Geun Ho; Mullen, Charles A; Boateng, Akwasi A; Vlachos, Dionisios G

    2015-01-01

    Density functional theory is used to study the adsorption of guaiacol and its initial hydrodeoxygenation (HDO) reactions on Pt(111). Previous Brønsted-Evans-Polanyi (BEP) correlations for small open-chain molecules are inadequate in estimating the reaction barriers of phenolic compounds except for the side group (methoxy) carbon-dehydrogenation. New BEP relations are established using a select group of phenolic compounds. These relations are applied to construct a potential-energy surface of guaiacol-HDO to catechol. Analysis shows that catechol is mainly produced via dehydrogenation of the methoxy functional group followed by the CHx (x<3) removal of the functional group and hydrogenation of the ring carbon, in contrast to a hypothesis of a direct demethylation path. Dehydroxylation and demethoxylation are slow, implying that phenol is likely produced from catechol but not through its direct dehydroxylation followed by aromatic carbon-ring hydrogenation. PMID:25470789

  7. Guaiacol hydrodeoxygenation mechanism on Pt(111): insights from density functional theory and linear free energy relations.

    PubMed

    Lee, Kyungtae; Gu, Geun Ho; Mullen, Charles A; Boateng, Akwasi A; Vlachos, Dionisios G

    2015-01-01

    Density functional theory is used to study the adsorption of guaiacol and its initial hydrodeoxygenation (HDO) reactions on Pt(111). Previous Brønsted-Evans-Polanyi (BEP) correlations for small open-chain molecules are inadequate in estimating the reaction barriers of phenolic compounds except for the side group (methoxy) carbon-dehydrogenation. New BEP relations are established using a select group of phenolic compounds. These relations are applied to construct a potential-energy surface of guaiacol-HDO to catechol. Analysis shows that catechol is mainly produced via dehydrogenation of the methoxy functional group followed by the CHx (x<3) removal of the functional group and hydrogenation of the ring carbon, in contrast to a hypothesis of a direct demethylation path. Dehydroxylation and demethoxylation are slow, implying that phenol is likely produced from catechol but not through its direct dehydroxylation followed by aromatic carbon-ring hydrogenation.

  8. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

    PubMed

    Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O

    2016-07-25

    Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467

  9. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

    PubMed

    Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O

    2016-07-25

    Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation.

  10. Rovibrational energies, partition functions and equilibrium fractionation of the CO2 isotopologues

    NASA Astrophysics Data System (ADS)

    Cerezo, J.; Bastida, A.; Requena, A.; Zúñiga, J.

    2014-11-01

    Rovibrational energy levels, partition functions and relative abundances of the stable isotopologues of CO2 in gas phase at equilibrium are calculated using an empirical Morse-cosine potential energy surface (PES) refined by fitting to the updated pure (l2=0) vibrational frequencies observed for the main 12C16O2 isotopologue. The rovibrational energy levels are calculated variationally using a system of optimized hyperspherical normal coordinates, and from these the vibrational terms Gv and rotational constants Bv of the isotopologues are determined. The refined potential surface is shown to be clearly superior to the original potential surface, with the former reproducing the observed values of the spectroscopic constants Gv and Bv with accuracies of about 0.1 cm-1 and 0.00020 cm-1, respectively, for levels with l2≥0 up to 10,000 cm-1 above the ground state. The internal partition functions of the isotopologues are calculated by approximated direct summation over the rovibrational energies and compared with both previous partition sums and values obtained from analytical expressions based on the harmonic oscillator and rigid rotor models. The partition functions calculated by approximated direct summation are then used to determine the abundances of the CO2 isotopologues at thermodynamic equilibrium using the method developed by Wang et al. [74]. Significant variations in the relative abundances of some of the CO2 multiple substituted isotopologues at terrestrial temperatures with respect to those provided by the classical harmonic-based Urey theory are found, which may be of relevance in geochemical processes.

  11. Modern money theory and ecological tax reform: A functional finance approach to energy conservation

    NASA Astrophysics Data System (ADS)

    McConnell, Scott L. B.

    This dissertation contributes to heterodox economics by developing a theoretical and policy-relevant link that will promote the conservation of energy while driving the value of the domestic currency. The analysis relies upon the theoretical foundation of modern money theory and functional finance, which states that "taxes-drive-money" where the value of a sovereign nation's currency is imputed through the acceptance by the sovereign nation of the currency in payment of taxation. This theoretical perspective lends itself to various public policy prescriptions, such as government employment policies or the employer of last resort (ELR), which has been discussed at length elsewhere (Wray 1998; Tcherneva 2007, Forstater 2003). This research contributes to this overall program by arguing that the basis for taxation under modern money theory allows public policy makers various alternatives regarding the make-up of the tax system in place. In particular, following functional finance, taxes do not have the sole purpose of paying for government spending, but rather drive the value of the currency and may be designed to perform other functions as well, such as penalizing socially undesirable behavior. The focus in this dissertation is on the amelioration of pollution and increasing energy conservation. The research question for this dissertation is this: what federally implemented tax would best serve the multiple criteria of 1) driving the value of the currency, 2) promoting energy conservation and 3) ameliorating income and wealth disparities inherent in a monetary production economy? This dissertation provides a suggestion for such a tax that would be part of a much larger overall policy program based upon the tenets of modern money theory and functional finance. Additionally, this research seeks to provide an important theoretical contribution to the emerging Post Keynesian and ecological economics dialog.

  12. Effect of fatigue loading on structure and functional behaviour of fascicles from energy-storing tendons.

    PubMed

    Thorpe, Chavaunne T; Riley, Graham P; Birch, Helen L; Clegg, Peter D; Screen, Hazel R C

    2014-07-01

    Tendons can broadly be categorized according to their function: those that act purely to position the limb and those that have an additional function as energy stores. Energy-storing tendons undergo many cycles of large deformations during locomotion, and so must be able to extend and recoil efficiently, rapidly and repeatedly. Our previous work has shown rotation in response to applied strain in fascicles from energy-storing tendons, indicating the presence of helical substructures which may provide greater elasticity and recovery. In the current study, we assessed how preconditioning and fatigue loading affect the ability of fascicles from the energy-storing equine superficial digital flexor tendon to extend and recoil. We hypothesized that preconditioned samples would exhibit changes in microstructural strain response, but would retain their ability to recover. We further hypothesized that fatigue loading would result in sample damage, causing further alterations in extension mechanisms and a significant reduction in sample recovery. The results broadly support these hypotheses: preconditioned samples showed some alterations in microstructural strain response, but were able to recover following the removal of load. However, fatigue loaded samples showed visual evidence of damage and exhibited further alterations in extension mechanisms, characterized by decreased rotation in response to applied strain. This was accompanied by increased hysteresis and decreased recovery. These results suggest that fatigue loading results in a compromised helix substructure, reducing the ability of energy-storing tendons to recoil. A decreased ability to recoil may lead to an impaired response to further loading, potentially increasing the likelihood of injury.

  13. Performance of Density Functionals for Activation Energies of Zr-Mediated Reactions.

    PubMed

    Sun, Yuanyuan; Chen, Hui

    2013-11-12

    Coupled cluster CCSD(T) calculations with core-valence correlation and complete basis set (CBS) limit extrapolation are used to benchmark the performance of commonly used density functionals in computing energy barriers for Zr-mediated reactions involving zirconocene species. These reactions include (a) insertions of the Zr-H bond of Cp2Zr(H)Cl into C═C, C≡C, and C═O bonds and (b) C-H activations by Zr═N bond in Cp2Zr═NH. The best performing functionals are M06-L, M06, and M06-2X in the M06 series, all having mean unsigned deviations (MUD) less than 2 kcal/mol. The worst performing functional is OLYP, with a distinctly large MUD of more than 10 kcal/mol. Considering also the trends in barrier heights and the systematic barrier height deviation, our best recommended functional is M06-2X. In this work, DFT empirical dispersion correction (DFT-D3) is found to improve the performance of barrier height values for most functionals (especially of OLYP and B3LYP). With DFT empirical dispersion correction, we also recommend M06-2X for reaction barrier calculations of Zr-mediated reactions.

  14. Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory

    SciTech Connect

    Gunawardana, K. G.S.H.; Song, Xueyu

    2014-12-22

    Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB2 and AB13 crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu5Zr(C15b), Cu51Zr14(β), Cu10Zr7(φ), CuZr(B2) and CuZr2 (C11b), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of the hard sphere crystal complexes in the two dimensional Gaussian space, namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu10Zr7(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.

  15. Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory

    DOE PAGES

    Gunawardana, K. G.S.H.; Song, Xueyu

    2014-12-22

    Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB2 and AB13 crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu5Zr(C15b), Cu51Zr14(β), Cu10Zr7(φ), CuZr(B2) and CuZr2 (C11b), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of the hard sphere crystal complexes in the two dimensional Gaussian space,more » namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu10Zr7(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.« less

  16. Microscopic description of fission in neutron-rich radium isotopes with the Gogny energy density functional

    NASA Astrophysics Data System (ADS)

    Rodrıguez-Guzmán, R.; Robledo, L. M.

    2016-01-01

    Mean-field calculations, based on the D1S, D1N and D1M parametrizations of the Gogny energy density functional, have been carried out to obtain the potential energy surfaces relevant to fission in several Ra isotopes with the neutron number 144≤ N≤ 176. Inner and outer barrier heights as well as first and second isomer excitation energies are given. The existence of a well-developed third minimum along the fission paths of Ra nuclei is analyzed in terms of the energetics of the "fragments" defining such elongated configuration. The masses and charges of the fission fragments are studied as functions of the neutron number in the parent Ra isotope. The comparison between fission and α -decay half-lives, reveals that the former becomes faster for increasing neutron numbers. Though there exists a strong variance of the results with respect to the parameters used in the computation of the spontaneous fission rate, a change in tendency is observed at N=164 with a steady increase that makes heavier neutron-rich Ra isotopes stable against fission, diminishing the importance of fission recycling in the r-process.

  17. Uncertainty analysis of continuum scale ferroelectric energy landscapes using density functional theory

    NASA Astrophysics Data System (ADS)

    Oates, William S.; Miles, Paul; Leon, Lider; Smith, Ralph

    2016-04-01

    Density functional theory (DFT) provides exceptional predictions of material properties of ideal crystal structures such as elastic modulus and dielectric constants. This includes ferroelectric crystals where excellent predictions of spontaneous polarization, lattice strain, and elastic moduli have been predicted using DFT. Less analysis has focused on quantifying uncertainty of the energy landscape over a broad range of polarization states in ferroelectric materials. This is non-trivial because the degrees of freedom contained within a unit cell are reduced to a single vector order parameter which is normally polarization. For example, lead titanate contains five atoms and 15 degrees of freedom of atomic nuclei motion which contribute to the overall unit cell polarization. Bayesian statistics is used to identify the uncertainty and propagation of error of a continuum scale, Landau energy function for lead titanate. Uncertainty in different parameters is quantified and this uncertainty is propagated through the model to illustrate error propagation over the energy surface. Such results are shown to have an impact in integration of quantum simulations within a ferroelectric phase field continuum modeling framework.

  18. SCAN: An Efficient Density Functional Yielding Accurate Structures and Energies of Diversely-Bonded Materials

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei

    The accuracy and computational efficiency of the widely used Kohn-Sham density functional theory (DFT) are limited by the approximation to its exchange-correlation energy Exc. The earliest local density approximation (LDA) overestimates the strengths of all bonds near equilibrium (even the vdW bonds). By adding the electron density gradient to model Exc, generalized gradient approximations (GGAs) generally soften the bonds to give robust and overall more accurate descriptions, except for the vdW interaction which is largely lost. Further improvement for covalent, ionic, and hydrogen bonds can be obtained by the computationally more expensive hybrid GGAs, which mix GGAs with the nonlocal exact exchange. Meta-GGAs are still semilocal in computation and thus efficient. Compared to GGAs, they add the kinetic energy density that enables them to recognize and accordingly treat different bonds, which no LDA or GGA can. We show here that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-GGA improves significantly over LDA and the standard Perdew-Burke-Ernzerhof GGA for geometries and energies of diversely-bonded materials (including covalent, metallic, ionic, hydrogen, and vdW bonds) at comparable efficiency. Often SCAN matches or improves upon the accuracy of a hybrid functional, at almost-GGA cost. This work has been supported by NSF under DMR-1305135 and CNS-09-58854, and by DOE BES EFRC CCDM under DE-SC0012575.

