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Sample records for binding energy calculated

  1. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Perturbation method is used to calculate the binding energy within the framework of effective mass approximation and taking into account the effect of dielectric mismatch between the dot and the barrier material. The ground-state binding energy of the donor is computed as a function of dot size for finite confinement.

  2. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Nilanjan Sil

    2017-12-18

    Dec 18, 2017 ... Abstract. In the present paper, we have studied the binding energy of the shallow donor hydrogenic impurity, which is confined in an inhomogeneous cylindrical quantum dot (CQD) of GaAs-AlxGa1−xAs. Perturbation method is used to calculate the binding energy within the framework of effective mass ...

  3. Using the fast fourier transform in binding free energy calculations.

    Science.gov (United States)

    Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L

    2018-04-30

    According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  4. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  5. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  6. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

    Science.gov (United States)

    2016-01-01

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  7. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  8. Perturbation method for calculating impurity binding energy in an ...

    Indian Academy of Sciences (India)

    Nilanjan Sil

    2017-12-18

    Dec 18, 2017 ... the physical properties in them. As a result, the energy of the electrons in the confined directions become quan- tized and forms a discrete energy spectrum. For such size-quantized electrons, the scattering probability is drastically suppressed [15]. The donor impurity in semiconductor nanoheterostru-.

  9. Calculation of the Relative Change in Binding Free Energy of a Protein-Inhibitor Complex

    Science.gov (United States)

    Bash, Paul A.; Singh, U. Chandra; Brown, Frank K.; Langridge, Robert; Kollman, Peter A.

    1987-01-01

    By means of a thermodynamic perturbation method implemented with molecular dynamics, the relative free energy of binding was calculated for the enzyme thermolysin complexed with a pair of phosphonamidate and phosphonate ester inhibitors. The calculated difference in free energy of binding was 4.21 ± 0.54 kilocalories per mole. This compares well with the experimental value of 4.1 kilocalories per mole. The method is general and can be used to determine a change or ``mutation'' in any system that can be suitably represented. It is likely to prove useful for protein and drug design.

  10. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

  11. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A

    Directory of Open Access Journals (Sweden)

    Manuela Maurer

    2016-04-01

    Full Text Available The periplasmic oligopeptide binding protein A (OppA represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK, but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.

  12. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

    2018-03-26

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  13. Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.

    Science.gov (United States)

    Miranda, Williams E; Noskov, Sergei Yu; Valiente, Pedro A

    2015-09-28

    In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The protocol, coined LIE-D, builds on the linear relationship between the empirical coefficient γ in the standard LIE scheme and the D parameter, introduced in our work. The D-parameter encompasses the balance (difference) between electrostatic (polar) and van der Waals (nonpolar) energies in protein–ligand complexes. Leave-one-out cross-validation showed that LIE-D reproduced accurately the absolute binding free energies for our training set of protein–ligand complexes ( = 0.92 kcal/mol, SDerror = 0.66 kcal/mol, R(2) = 0.90, QLOO(2) = 0.89, and sPRESS(LOO) = 1.28 kcal/mol). We also demonstrated LIE-D robustness by predicting accurately the binding free energies for three different protein–ligand systems outside the training data set, where the electrostatic and van der Waals interaction energies were calculated with different force fields.

  14. Binding free-energy calculation is a powerful tool for drug optimization: calculation and measurement of binding free energy for 7-azaindole derivatives to glycogen synthase kinase-3β.

    Science.gov (United States)

    Kitamura, Kunihiro; Tamura, Yunoshin; Ueki, Tomokazu; Ogata, Koji; Noda, Shigeho; Himeno, Ryutaro; Chuman, Hiroshi

    2014-06-23

    Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine whether calculation of binding free-energy change (ΔG) is effective for the lead-optimization process, binding ΔGs of 7-azaindole derivatives to the ATP binding site of glycogen synthase kinase-3β (GSK-3β) were calculated. The result was a significant correlation coefficient of r = 0.895 between calculated and observed ΔGs. This indicates that calculated ΔG reflects the inhibitory activities of 7-azaindole derivatives. In addition to quantitative estimation of activity, ΔG calculation characterizes the thermodynamic behavior of 7-azaindole derivatives, providing also useful information for inhibitor optimization on affinity to water molecules.

  15. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.

    Science.gov (United States)

    Deng, Nanjie; Flynn, William F; Xia, Junchao; Vijayan, R S K; Zhang, Baofeng; He, Peng; Mentes, Ahmet; Gallicchio, Emilio; Levy, Ronald M

    2016-09-01

    We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate

  16. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....

  17. Electron binding energies of organic azides: Green’s function and density functional theory versus Hartree Fock calculations

    Science.gov (United States)

    Mateus, Margarida P. S.; Cabral, Benedito J. C.

    2007-11-01

    Theoretical calculations for the electron binding energies (EBEs) of several organic azides including hydrazoic acid, methyl azide, ethyl azide, 2-chloroethyl azide, 2-azidoethanol, azidoacetone, 2-azidoacetic acid, 3-azido-2-butanone, and 2-azidoethyl acetate are reported. EBEs were calculated with ab initio Green's function (GF) and density functional theory (DFT). Complete basis-set extrapolated coupled cluster calculations with single, double, and perturbative triple excitations [CCSD(T)] for the first ionization energy of azides are also reported. It is shown that EBEs from GF and DFT calculations are in better agreement with experiment than Hartree-Fock predictions.

  18. Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.

    Science.gov (United States)

    Palma, P Nuno; Bonifácio, Maria João; Loureiro, Ana Isabel; Soares-da-Silva, Patrício

    2012-04-05

    Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein-ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low-energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol-O-methyltransferase and BIA 9-1067, a newly developed tight-binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high-binding affinity (K(d) in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O-methylated product. By comparing the experimental catalytic rate (k(cat)) and the estimated dissociation rate (k(off)) constants of the enzyme-inhibitor complex, one can conclude that the observed inhibition potency (K(i)) is primarily dependent on the catalytic rate constant of the inhibitor's O-methylation, rather than the rate constant of dissociation of the complex. Copyright © 2012 Wiley Periodicals, Inc.

  19. A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Abel, Robert; Wang, Lingle; Mobley, David L; Friesner, Richard A

    2017-01-01

    Protein-ligand binding is among the most fundamental phenomena underlying all molecular biology, and a greater ability to more accurately and robustly predict the binding free energy of a small molecule ligand for its cognate protein is expected to have vast consequences for improving the efficiency of pharmaceutical drug discovery. We briefly reviewed a number of scientific and technical advances that have enabled alchemical free energy calculations to recently emerge as a preferred approach, and critically considered proper validation and effective use of these techniques. In particular, we characterized a selection bias effect which may be important in prospective free energy calculations, and introduced a strategy to improve the accuracy of the free energy predictions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  20. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.

    Science.gov (United States)

    Mermelstein, Daniel J; Lin, Charles; Nelson, Gard; Kretsch, Rachael; McCammon, J Andrew; Walker, Ross C

    2018-03-12

    Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  1. Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

    Science.gov (United States)

    Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

    2016-01-01

    Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

  2. Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies.

    Science.gov (United States)

    Genheden, Samuel; Ryde, Ulf

    2011-11-08

    We have evaluated the efficiency of two popular end-point methods to calculate ligand-binding free energies, LIE (linear interaction energy) and MM/GBSA (molecular mechanics with generalized Born surface-area solvation), i.e. the computational effort needed to obtain estimates of a similar precision. As a test case, we use the binding of seven biotin analogues to avidin. The energy terms used by MM/GBSA and LIE exhibit a similar correlation time (∼5 ps), and the equilibration time seems also to be similar, although it varies much between the various ligands. The results show that the LIE method is more effective than MM/GBSA, by a factor of 2-7 for a truncated spherical system with a radius of 26 Å and by a factor of 1.0-2.4 for the full avidin tetramer (radius 47 Å). The reason for this is the cost for the MM/GBSA entropy calculations, which more than compensates for the extra simulation of the free ligand in LIE. On the other hand, LIE requires that the protein is neutralized, whereas MM/GBSA has no such requirements. Our results indicate that both the truncation and neutralization of the proteins may slow the convergence and emphasize small differences in the calculations, e.g., differences between the four subunits in avidin. Moreover, LIE cannot take advantage of the fact that avidin is a tetramer. For this test case, LIE gives poor results with the standard parametrization, but after optimizing the scaling factor of the van der Waals terms, reasonable binding affinities can be obtained, although MM/GBSA still gives a significantly better predictive index and correlation to the experimental affinities.

  3. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

  4. RECOGNITION DYNAMICS OF ESCHERICHIA COLI THIOREDOXIN PROBED USING MOLECULAR DYNAMICS AND BINDING FREE ENERGY CALCULATIONS

    Directory of Open Access Journals (Sweden)

    M. S. Shahul Hameed

    2016-03-01

    Full Text Available E. coli thioredoxin has been regarded as a hub protein as it interacts with, and regulates, numerous target proteins involved in a wide variety of cellular processes. Thioredoxin can form complexes with a variety of target proteins with a wide range of affinity, using a consensus binding surface. In this study an attempt to deduce the molecular basis for the observed multispecificity of E. coli thioredoxin has been made. In this manuscript it has been shown that structural plasticity, adaptable and exposed hydrophobic binding surface, surface electrostatics, closely clustered multiple hot spot residues and conformational changes brought about by the redox status of the protein have been shown to account for the observed multispecificity and molecular recognition of thioredoxin. Dynamical differences between the two redox forms of the enzyme have also been studied to account for their differing interactions with some target proteins.

  5. Ligand-induced structural changes in TEM-1 probed by molecular dynamics and relative binding free energy calculations.

    Science.gov (United States)

    Pimenta, A C; Martins, J M; Fernandes, R; Moreira, I S

    2013-10-28

    The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM-1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70-Oγ and Lys73-Nζ, Lys73-Nζ and Ser130-Oγ, and Ser70-Oγ-Ser130-Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

  6. Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution.

    Science.gov (United States)

    Niskanen, Johannes; Arul Murugan, N; Rinkevicius, Zilvinas; Vahtras, Olav; Li, Cui; Monti, Susanna; Carravetta, Vincenzo; Agren, Hans

    2013-01-07

    We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

  7. Binding energies and energy differences for p-shell nuclei from ab initio calculations with natural orbitals

    Science.gov (United States)

    Fasano, Patrick J.; Caprio, Mark A.; Constantinou, Chrysovalantis; Maris, Pieter; Vary, James P.