  19. Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory

    PubMed Central

    Bao, Peng

    2013-01-01

    An interaction energy decomposition analysis method based on the block-localized wavefunction (BLW-ED) approach is described. The first main feature of the BLW-ED method is that it combines concepts of valence bond and molecular orbital theories such that the intermediate and physically intuitive electron-localized states are variationally optimized by self-consistent field calculations. Furthermore, the block-localization scheme can be used both in wave function theory and in density functional theory, providing a useful tool to gain insights on intermolecular interactions that would otherwise be difficult to obtain using the delocalized Kohn–Sham DFT. These features allow broad applications of the BLW method to energy decomposition (BLW-ED) analysis for intermolecular interactions. In this perspective, we outline theoretical aspects of the BLW-ED method, and illustrate its applications in hydrogen-bonding and π–cation intermolecular interactions as well as metal–carbonyl complexes. Future prospects on the development of a multistate density functional theory (MSDFT) are presented, making use of block-localized electronic states as the basis configurations. PMID:21369567

  20. SirT1 gain-of-function increases energy efficiency and prevents diabetes in mice

    PubMed Central

    Banks, Alexander S.; Kon, Ning; Knight, Colette; Matsumoto, Michihiro; Gutiérrez-Juárez, Roger; Rossetti, Luciano; Gu, Wei; Accili, Domenico

    2011-01-01

    Summary In yeast, worms and flies, an extra copy of the gene encoding the Sirtuin Sir2 increases metabolic efficiency, as does administration of polyphenols like resveratrol, thought to act through Sirtuins. But evidence that Sirtuin gain-of-function results in increased metabolic efficiency in mammals is limited. We generated transgenic mice with moderate overexpression of SirT1, designed to mimic the Sirtuin gain-of-function that improves metabolism in C.elegans. These mice exhibit normal insulin sensitivity, but decreased food intake and locomotor activity, resulting in decreased energy expenditure. However, in various models of insulin resistance and diabetes, SirT1 transgenics display improved glucose tolerance due to decreased hepatic glucose production and increased adiponectin levels, without changes in body weight or composition. We conclude that SirT1 gain-of-function primes the organism for metabolic adaptation to insulin resistance, increasing hepatic insulin sensitivity and decreasing whole-body energy requirements. These findings have important implications for Sirtuin-based therapies in humans. PMID:18840364

  1. Multi-term approximation to the Boltzmann transport equation for electron energy distribution functions in nitrogen

    NASA Astrophysics Data System (ADS)

    Feng, Yue

    Plasma is currently a hot topic and it has many significant applications due to its composition of both positively and negatively charged particles. The energy distribution function is important in plasma science since it characterizes the ability of the plasma to affect chemical reactions, affect physical outcomes, and drive various applications. The Boltzmann Transport Equation is an important kinetic equation that provides an accurate basis for characterizing the distribution function---both in energy and space. This dissertation research proposes a multi-term approximation to solve the Boltzmann Transport Equation by treating the relaxation process using an expansion of the electron distribution function in Legendre polynomials. The elastic and 29 inelastic cross sections for electron collisions with nitrogen molecules (N2) and singly ionized nitrogen molecules ( N+2 ) have been used in this application of the Boltzmann Transport Equation. Different numerical methods have been considered to compare the results. The numerical methods discussed in this thesis are the implicit time-independent method, the time-dependent Euler method, the time-dependent Runge-Kutta method, and finally the implicit time-dependent relaxation method by generating the 4-way grid with a matrix solver. The results show that the implicit time-dependent relaxation method is the most accurate and stable method for obtaining reliable results. The results were observed to match with the published experimental data rather well.

  2. The origin of neutron biological effectiveness as a function of energy

    PubMed Central

    Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

    2016-01-01

    The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data. PMID:27654349

  3. Electron energy probability function and L-p similarity in low pressure inductively coupled bounded plasma

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Sudeep; Chatterjee, Sanghamitro; Charles, Christine; Boswell, Roderick

    2015-02-01

    Particle-In-Cell (PIC) simulations are carried out to investigate the effect of discharge length (L) and pressure (p) on Electron Energy Probability Function (EEPF) in a low pressure radio frequency (rf) inductively coupled plasma at 13.56 MHz. It is found that for both cases of varying L (0.1 - 0.5 m) and p (1 - 10 mTorr), the EEPF is a bi-Maxwellian with a step in the bounded direction (x) and in the symmetric unbounded directions (y, z) the EEPF are a Maxwellian with a hot tail. The plasma space potential decreases with increase in both L and p, the trapped electrons having energies in the range 0 to 20 eV. In a conventional discharge bounded in all directions, we infer that L and p are similarity parameters for low energy electrons trapped in the bulk plasma that have energies below the plasma space potential (eVp). The simulation results are consistent with a particle balance model.

  4. Kinetic energies to analyze the experimental auger electron spectra by density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Endo, Kazunaka

    2016-02-01

    In the Auger electron spectra (AES) simulations, we define theoretical modified kinetic energies of AES in the density functional theory (DFT) calculations. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. This method is applied to simulate Auger electron spectra (AES) of 2nd periodic atom (Li, Be, B, C, N, O, F)-involving substances (LiF, beryllium, boron, graphite, GaN, SiO2, PTFE) by deMon DFT calculations using the model molecules of the unit cell. Experimental KVV (valence band electrons can fill K-shell core holes or be emitted during KVV-type transitions) AES of the (Li, O) atoms in the substances agree considerably well with simulation of AES obtained with the maximum kinetic energies of the atoms, while, for AES of LiF, and PTFE substance, the experimental F KVV AES is almost in accordance with the spectra from the transitionstate kinetic energy calculations.

  5. The origin of neutron biological effectiveness as a function of energy

    NASA Astrophysics Data System (ADS)

    Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

    2016-09-01

    The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data.

  6. Modification Of The Electron Energy Distribution Function During Lithium Experiments On The National Spherical Torus Experiment

    SciTech Connect

    Jaworski, M A; Gray, T K; Kaita, R; Kallman, J; Kugel, H; LeBlanc, B; McLean, A; Sabbagh, S A; Soukanovskii, V; Stotler, D P

    2011-06-03

    The National Spherical Torus Experiment (NSTX) has recently studied the use of a liquid lithium divertor (LLD). Divertor Langmuir probes have also been installed for making measurements of the local plasma conditions. A non-local probe interpretation method is used to supplement the classical probe interpretation and obtain measurements of the electron energy distribution function (EEDF) which show the occurrence of a hot-electron component. Analysis is made of two discharges within a sequence that exhibited changes in plasma fueling efficiency. It is found that the local electron temperature increases and that this increase is most strongly correlated with the energy contained within the hot-electron population. Preliminary interpretative modeling indicates that kinetic effects are likely in the NSTX.

  7. Hydrogen atom wave function and eigen energy in the Rindler space

    NASA Astrophysics Data System (ADS)

    Dai, De-Chang

    2016-10-01

    We study the hydrogen atom eigenstate energy and wave function in the Rindler space. The probability distribution is tilted because the electric field of the nucleus is no longer spherically symmetric. The hydrogen atom therefore cannot be treated exactly in the same way as what it is in an inertial frame. We also find that if the external force accelerates only the nucleus and then the nucleus accelerates its surrounding electrons through electromagnetic force, the electrons can tunnel through the local energy gap and split the hydrogen atom into an ion. This is similar to what one expects from the Stark effect. However, the critical acceleration is about 3 ×1022 m /s2. It is well beyond the gravitational acceleration on a regular star surface.

  8. Squeeze-out of nuclear matter as a function of projectile energy and mass

    NASA Astrophysics Data System (ADS)

    Gutbrod, H. H.; Kampert, K. H.; Kolb, B.; Poskanzer, A. M.; Ritter, H. G.; Schicker, R.; Schmidt, H. R.

    1990-08-01

    Squeeze-out, a component of the collective flow of nuclear matter, is the preferential emission of particles out of the reaction plane. Using the sphericity method the out-of-plane/in-plane ratio of the kinetic energy flow has been analyzed as a function of multiplicity and beam energy for Ca+Ca, Nb+Nb, and Au+Au collisions measured with the Plastic Ball detector at the Bevalac. Also, azimuthal distribution of the particles around the flow axis are presented together with the extracted out-of-plane/in-plane ratios. Finally, the rapidity dependence of the out-of-plane/in-plane ratio has been investigated with a new method using the transverse momentum components of the particles.

  9. Random phase approximation correlation energy using a compact representation for linear response functions: application to solids

    NASA Astrophysics Data System (ADS)

    Kaoui, Fawzi; Rocca, Dario

    2016-01-01

    A new approach was recently presented to compute correlation energies within the random phase approximation using Lanczos chains and an optimal basis set (Rocca 2014 J. Chem. Phys. 140 18A501). This novel method avoids the explicit calculation of conduction states and represents linear response functions on a compact auxiliary basis set obtained from the diagonalization of an approximate dielectric matrix that contains only the kinetic energy contribution. Here, we extend this formalism, originally implemented for molecular systems, to treat periodic solids. In particular, the approximate dielectric matrix used to build the auxiliary basis set is generalized to avoid unphysical negative gaps, that make the model inefficient. The numerical convergence of the method is discussed and the accuracy is demonstrated considering a set including three covalently bonded (C, Si, and SiC) and three weakly bonded (Ne, Ar, and Kr) solids.

  10. LDRD final report : energy conversion using chromophore-functionalized carbon nanotubes.

    SciTech Connect

    Vance, Andrew L.; Zifer, Thomas; Zhou, Xinjian; Leonard, Francois Leonard; Wong, Bryan Matthew; Kane, Alexander; Katzenmeyer, Aaron Michael; Krafcik, Karen Lee

    2010-09-01

    With the goal of studying the conversion of optical energy to electrical energy at the nanoscale, we developed and tested devices based on single-walled carbon nanotubes functionalized with azobenzene chromophores, where the chromophores serve as photoabsorbers and the nanotube as the electronic read-out. By synthesizing chromophores with specific absorption windows in the visible spectrum and anchoring them to the nanotube surface, we demonstrated the controlled detection of visible light of low intensity in narrow ranges of wavelengths. Our measurements suggested that upon photoabsorption, the chromophores isomerize to give a large change in dipole moment, changing the electrostatic environment of the nanotube. All-electron ab initio calculations were used to study the chromophore-nanotube hybrids, and show that the chromophores bind strongly to the nanotubes without disturbing the electronic structure of either species. Calculated values of the dipole moments supported the notion of dipole changes as the optical detection mechanism.

  11. Enhancement of energy storage capacity of Mg functionalized silicene and silicane under external strain

    SciTech Connect

    Hussain, Tanveer; Ahuja, Rajeev; Chakraborty, Sudip; De Sarkar, Abir; Johansson, Börje

    2014-09-22

    The electronic structure, stability, and hydrogen storage capacity of strain induced Mg functionalized silicene (SiMg) and silicane (SiHMg) monolayers have been studied by means of van der Waals induced first principles calculations. A drastic increase in the binding energy of Mg adatoms on both the monolayers under the biaxial symmetric strain of 10% ensures the uniform distribution of dopants over the substrates. A significant positive charge on each Mg accumulates a maximum of six H{sub 2} molecules with H{sub 2} storage capacity of 8.10% and 7.95% in case of SiMg and SiHMg, respectively. The average adsorption energy for H{sub 2} molecules has been found ideal for practical H{sub 2} storage materials.

  12. Orbital relaxation effects on Kohn–Sham frontier orbital energies in density functional theory

    SciTech Connect

    Zhang, DaDi; Zheng, Xiao; Li, Chen; Yang, Weitao

    2015-04-21

    We explore effects of orbital relaxation on Kohn–Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn–Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn–Sham frontier orbital energies by Hartree–Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scaling correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems.

  13. Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory

    NASA Astrophysics Data System (ADS)

    Zhang, DaDi; Zheng, Xiao; Li, Chen; Yang, Weitao

    2015-04-01

    We explore effects of orbital relaxation on Kohn-Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn-Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn-Sham frontier orbital energies by Hartree-Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scaling correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems.

  14. Thermodynamic constraints on effective energy and mass transfer and catchment function

    NASA Astrophysics Data System (ADS)

    Rasmussen, C.

    2012-03-01

    Understanding how water, energy and carbon are partitioned to primary production and effective precipitation is central to quantifying the limits on critical zone evolution. Recent work suggests quantifying energetic transfers to the critical zone in the form of effective precipitation and primary production provides a first order approximation of critical zone process and structural organization. However, explicit linkage of this effective energy and mass transfer (EEMT; W m-2) to critical zone state variables and well defined physical limits remains to be developed. The objective of this work was to place EEMT in the context of thermodynamic state variables of temperature and vapor pressure deficit, with explicit definition of EEMT physical limits using a global climate dataset. The relation of EEMT to empirical measures of catchment function was also examined using a subset of the Model Parameter Estimation Experiment (MOPEX) catchments. The data demonstrated three physical limits for EEMT: (i) an absolute vapor pressure deficit threshold of 1200 Pa above which EEMT is zero; (ii) a temperature dependent vapor pressure deficit limit following the saturated vapor pressure function up to a temperature of 292 K; and (iii) a minimum precipitation threshold required from EEMT production at temperatures greater than 292 K. Within these limits, EEMT scales directly with precipitation, with increasing conversion of the precipitation to EEMT with increasing temperature. The state-space framework derived here presents a simplified framework with well-defined physical limits that has the potential for directly integrating regional to pedon scale heterogeneity in effective energy and mass transfer relative to critical zone structure and function within a common thermodynamic framework.

  15. Thermodynamic constraints on effective energy and mass transfer and catchment function

    NASA Astrophysics Data System (ADS)

    Rasmussen, C.

    2011-07-01

    Understanding how water, energy and carbon are partitioned to primary production and effective precipitation is central to quantifying the limits on critical zone evolution. Recent work suggests quantifying energetic transfers to the critical zone in the form of effective precipitation and primary production provides a first order approximation of critical zone process and structural organization. However, explicit linkage of this effective energy and mass transfer (EEMT; W m-2) to critical zone state variables and well defined physical limits remains to be developed. The objective of this work was to place EEMT in the context of thermodynamic state variables of temperature and vapor pressure deficit, with explicit definition of EEMT physical limits using a global climate dataset. The relation of EEMT to empirical measures of catchment function was also examined using a subset of the Model Parameter Estimation Experiment (MOPEX) catchments. The data demonstrated three physical limits for EEMT: (i) an absolute vapor pressure deficit threshold of 1200 Pa above which EEMT is zero; (ii) a temperature dependent vapor pressure deficit limit following the saturated vapor pressure function up to a temperature of 292 K; and (iii) a minimum precipitation threshold required from EEMT production at temperatures greater than 292 K. Within these limits, EEMT scales directly with precipitation, with increasing conversion of the precipitation to EEMT with increasing temperature. The state-space framework derived here presents a simplified framework with well-defined physical limits that has the potential for directly integrating regional to pedon scale heterogeneity in effective energy and mass transfer relative to critical zone structure and function within a common thermodynamic framework.

  16. Reliable Energy Level Alignment at Physisorbed Molecule–Metal Interfaces from Density Functional Theory

    PubMed Central

    2015-01-01

    A key quantity for molecule–metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal–molecule interfaces. The method builds on the “DFT+Σ” approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule–metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors. PMID:25741626

  17. Reliable energy level alignment at physisorbed molecule-metal interfaces from density functional theory.

    PubMed

    Egger, David A; Liu, Zhen-Fei; Neaton, Jeffrey B; Kronik, Leeor

    2015-04-01

    A key quantity for molecule-metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal-molecule interfaces. The method builds on the "DFT+Σ" approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule-metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors. PMID:25741626

  18. Enforcing the linear behavior of the total energy with hybrid functionals: Implications for charge transfer, interaction energies, and the random-phase approximation

    NASA Astrophysics Data System (ADS)

    Atalla, Viktor; Zhang, Igor Ying; Hofmann, Oliver T.; Ren, Xinguo; Rinke, Patrick; Scheffler, Matthias

    2016-07-01

    We obtain the exchange parameter of hybrid functionals by imposing the fundamental condition of a piecewise linear total energy with respect to electron number. For the Perdew-Burke-Ernzerhof (PBE) hybrid family of exchange-correlation functionals (i.e., for an approximate generalized Kohn-Sham theory) this implies that (i) the highest occupied molecular orbital corresponds to the ionization potential (I ), (ii) the energy of the lowest unoccupied molecular orbital corresponds to the electron affinity (A ), and (iii) the energies of the frontier orbitals are constant as a function of their occupation. In agreement with a previous study [N. Sai et al., Phys. Rev. Lett. 106, 226403 (2011), 10.1103/PhysRevLett.106.226403], we find that these conditions are met for high values of the exact exchange admixture α and illustrate their importance for the tetrathiafulvalene-tetracyanoquinodimethane complex for which standard density functional theory functionals predict artificial electron transfer. We further assess the performance for atomization energies and weak interaction energies. We find that atomization energies are significantly underestimated compared to PBE or PBE0, whereas the description of weak interaction energies improves significantly if a 1 /R6 van der Waals correction scheme is employed.

  19. Neuroendocrine circuits governing energy balance and stress regulation: functional overlap and therapeutic implications

    PubMed Central

    Ulrich-Lai, Yvonne M.; Ryan, Karen K.

    2014-01-01

    Significant co-morbidities between obesity-related metabolic disease and stress-related psychological disorders suggest important functional interactions between energy balance and brain stress integration. Largely overlapping neural circuits control these systems, and this anatomical arrangement optimizes opportunities for mutual influence. Here we first review the current literature identifying effects of metabolic neuroendocrine signals on stress regulation, and vice versa. Next, the contributions of reward driven food intake to these metabolic and stress interactions are discussed. Lastly, we consider the inter-relationships among metabolism, stress and reward in light of their important implications in the development of therapies for metabolism- or stress-related disease. PMID:24630812

  20. Matrix coefficient identification in an elliptic equation with the convex energy functional method

    NASA Astrophysics Data System (ADS)

    Hinze, Michael; Nhan Tam Quyen, Tran

    2016-08-01

    In this paper we study the inverse problem of identifying the diffusion matrix in an elliptic PDE from measurements. The convex energy functional method with Tikhonov regularization is applied to tackle this problem. For the discretization we use the variational discretization concept, where the PDE is discretized with piecewise linear, continuous finite elements. We show the convergence of approximations. Using a suitable source condition, we prove an error bound for discrete solutions. For the numerical solution we propose a gradient-projection algorithm and prove the strong convergence of its iterates to a solution of the identification problem. Finally, we present a numerical experiment which illustrates our theoretical results.

  1. Skeleton series and multivaluedness of the self-energy functional in zero space-time dimensions

    NASA Astrophysics Data System (ADS)

    Rossi, Riccardo; Werner, Félix

    2015-12-01

    Recently, Kozik, Ferrero and Georges discovered numerically that for a family of fundamental models of interacting fermions, the self-energy {{Σ }}[G] is a multi-valued functional of the fully dressed single-particle propagator G, and that the skeleton diagrammatic series {{{Σ }}}{{bold}}[G] converges to the wrong branch above a critical interaction strength. We consider the zero space-time dimensional case, where the same mathematical phenomena appear from elementary algebra. We also find a similar phenomenology for the fully bold formalism built on the fully dressed single-particle propagator and pair propagator.

  2. Tribo-Mechanical Investigation of the Functional Components used in Flexible Energy Harvesting Devices

    NASA Astrophysics Data System (ADS)

    Morris, Nicholas J.

    During the previous decade, the development of energy harvesting devices based on piezoelectric materials has garnered great interest. The ability to capture ambient mechanical energy and convert it to useable electricity is a potential solution to the ever-growing energy crisis. One of the most attractive functional materials used in these devices is zinc oxide (ZnO). This material's relative low cost and ease of large-area processing has spurred numerous device designs based around it. The ability to grow ZnO nanostructures of various geometries with low-temperature chemical methods makes this material even more attractive for flexible devices. Although numerous device architectures have been developed, the long-term mechanical reliability has not been addressed. This work focuses on the fabrication and mechanical failure analysis of the flexible components typically used in piezoelectric energy harvesting devices. A three-phase iterative design process was used to fabricate prototypical piezoelectric nanogenerators, based on ZnO nanowires. An output of several millivolts was achieved under normal contact and microtensile loading, but device failure occurred after only a few loading cycles, in all cases. Ex situ failure analysis confirmed the primary sources of failure, which became the focus of further, component-level studies. Failure was primarily seen in the flexible electrodes of the nanogenerating devices, but was also observed in the functional piezoelectric layer itself. Flexible electrodes comprised of polyester substrates with transparent conductive oxide (TCO) coatings were extensively investigated under various loading scenarios to mimic tribo-mechanical stresses applied during fabrication and use in flexible contact-based devices. The durability of these films was explored using microtensile testing, spherical nanoindentation, controlled mechanical buckling, stress corrosion cracking, and shear-contact reciprocating wear. The electro

  3. On modified finite difference method to obtain the electron energy distribution functions in Langmuir probes

    NASA Astrophysics Data System (ADS)

    Kang, Hyun-Ju; Choi, Hyeok; Kim, Jae-Hyun; Lee, Se-Hun; Yoo, Tae-Ho; Chung, Chin-Wook

    2016-06-01

    A modified central difference method (MCDM) is proposed to obtain the electron energy distribution functions (EEDFs) in single Langmuir probes. Numerical calculation of the EEDF with MCDM is simple and has less noise. This method provides the second derivatives at a given point as the weighted average of second order central difference derivatives calculated at different voltage intervals, weighting each by the square of the interval. In this paper, the EEDFs obtained from MCDM are compared to those calculated via the averaged central difference method. It is found that MCDM effectively suppresses the noises in the EEDF, while the same number of points are used to calculate of the second derivative.

  4. Constitutive Modeling of Skeletal Muscle Tissue with an Explicit Strain-Energy Function

    PubMed Central

    Odegard, G.M.; Donahue, T.L. Haut; Morrow, D.A.; Kaufman, K.R.

    2010-01-01

    While much work has previously been done in the modeling of skeletal muscle, no model has, to date, been developed that describes the mechanical behavior with an explicit strain-energy function associated with the active response of skeletal muscle tissue. A model is presented herein that has been developed to accommodate this design consideration using a robust dynamical approach. The model shows excellent agreement with a previously published model of both the active and passive length-tension properties of skeletal muscle. PMID:19045546

  5. Using an iterative eigensolver to compute vibrational energies with phase-spaced localized basis functions

    SciTech Connect

    Brown, James Carrington, Tucker

    2015-07-28

    Although phase-space localized Gaussians are themselves poor basis functions, they can be used to effectively contract a discrete variable representation basis [A. Shimshovitz and D. J. Tannor, Phys. Rev. Lett. 109, 070402 (2012)]. This works despite the fact that elements of the Hamiltonian and overlap matrices labelled by discarded Gaussians are not small. By formulating the matrix problem as a regular (i.e., not a generalized) matrix eigenvalue problem, we show that it is possible to use an iterative eigensolver to compute vibrational energy levels in the Gaussian basis.

  6. Effective Ginzburg-Landau free energy functional for multi-band isotropic superconductors

    NASA Astrophysics Data System (ADS)

    Grigorishin, Konstantin V.

    2016-04-01

    It has been shown that interband mixing of gradients of two order parameters (drag effect) in an isotropic bulk two-band superconductor plays important role - such a quantity of the intergradients coupling exists that the two-band superconductor is characterized with a single coherence length and a single Ginzburg-Landau (GL) parameter. Other quantities or neglecting of the drag effect lead to existence of two coherence lengths and dynamical instability due to violation of the phase relations between the order parameters. Thus so-called type-1.5 superconductors are impossible. An approximate method for solving of set of GL equations for a multi-band superconductor has been developed: using the result about the drag effect it has been shown that the free-energy functional for a multi-band superconductor can be reduced to the GL functional for an effective single-band superconductor.

  7. High-Resolution Rotational Spectrum, Dunham Coefficients, and Potential Energy Function of NaCl

    PubMed Central

    Cabezas, C.; Cernicharo, J.; Quintana-Lacaci, G.; Peña, I.; Agundez, M.; Prieto, L. Velilla; Castro-Carrizo, A.; Zuñiga, J.; Bastida, A.; Alonso, J. L.; Requena, A.

    2016-01-01

    We report laboratory spectroscopy for the first time of the J = 1–0 and J = 2–1 lines of Na35Cl and Na37Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δv = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted. PMID:27733778

  8. Quasi-particle energy spectra in local reduced density matrix functional theory.

    PubMed

    Lathiotakis, Nektarios N; Helbig, Nicole; Rubio, Angel; Gidopoulos, Nikitas I

    2014-10-28

    Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C20 isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids. PMID:25362285

  9. Quasi-particle energy spectra in local reduced density matrix functional theory

    SciTech Connect

    Lathiotakis, Nektarios N.; Helbig, Nicole; Rubio, Angel

    2014-10-28

    Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C{sub 20} isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.

  10. The diene isomerization energies dataset: A difficult test for double-hybrid density functionals?

    NASA Astrophysics Data System (ADS)

    Wykes, M.; Pérez-Jiménez, A. J.; Adamo, C.; Sancho-García, J. C.

    2015-06-01

    We have systematically analyzed the performance of some representative double-hybrid density functionals (including PBE0-DH, PBE-QIDH, PBE0-2, XYG3, XYGJ-OS, and xDH-PBE0) for a recently introduced database of diene isomerization energies. Double-hybrid models outperform their corresponding hybrid forms (for example, PBE0-DH, PBE0-2, and PBE-QIDH are more accurate than PBE0) and the XYG3, XYGJ-OS, and xDH-PBE0 functionals perform excellently, providing root mean square deviation values within "calibration accuracy." XYGJ-OS and xDH-PBE0 also rival the best performing post-Hartree-Fock methods at a substantially lower cost.

  11. Stored energy function and compressibility of compressible rubberlike materials under large strain

    NASA Technical Reports Server (NTRS)

    Peng, S. T. J.; Landel, R. F.

    1975-01-01

    By using new invariants in the theory of finite elasticity an expression is obtained for the stored energy function of slightly compressible materials in which the effects of the distortional change (change of shape) and of the volume change are clearly separated. The volume-related terms are expressed as a function of the third invariant, the classical compressibility, and an induced anisotropy of the effective compressibility which is due to the large deformations. After evaluating the terms, using data on pressure, volume, uniaxial strain, and fractional volume change vs strain data on natural rubber from the literature, it is shown that the volume change contribution to the total stress observed in a simple tensile experiment can be clearly separated from the distortional contribution, even at finite strains.

  12. High-resolution Rotational Spectrum, Dunham Coefficients, and Potential Energy Function of NaCl

    NASA Astrophysics Data System (ADS)

    Cabezas, C.; Cernicharo, J.; Quintana-Lacaci, G.; Peña, I.; Agundez, M.; Velilla Prieto, L.; Castro-Carrizo, A.; Zuñiga, J.; Bastida, A.; Alonso, J. L.; Requena, A.

    2016-07-01

    We report laboratory spectroscopy for the first time of the J = 1-0 and J = 2-1 lines of Na35Cl and Na37Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δv = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.

  13. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749

  14. Tunable fluorescence in chromophore-functionalized nanodiamond induced by energy transfer.

    PubMed

    Maitra, Urmimala; Jain, Ankit; George, Subi J; Rao, C N R

    2011-08-01

    Hybrid materials comprising diamond nanoparticles (ND) and oligo(phenylenevinylenes) (OPVs) have been synthesized by the covalent linking of acid-functionalized ND and OPV-amine. Chromophore-functionalized ND particles with long alkyl and π-conjugated groups are readily dispersed in various organic solvents without any precipitation after several hours. A careful study of the properties of the hybrid materials revealed an aggregation-induced energy transfer from the blue fluorescent nanodiamonds to green emitting OPVs. At very low concentrations the hybrid emits in the blue region, but as the concentration is increased a gradual transition from blue to green emission occurs. Competitive processes such as aggregation-induced enhanced emission and self-absorption have been ruled out and a molecular picture of the phenomenon is proposed. This strategy can open a plethora of new avenues for fluorescent nanodiamonds in optoelectronics and light harvesting apart from bio-imaging.

  15. Tunable fluorescence in chromophore-functionalized nanodiamond induced by energy transfer

    NASA Astrophysics Data System (ADS)

    Maitra, Urmimala; Jain, Ankit; George, Subi J.; Rao, C. N. R.