    2017-09-01

    Ab initio methods in nuclear theory strive to make quantitative predictions of nuclear observables, starting with the internucleon interaction. In the no-core configuration interaction (NCCI) approach, the nuclear many-body problem is solved in a basis of Slater determinants constructed from single-particle states. NCCI calculations are computationally limited by combinatorial explosion of the many-body basis size; as such, choice of basis greatly influences convergence. Natural orbitals, constructed by diagonalizing the one-body density matrix from an initial many-body calculation, maximize occupation of the lowest single-particle states and thereby reduce the importance of higher-lying many-body basis states. We use natural orbitals to explore energies and energy differences in p-shell nuclei. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DE-FG02-91ER-40608, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. NSF-PHY05-52843. Computational resources provided by NERSC (DOE Contract DE-AC02-05CH11231).

  8. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen

    2010-01-01

    , and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set includes both...... substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 kJ/mol. Subsequent......Predicting binding affinities for receptor-ligand complexes is still one of the challenging processes in computational structure-based ligand design. Many computational methods have been developed to achieve this goal, such as docking and scoring methods, the linear interaction energy (LIE) method...

  9. Electron binding energies of aqueous alkali and halide ions: EUV photoelectron spectroscopy of liquid solutions and combined ab initio and molecular dynamics calculations.

    Science.gov (United States)

    Winter, Bernd; Weber, Ramona; Hertel, Ingolf V; Faubel, Manfred; Jungwirth, Pavel; Brown, Eric C; Bradforth, Stephen E

    2005-05-18

    Photoelectron spectroscopy combined with the liquid microjet technique enables the direct probing of the electronic structure of aqueous solutions. We report measured and calculated lowest vertical electron binding energies of aqueous alkali cations and halide anions. In some cases, ejection from deeper electronic levels of the solute could be observed. Electron binding energies of a given aqueous ion are found to be independent of the counterion and the salt concentration. The experimental results are complemented by ab initio calculations, at the MP2 and CCSD(T) level, of the ionization energies of these prototype ions in the aqueous phase. The solvent effect was accounted for in the electronic structure calculations in two ways. An explicit inclusion of discrete water molecules using a set of snapshots from an equilibrium classical molecular dynamics simulations and a fractional charge representation of solvent molecules give good results for halide ions. The electron binding energies of alkali cations computed with this approach tend to be overestimated. On the other hand, the polarizable continuum model, which strictly provides adiabatic binding energies, performs well for the alkali cations but fails for the halides. Photon energies in the experiment were in the EUV region (typically 100 eV) for which the technique is probing the top layers of the liquid sample. Hence, the reported energies of aqueous ions are closely connected with both structures and chemical reactivity at the liquid interface, for example, in atmospheric aerosol particles, as well as fundamental bulk solvation properties.

  10. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors

    Science.gov (United States)

    Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

    2018-02-01

    Optimization of fragment size d-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

  11. Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.

    Science.gov (United States)

    Shi, Danfeng; Bai, Qifeng; Zhou, Shuangyan; Liu, Xuewei; Liu, Huanxiang; Yao, Xiaojun

    2018-01-01

    As co-chaperones of the 90-kDa heat shock protein(HSP90), FK506 binding protein 51 (FKBP51) and FK506 binding protein 52 (FKBP52) modulate the maturation of steroid hormone receptor through their specific FK1 domains (FKBP12-like domain 1). The inhibitors targeting FK1 domains are potential therapies for endocrine-related physiological disorders. However, the structural conservation of the FK1 domains between FKBP51 and FKBP52 make it difficult to obtain satisfactory selectivity in FK506-based drug design. Fortunately, a series of iFit ligands synthesized by Hausch et al exhibited excellent selectivity for FKBP51, providing new opportunity for design selective inhibitors. We performed molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis to reveal selective mechanism for the inhibitor iFit4 binding with FKBP51 and FKBP52. The conformational stability evaluation of the "Phe67-in" and "Phe67-out" states implies that FKBP51 and FKBP52 have different preferences for "Phe67-in" and "Phe67-out" states, which we suggest as the determinant factor for the selectivity for FKBP51. The binding free energy calculations demonstrate that nonpolar interaction is favorable for the inhibitors binding, while the polar interaction and entropy contribution are adverse for the inhibitors binding. According to the results from binding free energy decomposition, the electrostatic difference of residue 85 causes the most significant thermodynamics effects on the binding of iFit4 to FKBP51 and FKBP52. Furthermore, the importance of substructure units on iFit4 were further evaluated by unbinding pathway analysis and residue-residue contact analysis between iFit4 and the proteins. The results will provide new clues for the design of selective inhibitors for FKBP51. © 2017 Wiley Periodicals, Inc.

  12. Binding Energy calculation of GSK-3 protein of Human against some anti-diabetic compounds of Momordica charantia linn (Bitter melon).

    Science.gov (United States)

    Hazarika, Ridip; Parida, Pratap; Neog, Bijoy; Yadav, Raj Narain Singh

    2012-01-01

    Diabetes is one of the major life threatening diseases worldwide. It creates major health problems in urban India. Glycogen Synthase Kinase-3 (GSK-3) protein of human is known for phosphorylating and inactivating glycogen synthase which also acts as a negative regulator in the hormonal control of glucose homeostasis. In traditional medicine, Momordica charantia is used as antidiabetic plant because of its hypoglycemic effect. Hence to block the active site of the GSK-3 protein three anti-diabetic compounds namely, charantin, momordenol & momordicilin were taken from Momordica charantia for docking study and calculation of binding energy. The aim of present investigation is to find the binding energy of three major insulin-like active compounds against glycogen synthase kinase-3 (GSK-3), one of the key proteins involved in carbohydrate metabolism, with the help of molecular docking using ExomeTM Horizon suite. The study recorded minimum binding energy by momordicilin in comparison to the others.

  13. Binding Energies of the pi-Stacked Anisole Dimer: New Molecular Beam-Laser Spectroscopy Experiments and CCSD(T) Calculations

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Nachtigallová, Dana; Mazzoni, F.; Pasquini, M.; Pietraperzia, G.; Becucci, M.; Müller-Dethlefs, K.; Hobza, Pavel

    2015-01-01

    Roč. 21, č. 18 (2015), s. 6740-6746 ISSN 0947-6539 R&D Projects: GA ČR GBP208/12/G016 Grant - others:GA MŠk(CZ) ED2.1.00/03.0058 Program:ED Institutional support: RVO:61388963 Keywords : binding energy * noncovalent interactions * pi stacking * laser spectroscopy * CCSD(T) calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.771, year: 2015

  14. Calculating the Na⁺ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation.

    Science.gov (United States)

    Muhammed, Zahed; Arai, Satoshi; Saijo, Shinya; Yamato, Ichiro; Murata, Takeshi; Suenaga, Atsushi

    2012-07-01

    Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble catalytic domain (V₁; NtpA₃-B₃-D-G) and an integral membrane domain (V₀; NtpI-K₁₀) connected by a central and two peripheral stalks (NtpC, NtpD-G and NtpE-F). Recently nucleotide binding of catalytic NtpA monomer has been reported (Arai et al.). In the present study, we calculated the nucleotide binding affinity of NtpA by molecular dynamics (MD) simulation/free energy calculation using MM-GBSA approach based on homology modeled structure of NtpA monomer docked with ATP analogue, adenosine 5'-[β, γ-imido] triphosphate (AMP-PNP). The calculated binding free energies showed qualitatively good agreement with experimental data. The calculation was cross-validated further by the rigorous method, thermodynamic integration (TI) simulation. Finally, the interaction between NtpA and nucleotides at the atomic level was investigated by the analyses of components of free energy and the optimized model structures obtained from MD simulations, suggesting that electrostatic contribution is responsible for the difference in nucleotide binding to NtpA monomer. This is the first observation and suggestion to explain the difference of nucleotide binding properties in V-ATPase NtpA subunit, and our method can be a valuable primary step to predict nucleotide binding affinity to other subunits (NtpAB, NtpA₃B₃) and to explore subunit interactions and eventually may help to understand energy transduction mechanism of E. hirae V-ATPase. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations.

    Science.gov (United States)

    Řezáč, Jan; Nachtigallová, Dana; Mazzoni, Federico; Pasquini, Massimiliano; Pietraperzia, Giangaetano; Becucci, Maurizio; Müller-Dethlefs, Klaus; Hobza, Pavel

    2015-04-27

    Among noncovalent interactions, π-π stacking is a very important binding motif governed mainly by London dispersion. Despite its importance, for instance, for the structure of bio-macromolecules, the direct experimental measurement of binding energies in π-π stacked complexes has been elusive for a long time. Only recently, an experimental value for the binding energy of the anisole dimer was presented, determined by velocity mapping ion imaging in a two-photon resonant ionisation molecular beam experiment. However, in that paper, a discrepancy was already noted between the obtained experimental value and a theoretical estimate. Here, we present an accurate recalculation of the binding energy based on the combination of the CCSD(T)/CBS interaction energy and a DFT-D3 vibrational analysis. This proves unambiguously that the previously reported experimental value is too high and a new series of measurements with a different, more sensitive apparatus was performed. The new experimental value of 1800±100 cm(-1) (5.15±0.29 kcal mol(-1)) is close to the present theoretical prediction of 5.04±0.40 kcal mol(-1). Additional calculations of the properties of the cationic and excited states involved in the photodissociation of the dimer were used to identify and rationalise the difficulties encountered in the experimental work. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.

    Directory of Open Access Journals (Sweden)

    Yuzhen Niu

    Full Text Available As a promising target for the treatment of lung cancer, the MutT Homolog 1 (MTH1 protein can be inhibited by crizotinib. A recent work shows that the inhibitory potency of (S-crizotinib against MTH1 is about 20 times over that of (R-crizotinib. But the detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD simulations and free energy calculations were used to elucidate the mechanism about the effect of chirality of crizotinib on the inhibitory activity against MTH1. The binding free energy of (S-crizotinib predicted by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA and Adaptive biasing force (ABF methodologies is much lower than that of (R-crizotinib, which is consistent with the experimental data. The analysis of the individual energy terms suggests that the van der Waals interactions are important for distinguishing the binding of (S-crizotinib and (R-crizotinib. The binding free energy decomposition analysis illustrated that residues Tyr7, Phe27, Phe72 and Trp117 were important for the selective binding of (S-crizotinib to MTH1. The adaptive biasing force (ABF method was further employed to elucidate the unbinding process of (S-crizotinib and (R-crizotinib from the binding pocket of MTH1. ABF simulation results suggest that the reaction coordinates of the (S-crizotinib from the binding pocket is different from (R-crizotinib. The results from our study can reveal the details about the effect of chirality on the inhibition activity of crizotinib to MTH1 and provide valuable information for the design of more potent inhibitors.

  17. Quarkeosynthesis Binding Energy

    Science.gov (United States)

    Webb, Bill

    2009-05-01

    Quarkeosynthesis shows that the binding energy of a nucleus is the difference between the relativistic kinetic energies of its threesome of Jumbo Quarks and that of its building block quarks from neutrons and protons. There is no involvement of a nuclear strong force or gluon material.

  18. Binding energy of protonium ions

    Science.gov (United States)

    Assad Abdel-Raouf, Mohamed

    2009-11-01

    The goal of the present work is to calculate the binding energy of the protonium ions bar PPe+ and bar PPe- using Rayleigh- Ritz variational method. It is indicated that an employment of 21 components of the trial wavefunction yields -0.08793 eV as the ground state energy of these ions. Our result agrees quite well with recently obtained results based on elaborate Monte Carlo approximations. It confirms the possible formation of these ions in laboratory.

  19. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method

    NARCIS (Netherlands)

    Stjernschantz, E.M.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N.P.E.; Oostenbrink, C.

    2006-01-01

    An extensive evaluation of the linear interaction energy (LIE) method for the prediction of binding affinity of docked compounds has been performed, with an emphasis on its applicability in lead optimization. An automated setup is presented, which allows for the use of the method in an industrial

  20. Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study.

    Directory of Open Access Journals (Sweden)

    Dimitrios Spiliotopoulos

    Full Text Available PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0. As a case study we focused on the first PHD finger of autoimmune regulator protein (AIRE-PHD1 in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a "flapping" movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.

  1. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

    Science.gov (United States)

    Athanasiou, Christina; Vasilakaki, Sofia; Dellis, Dimitris; Cournia, Zoe

    2018-01-01

    Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of

  2. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.

    Science.gov (United States)

    Athanasiou, Christina; Vasilakaki, Sofia; Dellis, Dimitris; Cournia, Zoe

    2018-01-01

    Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of

  3. Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Świderek, Katarzyna; Martins, João B L; Andrés, Juan

    2017-04-24

    In the present study, the binding free energy of some classical inhibitors (DMT, DNP, GNT, HUP, THA) with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation (FEP) method based on hybrid quantum mechanics and molecular mechanics (QM/MM) potentials. The results highlight the key role of the van der Waals interaction for the inhibition process, since the contribution of this term to the binding free energy is almost as decisive as the electrostatic one. The analysis of the geometrical parameters and the interaction energy per residue along the QM/MM molecular dynamics (MD) simulations highlights the most relevant interactions in the different AChE-ligand systems, showing that the charged residues with a more prominent contribution to the interaction energy are Asp72 and Glu199, although the relative importance depends on the molecular size of the ligand. A correlation between the binding free energy and the number of cation-π interactions present in the systems has been established, DMT being the most potent inhibitor, capable of forming four cation-π interactions. A layer of water molecules surrounding the inhibitors has been observed, which act as bridges along a network formed by the ligands and the residues of the gorge and also between different residues. Although several hydrogen bonds between ligands and AChE do appear, no significant values of BIEs have been recorded. This behavior can be accounted for by the special features of AChE, such as the presence of several subsites of different natures in the gorge or the existence of several water molecules that act as bridges in the electrostatic interactions.

  4. Binding energy of the barbell exciton

    Science.gov (United States)

    Peeters, F. M.; Golub, J. E.

    1991-02-01

    The exciton binding energy in asymmetric coupled double quantum wells is calculated. As the system is electrically tuned from type I to type II, the exciton binding energy decreases from that of a two-dimensional exciton to the binding energy of a spatially separated electron-hole pair, i.e., the barbell exciton.$-- We compare our theoretical results with a recent experiment and find good agreement.

  5. Calculation of Positron Binding Energies and Electron-Positron Annihilation Rates for Atomic Systems with the Reduced Explicitly Correlated Hartree-Fock Method in the Nuclear-Electronic Orbital Framework.

    Science.gov (United States)

    Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

    2017-01-19

    Although the binding of a positron to a neutral atom has not been directly observed experimentally, high-level theoretical methods have predicted that a positron will bind to a neutral atom. In the present study, the binding energies of a positron to lithium, sodium, beryllium, and magnesium, as well as the electron-positron annihilation rates for these systems, are calculated using the reduced explicitly correlated Hartree-Fock (RXCHF) method within the nuclear-electronic orbital (NEO) framework. Due to the lack of explicit electron-positron correlation, NEO Hartree-Fock and full configuration interaction calculations with reasonable electronic and positronic basis sets do not predict positron binding to any of these atoms. In contrast, the RXCHF calculations predict positron binding energies and electron-positron annihilation rates in qualitative agreement with previous highly accurate but computationally expensive stochastic variational method calculations. These results illustrate that the RXCHF method can successfully describe the binding of a positron to a neutral species with no dipole moment. Moreover, the RXCHF method will be computationally tractable for calculating positron binding to molecular systems. The RXCHF approach offers a balance of accuracy and computational tractability for studying these types of positronic systems.

  6. Landfill Gas Energy Benefits Calculator

    Science.gov (United States)

    This page contains the LFG Energy Benefits Calculator to estimate direct, avoided, and total greenhouse gas reductions, as well as environmental and energy benefits, for a landfill gas energy project.

  7. Biogas - the calculable energy

    Science.gov (United States)

    Kith, Károly; Nagy, Orsolya; Balla, Zoltán; Tamás, András

    2015-04-01

    EU actions against climate change are rising energy prices, both have emphasized the use of renewable energy,increase investments and energy efficiency. A number of objectives formulated in the EC decree no. 29/2009 by 2020. This document is based on the share of renewable energies in energy consumption should be increased to 20% (EC, 2009). The EU average is 20% but the share of renewables vary from one member state to another. In Hungary in 2020, 14.65% renewable energy share is planned to be achieved. According to the latest Eurostat data, the share of renewable energy in energy consumption of the EU average was 14.1%, while in Hungary, this share was 9.6% in 2012. (EUROSTAT, 2014). The use of renewable energy plant level is influenced by several factors. The most important of these is the cost savings and efficiency gains. Hungarian investments in renewable energy production usually have high associated costs and the payback period is substantially more than five years, depending on the support rate. For example, the payback period is also influenced by the green electricity generated feed prices, which is one of the lowest in Hungary compared the Member States of the European Union. Consequently, it is important to increase the production of green energy. Nowadays, predictable biogas energy is an outstanding type of decentralized energy production. It follows directly that agricultural by-products can be used to produce energy and they also create jobs by the construction of a biogas plant. It is important to dispose of and destroy hazardous and noxious substances in energy production. It follows from this that the construction of biogas plants have a positive impact, in addition to green energy which is prepared to reduce the load on the environment. The production of biogas and green electricity is one of the most environment friendly forms of energy production. Biogas production also has other important ecological effects, such as the substitution of

  8. Binding energies of hypernuclei and hypernuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1996-05-01

    In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

  9. Binding energies of hypernuclei and hypernuclear interactions

    International Nuclear Information System (INIS)

    Bodmer, A.R.; Univ. of Illinois, Chicago, IL; Murali, S.; Usmani, Q.N.

    1996-01-01

    In part 1 the effect of nuclear core dynamics on the binding energies of Λ hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the Λ single-particle energy in terms of basic Λ-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body ΛNN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei

  10. Binding energy and preferred adsorption sites of CO on gold and silver-gold cluster cations: adsorption kinetics and quantum chemical calculations.

    Science.gov (United States)

    Neumaier, Marco; Weigend, Florian; Hampe, Oliver; Kappes, Manfred M

    2008-01-01

    We revisit the reactivity of trapped pure gold (Au(n)+, n cluster cations (Ag(m)Au(n)+, m + n adsorption sites, associated vibrational frequencies) of CO to the noble metal as a function of cluster size and composition. Starting from results for pure gold cluster cations for which an overall decrease of CO binding energy with increasing cluster size was experimentally observed--from about 1.09 +/- 0.1 eV (for n = 6) to below 0.65 +/- 0.1 eV (for n > 26) we demonstrate that metal--CO bond energies correlate with the total electron density and with the energy of the lowest unoccupied molecular orbital (LUMO) on the bare metal cluster cation as obtained by density functional theory (DFT) computations. This is a consequence of the predominantly sigma-donating character of the CO-M bond. Further support for this concept is found by contrasting the predictions of binding energies to the experimental results for small alloy cluster cations (Ag(m)Au(n)+, 4 adsorption sites and pre-screen favorable isomers.

  11. Characterization of the ligand binding of PGRP-L in half-smooth tongue sole (Cynoglossus semilaevis by molecular dynamics and free energy calculation

    Directory of Open Access Journals (Sweden)

    Zisheng Wang

    2018-01-01

    Conclusions: The 3-D structure of csPGRP-L possessed typical PGRP structure and might selectively bind both types of MTP- and MPP-PGNs, which provided useful insights to understanding the functions of fish PGRPs.

  12. Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

    Science.gov (United States)

    2015-01-01

    We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van’t Hoff equation. Excellent agreement between the direct and van’t Hoff methods is demonstrated for both host–guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design. PMID:26523125

  13. Binding energy and formation heat of UO2

    International Nuclear Information System (INIS)

    Almeida, M.R. de; Veado, J.T.; Siqueira, M.L. de

    The Born-Haber cycle is utilized for the calculation of the heat of formation of UO 2 , on the assumption that the binding energy is predominantly ionic in character. The ionization potentials of U and the repulsion energy are two critical values that influence calculations. Calculations of the ionization potentials with non-relativistic Hartree-Fock-Gaspar-Kohn-Sham approximation are presented [pt

  14. CALCULATION OF PHYSISORPTION ENERGIES OF

    African Journals Online (AJOL)

    definition of physisorption energy, a quantity of interest to us here. It seems to us more reasonable, in the case of the transition metal oxides, to define the physisorption energy in terms of the effects of the adsorbates in the crystal field of a surface cluster. This takes full account of the local symmetry at the adsorption site.

  15. Large-dimension configuration-interaction calculations of positron binding to the group-II atoms

    International Nuclear Information System (INIS)

    Bromley, M. W. J.; Mitroy, J.

    2006-01-01

    The configuration-interaction (CI) method is applied to the calculation of the structures of a number of positron binding systems, including e + Be, e + Mg, e + Ca, and e + Sr. These calculations were carried out in orbital spaces containing about 200 electron and 200 positron orbitals up to l=12. Despite the very large dimensions, the binding energy and annihilation rate converge slowly with l, and the final values do contain an appreciable correction obtained by extrapolating the calculation to the l→∞ limit. The binding energies were 0.00317 hartree for e + Be, 0.0170 hartree for e + Mg, 0.0189 hartree for e + Ca, and 0.0131 hartree for e + Sr

  16. eqpair: Electron energy distribution calculator

    Science.gov (United States)

    Coppi, Paolo S.