    2011-08-01

    Hybrid materials comprising diamond nanoparticles (ND) and oligo(phenylenevinylenes) (OPVs) have been synthesized by the covalent linking of acid-functionalized ND and OPV-amine. Chromophore-functionalized ND particles with long alkyl and π-conjugated groups are readily dispersed in various organic solvents without any precipitation after several hours. A careful study of the properties of the hybrid materials revealed an aggregation-induced energy transfer from the blue fluorescent nanodiamonds to green emitting OPVs. At very low concentrations the hybrid emits in the blue region, but as the concentration is increased a gradual transition from blue to green emission occurs. Competitive processes such as aggregation-induced enhanced emission and self-absorption have been ruled out and a molecular picture of the phenomenon is proposed. This strategy can open a plethora of new avenues for fluorescent nanodiamonds in optoelectronics and light harvesting apart from bio-imaging.Hybrid materials comprising diamond nanoparticles (ND) and oligo(phenylenevinylenes) (OPVs) have been synthesized by the covalent linking of acid-functionalized ND and OPV-amine. Chromophore-functionalized ND particles with long alkyl and π-conjugated groups are readily dispersed in various organic solvents without any precipitation after several hours. A careful study of the properties of the hybrid materials revealed an aggregation-induced energy transfer from the blue fluorescent nanodiamonds to green emitting OPVs. At very low concentrations the hybrid emits in the blue region, but as the concentration is increased a gradual transition from blue to green emission occurs. Competitive processes such as aggregation-induced enhanced emission and self-absorption have been ruled out and a molecular picture of the phenomenon is proposed. This strategy can open a plethora of new avenues for fluorescent nanodiamonds in optoelectronics and light harvesting apart from bio-imaging. Electronic

  16. Radiated Energy of Great Earthquakes from Teleseismic Empirical Green's Function Deconvolution

    NASA Astrophysics Data System (ADS)

    Baltay, Annemarie S.; Beroza, Gregory C.; Ide, Satoshi

    2014-10-01

    We expand on the empirical Green's function deconvolution method of Ide et al. (2011) to estimate radiated energy for the six largest earthquakes worldwide over the last 10 years: 2011 M w 9.0 Tohoku-Oki, 2004 M w 9.1 Sumatra, 2010 M w 8.8 Maule, 2005 M w 8.7 Nias, 2007 M w 8.5 Bengkulu, and 2012 M w 8.6 off-Sumatra. Deconvolution of P, SV and SH components gives consistent energy results that are comparable to estimates found independently by other researchers. Apparent stress for the five great thrust earthquakes is between 0.4 and 0.8 MPa, while the 2012 off-Sumatra strike-slip earthquake has a higher apparent stress of 3 MPa, which is consistent with other studies that find a tendency for strike-slip events to be more energetic. Our results are within the spread of apparent stress from the wider global earthquake population over a large magnitude range. The azimuthal distribution of energy in each case shows signs of directivity, and in some cases, shows less energy radiated in the trench-ward direction, which may suggest enhanced tsunami potential. We find that eGfs as small as ~M 6.5 can be used for teleseismic deconvolution, and that an eGf-mainshock magnitude difference of 1.5 units yields stable results. This implies that M 8 is the minimum mainshock size for which teleseismic eGf deconvolution will work well. We propose that a database of eGf events could be used to calculate radiated energy and apparent stress of great, hazardous events in near real time, i.e., promptly enough that it could contribute to rapid response measures.

  17. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction

    PubMed Central

    CAO, Song; CHEN, Shi-Jie

    2016-01-01

    In spite of the success of computational methods for predicting RNA secondary structure, the problem of predicting RNA tertiary structure folding remains. Low-resolution structural models show promise as they allow for rigorous statistical mechanical computation for the conformational entropies, free energies, and the coarse-grained structures of tertiary folds. Molecular dynamics refinement of coarse-grained structures leads to all-atom 3D structures. Modeling based on statistical mechanics principles also has the unique advantage of predicting the full free energy landscape, including local minima and the global free energy minimum. The energy landscapes combined with the 3D structures form the basis for quantitative predictions of RNA functions. In this chapter, we present an overview of statistical mechanical models for RNA folding and then focus on a recently developed RNA statistical mechanical model -- the Vfold model. The main emphasis is placed on the physics underpinning the models, the computational strategies, and the connections to RNA biology. PMID:27293312

  18. Extra-galactic high-energy transients: event rate density and luminosity function

    NASA Astrophysics Data System (ADS)

    Sun, Hui; Zhang, Bing; Li, Zhuo

    2015-08-01

    Several types of extra-galactic high-energy transients have been discovered, which include high-luminosity and low-luminosity long-duration gamma-ray bursts (GRBs), short-duration GRBs, supernova shock breakouts (SBOs), and tidal disruption events (TDEs) without or with a relativistic jet. In this paper, we apply a unified method to systematically study the reshift-dependent event rate densities and luminosity functions of these extra-galactic high-energy transients. We consider star formation history as the tracer of the redshift distribution for long GRBs and SBOs. For short GRBs, we consider the compact star merger model to introduce several possible merger delay time distribution models. For TDEs, we consider the mass distribution of supermassive black holes as a function of redshift. We derive some empirical formulae for the redshift-dependent event rate density for different types of transients. Based on the observed events, we derive the local specific event rate density, ρ0,L ∝ dρ0/dL for each type of transient, which represents its luminosity function. All the transients are consistent with having a single power law luminosity function, except the high luminosity long GRBs (HL-lGRBs), whose luminosity function can be well described by a broken power law. The total event rate density for a particular transient depends on the luminosity threshold, and we obtain the following values in units of Gpc-3 yr-1: 2.82^{+0.41}_{-0.36} for HL-lGRBs above 4×1049 erg s-1 218^{+130}_{-86} for low luminosity long GRBs above 6×1046 erg s-1 3.18^{+0.88}_{-0.70}, 2.87^{+0.80}_{-0.64}, and 6.25^{+1.73}_{-1.38} above 5×1049 erg s-1 for short GRBs with three different merger delay models (Gaussian, log-normal, and power law); 2.0^{+2.6}_{-1.3}×104 above 9×1043 erg s-1 for SBOs, 3.0^{+1.0}_{-0.8}×105 for normal TDEs above 1042 erg s-1 and 6.2^{+8.2}_{-4.0} above 3×1047 erg s-1for TDE jets as discovered by Swift. Intriguingly, the global specific event rate densities

  19. On the evaluation of the non-interacting kinetic energy in density functional theory.

    PubMed

    Peach, Michael J G; Griffiths, David G J; Tozer, David J

    2012-04-14

    The utility of both an orbital-free and a single-orbital expression for computing the non-interacting kinetic energy in density functional theory is investigated for simple atomic systems. The accuracy of both expressions is governed by the extent to which the Kohn-Sham equation is solved for the given exchange-correlation functional and so special attention is paid to the influence of finite Gaussian basis sets. The orbital-free expression is a statement of the virial theorem and its accuracy is quantified. The accuracy of the single-orbital expression is sensitive to the choice of Kohn-Sham orbital. The use of particularly compact orbitals is problematic because the failure to solve the Kohn-Sham equation exactly in regions where the orbital has decayed to near-zero leads to unphysical behaviour in regions that contribute to the kinetic energy, rendering it inaccurate. This problem is particularly severe for core orbitals, which would otherwise appear attractive due to their formally nodeless nature. The most accurate results from the single-orbital expression are obtained using the relatively diffuse, highest occupied orbitals, although special care is required at orbital nodes.

  20. Method for Determining the Activation Energy Distribution Function of Complex Reactions by Sieving and Thermogravimetric Measurements.

    PubMed

    Bufalo, Gennaro; Ambrosone, Luigi

    2016-01-14

    A method for studying the kinetics of thermal degradation of complex compounds is suggested. Although the method is applicable to any matrix whose grain size can be measured, herein we focus our investigation on thermogravimetric analysis, under a nitrogen atmosphere, of ground soft wheat and ground maize. The thermogravimetric curves reveal that there are two well-distinct jumps of mass loss. They correspond to volatilization, which is in the temperature range 298-433 K, and decomposition regions go from 450 to 1073 K. Thermal degradation is schematized as a reaction in the solid state whose kinetics is analyzed separately in each of the two regions. By means of a sieving analysis different size fractions of the material are separated and studied. A quasi-Newton fitting algorithm is used to obtain the grain size distribution as best fit to experimental data. The individual fractions are thermogravimetrically analyzed for deriving the functional relationship between activation energy of the degradation reactions and the particle size. Such functional relationship turns out to be crucial to evaluate the moments of the activation energy distribution, which is unknown in terms of the distribution calculated by sieve analysis. From the knowledge of moments one can reconstruct the reaction conversion. The method is applied first to the volatilization region, then to the decomposition region. The comparison with the experimental data reveals that the method reproduces the experimental conversion with an accuracy of 5-10% in the volatilization region and of 3-5% in the decomposition region.

  1. On the evaluation of the non-interacting kinetic energy in density functional theory.

    PubMed

    Peach, Michael J G; Griffiths, David G J; Tozer, David J

    2012-04-14

    The utility of both an orbital-free and a single-orbital expression for computing the non-interacting kinetic energy in density functional theory is investigated for simple atomic systems. The accuracy of both expressions is governed by the extent to which the Kohn-Sham equation is solved for the given exchange-correlation functional and so special attention is paid to the influence of finite Gaussian basis sets. The orbital-free expression is a statement of the virial theorem and its accuracy is quantified. The accuracy of the single-orbital expression is sensitive to the choice of Kohn-Sham orbital. The use of particularly compact orbitals is problematic because the failure to solve the Kohn-Sham equation exactly in regions where the orbital has decayed to near-zero leads to unphysical behaviour in regions that contribute to the kinetic energy, rendering it inaccurate. This problem is particularly severe for core orbitals, which would otherwise appear attractive due to their formally nodeless nature. The most accurate results from the single-orbital expression are obtained using the relatively diffuse, highest occupied orbitals, although special care is required at orbital nodes. PMID:22502495

  2. Analytical potential energy function for the Van der Waals molecule He 2Ne +

    NASA Astrophysics Data System (ADS)

    Huang, Z.; Zhu, Z. H.

    1998-01-01

    A potential energy function has been derived for the two linear isomer structures He 2Ne +(X 2Σ +) using ab initio calculations with the {QCISD(T)}/{6-31++ G(d,p)} method. Because we use the reasonable dissociation limit (3) instead of the unacceptable one (1), our potential energy function represents considerable topographical features in detail, including the linear [HeNe +He] structure ( R HeNe = 1.4694 Å, R He'Ne = 2.0069 Å ∠HeNeHe = 180°) with two symmetric linear saddles ( R HeNe = R He'Ne = 1.80 Å, ∠HeNeHe = 180° and R HeNe = 1.5 Å, R He'Ne = 3.2 A°, ∠HeNeHe = 180°), and the topographical minimum of the [HeHeNe +] structure ( R HeHe = 2.2217 Å, R HeNe = 1.4426 Å, ∠HeHeNe = 180°), with a linear saddle ( R HeHe' = 3.0 Å, R HeNe = 1.8 Å, ∠HeHeNe = 180°).

  3. Building a Universal Nuclear Energy Density Functional (UNEDF): SciDAC-2 Project

    SciTech Connect

    Carlson, Joe; Furnstahl, Dick; Lusk, Rusty; Nazarewicz, Witek; Ng, Esmond; Thompson, Ian; Vary, James

    2012-06-30

    An understanding of the properties of atomic nuclei is crucial for a complete nuclear theory, for element formation, for properties of stars, and for present and future energy and defense applications. During the period of Dec. 1, 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; and third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.

  4. Convexity of Energy-Like Functions: Theoretical Results and Applications to Power System Operations

    SciTech Connect

    Dvijotham, Krishnamurthy; Chertkov, Michael; Low, Steven

    2015-01-22

    Power systems are undergoing unprecedented transformations with increased adoption of renewables and distributed generation, as well as the adoption of demand response programs. All of these changes, while making the grid more responsive and potentially more efficient, pose significant challenges for power systems operators. Conventional operational paradigms are no longer sufficient as the power system may no longer have big dispatchable generators with sufficient positive and negative reserves. This increases the need for tools and algorithms that can efficiently predict safe regions of operation of the power system. In this paper, we study energy functions as a tool to design algorithms for various operational problems in power systems. These have a long history in power systems and have been primarily applied to transient stability problems. In this paper, we take a new look at power systems, focusing on an aspect that has previously received little attention: Convexity. We characterize the domain of voltage magnitudes and phases within which the energy function is convex in these variables. We show that this corresponds naturally with standard operational constraints imposed in power systems. We show that power of equations can be solved using this approach, as long as the solution lies within the convexity domain. We outline various desirable properties of solutions in the convexity domain and present simple numerical illustrations supporting our results.

  5. Complex carbohydrates as a possible source of high energy to formulate functional feeds.

    PubMed

    Ochoa, Leonel; Paniagua Michel, José de Jesús; Olmos-Soto, Jorge

    2014-01-01

    Carbohydrates (CHOs) are the most abundant organic compounds found in living organisms and are a great source of metabolic energy, both for plants and animals. Besides of CHOs great potential to solve animal's energy requirements and diminishing high feed cost, we first must to understand its digestibility and assimilation to avoid several inconvenients. Today, CHOs feed animal inclusions are of great concern about cost-benefits, animal's health status, and environmental pollution. In this chapter, we make a brief description about sugars (DP1-2), oligosaccharides (DP3-9), polysaccharides (DP ≥10), and their essential characteristics to understand the role of marine and terrestrial CHOs in animal nutrition. Subsequently, we talk about basic concepts, CHOs functional benefits, suggestions about their application and successful cases. This information will contribute to produce a new generation of high-quality and energetic functional feed formulations for livestock and aquaculture farms; which must be of low cost, healthy, and environmentally friendly, with the inclusion of prebiotics and probiotics. PMID:25300550

  6. Microscopic distribution functions, structure, and kinetic energy of liquid and solid neon: quantum Monte Carlo simulations.

    PubMed

    Neumann, Martin; Zoppi, Marco

    2002-03-01

    We have performed extensive path integral Monte Carlo simulations of liquid and solid neon, in order to derive the kinetic energy as well as the single-particle and pair distribution functions of neon atoms in the condensed phases. From the single-particle distribution function n(r) one can derive the momentum distribution and thus obtain an independent estimate of the kinetic energy. The simulations have been carried out using mostly the semiempirical HFD-C2 pair potential by Aziz et al. [R. A. Aziz, W. J. Meath, and A. R. Allnatt, Chem. Phys. 79, 295 (1983)], but, in a few cases, we have also used the Lennard-Jones potential. The differences between the potentials, as measured by the properties investigated, are not very large, especially when compared with the actual precision of the experimental data. The simulation results have been compared with all the experimental information that is available from neutron scattering. The overall agreement with the experiments is very good.

  7. Complex carbohydrates as a possible source of high energy to formulate functional feeds.

    PubMed

    Ochoa, Leonel; Paniagua Michel, José de Jesús; Olmos-Soto, Jorge

    2014-01-01

    Carbohydrates (CHOs) are the most abundant organic compounds found in living organisms and are a great source of metabolic energy, both for plants and animals. Besides of CHOs great potential to solve animal's energy requirements and diminishing high feed cost, we first must to understand its digestibility and assimilation to avoid several inconvenients. Today, CHOs feed animal inclusions are of great concern about cost-benefits, animal's health status, and environmental pollution. In this chapter, we make a brief description about sugars (DP1-2), oligosaccharides (DP3-9), polysaccharides (DP ≥10), and their essential characteristics to understand the role of marine and terrestrial CHOs in animal nutrition. Subsequently, we talk about basic concepts, CHOs functional benefits, suggestions about their application and successful cases. This information will contribute to produce a new generation of high-quality and energetic functional feed formulations for livestock and aquaculture farms; which must be of low cost, healthy, and environmentally friendly, with the inclusion of prebiotics and probiotics.