    2018-02-01

    eqpair computes the electron energy distribution resulting from a balance between heating and direct acceleration of particles, and cooling processes. Electron-positron pair balance, bremstrahlung, and Compton cooling, including external soft photon input, are among the processes considered, and the final electron distribution can be hybrid, thermal, or non-thermal.

  17. Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Zhu, Bairen; Chen, Xi; Cui, Xiaodong

    2015-03-01

    The optical properties of monolayer transition metal dichalcogenides (TMDC) feature prominent excitonic natures. Here we report an experimental approach to measuring the exciton binding energy of monolayer WS2 with linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE). TP-PLE measurements show the exciton binding energy of 0.71 +/- 0.01 eV around K valley in the Brillouin zone.

  18. Considerations for dosimetry calculations with neuroreceptor binding radioligands

    International Nuclear Information System (INIS)

    Wong, D.F.; Bice, A.N.; Beck, T.; Dannals, R.F.; Links, J.M.; Wagner, H.N. Jr.

    1986-01-01

    Neuroreceptor binding radiotracers have unique characteristics which must be considered in absorbed dose calculations. In this article the authors outline some of the important issues to be considered such as the high specific binding to various receptor bearing tissue regions, the receptor kinetics, the specific activity of the injected ligand and the presence of competing unlabeled substances. As an example of these considerations they have shown the outline of the measurements for animal and human biodistribution data of the D2 dopamine receptor binding ligand 11 C-3N-methylspiperone (NMSP) and they calculated the absorbed doses for the important body organs. This includes dose estimates using various species including mice, followed by primate and human data. Because of the selective uptake of NMSP to brain regions such as the basal ganglia they calculated values specifically for these areas in the cerebellum. Since kinetic modeling and therapeutic drug monitoring employ competing unlabeled ligands such as haloperidol which alter the NMSP distribution they estimated the dose in both unblocked and cases blocked with haloperidol. In such cases the doses were about 50% lower in the blocked cases for the basal ganglia. Target organs such as the bladder using external probes and a model based upon changing urine volumes suggests a 30% decrease from mouse estimates. 13 references, 4 figures, 7 tables

  19. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  20. Calculating zeros: Non-equilibrium free energy calculations

    International Nuclear Information System (INIS)

    Oostenbrink, Chris; Gunsteren, Wilfred F. van

    2006-01-01

    Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations

  1. Funnel metadynamics as accurate binding free-energy method

    Science.gov (United States)

    Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele

    2013-01-01

    A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficient characterization of the binding free-energy surface and an accurate calculation of the absolute protein–ligand binding free energy. We illustrate our protocol in two systems, benzamidine/trypsin and SC-558/cyclooxygenase 2. In both cases, the X-ray conformation has been found as the lowest free-energy pose, and the computed protein–ligand binding free energy in good agreement with experiments. Furthermore, funnel metadynamics unveils important information about the binding process, such as the presence of alternative binding modes and the role of waters. The results achieved at an affordable computational cost make funnel metadynamics a valuable method for drug discovery and for dealing with a variety of problems in chemistry, physics, and material science. PMID:23553839

  2. Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

    Science.gov (United States)

    Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

    2018-03-01

    The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

  3. Good Practices in Free-energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher

    2013-01-01

    As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

  4. The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

    Science.gov (United States)

    2011-01-01

    The adsorption of Ag, Au, and Pd atoms on benzene, coronene, and graphene has been studied using post Hartree–Fock wave function theory (CCSD(T), MP2) and density functional theory (M06-2X, DFT-D3, PBE, vdW-DF) methods. The CCSD(T) benchmark binding energies for benzene–M (M = Pd, Au, Ag) complexes are 19.7, 4.2, and 2.3 kcal/mol, respectively. We found that the nature of binding of the three metals is different: While silver binds predominantly through dispersion interactions, the binding of palladium has a covalent character, and the binding of gold involves a subtle combination of charge transfer and dispersion interactions as well as relativistic effects. We demonstrate that the CCSD(T) benchmark binding energies for benzene–M complexes can be reproduced in plane-wave density functional theory calculations by including a fraction of the exact exchange and a nonempirical van der Waals correction (EE+vdW). Applying the EE+vdW method, we obtained binding energies for the graphene–M (M = Pd, Au, Ag) complexes of 17.4, 5.6, and 4.3 kcal/mol, respectively. The trends in binding energies found for the benzene–M complexes correspond to those in coronene and graphene complexes. DFT methods that use empirical corrections to account for the effects of vdW interactions significantly overestimate binding energies in some of the studied systems. PMID:22076121

  5. Li+-ligand binding energies and the effect of ligand fluorination on the binding energies

    Science.gov (United States)

    Bauschlicher, Charles W.

    2018-02-01

    The Li+-ligand binding energies are computed for seven ligands and their perfluoro analogs using Density Functional Theory. The bonding is mostly electrostatic in origin. Thus the size of the binding energy tends to correlate with the ligand dipole moment, however, the charge-induced dipole contribution can be sufficiently large to affect the dipole-binding energy correlation. The perfluoro species are significantly less strongly bound than their parents, because the electron withdrawing power of the fluorine reduces the ligand dipole moment.

  6. Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases.

    Science.gov (United States)

    Sadiq, S Kashif; Wright, David; Watson, Simon J; Zasada, Stefan J; Stoica, Ileana; Coveney, Peter V

    2008-09-01

    The successful application of high throughput molecular simulations to determine biochemical properties would be of great importance to the biomedical community if such simulations could be turned around in a clinically relevant timescale. An important example is the determination of antiretroviral inhibitor efficacy against varying strains of HIV through calculation of drug-protein binding affinities. We describe the Binding Affinity Calculator (BAC), a tool for the automated calculation of HIV-1 protease-ligand binding affinities. The tool employs fully atomistic molecular simulations alongside the well established molecular mechanics Poisson-Boltzmann solvent accessible surface area (MMPBSA) free energy methodology to enable the calculation of the binding free energy of several ligand-protease complexes, including all nine FDA approved inhibitors of HIV-1 protease and seven of the natural substrates cleaved by the protease. This enables the efficacy of these inhibitors to be ranked across several mutant strains of the protease relative to the wildtype. BAC is a tool that utilizes the power provided by a computational grid to automate all of the stages required to compute free energies of binding: model preparation, equilibration, simulation, postprocessing, and data-marshaling around the generally widely distributed compute resources utilized. Such automation enables the molecular dynamics methodology to be used in a high throughput manner not achievable by manual methods. This paper describes the architecture and workflow management of BAC and the function of each of its components. Given adequate compute resources, BAC can yield quantitative information regarding drug resistance at the molecular level within 96 h. Such a timescale is of direct clinical relevance and can assist in decision support for the assessment of patient-specific optimal drug treatment and the subsequent response to therapy for any given genotype.

  7. Tseng's calculations of low energy pair production

    International Nuclear Information System (INIS)

    Pratt, R.H.

    2006-01-01

    We review the theoretical work 1971-1997 of H.K. Tseng on low energy pair production. In this work numerical calculations were performed in independent particle approximation in a screened self-consistent central potential, expanding the S-matrix element in partial waves and multipoles. Sampling techniques in partial waves and multipoles were used to extend the calculations to higher energies (up to 10 Mev). Total cross sections, the positron energy spectrum, the positron angular distributions, and the positron-photon polarization correlations were studied. Agreement was obtained with most experiments, although some anomalies remained at the lowest energies (particularly at 1082 keV). Atomic screening of the nuclear charge decreases cross sections at higher energies, as described by a form factor in the momentum transfer to the nucleus. In an intermediate energy regime point Coulomb results in a shifted energy spectrum may be used. At low energies screening increases cross sections, and this is characterized in terms of a normalization screening factor which describes the change in magnitude of electron and positron wave functions at small distances. In this low energy regime angular distribution shapes and polarization correlations are independent of screening

  8. Binding Energy and Equilibrium of Compact Objects

    Directory of Open Access Journals (Sweden)

    Germano M.

    2014-04-01

    Full Text Available The theoretical analysis of the existence of a limit mass for compact astronomic ob- jects requires the solution of the Einstein’s equations of g eneral relativity together with an appropriate equation of state. Analytical solutions exi st in some special cases like the spherically symmetric static object without energy sou rces that is here considered. Solutions, i.e. the spacetime metrics, can have a singular m athematical form (the so called Schwarzschild metric due to Hilbert or a nonsingula r form (original work of Schwarzschild. The former predicts a limit mass and, conse quently, the existence of black holes above this limit. Here it is shown that, the origi nal Schwarzschild met- ric permits compact objects, without mass limit, having rea sonable values for central density and pressure. The lack of a limit mass is also demonst rated analytically just imposing reasonable conditions on the energy-matter densi ty, of positivity and decreas- ing with radius. Finally the ratio between proper mass and to tal mass tends to 2 for high values of mass so that the binding energy reaches the lim it m (total mass seen by a distant observer. As it is known the negative binding energ y reduces the gravitational mass of the object; the limit of m for the binding energy provides a mechanism for stable equilibrium of any amount of mass to contrast the gravitatio nal collapse.

  9. Impurity binding energy for δ-doped quantum well structures

    Indian Academy of Sciences (India)

    Administrator

    Abstract. The binding energy of an impurity delta layer situated either in the centre or at the edge of a quantum well (QW) is theoretically considered for the example of n-type Si0∙8Ge0∙2/Si/Si0∙8Ge0∙2 QW doped with phosphorus. Calculations are made for the case of not so big impurity concentrations, when impurity.

  10. Binding of hydrogen on benzene, coronene, and graphene from quantum Monte Carlo calculations

    Science.gov (United States)

    Ma, Jie; Michaelides, Angelos; Alfè, Dario

    2011-04-01

    Quantum Monte Carlo calculations with the diffusion Monte Carlo (DMC) method have been used to compute the binding energy curves of hydrogen on benzene, coronene, and graphene. The DMC results on benzene agree with both Møller-Plessett second order perturbation theory (MP2) and coupled cluster with singles, doubles, and perturbative triples [CCSD(T)] calculations, giving an adsorption energy of ˜25 meV. For coronene, DMC agrees well with MP2, giving an adsorption energy of ˜40 meV. For physisorbed hydrogen on graphene, DMC predicts a very small adsorption energy of only 5 ± 5 meV. Density functional theory (DFT) calculations with various exchange-correlation functionals, including van der Waals corrected functionals, predict a wide range of binding energies on all three systems. The present DMC results are a step toward filling the gap in accurate benchmark data on weakly bound systems. These results can help us to understand the performance of current DFT based methods, and may aid in the development of improved approaches.

  11. Calculating Free Energies Using Average Force

    Science.gov (United States)

    Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.