  8. Critical points and symmetries of a free energy function for biaxial nematic liquid crystals

    NASA Astrophysics Data System (ADS)

    Chillingworth, D. R. J.

    2015-05-01

    We describe a general mean field model for the free energy function for a homogeneous medium of mutually interacting molecules, based on the formalism for a biaxial nematic liquid crystal set out by Katriel et al (1986) in an influential paper in Liquid Crystals 1 and subsequently called the KKLS formalism. The free energy is expressed as the sum of an entropy term and an interaction (Hamiltonian) term. Using the language of group representation theory we identify the order parameters as averaged components of a linear transformation, and characterize the full symmetry group of the entropy term in the liquid crystal context as a wreath product SO(3) ≀ Z2. The symmetry-breaking role of the Hamiltonian, pointed out by Katriel et al, is here made explicit in terms of centre manifold reduction at bifurcation from isotropy. We use tools and methods of equivariant singularity theory to reduce the bifurcation study to that of a D3-invariant function on R2, ubiquitous in liquid crystal theory, and to describe the ‘universal’ bifurcation geometry in terms of the superposition of a familiar swallowtail surface controlling uniaxial equilibria and another less familiar surface controlling biaxial equilibria. In principle this provides a template for all nematic liquid crystal phase transitions close to isotropy, although further work is needed to identify the absolute minima that are the critical points representing stable phases.

  9. Energy distribution functions of kilovolt ions parallel and perpendicular to the magnetic field of a modified Penning discharge

    NASA Technical Reports Server (NTRS)

    Roth, R. J.

    1973-01-01

    The distribution function of ion energy parallel to the magnetic field of a modified Penning discharge has been measured with a retarding potential energy analyzer. These ions escaped through one of the throats of the magnetic mirror geometry. Simultaneous measurements of the ion energy distribution function perpendicular to the magnetic field have been made with a charge exchange neutral detector. The ion energy distribution functions are approximately Maxwellian, and the parallel and perpendicular kinetic temperatures are equal within experimental error. These results suggest that turbulent processes previously observed in this discharge Maxwellianize the velocity distribution along a radius in velocity space and cause an isotropic energy distribution. When the distributions depart from Maxwellian, they are enhanced above the Maxwellian tail.

  10. Kinetic energy and spatial variability of throughfall in forest ecosystems as a function of biodiversity

    NASA Astrophysics Data System (ADS)

    Goebes, Philipp; Seitz, Steffen; Kühn, Peter; Scholten, Thomas

    2014-05-01

    Soil erosion by water is an important process regarding ecosystem stability and ecosystem functions; this is especially true for subtropical regions with high intensity rainfall. Rainfall erosivity is one important factor in estimating soil erosion as an ecosystem function under forest. The power of raindrops to detach sediment at the soil surface is influenced by drop size and velocity. When passing through vegetation, rain drop size as well as rain drop velocity are changed depending on several vegetation parameters e.g. leaf area index (LAI). The role of biodiversity as one of these vegetation parameters on soil erosion processes is not yet clear and more information on the spatial distribution of throughfall under vegetation canopies is needed. In this study throughfall kinetic energy (TKE) as a unit of rainfall erosivity was measured and the effect of biodiversity on TKE and their spatial distribution was investigated. The experiment was carried out within the DFG research unit "Biodiversity and Ecosystem Functioning (BEF)-China" in subtropical China. To measure biodiversity effects, splash cups have been used as a high-precision device with a high number of replications possible. 1800 Splash Cups were installed in the field during five different rainfall events on 40 plots with different tree diversity levels with a total of 24 tree species. For investigating spatial distribution of TKE, these splash cups have been set up in distinct distances from tree individuals (15cm, 30cm and 45cm away from stem, in the middle of two and four individuals, under the first branch, at the intersection of a 45cm and 105cm circle around two stems and one free from vegetation to determine freefall kinetic energy). Additional vegetation parameters have been measured: LAI and ground coverage under each splash cup, height, stem diameter, crown expansion in north-south and west-east direction, number of branches and crown height of each tree individual. First results show a higher

  11. Electron energy distribution function in the divertor region of the COMPASS tokamak

    NASA Astrophysics Data System (ADS)

    Dimitrova, M.; Hasan, E.; Ivanova, P.; Vasileva, E.; Popov, Tsv; Dejarnac, R.; Stöckel, J.; Panek, R.

    2016-03-01

    The plasma parameters during an L-mode hydrogen discharge in the COMPASS tokamak with a toroidal magnetic field BT =1.15 T, line-averaged electron density ne = 6×1019 m-3 and a plasma current variation from 209 kA to 100 kA were studied in the divertor region. The electron energy distribution function for 209 kA at the high-field side and the private region is Maxwellian with a temperature in the range of 5 -- 9 eV, while around the outer strike point and the low-field side it is bi-Maxwellian with a low-energy electron group (4 -- 5 eV) and higher energy electrons (10 -- 20 eV). As the plasma current decreases, the appearance of the bi-Maxwellian EEDF is shifted towards the low-field side; at plasma current of 100 kA, the EEDF is Maxwellian in the whole divertor region.

  12. Multi-functional electrospun nanofibres for advances in tissue regeneration, energy conversion & storage, and water treatment.

    PubMed

    Peng, Shengjie; Jin, Guorui; Li, Linlin; Li, Kai; Srinivasan, Madhavi; Ramakrishna, Seeram; Chen, Jun

    2016-03-01

    Tissue regeneration, energy conversion & storage, and water treatment are some of the most critical challenges facing humanity in the 21st century. In order to address such challenges, one-dimensional (1D) materials are projected to play a key role in developing emerging solutions for the increasingly complex problems. Eletrospinning technology has been demonstrated to be a simple, versatile, and cost-effective method in fabricating a rich variety of materials with 1D nanostructures. These include polymers, composites, and inorganic materials with unique chemical and physical properties. In this tutorial review, we first give a brief introduction to electrospun materials with a special emphasis on the design, fabrication, and modification of 1D functional materials. Adopting the perspective of chemists and materials scientists, we then focus on the recent significant progress made in the domains of tissue regeneration (e.g., skin, nerve, heart and bone) and conversion & storage of clean energy (e.g., solar cells, fuel cells, batteries, and supercapacitors), where nanofibres have been used as active nanomaterials. Furthermore, this review's scope also includes the advances in the use of electrospun materials for the removal of heavy metal ions, organic pollutants, gas and bacteria in water treatment applications. Finally a conclusion and perspective is provided, in which we discuss the remaining challenges for 1D electrospun nanomaterials in tissue regeneration, energy conversion & storage, and water treatment. PMID:26727278

  13. Sub-barrier fusion excitation function data and energy dependent Woods-Saxon potential

    NASA Astrophysics Data System (ADS)

    Gautam, Manjeet Singh

    2016-07-01

    This paper analyzed the role of intrinsic degrees of freedom of colliding nuclei in the enhancement of sub-barrier fusion cross-section data of various heavy ion fusion reactions. The influences of inelastic surface vibrations of colliding pairs are found to be dominant and their couplings result in the significantly larger fusion enhancement over the predictions of the one dimensional barrier penetration model at sub-barrier energies. The theoretical calculations are performed by using energy dependent Woods-Saxon potential model (EDWSP model) in conjunction with the one dimensional Wong formula. The effects of dominant intrinsic channels are entertained within framework of the coupled channel calculations obtained by using the code CCFULL. It is quite interesting to note that the energy dependence in Woods-Saxon potential simulates the effects of inelastic surface vibrational states of reactants wherein significantly larger value of diffuseness parameter ranging from a = 0.85 fm to a = 0.95 fm is required to address the observed fusion excitation function data of the various heavy ion fusion reactions.

  14. Energy substrates to support glutamatergic and GABAergic synaptic function: role of glycogen, glucose and lactate.

    PubMed

    Schousboe, Arne; Bak, Lasse K; Sickmann, Helle M; Sonnewald, Ursula; Waagepetersen, Helle S

    2007-12-01

    Maintenance of glutamatergic and GABAergic activity requires a continuous supply of energy since the exocytotic processes as well as high affinity glutamate and GABA uptake and subsequent metabolism of glutamate to glutamine are energy demanding processes. The main energy substrate for the brain under normal conditions is glucose but at the cellular level, i.e., neurons and astrocytes, lactate may play an important role as well. In addition to this the possibility exists that glycogen, which functions as a glucose storage molecule and which is only present in astrocytes, could play a role not only during aglycemia but also during normoglycemia. These issues are discussed and it is concluded that both glucose and lactate are of importance for the maintenance of normal glutamatergic and GABAergic activity. However, with regard to maintenance of an adequate capacity for glutamate transport, it appears that glucose metabolism via the glycolytic pathway plays a fundamental role. Additionally, evidence is presented to support the notion that glycogen turnover may play an important role in this context. Moreover, it should be noted that the amino acid neurotransmitters can be used as metabolic substrates. This requires pyruvate recycling, a process that is discussed as well.

  15. Influence of a Geometrically Induced Space Charge on the Electron Energy Distribution Function

    NASA Astrophysics Data System (ADS)

    Tersigni, F. A.; Bailey, Wm. F.

    1999-04-01

    Space charge effects on the Electron Energy Distribution Function (EEDF) were explored using an approximate, nonlocal solution to the collisional Boltzmann equation after Godyak(Godyak, V., R. Lagushenko, and J. Maya. "Spatial evolution of the electron energy distribution in the vicinity of a discharge tube constriction," Phys. Rev. A 38(4):2044-2055 (August 1988).). The method was implemented, extended and the results assessed within the experimental data of Godyak and Sirghi(Sirghi, L., K Ohe, and G. Popa "Interactions between ionization waves and potential structure formed at a constriction of the DC He positive column," J. Phys. D: Appl. Phys. 30:2431-2440 (1997).). In the region upstream of the constriction, the approximate solution captured the aspects of the nonlocal plasma response. Using a simplified set of inelastic collisions, neglecting the influx of energy degraded electrons above the inelastic threshold and introducing an approximate form for the spatial variation of the field restricted quantitative comparisons with experiment. Downstream of the constriction, the original formalism led to discontinuities and singularities in the EEDF. Attempts at remedying these deficiencies are discussed.

  16. Dual-Functional Energy-Harvesting and Vibration Control: Electromagnetic Resonant Shunt Series Tuned Mass Dampers.

    PubMed

    Zuo, Lei; Cui, Wen

    2013-10-01

    This paper proposes a novel retrofittable approach for dual-functional energy-harvesting and robust vibration control by integrating the tuned mass damper (TMD) and electromagnetic shunted resonant damping. The viscous dissipative element between the TMD and primary system is replaced by an electromagnetic transducer shunted with a resonant RLC circuit. An efficient gradient based numeric method is presented for the parameter optimization in the control framework for vibration suppression and energy harvesting. A case study is performed based on the Taipei 101 TMD. It is found that by tuning the TMD resonance and circuit resonance close to that of the primary structure, the electromagnetic resonant-shunt TMD achieves the enhanced effectiveness and robustness of double-mass series TMDs, without suffering from the significantly amplified motion stroke. It is also observed that the parameters and performances optimized for vibration suppression are close to those optimized for energy harvesting, and the performance is not sensitive to the resistance of the charging circuit or electrical load.

  17. Dual-Functional Energy-Harvesting and Vibration Control: Electromagnetic Resonant Shunt Series Tuned Mass Dampers.

    PubMed

    Zuo, Lei; Cui, Wen

    2013-10-01

    This paper proposes a novel retrofittable approach for dual-functional energy-harvesting and robust vibration control by integrating the tuned mass damper (TMD) and electromagnetic shunted resonant damping. The viscous dissipative element between the TMD and primary system is replaced by an electromagnetic transducer shunted with a resonant RLC circuit. An efficient gradient based numeric method is presented for the parameter optimization in the control framework for vibration suppression and energy harvesting. A case study is performed based on the Taipei 101 TMD. It is found that by tuning the TMD resonance and circuit resonance close to that of the primary structure, the electromagnetic resonant-shunt TMD achieves the enhanced effectiveness and robustness of double-mass series TMDs, without suffering from the significantly amplified motion stroke. It is also observed that the parameters and performances optimized for vibration suppression are close to those optimized for energy harvesting, and the performance is not sensitive to the resistance of the charging circuit or electrical load. PMID:23918165

  18. Strain and Cohesive Energy of TiN Deposit on Al(001) Surface: Density Functional Calculation

    NASA Astrophysics Data System (ADS)

    Ren, Yuan; Liu, Xuejie

    2016-07-01

    To apply the high hardness of TiN film to soft and hard multilayer composite sheets, we constructed a new type of composite structural material with ultra-high strength. The strain of crystal and cohesive energy between the atoms in the eight structures of N atom, Ti atom, 2N2Ti island and TiN rock salt deposited on the Al(001) surface were calculated with the first-principle ultra-soft pseudopotential approach of the plane wave based on the density functional theory. The calculations of the cohesive energy showed that N atoms could be deposited in the face-centered-cubic vacancy position of the Al(001) surface and results in a cubic structure AlN surface. The TiN film could be deposited on the interface of β-AlN. The calculations of the strains showed that the strain in the TiN film deposited on the Al(001) surface was less than that in the 2N2Ti island deposited on the Al(001) surface. The diffusion behavior of interface atom N was investigated by a nudged elastic band method. Diffusion energy calculation showed that the N atom hardly diffused to the substrate Al layer.

  19. Dye-sensitized solar cell with energy storage function through PVDF/ZnO nanocomposite counter electrode.

    PubMed

    Zhang, Xi; Huang, Xuezhen; Li, Chensha; Jiang, Hongrui

    2013-08-14

    Dye-sensitized solar cells with an energy storage function are demonstrated by modifying its counter electrode with a poly (vinylidene fluoride)/ZnO nanowire array composite. This simplex device could still function as an ordinary solar cell with a steady photocurrent output even after being fully charged. An energy storage density of 2.14 C g(-1) is achieved, while simultaneously a 3.70% photo-to-electric conversion efficiency is maintained.

  20. ATOMIC AND MOLECULAR PHYSICS: Calculation of Energy and Other Properties of Muonic Helium Atom Using Boundary Conditions of Wave Function

    NASA Astrophysics Data System (ADS)

    Rezaei, B.

    2010-09-01

    The properties of muonic helium atom (4He+2μ-e-) in ground state are considered. In this work, the energy and average distance between particles have been obtained using a wave function, which satisfies boundary conditions. It is shown that the obtained energy are very close to the values calculated by others. But the small differences of the expectation values of r2n are due to the incorporated boundary conditions in proposed wave function and are expected.

  1. On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.

    PubMed

    Li, Lin; Li, Chuan; Alexov, Emil

    2014-05-01

    Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute-water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.

  2. Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Tantakitti, Faifan

    Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while

  3. Three layer functional model and energy exchange concept of aging process

    PubMed Central

    Mihajlovic, William

    2006-01-01

    Relying on a certain degree of abstraction, we can propose that no particular distinction exists between animate or living matter and inanimate matter. While focusing attention on some specifics, the dividing line between the two can be drawn. The most apparent distinction is in the level of structural and functional organization with the dissimilar streams of ‘energy flow’ between the observed entity and the surrounding environment. In essence, living matter is created from inanimate matter which is organized to contain internal intense energy processes and maintain lower intensity energy exchange processes with the environment. Taking internal and external energy processes into account, we contend in this paper that living matter can be referred to as matter of dissipative structure, with this structure assumed to be a common quality of all living creatures and living matter in general. Interruption of internal energy conversion processes and terminating the controlled energy exchange with the environment leads to degeneration of dissipative structure and reduction of the same to inanimate matter, (gas, liquid and/or solid inanimate substances), and ultimately what can be called ‘death.’ This concept of what we call dissipative nature can be extended from living organisms to social groups of animals, to mankind. An analogy based on the organization of matter provides a basis for a functional model of living entities. The models relies on the parallels among the three central structures of any cell (nucleus, cytoplasm and outer membrane) and the human body (central organs, body fluids along with the connective tissues, and external skin integument). This three-part structural organization may be observed almost universally in nature. It can be observed from the atomic structure to the planetary and intergalactic organizations. This similarity is corroborated by the membrane theory applied to living organisms. According to the energy nature of living matter

  4. Characterization of anisotropic elastic properties of the arteries by exponential and polynomial strain energy functions.

    PubMed

    Hudetz, A G; Monos, E

    1981-01-01

    Three-dimensional quasi-static mechanical measurements were carried out on cylindrical segments of the dog carotid and iliac arteries for determination of the passive anisotropic elastic properties of the vessel wall. On the basis of passive characteristics of outer diameter vs. intraluminal pressure, and axial extending force vs. intraluminal pressure, picked up at various fixed initial vascular length values, the incremental Young moduli and poisson ratios of the vessel wall were calculated in the 0--33 kPa (0--250 mm Hg) pressure range. The strain energy function of the arteries was approximated by polynomial and exponential models. We found that an exponential energy function with 4-parameters gives more accurate results than the 7- or 12-parameter polynomial functions. According to the results the axial modulus reaches higher values than the tangential and radial moduli at a low tangential stretch level, while at high tangential stretch the tangential modulus is the highest in both carotid and iliac arteries. After elevation of the initial tangential stretch the increase in the tangential modulus is the most pronounced, while the values of radial and axial moduli increased less. A change in the initial axial stretch influences the axial and radial moduli to a similar extent, but has no substantial effect on the value of the tangential modulus. The values of corresponding poisson ratios depend in a similar way on the initial deformation state. The different behaviour of the two Poisson ratios characterizing the mechanical coupling between tangential and axial directions, indicates that the structural coupling between the two main directions is asymmetrical. It is assumed that this property of the passive vascular structure can be explained by the network arrangement of collagen fibres in the vessel wall.

  5. Alcohol Mixed With Energy Drinks: Associations with Risky Drinking and Functioning in High School

    PubMed Central

    Tucker, Joan S.; Troxel, Wendy M.; Ewing, Brett A.; D’Amico, Elizabeth J.

    2016-01-01

    Background Mixing alcohol with energy drinks is associated with heavier drinking and related problems among college students. However, little is known about how high school drinkers who mix alcohol with energy drinks (AmED) compare to those who do not (AwoED). This study compares high school AmED and AwoED users on their alcohol use during middle and high school, as well as key domains of functioning in high school. Methods Two surveys were conducted three years apart in adolescents initially recruited from 16 middle schools in Southern California. The analytic sample consists of 696 past month drinkers. Multivariable models compared AmED and AwoED users on alcohol use, mental health, social functioning, academic orientation, delinquency and other substance use at age 17, and on their alcohol use and related cognitions at age 14. Results AmED was reported by 13% of past month drinkers. AmED and AwoED users did not differ on alcohol use or cognitions in middle school, but AmED users drank more often, more heavily, and reported more negative consequences in high school. AmED users were also more likely to report poor grades, delinquent behavior, substance use-related unsafe driving, public intoxication, and drug use than AwoED users in high school. Group differences were not found on mental health, social functioning, or academic aspirations. Conclusions AmED use is common among high school drinkers. The higher risk behavioral profile of these young AmED users, which includes drug use and substance use-related unsafe driving, is a significant cause for concern and warrants further attention. PMID:27522534

  6. Graphene nanoplatelets with selectively functionalized edges as electrode material for electrochemical energy storage.

    PubMed

    Bhattacharjya, Dhrubajyoti; Jeon, In-Yup; Park, Hyean-Yeol; Panja, Tandra; Baek, Jong-Beom; Yu, Jong-Sung

    2015-05-26

    In recent years, graphene-based materials have been in the forefront as electrode material for electrochemical energy generation and storage. Despite this prevalent interest, synthesis procedures have not attained three important efficiency requirements, that is, cost, energy, and eco-friendliness. In this regard, in the present work, graphene nanoplatelets with selectively functionalized edges (XGnPs) are prepared through a simple, eco-friendly and efficient method, which involves ball milling of graphite in the presence of hydrogen (H2), bromine (Br2), and iodine (I2). The resultant HGnP, BrGnP, and IGnP reveal significant exfoliation of graphite layers, as evidenced by high BET surface area of 414, 595, and 772 m(2) g(-1), respectively, in addition to incorporation of H, Br, and I along with other oxygen-containing functional groups at the graphitic edges. The BrGnP and IGnP are also found to contain 4.12 and 2.20 at % of Br and I, respectively in the graphene framework. When tested as supercapacitor electrode, all XGnPs show excellent electrochemical performance in terms of specific capacitance and durability at high current density and long-term operation. Among XGnPs, IGnP delivers superior performance of 172 F g(-1) at 1 A g(-1) compared with 150 F g(-1) for BrGnP and 75 F g(-1) for HGnP because the large surface area and high surface functionality in the IGnP give rise to the outstanding capacitive performance. Moreover, all XGnPs show excellent retention of capacitance at high current density of 10 A g(-1) and for long-term operation up to 1000 charge-discharge cycles.

  7. Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.

    PubMed

    Tian, Ye; Huang, Xiaoqiang; Zhu, Yushan

    2015-08-01

    Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts.

  8. Sensory profile of a model energy drink with varying levels of functional ingredients-caffeine, ginseng, and taurine.

    PubMed

    Tamamoto, Lauren C; Schmidt, Shelly J; Lee, Soo-Yeun

    2010-08-01

    Energy drinks have increased in popularity in recent years due to the claimed energy boost provided by functional ingredients. A multitude of functional ingredients have been utilized; however, there is limited research on their sensory effects in energy drink formulations. A 13-member descriptive analysis panel was conducted to investigate the effects on the sensory and rheological properties of 3 common functional ingredients-caffeine, ginseng, and taurine-in a noncarbonated model energy drink solution. Combinations of these functional ingredients at 3 levels (low, medium, high) were added to create a total of 27 different solutions (3 x 3 x 3 factorial design). Analysis of variance was performed to evaluate the sensory effects of the varying concentrations of functional ingredients in solution. Principal component analysis (PCA) was performed to summarize the relationship among the attributes and solutions. In general, high levels of caffeine in solution resulted in low ratings of fruity attributes and high ratings of bitter tea and fruit bitter attributes. The high level of ginseng in solution was characterized by high ratings of bitter attributes. A horns effect was observed as the sweet, artificial lemon-lime, pear, mango, and pineapple attributes were rated lower in intensity with increased ginseng levels. Taurine levels of up to 416 mg/100 mL had no significant effect on the sensory attribute ratings of the model energy drink solutions. These findings can be utilized to predict the changes in sensory characteristics when formulating energy drinks containing these popular functional ingredients.

  9. PTENα, a PTEN isoform translated through alternative initiation, regulates mitochondrial function and energy metabolism.

    PubMed

    Liang, Hui; He, Shiming; Yang, Jingyi; Jia, Xinying; Wang, Pan; Chen, Xi; Zhang, Zhong; Zou, Xiajuan; McNutt, Michael A; Shen, Wen Hong; Yin, Yuxin

    2014-05-01

    PTEN is one of the most frequently mutated genes in human cancer. It is known that PTEN has a wide range of biological functions beyond tumor suppression. Here, we report that PTENα, an N-terminally extended form of PTEN, functions in mitochondrial metabolism. Translation of PTENα is initiated from a CUG codon upstream of and in-frame with the coding region of canonical PTEN. Eukaryotic translation initiation factor 2A (eIF2A) controls PTENα translation, which requires a CUG-centered palindromic motif. We show that PTENα induces cytochrome c oxidase activity and ATP production in mitochondria. TALEN-mediated somatic deletion of PTENα impairs mitochondrial respiratory chain function. PTENα interacts with canonical PTEN to increase PINK1 protein levels and promote energy production. Our studies demonstrate the importance of eIF2A-mediated alternative translation for generation of protein diversity in eukaryotic systems and provide insights into the mechanism by which the PTEN family is involved in multiple cellular processes.

  10. Identical Binding Energies and Work Functions for Distinct Adsorption Structures: Olympicenes on the Cu(111) Surface.

    PubMed

    Liu, Wei; Schuler, Bruno; Xu, Yong; Moll, Nikolaj; Meyer, Gerhard; Gross, Leo; Tkatchenko, Alexandre

    2016-03-17

    Reliability is one of the major concerns and challenges in designing organic/inorganic interfaces for (opto)electronic applications. Even small structural differences for molecules on substrates can result in a significant variation in the interface functionality, due to the strong correlation between geometry, stability, and electronic structure. Here, we employed state-of-the-art first-principles calculations with van der Waals interactions, in combination with atomic force microscopy experiments, to explore the interaction mechanism for three structurally related olympicene molecules adsorbed on the Cu(111) surface. The substitution of a single atom in the olympicene molecule switches the nature of adsorption from predominantly physisorptive character [olympicene on Cu(111)], to an intermediate state [olympicene-derived ketone on Cu(111)], then to chemisorptive character [olympicene radical on Cu(111)]. Despite the remarkable difference in adsorption structures (by up to 0.9 Å in adsorption height) and different nature of bonding, the olympicene, its ketone, and its radical derivatives have essentially identical binding energies and work functions upon interaction with the metal substrate. Our findings suggest that the stability and work functions of molecular adsorbates could be rendered insensitive to their adsorption structures, which could be a useful property for (opto)electronic applications. PMID:26928143

  11. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L.; Perdew, John P.

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  12. A coherent neurobiological framework for functional neuroimaging provided by a model integrating compartmentalized energy metabolism.

    PubMed

    Aubert, Agnès; Pellerin, Luc; Magistretti, Pierre J; Costalat, Robert

    2007-03-01

    Functional neuroimaging has undergone spectacular developments in recent years. Paradoxically, its neurobiological bases have remained elusive, resulting in an intense debate around the cellular mechanisms taking place upon activation that could contribute to the signals measured. Taking advantage of a modeling approach, we propose here a coherent neurobiological framework that not only explains several in vitro and in vivo observations but also provides a physiological basis to interpret imaging signals. First, based on a model of compartmentalized energy metabolism, we show that complex kinetics of NADH changes observed in vitro can be accounted for by distinct metabolic responses in two cell populations reminiscent of neurons and astrocytes. Second, extended application of the model to an in vivo situation allowed us to reproduce the evolution of intraparenchymal oxygen levels upon activation as measured experimentally without substantially altering the initial parameter values. Finally, applying the same model to functional neuroimaging in humans, we were able to determine that the early negative component of the blood oxygenation level-dependent response recorded with functional MRI, known as the initial dip, critically depends on the oxidative response of neurons, whereas the late aspects of the signal correspond to a combination of responses from cell types with two distinct metabolic profiles that could be neurons and astrocytes. In summary, our results, obtained with such a modeling approach, support the concept that both neuronal and glial metabolic responses form essential components of neuroimaging signals. PMID:17360498

  13. Ion Binding Energies Determining Functional Transport of ClC Proteins

    NASA Astrophysics Data System (ADS)

    Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

    2014-06-01

    The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

  14. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

    PubMed

    Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science. PMID:27554409

  15. A comparison of global optimization algorithms with standard benchmark functions and real-world applications using Energy Plus

    SciTech Connect

    Kamph, Jerome Henri; Robinson, Darren; Wetter, Michael

    2009-09-01

    There is an increasing interest in the use of computer algorithms to identify combinations of parameters which optimise the energy performance of buildings. For such problems, the objective function can be multi-modal and needs to be approximated numerically using building energy simulation programs. As these programs contain iterative solution algorithms, they introduce discontinuities in the numerical approximation to the objective function. Metaheuristics often work well for such problems, but their convergence to a global optimum cannot be established formally. Moreover, different algorithms tend to be suited to particular classes of optimization problems. To shed light on this issue we compared the performance of two metaheuristics, the hybrid CMA-ES/HDE and the hybrid PSO/HJ, in minimizing standard benchmark functions and real-world building energy optimization problems of varying complexity. From this we find that the CMA-ES/HDE performs well on more complex objective functions, but that the PSO/HJ more consistently identifies the global minimum for simpler objective functions. Both identified similar values in the objective functions arising from energy simulations, but with different combinations of model parameters. This may suggest that the objective function is multi-modal. The algorithms also correctly identified some non-intuitive parameter combinations that were caused by a simplified control sequence of the building energy system that does not represent actual practice, further reinforcing their utility.