  12. Total energy calculations and bonding at interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Louie, S.G.

    1984-08-01

    Some of the concepts and theoretical techniques employed in recent ab initio studies of the electronic and structural properties of surfaces and interfaces are discussed. Results of total energy calculations for the 2 x 1 reconstructed diamond (111) surface and for stacking faults in Si are reviewed. 30 refs., 8 figs.

  13. On energy calculation for Coulomb systems

    International Nuclear Information System (INIS)

    Rebane, T.K.

    1993-01-01

    The problem of energy calculation for a Coulomb atomic-molecular system with arbitrary number N of particles is studied. The exponential wave functions explicitly depending on all N(N-1)/2 interparticle separations and taking into account the effects of correlation and nonadiabaticity are used. Straightforward use of these functions in many-particle systems with N > 3 is faced by time-consuming calculations of various multidimensional integrals with nonseparable variables. The number of these integrals increases as N 3 . This main obstacle can be obviated in the approach developed, based on the model Schroedinger equation combined with the virial and Hellmann-Feynman theorems. In this way the number of integrals in the expression for the matrix element of the many-particle Coulomb system Hamiltonian is significantly reduced: indeed, for a system with N = 4 particles only 7 instead of 43 integrals must be evaluated, for N = 5 only 10 instead of 101 integrals, etc. The number of different types of integral is also reduced. For a calculation of the energy of a 4-particle Coulomb system it is sufficient to calculate only 6 integrals of interparticle Coulomb interaction and the normalization integral. The results obtained offer a practical possibility for high-precision calculations of many-particle atomic-molecular systems with a detailed account of correlation and nonadiabaticity. 9 refs

  14. Magnetic properties and core electron binding energies of liquid water

    Science.gov (United States)

    Galamba, N.; Cabral, Benedito J. C.

    2018-01-01

    The magnetic properties and the core and inner valence electron binding energies of liquid water are investigated. The adopted methodology relies on the combination of molecular dynamics and electronic structure calculations. Born-Oppenheimer molecular dynamics with the Becke and Lee-Yang-Parr functionals for exchange and correlation, respectively, and includes an empirical correction (BLYP-D3) functional and classical molecular dynamics with the TIP4P/2005-F model were carried out. The Keal-Tozer functional was applied for predicting magnetic shielding and spin-spin coupling constants. Core and inner valence electron binding energies in liquid water were calculated with symmetry adapted cluster-configuration interaction. The relationship between the magnetic shielding constant σ(17O), the role played by the oxygen atom as a proton acceptor and donor, and the tetrahedral organisation of liquid water are investigated. The results indicate that the deshielding of the oxygen atom in water is very dependent on the order parameter (q) describing the tetrahedral organisation of the hydrogen bond network. The strong sensitivity of magnetic properties on changes of the electronic density in the nuclei environment is illustrated by a correlation between σ(17O) and the energy gap between the 1a1[O1s] (core) and the 2a1 (inner valence) orbitals of water. Although several studies discussed the eventual connection between magnetic properties and core electron binding energies, such a correlation could not be clearly established. Here, we demonstrate that for liquid water this correlation exists although involving the gap between electron binding energies of core and inner valence orbitals.

  15. Application of Henry's Law for Binding Energies of Adsorbed Hydrogen

    Science.gov (United States)

    Gillespie, Andrew; Dohnke, Elmar; Stalla, David; Sweany, Mark; Pfeifer, Peter

    2015-03-01

    The method of isosteres is the simplest method used to calculate the differential enthalpy of adsorption. However, it is incredibly sensitive to the choice of model and respective fitting parameters. For a set of isotherms measured on a specific sample, most models converge upon a similar value at high coverage, but are inconsistent in the low pressure regime. In this talk, we investigate the application of various models for localized and mobile adsorption at low pressures in order to obtain binding energy of hydrogen to the adsorbent surface. Henry's Law analysis of the Langmuir Model of adsorption yield binding energies in excellent agreement with those obtained from the Clausius Clapeyron relation. Work supported by DOE-EERE, Award No. DE-FG36-08GO18142.

  16. Calculated stacking-fault energies of elemental metals

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1993-01-01

    We have performed ab initio calculations of twin, intrinsic, and extrinsic face-centered-cubic stacking faults for all the 3d, 4d, and 5d transition metals by means of a Green's-function technique, based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approxima......We have performed ab initio calculations of twin, intrinsic, and extrinsic face-centered-cubic stacking faults for all the 3d, 4d, and 5d transition metals by means of a Green's-function technique, based on the linear-muffin-tin-orbitals method within the tight-binding and atomic......-sphere approximations. The results are in excellent agreement with recent layer Korringa-Kohn-Rostoker Green's-function calculations where stacking-fault energies for Ni, Cu, Rh, Pd, Ag, Ir, and Au were found by means of the the so-called force theorem. We find that the self-consistent fault energies for all the metals...... on the local atomic coordination are obeyed to a high degree of accuracy....

  17. Calculation of elastic constants of BCC transition metals: tight-binding recursion method

    International Nuclear Information System (INIS)

    Masuda, K.; Hamada, N.; Terakura, K.

    1984-01-01

    The elastic constants of BCC transition metals (Fe, Nb, Mo and W) are calculated by using the tight-binding d band and the Born-Mayer repulsive potential. Introducing a small distortion characteristic to C 44 (or C') elastic deformation and calculating the energy change up to second order in the atomic displacement, the shear elastic constants C 44 and C' are determined. The elastic constants C 11 and C 12 are then calculated by using the relations B=1/3(C 11 + 2C 12 ) and C'=1/2(C 11 -C 12 ), where B is the bulk modulus. In general, the agreement between the present results and the experimental values is satisfactory. The characteristic elasticity behaviour, i.e. the strong Nsub(d) (number of d electrons) dependence of the observed anisotropy factor A=C 44 /C', will also be discussed. (author)

  18. Zero energy scattering calculation in Euclidean space

    International Nuclear Information System (INIS)

    Carbonell, J.; Karmanov, V.A.

    2016-01-01

    We show that the Bethe–Salpeter equation for the scattering amplitude in the limit of zero incident energy can be transformed into a purely Euclidean form, as it is the case for the bound states. The decoupling between Euclidean and Minkowski amplitudes is only possible for zero energy scattering observables and allows determining the scattering length from the Euclidean Bethe–Salpeter amplitude. Such a possibility strongly simplifies the numerical solution of the Bethe–Salpeter equation and suggests an alternative way to compute the scattering length in Lattice Euclidean calculations without using the Luscher formalism. The derivations contained in this work were performed for scalar particles and one-boson exchange kernel. They can be generalized to the fermion case and more involved interactions.

  19. Zero energy scattering calculation in Euclidean space

    Energy Technology Data Exchange (ETDEWEB)

    Carbonell, J. [Institut de Physique Nucléaire, Université Paris-Sud, IN2P3-CNRS, 91406 Orsay Cedex (France); Karmanov, V.A., E-mail: karmanov@sci.lebedev.ru [Lebedev Physical Institute, Leninsky Prospekt 53, 119991 Moscow (Russian Federation)

    2016-03-10

    We show that the Bethe–Salpeter equation for the scattering amplitude in the limit of zero incident energy can be transformed into a purely Euclidean form, as it is the case for the bound states. The decoupling between Euclidean and Minkowski amplitudes is only possible for zero energy scattering observables and allows determining the scattering length from the Euclidean Bethe–Salpeter amplitude. Such a possibility strongly simplifies the numerical solution of the Bethe–Salpeter equation and suggests an alternative way to compute the scattering length in Lattice Euclidean calculations without using the Luscher formalism. The derivations contained in this work were performed for scalar particles and one-boson exchange kernel. They can be generalized to the fermion case and more involved interactions.

  20. Electronic transport properties of fullerene functionalized carbon nanotubes: Ab initio and tight-binding calculations

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Hashemi, J.; Markussen, Troels

    2009-01-01

    techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure......Fullerene functionalized carbon nanotubes-NanoBuds-form a novel class of hybrid carbon materials, which possesses many advantageous properties as compared to the pristine components. Here, we report a theoretical study of the electronic transport properties of these compounds. We use both ab initio...

  1. Effect of magnetic field on the impurity binding energy of the excited ...

    Indian Academy of Sciences (India)

    Abstract. The effect of external magnetic field on the excited state energies in a spher- ical quantum dot was studied. The impurity energy and binding energy were calculated using the variational method within the effective mass approximation and finite barrier potential. The results showed that by increasing the magnetic ...

  2. Effect of magnetic field on the impurity binding energy of the excited ...

    Indian Academy of Sciences (India)

    The effect of external magnetic field on the excited state energies in a spherical quantum dot was studied. The impurity energy and binding energy were calculated using the variational method within the effective mass approximation and finite barrier potential. The results showed that by increasing the magnetic field, the ...

  3. Binding-energy distribution and dephasing of localized biexcitons

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher; Umlauff, M.

    1997-01-01

    We report on the binding energy and dephasing of localized biexciton states in narrow ZnSe multiple quantum wells. The measured binding-energy distribution of the localized biexcitons shows a width of 2.2 meV centered at 8.5 meV, and is fairly independent of the exciton localization energy. In four...

  4. Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Matei, Iulia; Ionescu, Sorana [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania); Hillebrand, Mihaela, E-mail: mihh@gw-chimie.math.unibuc.ro [Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta 4-12, 030018 Bucharest (Romania)

    2011-08-15

    The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 10{sup 5} M{sup -1} was evidenced. Foerster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes in the CD band of HSA indicate a decrease in the {alpha}-helix content upon binding. An induced CD signal for bound fisetin was observed and rationalized in terms of density functional theory calculations. - Highlights: > Fisetin-BSA system was studied by fluorescence spectroscopy. > Binding parameters, association constant and number of sites were estimated. > Binding site of fisetin was identified by competitive experiments. > Conformational changes in HSA and fisetin were evidenced by circular dichroism. > TDDFT calculated CD spectra supported the experimental data.

  5. A robust force field based method for calculating conformational energies of charged drug-like molecules

    DEFF Research Database (Denmark)

    Pøhlsgaard, Jacob; Harpsøe, Kasper; Jørgensen, Flemming Steen

    2012-01-01

    The binding affinity of a drug like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, the molecule is unlikely to bind to its target. Determination...... of the global minimum energy conformation and calculation of conformational penalties of binding are prerequisites for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse...... molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force-field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic...

  6. Influence of host matrices on krypton electron binding energies and KLL Auger transition energies

    Czech Academy of Sciences Publication Activity Database

    Inoyatov, A. K.; Perevoshchikov, L. L.; Kovalík, Alojz; Filosofov, D. V.; Yushkevich, Yu. V.; Ryšavý, Miloš; Lee, B. Q.; Kibédi, T.; Stuchbery, A. E.; Zhdanov, V. S.

    2014-01-01

    Roč. 197, DEC (2014), s. 64-71 ISSN 0368-2048 R&D Projects: GA ČR(CZ) GAP203/12/1896; GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : Kr-83 * Rb-83 * Sr-83 * electron binding energy * KLL transitions * natural atomic level width * multiconfiguration Dirac-Fock calculations Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.436, year: 2014

  7. Free-Energy Calculations. A Mathematical Perspective

    Science.gov (United States)

    Pohorille, Andrzej

    2015-01-01

    conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

  8. Sampling and energy evaluation challenges in ligand binding protein design.

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David

    2017-12-01

    The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  9. CHP Energy and Emissions Savings Calculator

    Science.gov (United States)

    Download the CHP Emissions Calculator, a tool that calculates the difference between the anticipated carbon dioxide, methane, nitrous oxide, sulfur dioxide, and nitrogen oxide emissions from a CHP system to those of a separate heat and power system.

  10. Extrapolations of nuclear binding energies from new linear mass relations

    DEFF Research Database (Denmark)

    Hove, D.; Jensen, A. S.; Riisager, K.

    2013-01-01

    We present a method to extrapolate nuclear binding energies from known values for neighboring nuclei. We select four specific mass relations constructed to eliminate smooth variation of the binding energy as function nucleon numbers. The fast odd-even variations are avoided by comparing nuclei...

  11. Binding free energy analysis of protein-protein docking model structures by evERdock.

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  12. Binding free energy analysis of protein-protein docking model structures by evERdock

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-01

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  13. Exciton binding energy in a pyramidal quantum dot

    Science.gov (United States)

    Anitha, A.; Arulmozhi, M.

    2018-05-01

    The effects of spatially dependent effective mass, non-parabolicity of the conduction band and dielectric screening function on exciton binding energy in a pyramid-shaped quantum dot of GaAs have been investigated by variational method as a function of base width of the pyramid. We have assumed that the pyramid has a square base with area a× a and height of the pyramid H=a/2. The trial wave function of the exciton has been chosen according to the even mirror boundary condition, i.e. the wave function of the exciton at the boundary could be non-zero. The results show that (i) the non-parabolicity of the conduction band affects the light hole (lh) and heavy hole (hh) excitons to be more bound than that with parabolicity of the conduction band, (ii) the dielectric screening function (DSF) affects the lh and hh excitons to be more bound than that without the DSF and (iii) the spatially dependent effective mass (SDEM) affects the lh and hh excitons to be less bound than that without the SDEM. The combined effects of DSF and SDEM on exciton binding energy have also been calculated. The results are compared with those available in the literature.

  14. Computation of pH-Dependent Binding Free Energies

    Science.gov (United States)

    Kim, M. Olivia; McCammon, J. Andrew

    2015-01-01

    Protein-ligand binding accompanies changes in the surrounding electrostatic environments of the two binding partners and may lead to changes in protonation upon binding. In cases where the complex formation results in a net transfer of protons, the binding process is pH-dependent. However, conventional free energy computations or molecular docking protocols typically employ fixed protonation states for the titratable groups in both binding partners set a priori, which are identical for the free and bound states. In this review, we draw attention to these important yet largely ignored binding-induced protonation changes in protein-ligand association by outlining physical origins and prevalence of the protonation changes upon binding. Following a summary of various theoretical methods for pKa prediction, we discuss the theoretical framework to examine the pH dependence of protein-ligand binding processes. PMID:26202905

  15. Atomic Mass and Nuclear Binding Energy for Y-90 (Yttrium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume A `Nuclei with Z = 1 - 54' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms'. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Y-90 (Yttrium, atomic number Z = 39, mass number A = 90).

  16. Elucidating the structures and cooperative binding mechanism of cesium salts to the multitopic ion-pair receptor through density functional theory calculations.

    Science.gov (United States)

    Sadhu, Biswajit; Sundararajan, Mahesh; Velmurugan, Gunasekaran; Venuvanalingam, Ponnambalam

    2015-09-21

    Designing new and innovative receptors for the selective binding of radionuclides is central to nuclear waste management processes. Recently, a new multi-topic ion-pair receptor was reported which binds a variety of cesium salts. Due to the large size of the receptor, quantum chemical calculations on the full ion-pair receptors are restricted, thus the binding mechanisms are not well understood at the molecular level. We have assessed the binding strengths of various cesium salts to the recently synthesized multi-topic ion-pair receptor molecule using density functional theory based calculations. Our calculations predict that the binding of cesium salts to the receptor predominantly occurs via the cooperative binding mechanism. Cesium and the anion synergistically assist each other to bind favorably inside the receptor. Energy decomposition analysis on the ion-pair complexes shows that the Cs salts are bound to the receptor mainly through electrostatic interactions with small contribution from covalent interactions for large ionic radius anions. Further, QTAIM analysis characterizes the importance of different inter-molecular interactions between the ions and the receptor inside the ion-pair complexes. The role of the crystallographic solvent molecule contributes significantly by ~10 kcal mol(-1) to the overall binding affinities which is quite significant. Further, unlike the recent molecular mechanics (MM) calculations, our calculated binding affinity trends for various Cs ion-pair complexes (CsF, CsCl and CsNO3) are now in excellent agreement with the experimental binding affinity trends.

  17. Formation Mechanism and Binding Energy for Regular Octahedral Structure of Li6 Cluster

    Science.gov (United States)

    Zhao, Yan-Ping; Li, Ping; Gou, Qing-Quan; Liu, Wei-Na

    2008-12-01

    The formation mechanism for the regular octahedral structure of Li6cluster is proposed. The curve of the total energy versus the separation R between any two neighboring nuclei has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of -44.736 89 a.u. at R = 5.07a0. When R approaches infinity, the total energy of six lithium atoms has the value of -44.568 17 a.u. So the binding energy of Li6 with respect to six lithium atoms is 0.1687 a.u. Therefore, the binding energy per atom for Li6 is 0.028 12 a.u., or 0.7637 eV, which is greater than the binding energy per atom of 0.453 eV for Li2 and the binding energy per atom of 0.494 eV for Li3 calculated in our previous work. This means that the Li6 cluster may be formed in a regular octahedral structure with a greater binding energy.

  18. Structure-function relationships of Na+, K+, ATP, or Mg2+ binding and energy transduction in Na,K-ATPase

    DEFF Research Database (Denmark)

    Jorgensen, Peter L.; Pedersen, Per Amstrup

    2000-01-01

    Na,K-ATPase; Mutagenesis; Na+ binding; K+ binding; Tl+ binding; Mg2+ binding; ATP binding; Cation binding site; Energy transduction......Na,K-ATPase; Mutagenesis; Na+ binding; K+ binding; Tl+ binding; Mg2+ binding; ATP binding; Cation binding site; Energy transduction...

  19. Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas; Suárez, Ernesto

    2010-01-01

    Herein, we examine computationally the binding and hydrolysis reaction of the MMP-2 enzyme with two peptide substrates selected by the enzyme from a phage peptide library. Molecular dynamics simulations of the Michaelis complexes (25 ns) allow us to characterize the main enzyme/substrate contacts. Subsequently MM-PBSA calculations using independent trajectories for the complexes and the free substrates provide relative binding energies in good agreement with the experimental K(M) results. Computational alanine scanning analyses of the enzyme/substrate interaction energies confirm the relevance of the P(3), P(2), and P(1)' side chains for ligand binding. Finally, the hydrolysis of both peptides taking place at the MMP-2 active site is explored by means of hybrid quantum mechanical/molecular mechanics calculations. The computed reaction mechanisms result in rate-determining energy barriers being in consonance with the experimental k(cat) values. Overall, the computational protocol seems to capture the subtle differences in binding and catalysis experimentally observed for the two peptide substrates. Some implications of our results for the future design of novel and more specific MMP-2 inhibitors are also discussed. (c) 2009 Wiley-Liss, Inc.

  20. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations

    Science.gov (United States)

    Ngo, Son Tung; Nguyen, Minh Tung; Nguyen, Minh Tho

    2017-05-01

    The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding molecules by the fast pulling of ligand (FPL) process using non-equilibrium molecular dynamics (NEMD) simulations. The calculated free energy difference terms help clarifying the nature of the binding. Theoretical binding affinities are in good correlation with experimental data, with R = 0.89. The paradigm used is able to rank two inhibitors having the maximum difference of ∼1.5 kcal/mol in absolute binding free energies.

  1. A tool for calculating binding-site residues on proteins from PDB structures

    Directory of Open Access Journals (Sweden)

    Hu Jing

    2009-08-01

    Full Text Available Abstract Background In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB that consists of the protein of interest and its interacting partner(s and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. Results In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. Conclusion The developed tool is very useful for the research on protein binding site analysis and prediction.

  2. Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches

    National Research Council Canada - National Science Library

    Lee, Michael S; Olson, Mark A

    2006-01-01

    .... The results of this approach agree well with experimentally observed binding affinities. Also assessed is a commonly used approximate endpoint approach, which separately estimates enthalpy, solvation free energy, and entropy...

  3. Low-energy calculations for nuclear photodisintegration

    Directory of Open Access Journals (Sweden)

    Deflorian S.

    2016-01-01

    Full Text Available In the Standard Solar Model a central role in the nucleosynthesis is played by reactions of the kind XZ1A11+XZ2A22→YZ1+Z2A1+A2+γ${}_{{Z_1}}^{{A_1}}{X_1} + {}_{{Z_2}}^{{A_2}}{X_2} \\to {}_{{Z_1} + {Z_2}}^{{A_1} + {A_2}}Y + \\gamma $, which enter the proton-proton chains. These reactions can also be studied through the inverse photodisintegration reaction. One option is to use the Lorentz Integral Transform approach, which transforms the continuum problem into a bound state-like one. A way to check the reliability of such methods is a direct calculation, for example using the Kohn Variational Principle to obtain the scattering wave function and then directly calculate the response function of the reaction.

  4. To the calculation of energy resolution of ionization calorimeter

    International Nuclear Information System (INIS)

    Uchajkin, V.V.; Lagutin, A.A.

    1976-01-01

    The question of energy resolution of the ionization calorimeter is considered analytically. A method is discussed for calculating the probability characteristics (mean value and dispersion) of energy losses of an electron-photon shower by ionization in the calorimeter volume

  5. Consideration of relativistic effects in band structure calculations based on the empirical tight-binding method

    International Nuclear Information System (INIS)

    Hanke, M.; Hennig, D.; Kaschte, A.; Koeppen, M.