  16. Diode calibration of a Langmuir probe system for measurement of electron energy distribution functions in a plasma

    SciTech Connect

    DeJoseph, C.A. Jr.; Demidov, V.I.

    2005-08-15

    It is shown that a simple circuit consisting of a semiconductor diode, a resistor, and a dc voltage source can model a narrow-energy group of electrons in a plasma for the purpose of calibration of a Langmuir probe. The calibration is appropriate when the probe is used for measurement of the electron energy distribution function (EEDF). This simple circuit allows real-time determination of sensitivity, energy resolution, and signal-to-noise ratio for probe measurements of the EEDF.

  17. Synthesis and application of functional branched macromolecules: From site isolation and energy harvesting to catalysis

    NASA Astrophysics Data System (ADS)

    Hecht, Stefan

    The symbiosis of our understanding of structure property relationships in many biological macromolecules and our increased ability to prepare large synthetic macromolecules with exquisite structural precision has generated a new area of research where chemistry and materials science join with biology. For example, numerous biological systems utilize the concept of site isolation whereby an active center or catalytic site is encapsulated, frequently within a protein, to afford properties that would not be encountered in the bulk state. The ability of a dendritic shell to encapsulate functional core moieties and to create specific site-isolated nanoenvironments, thereby affecting molecular properties, not only mimics natural systems but affords novel materials with unique characteristics. Furthermore, introduction of donor chromophores at periphery of dendrimers having a central acceptor dye enables spatial and spectral energy concentration at the core. Continuing the effort towards designing bio-inspired macromolecules, this dissertation describes the use of different polymer architectures to encapsulate active sites that have either photophysical, photochemical, or catalytic functions and the evaluation of site isolation using a variety of different techniques. While the first part is mainly concerned with different synthetic approaches towards site isolation of porphyrin moieties, the second part describes the design of light-driven catalytic systems incorporating both light harvesting and energy conversion. The fundamental knowledge that can be gleaned from such investigations has implications that range from the preliminary design of artificial enzymes to the construction of molecular-scale devices. After an overview of dendritically encapsulated functions (Chapter 1) and a brief account of a novel synthetic approach to benzene core dendrimers (Chapter 2), site isolation of porphyrin moieties within dendrimers, their linear structural isomers, and branched star

  18. Effects of Corticosterone and Dietary Energy on Immune Function of Broiler Chickens

    PubMed Central

    Sheikhahmadi, Ardashir; Wang, Yufeng; Li, Congcong; Jiao, Hongchao; Lin, Hai; Song, Zhigang

    2015-01-01

    An experiment was conducted to investigate the effects of dietary energy level on the performance and immune function of stressed broiler chickens (Gallus gallus domesticus). A total of 96 three-day-old male broiler chickens (Ross × Ross) were divided into two groups. One group received a high energy (HE) diet and the other group received a low energy (LE) diet for 7 days. At 5 days of age, the chickens from each group were further divided into two sub-groups and received one of the following two treatments for 3 days: (1) subcutaneous injection of corticosterone, twice per day (CORT group; 2 mg of CORT/kg BW in corn oil) and (2) subcutaneous injection of corn oil, twice per day (Control/Sham treatment group). At 10 days of age, samples of blood, duodenum, jejunum, and ileum were obtained. Compared with the other three groups, the LE group treated with CORT had the lowest average daily gain (ADG) and the poorest feed conversion ratio (FCR, P < 0.05). Furthermore, CORT treatment decreased the relative weight (RW) of the bursa independent of the dietary energy level, but it decreased the RW of the thymus only in the chickens fed the LE diet. By contrast, CORT administration decreased the RW of the spleen only in the chickens fed the HE diet (P < 0.05). The plasma total protein, albumin, tumor necrosis factor alpha, interleukin 2 and immunoglobulin G (IgG) levels were affected by the CORT treatment (P < 0.05); however, these factors were not significantly affected by the dietary energy level. Toll-like receptor-5 mRNA level was down-regulated by CORT injection in the duodenum and ileum (P < 0.05) and showed a trend of down-regulation in the jejunum (P=0.0846). The present study showed that CORT treatment induced immunosuppressive effects on the innate immune system of broiler chickens, which were ameliorated by consumption of higher dietary energy. PMID:25803644

  19. Description of superheavy nuclei on the basis of a modified version of the DF3 energy functional

    SciTech Connect

    Tolokonnikov, S. V.; Saperstein, E. E.

    2010-10-15

    The possibility of describing nuclei of the uranium and transuranium region within the generalized method of the energy functional proposed by Fayans and his coauthors is studied. It turned out that, in the functional DF3, it is necessary, for this purpose, to modify the spin-orbit terms whose parameters were chosen in such a way as to describe the binding energies and charge radii of spherical nuclei from calcium to lead. The modified functional (DF3-a) describes well the energy features and charged radii for isotopic chains of uranium and neighboring elements. For deformed nuclei, the deformation was taken into account approximately. The nucleon-drip-line position obtained for these chains proved to be close to the predictions of one of the most successful calculations by the Skyrme-Hartree-Fock method with the HFB-17 functional. It is verified that the use of the functional DF3-a does not impair the description of the properties of lighter nuclei, for which the functional DF3 was devised. Moreover, the modified functional describes better, than the original one, new data on spin-orbit splitting in magic and semimagic nuclei. The calculation with the functional DF3-a confirms the doubly magic nature of the superheavy nuclide {sub 114}{sup 298}X{sub 184}. As for the neutron-separation energies S{sub n} along the isotopic chain of this element, our results are close to the predictions of the so-called micro-macro method.

  20. 23 CFR Appendix A to Part 772 - National Reference Energy Mean Emission Levels as a Function of Speed

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false National Reference Energy Mean Emission Levels as a Function of Speed A Appendix A to Part 772 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF... Function of Speed EC14OC91.013...

  1. Determination of Electron and Ion Energy Distribution Functions in a Plasma Ion Assisted Deposition (PIAD) Process

    NASA Astrophysics Data System (ADS)

    Harhausen, J.; Foest, R.; Ohl, A.

    2011-10-01

    High performance optical coatings are commonly produced by PIAD in order to achieve comparably high deposition rates. Here, the plasma source is a hot cathode direct current discharge with an auxiliary magnetic field (APS). Its design is such to generate a population of fast ions to be released into the deposition chamber. A detailed understanding of the plasma properties in the chamber is mandatory to increase the level of uniformity and reproducibility of the deposition process. In order to determine the electron and ion energy distribution functions (EEDF, IEDF) the concepts of the Langmuir probe, the retarding field energy analyzer and optical emission spectroscopy are employed. Fundamental findings are that the EEDF can be described in the framework of the non-local approximation and that the degree of ionization inside the APS is close to unity. The shape of the IEDF and its evolution along the beam path can be described consistently by considering charge exchange reactions with the background neutral gas and the profile of the plasma potential. High performance optical coatings are commonly produced by PIAD in order to achieve comparably high deposition rates. Here, the plasma source is a hot cathode direct current discharge with an auxiliary magnetic field (APS). Its design is such to generate a population of fast ions to be released into the deposition chamber. A detailed understanding of the plasma properties in the chamber is mandatory to increase the level of uniformity and reproducibility of the deposition process. In order to determine the electron and ion energy distribution functions (EEDF, IEDF) the concepts of the Langmuir probe, the retarding field energy analyzer and optical emission spectroscopy are employed. Fundamental findings are that the EEDF can be described in the framework of the non-local approximation and that the degree of ionization inside the APS is close to unity. The shape of the IEDF and its evolution along the beam path can be

  2. Density functional and theoretical study of the temperature and pressure dependency of the plasmon energy of solids

    SciTech Connect

    Attarian Shandiz, M. Gauvin, R.

    2014-10-28

    The temperature and pressure dependency of the volume plasmon energy of solids was investigated by density functional theory calculations. The volume change of crystal is the major factor responsible for the variation of valence electron density and plasmon energy in the free electron model. Hence, to introduce the effect of temperature and pressure for the density functional theory calculations of plasmon energy, the temperature and pressure dependency of lattice parameter was used. Also, by combination of the free electron model and the equation of state based on the pseudo-spinodal approach, the temperature and pressure dependency of the plasmon energy was modeled. The suggested model is in good agreement with the results of density functional theory calculations and available experimental data for elements with the free electron behavior.

  3. Comparison of measured and simulated electron energy distribution functions in low-pressure helium plasmas

    NASA Astrophysics Data System (ADS)

    Gruenwald, J.; Tskhakaya, D.; Kovačič, J.; Čerček, M.; Gyergyek, T.; Ionita, C.; Schrittwieser, R.

    2013-02-01

    Knowledge of the electron energy distribution function (EEDF) is of great interest in different branches of plasma physics ranging from laboratory to fusion plasmas. In the frame of this work systematic measurements of the EEDF in low temperature helium plasmas (Te ≈ 2 eV) at different working gas pressures and discharge currents (Idis between 1 and 2 A) will be presented and compared with numerical particle-in-cell (PIC) code simulations. The experiments were conducted in the Innsbruck double plasma machine and in the Ljubljana linear magnetic plasma device with helium as the working gas. The EEDF was obtained by the second derivative of the characteristic of a Langmuir probe. The PIC code was used to simulate the EEDF by taking into account most of the physical parameters in the plasma vessel.

  4. Equation satisfied by the energy-density functional for electron-electron mutual Coulomb repulsion

    SciTech Connect

    Joubert, Daniel P.

    2011-10-15

    It is shown that the electron-electron mutual Coulomb repulsion energy-density functional V{sub ee}{sup {gamma}}[{rho}] satisfies the equationV{sub ee}{sup {gamma}}[{rho}{sub N}{sup 1}]-V{sub ee}{sup {gamma}}[{rho}{sub N-1}{sup {gamma}}]={integral}d{sup 3}r({delta}V{sub ee}{sup {gamma}}[{rho}{sub N}{sup 1}]/{delta}{rho}{sub N}{sup 1}(r))[{rho}{sub N}{sup 1}(r)-{rho}{sub N-1}{sup {gamma}}(r)], where {rho}{sub N}{sup 1}(r) and {rho}{sub N-1}{sup {gamma}}(r) are N-electron and (N-1)-electron densities determined from the same adiabatic scaled external potential of the N-electron system at coupling strength {gamma}.

  5. Multidimensionally constrained covariant density functional theories—nuclear shapes and potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Zhou, Shan-Gui

    2016-06-01

    The intrinsic nuclear shapes deviating from a sphere not only manifest themselves in nuclear collective states but also play important roles in determining nuclear potential energy surfaces (PES’s) and fission barriers. In order to describe microscopically and self-consistently nuclear shapes and PES’s with as many shape degrees of freedom as possible included, we developed multidimensionally constrained covariant density functional theories (MDC-CDFTs). In MDC-CDFTs, the axial symmetry and the reflection symmetry are both broken and all deformations characterized by {β }λ μ with even μ are considered. We have used the MDC-CDFTs to study PES’s and fission barriers of actinides, the non-axial octupole Y 32 correlations in N = 150 isotones and shapes of hypernuclei. In this Review we will give briefly the formalism of MDC-CDFTs and present the applications to normal nuclei.

  6. 3D modeling of the electron energy distribution function in negative hydrogen ion sources.

    PubMed

    Terasaki, R; Fujino, I; Hatayama, A; Mizuno, T; Inoue, T

    2010-02-01

    For optimization and accurate prediction of the amount of H-ion production in negative ion sources, analysis of electron energy distribution function (EEDF) is necessary. We are developing a numerical code which analyzes EEDF in the tandem-type arc-discharge source. It is a three-dimensional Monte Carlo simulation code with realistic geometry and magnetic configuration. Coulomb collision between electrons is treated with the "binary collision" model and collisions with hydrogen species are treated with the "null-collision" method. We applied this code to the analysis of the JAEA 10 A negative ion source. The numerical result shows that the obtained EEDF is in good agreement with experimental results.

  7. Electro-magneto-thermo-elastic response of infinite functionally graded cylinders without energy dissipation

    NASA Astrophysics Data System (ADS)

    Zenkour, Ashraf M.; Abbas, Ibrahim A.

    2015-12-01

    The electro-magneto-thermo-elastic analysis problem of an infinite functionally graded (FG) hollow cylinder is studied in the context of Green-Naghdi's (G-N) generalized thermoelasticity theory (without energy dissipation). Material properties are assumed to be graded in the radial direction according to a novel power-law distribution in terms of the volume fractions of the metal and ceramic constituents. The inner surface of the FG cylinder is pure metal whereas the outer surface is pure ceramic. The equations of motion and the heat-conduction equation are used to derive the governing second-order differential equations. A finite element scheme is presented for the numerical purpose. The system of differential equations is solved numerically and some plots for displacement, radial and electromagnetic stresses, and temperature are presented. The radial displacement, mechanical stresses and temperature as well as the electromagnetic stress are all investigated along the radial direction of the infinite cylinder.

  8. Density functional theory calculations of magnetocrystalline anisotropy energies for (Fe1-xCox)2B

    DOE PAGES

    Daene, Markus; Kim, Soo Kyung; Surh, Michael P.; Aberg, Daniel; Benedict, Lorin X.