    1988-01-01

    The energy band structure of cadmium telluride and mercury telluride materials is investigated by means of the tight-binding (TB) method considering relativistic effects and the spin-orbit interaction. Taking into account relativistic effects in the method is rather simple though the size of the Hamilton matrix doubles. Such considerations are necessary for the interesting small-interstice semiconductors, and the experimental results are reflected correctly in the band structures. The transformation behaviour of the eigenvectors within the Brillouin zone gets more complicated, but is, nevertheless, theoretically controllable. If, however, the matrix elements of the Green operator are to be calculated, one has to use formula manipulation programmes in particular for non-diagonal elements. For defect calculations by the Koster-Slater theory of scattering it is necessary to know these matrix elements. Knowledge of the transformation behaviour of eigenfunctions saves frequent diagonalization of the Hamilton matrix and thus permits a numerical solution of the problem. Corresponding results for the sp 3 basis are available

  6. Calculation of molecular free energies in classical potentials

    International Nuclear Information System (INIS)

    Farhi, Asaf; Singh, Bipin

    2016-01-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations. (paper)

  7. Calculation of transportation energy for biomass collection

    Energy Technology Data Exchange (ETDEWEB)

    Kanai, G.; Takekura, K.; Kato, H.; Kobayashi, Y.; Yakushido, K. [National Agricultural Research Center, Tsukuba, Ibaraki (Japan)

    2010-07-01

    This paper reported on a study at a rice straw facility in Japan that produces bioethanol. Simulation modeling and calculations methods were used to examine the characteristics of field-to-facility transportation. Fuel consumption was found to be influenced by the conversion rate from straw to ethanol, the quantity of straw collected, and the ratio of the field area to that around the facility. Standard conditions were assumed based on reported data and actual observations for 15 ML/yr ethanol production, 0.3 kL output of ethanol from 1 t dry straw, 53.6 day/yr working days, 2.7 t truck load capacity, and 0.128 as the ratio of field to the area around the facility. According to calculations, a quantity of 50 kt dry straw requires 2.78 L of fuel to transport 1 t of dry straw, 109.5 trucks, and a 19.1 km collection area radius. The fuel consumption for transportation was found to be proportional to the quantity of straw to the 0.5 power, but inversely proportional to the ratio of field to the 0.5 power. The rate of increase in the number of trucks needed to collect straw increases with the decrease in the ratio of the field to area surface around the facility.

  8. A Python tool to set up relative free energy calculations in GROMACS.

    Science.gov (United States)

    Klimovich, Pavel V; Mobley, David L

    2015-11-01

    Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations.

  9. Enzyme activation through the utilization of intrinsic dianion binding energy.

    Science.gov (United States)

    Amyes, T L; Malabanan, M M; Zhai, X; Reyes, A C; Richard, J P

    2017-03-01

    We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.

  10. Entropy and energy quantization: Planck thermodynamic calculation

    International Nuclear Information System (INIS)

    Mota e Albuquerque, Ivone Freire da.

    1988-01-01

    This dissertation analyses the origins and development of the concept of entropy and its meaning of the second Law of thermodynamics, as well as the thermodynamics derivation of the energy quantization. The probabilistic interpretation of that law and its implication in physics theory are evidenciated. Based on Clausius work (which follows Carnot's work), we analyse and expose in a original way the entropy concept. Research upon Boltzmann's work and his probabilistic interpretation of the second Law of thermodynamics is made. The discuss between the atomistic and the energeticist points of view, which were actual at that time are also commented. (author). 38 refs., 3 figs

  11. Danish Sector Guide for Calculation of the Actual Energy Consumption

    DEFF Research Database (Denmark)

    Mortensen, Lone Hedegaard

    2016-01-01

    Energy calculations have for a long time been a controversial topic as building owners do not necessarily achieve the promised energy savings after a building upgrade, but is this due to incorrect calculations or rather the evidence of misunderstandings in the communication? In Denmark, the innov...

  12. Calculated distortions induced by metal-ion binding to simple oligonucleotide systems: Implications for toxicity

    Energy Technology Data Exchange (ETDEWEB)

    Turner, J.E.; Hingerty, B.E.; England, M.W.; Jacobson, K.B.

    1990-01-01

    We have previously published detailed results of calculations of the binding of the metal ions, Cd{sup 2+} and Ca{sup 2+}, to the dinucleoside monophosphate GpC in water. These ions, which have the same charge and radius, differ enormously in their toxicity to man and other biological systems. Our calculations showed contrasting behavior in the binding of these two metal ions to GpC. We suggest the hypothesis that structural distortions calculated for metal ions binding to simple nucleic-acid systems might serve as a indicator of an ion's potential ability to alter molecular activity and hence to be toxic to an organism. Furthermore, the degree of distortion might be correlated with the degree of toxicity as measured by some suitable criteria. The present paper reports the results of binding calculations for a number of other metal ions, of different valence states, with several dinucleoside monophosphates in water. A general trend of distortion with the type of binding of the metal ions is found. We are seeking quantitative measures of distortion to correlate with indicators of acute toxicity that we have measured for 24 metal ions using mice, Drosophila, and CHO cells. 3 refs., 3 figs.

  13. Binding analysis for interaction of diacetylcurcumin with β-casein nanoparticles by using fluorescence spectroscopy and molecular docking calculations

    Science.gov (United States)

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Fani, Najme; Keyhanfar, Mehrnaz

    2013-11-01

    The interaction of diacetylcurcumin (DAC), as a novel synthetic derivative of curcumin, with bovine β-casein (an abundant milk protein that is highly amphiphilic and self assembles into stable micellar nanoparticles in aqueous solution) was investigated using fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations. The fluorescence quenching measurements revealed the presence of a single binding site on β-casein for DAC with the binding constant value equals to (4.40 ± 0.03) × 104 M-1. Forster energy transfer measurements suggested that the distance between bound DAC and Trp143 residue is higher than the respective critical distance, hence, the static quenching is more likely responsible for fluorescence quenching other than the mechanism of non-radiative energy transfer. Our results from molecular docking calculations indicated that binding of DAC to β-casein predominantly occurred through hydrophobic contacts in the hydrophobic core of protein. Additionally, in vitro investigation of the cytotoxicity of free DAC and DAC-β-casein complex in human breast cancer cell line MCF7 revealed the higher cytotoxic effect of DAC-β-casein complex.

  14. Formation Mechanism and Binding Energy for Body-Centred Regular Icosahedral Structure of Li13 Cluster

    International Nuclear Information System (INIS)

    Liu Weina; Li Ping; Gou Qingquan; Zhao Yanping

    2008-01-01

    The formation mechanism for the body-centred regular icosahedral structure of Li 13 cluster is proposed. The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li 13 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of -96.951 39 a.u. at R = 5.46a 0 . When R approaches to infinity, the total energy of thirteen lithium atoms has the value of -96.564 38 a.u. So the binding energy of Li 13 with respect to thirteen lithium atoms is 0.387 01 a.u. Therefore the binding energy per atom for Li 13 is 0.029 77 a.u. or 0.810 eV, which is greater than the binding energy per atom of 0.453 eV for Li 2 , 0.494 eV for Li 3 , 0.7878 eV for Li 4 , 0.632 eV for Li 5 , and 0.674 eV for Li 7 calculated by us previously. This means that the Li 13 cluster may be formed stably in a body-centred regular icosahedral structure with a greater binding energy

  15. Formation Mechanism and Binding Energy for Body-Centred Regular Icosahedral Structure of Li13 Cluster

    Science.gov (United States)

    Liu, Wei-Na; Li, Ping; Gou, Qing-Quan; Zhao, Yan-Ping

    2008-11-01

    The formation mechanism for the body-centred regular icosahedral structure of Li13 cluster is proposed. The curve of the total energy versus the separation R between the nucleus at the centre and nuclei at the apexes for this structure of Li13 has been calculated by using the method of Gou's modified arrangement channel quantum mechanics (MACQM). The result shows that the curve has a minimal energy of 96.951 39 a.u. at R = 5.46a0. When R approaches to infinity, the total energy of thirteen lithium atoms has the value of 96.564 38 a.u. So the binding energy of Li13 with respect to thirteen lithium atoms is 0.387 01 a.u. Therefore the binding energy per atom for Li13 is 0.029 77 a.u. or 0.810 eV, which is greater than the binding energy per atom of 0.453 eV for Li2, 0.494 eV for Li3, 0.7878 eV for Li4, 0.632 eV for Li5, and 0.674 eV for Li7 calculated by us previously. This means that the Li13 cluster may be formed stably in a body-centred regular icosahedral structure with a greater binding energy.

  16. Atomic Mass and Nuclear Binding Energy for Cf-252 (Californium)

    Science.gov (United States)

    Sukhoruchkin, S. I.; Soroko, Z. N.

    This document is part of the Supplement containing the complete sets of data of Subvolume B `Nuclei with Z = 55 - 100' of Volume 22 `Nuclear Binding Energies and Atomic Masses' of Landolt-Börnstein - Group I `Elementary Particles, Nuclei and Atoms', and additionally including data for nuclei with Z = 101 - 130. It provides atomic mass, mass excess, nuclear binding energy, nucleon separation energies, Q-values, and nucleon residual interaction parameters for atomic nuclei of the isotope Cf-252 (Californium, atomic number Z = 98, mass number A = 252).

  17. Microwave emulations and tight-binding calculations of transport in polyacetylene

    Energy Technology Data Exchange (ETDEWEB)

    Stegmann, Thomas, E-mail: stegmann@icf.unam.mx [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Franco-Villafañe, John A., E-mail: jofravil@fis.unam.mx [Instituto de Física, Benemérita Universidad Autónoma de Puebla, Apartado Postal J-48, 72570 Puebla (Mexico); Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Ortiz, Yenni P. [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Kuhl, Ulrich [Université de Nice – Sophia Antipolis, Laboratoire de la Physique de la Matière Condensée, CNRS, Parc Valrose, 06108 Nice (France); Mortessagne, Fabrice, E-mail: fabrice.mortessagne@unice.fr [Université de Nice – Sophia Antipolis, Laboratoire de la Physique de la Matière Condensée, CNRS, Parc Valrose, 06108 Nice (France); Seligman, Thomas H. [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, 62210 Cuernavaca (Mexico); Centro Internacional de Ciencias, 62210 Cuernavaca (Mexico)

    2017-01-05

    A novel approach to investigate the electron transport of cis- and trans-polyacetylene chains in the single-electron approximation is presented by using microwave emulation measurements and tight-binding calculations. In the emulation we take into account the different electronic couplings due to the double bonds leading to coupled dimer chains. The relative coupling constants are adjusted by DFT calculations. For sufficiently long chains a transport band gap is observed if the double bonds are present, whereas for identical couplings no band gap opens. The band gap can be observed also in relatively short chains, if additional edge atoms are absent, which cause strong resonance peaks within the band gap. The experimental results are in agreement with our tight-binding calculations using the nonequilibrium Green's function method. The tight-binding calculations show that it is crucial to include third nearest neighbor couplings to obtain the gap in the cis-polyacetylene. - Highlights: • Electronic transport in individual polyacetylene chains is studied. • Microwave emulation experiments and tight-binding calculations agree well. • In long chains a band-gap opens due the dimerization of the chain. • In short chains edge atoms cause strong resonance peaks in the center of the band-gap.