    2015-06-15

    We present and discuss density functional theory calculations of magnetic properties of the family of ferromagnetic compounds, (Fe1-xCox)2B, focusing specifically on the magnetocrystalline anisotropy energy (MAE). Using periodic supercells of various sizes (up to 96 atoms), it is shown that the general qualitative features of the composition dependence of the MAE is in agreement with experimental findings, while our predicted magnitudes are larger than those of experiment. We find that the use of small supercells (6 and 12-atom) favors larger MAE values relative to a statistical sample of configurations constructed with 96-atom supercells. As a result, the effect of latticemore » relaxations is shown to be small. Calculations of the Curie temperature for this alloy are also presented.« less

  9. Effect of Red Bull energy drink on cardiovascular and renal function.

    PubMed

    Ragsdale, Frances R; Gronli, Tyler D; Batool, Narjes; Haight, Nicole; Mehaffey, April; McMahon, Erin C; Nalli, Thomas W; Mannello, Carla M; Sell, Crystal J; McCann, Patrick J; Kastello, Gary M; Hooks, Tisha; Wilson, Ted

    2010-04-01

    Energy drink consumption has been anecdotally linked to the development of adverse cardiovascular effects in consumers, although clinical trials to support this link are lacking. The effects of Red Bull energy drink on cardiovascular and neurologic functions were examined in college-aged students enrolled at Winona State University. In a double-blind experiment where normal calorie and low calorie Red Bull were compared to normal and low calorie placebos, no changes in overall cardiovascular function nor blood glucose (mg/dL) were recorded in any participant (n = 68) throughout a 2-h test period. However, in the second experiment, nine male and twelve female participants subjected to a cold pressor test (CPT) before and after Red Bull consumption showed a significant increase in blood sugar levels pre- and post Red Bull consumption. There was a significant increase in diastolic blood pressure of the male volunteers immediately after submersion of the hand in the 5 degrees C water for the CPT. Under the influence of Red Bull, the increase in diastolic pressure for the male participants during the CPT was negated. There were no significant changes in the blood pressure of the female participants for the CPT with or without Red Bull. Finally, the CPT was used to evaluate pain threshold and pain tolerance before and after Red Bull consumption. Red Bull consumption was associated with a significant increase in pain tolerance in all participants. These findings suggest that Red Bull consumption ameliorates changes in blood pressure during stressful experiences and increases the participants' pain tolerance.

  10. Fabricating of high-performance functional graphene fibers for micro-capacitive energy storage

    PubMed Central

    Fan, Tianju; Zhao, Chunyan; Xiao, Zhuangqing; Guo, Fangjun; Cai, Kaiyu; Lin, Hai; Liu, Yidong; Meng, Hong; Min, Yong; Epstein, Arthur J.

    2016-01-01

    Although graphene is a typical two dimensional materials, it has converted to multi-dimensional materials with many unique properties. As an example, the one dimensional graphene fiber is fabricated by utilizing ionic liquid as coagulation and functional diamines as cross-linkers to connect graphene oxide layers. The fibers show excellent mechanical properties and superior electrical performance. The tensile strength of the resultant fibers reaches ~729 MPa after a super high temperature thermal annealing treatment at 2800 °C. Additionally, quasi-solid-state flexible micro-capacitors are fabricated with promising result on energy storage. The device show a specific volumetric capacity as high as ~225 F/cm3 (measured at 103.5 mA cm−3 in a three-electrode cell), as well as a long cycle life of 2000 times. The initial results indicate that these fibers will be a good candidate to replace energy storage devices for miniaturized portable electronic applications. PMID:27390070

  11. Fabricating of high-performance functional graphene fibers for micro-capacitive energy storage

    NASA Astrophysics Data System (ADS)

    Fan, Tianju; Zhao, Chunyan; Xiao, Zhuangqing; Guo, Fangjun; Cai, Kaiyu; Lin, Hai; Liu, Yidong; Meng, Hong; Min, Yong; Epstein, Arthur J.

    2016-07-01

    Although graphene is a typical two dimensional materials, it has converted to multi-dimensional materials with many unique properties. As an example, the one dimensional graphene fiber is fabricated by utilizing ionic liquid as coagulation and functional diamines as cross-linkers to connect graphene oxide layers. The fibers show excellent mechanical properties and superior electrical performance. The tensile strength of the resultant fibers reaches ~729 MPa after a super high temperature thermal annealing treatment at 2800 °C. Additionally, quasi-solid-state flexible micro-capacitors are fabricated with promising result on energy storage. The device show a specific volumetric capacity as high as ~225 F/cm3 (measured at 103.5 mA cm‑3 in a three-electrode cell), as well as a long cycle life of 2000 times. The initial results indicate that these fibers will be a good candidate to replace energy storage devices for miniaturized portable electronic applications.

  12. Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Tantakitti, Faifan

    Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while

  13. A new Skyrme energy density functional for a better description of spin-isospin resonances

    NASA Astrophysics Data System (ADS)

    Roca-Maza, X.; Colò, G.; Cao, Li-Gang; Sagawa, H.

    2015-10-01

    A correct determination of the isospin and spin-isospin properties of the nuclear effective interaction should lead to an accurate description of the Gamow-Teller resonance (GT), the Spin Dipole Resonance (SDR), the Giant Dipole Resonance (GDR) or the Antianalog Giant Dipole Resonance (AGDR), among others. A new Skyrme energy density functional named SAMi is introduced with the aim of going a step forward in setting the bases for a more precise description of spin-isospin resonances [1, 2]. In addition, we will discuss some new features of our analysis on the AGDR in 208Pb [3] as compared with available experimental data on this resonance [4, 5, 6], and on the GDR [7]. Such study, guided by a simple yet physical pocket formula, has been developed by employing the so called SAMi-J family of systematically varied interactions. This set of interactions is compatible with experimental data for values of the symmetry energy at saturation J and slope parameter L falling in the ranges 31-33 MeV and 75-95 MeV, respectively.

  14. A new Skyrme energy density functional for a better description of spin-isospin resonances

    SciTech Connect

    Roca-Maza, X.; Colò, G.; Cao, Li-Gang; Sagawa, H.

    2015-10-15

    A correct determination of the isospin and spin-isospin properties of the nuclear effective interaction should lead to an accurate description of the Gamow-Teller resonance (GT), the Spin Dipole Resonance (SDR), the Giant Dipole Resonance (GDR) or the Antianalog Giant Dipole Resonance (AGDR), among others. A new Skyrme energy density functional named SAMi is introduced with the aim of going a step forward in setting the bases for a more precise description of spin-isospin resonances [1, 2]. In addition, we will discuss some new features of our analysis on the AGDR in {sup 208}Pb [3] as compared with available experimental data on this resonance [4, 5, 6], and on the GDR [7]. Such study, guided by a simple yet physical pocket formula, has been developed by employing the so called SAMi-J family of systematically varied interactions. This set of interactions is compatible with experimental data for values of the symmetry energy at saturation J and slope parameter L falling in the ranges 31−33 MeV and 75−95 MeV, respectively.

  15. The 14th Ile residue is essential for Leptin function in regulating energy homeostasis in rat.

    PubMed

    Xu, Shuyang; Zhu, Xianmin; Li, Hong; Hu, Youtian; Zhou, Jinping; He, Di; Feng, Yun; Lu, Lina; Du, Guizhen; Hu, Youjin; Liu, Tiancheng; Wang, Zhen; Ding, Guohui; Chen, Jiayu; Gao, Shaorong; Wu, Fang; Xue, Zhigang; Li, Yixue; Fan, Guoping

    2016-01-01

    LEPTIN (LEP) is a circulating hormone released primarily from white adipocytes and is crucial for regulating satiety and energy homeostasis in humans and animals. Using the CRISPR technology, we created a set of Lep mutant rats that carry either null mutations or a deletion of the 14(th) Ile (LEP(∆I14)) in the mature LEP protein. We examined the potential off-target sites (OTS) by whole-genome high-throughput sequencing and/or Sanger-sequencing analysis and found no OTS in mutant rats. Mature LEP(∆I14) is incessantly produced and released to blood at a much elevated level due to the feedback loop. Structure modeling of binding conformation between mutant LEP(∆I14) and LEPTIN receptor (LEPR) suggests that the conformation of LEP(∆I14) impairs its binding with LEPR, consistent with its inability to activate STAT3-binding element in the luciferase reporter assay. Phenotypic study demonstrated that Lep(∆I14) rats recapitulate phenotypes of Lep-null mutant rats including obesity, hyperinsulinemia, hepatic steatosis, nephropathy, and infertility. Compared to the existing ob/ob mouse models, this Lep(∆I14/∆I14) rat strain provides a robust tool for further dissecting the roles of LEP in the diabetes related kidney disease and reproduction problem, beyond its well established function in regulating energy homeostasis.

  16. Fabricating of high-performance functional graphene fibers for micro-capacitive energy storage.

    PubMed

    Fan, Tianju; Zhao, Chunyan; Xiao, Zhuangqing; Guo, Fangjun; Cai, Kaiyu; Lin, Hai; Liu, Yidong; Meng, Hong; Min, Yong; Epstein, Arthur J

    2016-01-01

    Although graphene is a typical two dimensional materials, it has converted to multi-dimensional materials with many unique properties. As an example, the one dimensional graphene fiber is fabricated by utilizing ionic liquid as coagulation and functional diamines as cross-linkers to connect graphene oxide layers. The fibers show excellent mechanical properties and superior electrical performance. The tensile strength of the resultant fibers reaches ~729 MPa after a super high temperature thermal annealing treatment at 2800 °C. Additionally, quasi-solid-state flexible micro-capacitors are fabricated with promising result on energy storage. The device show a specific volumetric capacity as high as ~225 F/cm(3) (measured at 103.5 mA cm(-3) in a three-electrode cell), as well as a long cycle life of 2000 times. The initial results indicate that these fibers will be a good candidate to replace energy storage devices for miniaturized portable electronic applications. PMID:27390070

  17. Nonequilibrium self-energy functional approach to the dynamical Mott transition

    NASA Astrophysics Data System (ADS)

    Hofmann, Felix; Eckstein, Martin; Potthoff, Michael

    2016-06-01

    The real-time dynamics of the Fermi-Hubbard model, driven out of equilibrium by quenching or ramping the interaction parameter, is studied within the framework of the nonequilibrium self-energy functional theory. A dynamical impurity approximation with a single auxiliary bath site is considered as a reference system, and the time-dependent hybridization is optimized as prescribed by the variational principle. The dynamical two-site approximation turns out to be useful to study the real-time dynamics on short and intermediate time scales. Depending on the strength of the interaction in the final state, two qualitatively different response regimes are observed. For both weak and strong couplings, qualitative agreement with previous results of nonequilibrium dynamical mean-field theory is found. The two regimes are sharply separated by a critical point at which the low-energy bath degree of freedom decouples in the course of time. We trace the dependence of the critical interaction of the dynamical Mott transition on the duration of the interaction ramp from sudden quenches to adiabatic dynamics and therewith link the dynamical to the equilibrium Mott transition.

  18. Structure and function of occupational health services within selected Department of Energy sites.

    PubMed

    Salazar, M K; Takaro, T K; Ertell, K; Gochfeld, M; O'Neill, S; Connon, C; Barnhart, S

    1999-12-01

    The mission of the United States Department of Energy sites has recently changed from nuclear weapons production to site remediation. Considering the mass of radiological and chemical contaminants at these sites, ensuring the health and safety of workers is a major challenge. This study used the findings from a written survey to describe occupational health services at 10 Department of Energy sites. The study aims were to describe and compare: (1) the primary hazards associated with the site activities; (2) the occupational safety and health structure, including service providers; and (3) the occupational health and safety functions, including surveillance, training, and service provision. Although explosions and radiological agents were identified as the hazards with the greatest associated risks, workers at these sites were most likely to be exposed to physical hazards, ergonomic hazards, and/or chemicals, including asbestos. Physicians accounted for 2.4% of service providers, nurses for 5.5%, industrial hygienists for 12.2%, safety personnel for 11.8%, and health physicists for 64.9%. It was concluded that there is an imbalance between the most important hazards and the types of health and safety personnel at these sites.

  19. Homeostatic functions of the p53 tumor suppressor: regulation of energy metabolism and antioxidant defense

    PubMed Central

    Olovnikov, Ivan A.; Kravchenko, Julia E.; Chumakov, Peter M.

    2008-01-01

    The p53 tumor suppressor plays pivotal role in the organism by supervising strict compliance of individual cells to needs of the whole organisms. It has been widely accepted that p53 acts in response to stresses and abnormalities in cell physiology by mobilizing the repair processes or by removing the diseased cells through initiating the cell death programs. Recent studies, however, indicate that even under normal physiological conditions certain activities of p53 participate in homeostatic regulation of metabolic processes and that these activities are important for prevention of cancer. These novel functions of p53 help to align metabolic processes with the proliferation and energy status, to maintain optimal mode of glucose metabolism and to boost the energy efficient mitochondrial respiration in response to ATP deficiency. Additional activities of p53 in non-stressed cells tune up the antioxidant defense mechanisms reducing the probability of mutations caused by DNA oxidation under conditions of daily stresses. The deficiency in the p53-mediated regulation of glycolysis and mitochondrial respiration greatly accounts for the deficient respiration of the predominance of aerobic glycolysis in cancer cells (the Warburg effect), while the deficiency in the p53-modulated antioxidant defense mechanisms contributes to mutagenesis and additionally boosts the carcinogenesis process. PMID:19101635

  20. Ion energy-angle distribution functions at the plasma-material interface in oblique magnetic fields

    SciTech Connect

    Khaziev, Rinat; Curreli, Davide

    2015-04-15

    The ion energy-angle distribution (IEAD) at the wall of a magnetized plasma is of fundamental importance for the determination of the material processes occurring at the plasma-material interface, comprising secondary emissions and material sputtering. Here, we present a numerical characterization of the IEAD at the wall of a weakly collisional magnetized plasma with the magnetic field inclined at an arbitrary angle with respect to the wall. The analysis has been done using two different techniques: (1) a fluid-Monte Carlo method, and (2) particle-in-cell simulations, the former offering a fast but approximate method for the determination of the IEADs, the latter giving a computationally intensive but self-consistent treatment of the plasma behavior from the quasi-neutral region to the material boundary. The two models predict similar IEADs, whose similarities and differences are discussed. Data are presented for magnetic fields inclined at angles from normal to grazing incidence (0°–85°). We show the scaling factors of the average and peak ion energy and trends of the pitch angle at the wall as a function of the magnetic angle, for use in the correlation of fluid plasma models to material models.