  18. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    Science.gov (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  19. Binding energy of impurity states in an inverse parabolic quantum well under magnetic field

    International Nuclear Information System (INIS)

    Kasapoglu, E.; Sari, H.; Soekmen, I.

    2007-01-01

    We have investigated the effects of the magnetic field which is directed perpendicular to the well on the binding energy of the hydrogenic impurities in an inverse parabolic quantum well (IPQW) with different widths as well as different Al concentrations at the well center. The Al concentration at the barriers was always x max =0.3. The calculations were performed within the effective mass approximation, using a variational method. We observe that IPQW structure turns into parabolic quantum well with the inversion effect of the magnetic field and donor impurity binding energy in IPQW strongly depends on the magnetic field, Al concentration at the well center and well dimensions

  20. A comparison of binding energy and metastable zone width for adipic acid with various additives

    Science.gov (United States)

    Myerson, Allan S.; Jang, Shyh M.

    1995-12-01

    The binding energy of nine alkanoic acids to the major crystal faces of adipic acid were calculated employing molecular modelling techniques. The results indicate that the alkanoic acids bind strongly to the surface when compared to solvents and to adipic acid itself indicating that the alkanoic acids could be potential growth and nucleation inhibitors. The binding energies were found to increase with increasing carbon number to C 14 to decrease from C 14 to C 16 and then to increase again. The effect of the alkanoic acids on the metastable zone width of adipic acid in ethanol solution were measured employing a differential scanning calorimeter. The results showed that each of the nine alkanoic acids increased the metastable zone width. The metastable zone widths were found to increase with increasing carbon number to C 14 to decrease from C 14 to C 16 and to then increase again thus correlating well with the results obtained from binding energies. These results indicate that binding energy calculations appear to provide a valid method to screen impurities as potential nucleation inhibitors.

  1. Guidelines for the analysis of free energy calculations.

    Science.gov (United States)

    Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

    2015-05-01

    Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.

  2. First principle prediction of shallow defect level binding energies and deep level nonradiative recombination rates

    Science.gov (United States)

    Wang, Linwang

    2014-03-01

    Accurate calculation of defect level energies in semiconductors and their carrier capturing rate is an important issue in ab initio prediction of semiconductor properties. In this talk, I will present our result work in ab initio shallow level calculation and deep level caused nonradiative recombination rate calculation. In the shallow acceptor level calculation, a large system up to 64,000 atoms needs to be used to properly describe the weakly bounded hole wave functions. The single particle Hamiltonian of that system is patched from bulk potential and central potential. Furthermore, GW calculation is used to correct the one site potential of the impurity atom. The resulting binding energy agrees excellently with the experiments within 10 meV. To calculate the nonradiative decay rate, the electron-phonon coupling constants in the defect system are calculated all at once using a new variational algorithm. Multiphonon process formalism is used to calculate the nonradiative decay rate. It is found that the transition is induced by the electron and the optical phonon coupling, but the energy conservation is mostly satisfied by the acoustic phonons. The new algorithm allows fast calculation of such nonradiative decay rate for any defect levels, as well as other multiphonon processes in nanostructures. This work was supported by the Director, Office of Science (SC), Basic Energy Science (BES)/Materials Science and Engineering Division (MSED) of the U.S. Department of Energy (DOE) under the contract No. DE-AC02-05CH11231.

  3. A general scheme for the estimation of oxygen binding energies on binary transition metal surface alloys

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Nørskov, Jens Kehlet

    2005-01-01

    A simple scheme for the estimation of oxygen binding energies on transition metal surface alloys is presented. It is shown that a d-band center model of the alloy surfaces is a convenient and appropriate basis for this scheme; variations in chemical composition, strain effects, and ligand effects...... are all incorporated into the binding energy analysis through this parameter. With few exceptions, the agreement of the results from the simple model with full DFT calculations on hundreds of binary surface alloys is remarkable. The scheme should therefore provide a fast and effective method...... for the estimation of oxygen binding energies on a wide variety of transition metal alloys. (c) 2005 Elsevier B.V. All rights reserved....

  4. Analysis of experimental positron-molecule binding energies

    International Nuclear Information System (INIS)

    Danielson, J R; Surko, C M; Young, J A

    2010-01-01

    Experiments show that positron annihilation on molecules frequently occurs via capture into vibrational Feshbach resonances. In these cases, the downshifts in the annihilation spectra from the vibrational mode spectra provide measures of the positron-molecule binding energies. An analysis of these binding energy data is presented in terms of the molecular dipole polarizability, the permanent dipole moment, and the number of π bonds in aromatic molecules. The results of this analysis are in reasonably good agreement with other information about positron-molecule bound states. Predictions for other targets and promising candidate molecules for further investigation are discussed.

  5. Calculation of energy spectrum of C isotope with modified Yukawa ...

    Indian Academy of Sciences (India)

    2016-09-12

    Sep 12, 2016 ... Abstract. In this paper, we have calculated the energy spectrum of 12C isotope in two-cluster models, 3α cluster model and 8Be + α cluster model. We use the modified Yukawa potential for interaction between the clusters and solve the Schrödinger equation using Nikiforov–Uvarov method to calculate the ...

  6. Precise calculation of the energies of heavy hydrogenlike ions

    International Nuclear Information System (INIS)

    Driker, M.N.; Ivanova, E.P.; Ivanov, L.N.

    1983-01-01

    Energies of the 1s, 2s, and 2p states are calculated for hydrogenlike ions with z = 30--170. The calculation is based on Dirac's equation taking into account radiation effects and the finiteness of the nucleus. The hyperfine splitting constants are calculated taking the finiteness of the nucleus into account, and derivatives are taken with respect to the volume of the nucleus for all S-state characteristics

  7. Equivalence of Stress and Energy Calculations of Mean Stress

    DEFF Research Database (Denmark)

    Pedersen, Ole Bøcker; Brown, L. M.

    1977-01-01

    Calculations of the mean stress in a plastically deformed matrix containing randomly distributed elastic inclusions are considered. The mean stress for an elastically homogeneous material is calculated on the basis of an energy consideration which completely accounts for elastic interactions....... The result is shown to be identical to that obtained from a stress calculation. The possibility of including elastic interactions in the case of elastic inhomogeneity is discussed....

  8. Lanthanide 4f-electron binding energies and the nephelauxetic effect in wide band gap compounds

    International Nuclear Information System (INIS)

    Dorenbos, Pieter

    2013-01-01

    Employing data from luminescence spectroscopy, the inter 4f-electron Coulomb repulsion energy U(6, A) in Eu 2+/3+ impurities together with the 5d-centroid energy shift ϵ c (1,3+,A) in Ce 3+ impurities in 40 different fluoride, chloride, bromide, iodide, oxide, sulfide, and nitride compounds has been determined. This work demonstrates that the chemical environment A affects the two energies in a similar fashion; a fashion that follows the anion nephelauxetic sequence F, O, Cl, Br, N, I, S, Se. One may then calculate U(6, A) from well established and accurate ϵ c (1,3+,A) values which are then used as input to the chemical shift model proposed in Dorenbos (2012) [19]. As output it provides the chemical shift of 4f-electron binding energy and therewith the 4f-electron binding energy relative to the vacuum energy. In addition this method provides a tool to routinely establish the binding energy of electrons at the top of the valence band (work function) and the bottom of the conduction band (electron affinity) throughout the entire family of inorganic compounds. How the electronic structure of the compound and lanthanide impurities therein change with type of compound and type of lanthanide is demonstrated. -- Highlights: ► A relationship between 5d centroid shift and 4f-electron Coulomb repulsion energy is established. ► Information on the absolute 4f-electron binding energy of lanthanides in 40 compounds is provided. ► A new tool to determine absolute binding energies of electrons in valence and conduction bands is demonstrated

  9. Predicting accurate absolute binding energies in aqueous solution

    DEFF Research Database (Denmark)

    Jensen, Jan Halborg

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal...

  10. Nuclear Cartography: Patterns in Binding Energies and Subatomic Structure

    Science.gov (United States)

    Simpson, E. C.; Shelley, M.

    2017-01-01

    Nuclear masses and binding energies are some of the first nuclear properties met in high school physics, and can be used to introduce radioactive decays, fusion, and fission. With relatively little extension, they can also illustrate fundamental concepts in nuclear physics, such as shell structure and pairing, and to discuss how the elements…

  11. 18 CFR 11.13 - Energy gains calculations.

    Science.gov (United States)

    2010-04-01

    ... (HWBEG) Model Description and Users Manual, which is available for the National Technical Information... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY...

  12. User guide – COE Calculation Tool for Wave Energy Converters

    DEFF Research Database (Denmark)

    Chozas, Julia Fernandez; Kofoed, Jens Peter; Jensen, Niels Ejner Helstrup

    Aalborg University together with Energinet.dk and Julia F. Chozas Consulting Engineer, have released a freely available online spreadsheet to evaluate the Levelised Cost of Energy (LCOE) for wave energy projects. The open-access tool calculates the LCOE based on the power production of a Wave...

  13. Rapid calculation of partition functions and free energies of fluids.

    Science.gov (United States)

    Do, Hainam; Hirst, Jonathan D; Wheatley, Richard J

    2011-11-07

    The partition function (Q) is a central quantity in statistical mechanics. All the thermodynamic properties can be derived from it. Here we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the Helmholtz free energy (F) via F = -k(B)T ln Q. In our approach, we divide the density of states, assigning half of the configurations found in a simulation to a high-energy partition and half to a low-energy partition. By recursively dividing the low-energy partition into halves, we map out the complete density of states for a continuous system. The result allows free energy to be calculated directly as a function of temperature. We illustrate our method in the context of the free energy of water.

  14. Energy mesh optimization for multi-level calculation schemes

    International Nuclear Information System (INIS)

    Mosca, P.; Taofiki, A.; Bellier, P.; Prevost, A.

    2011-01-01

    The industrial calculations of third generation nuclear reactors are based on sophisticated strategies of homogenization and collapsing at different spatial and energetic levels. An important issue to ensure the quality of these calculation models is the choice of the collapsing energy mesh. In this work, we show a new approach to generate optimized energy meshes starting from the SHEM 281-group library. The optimization model is applied on 1D cylindrical cells and consists of finding an energy mesh which minimizes the errors between two successive collision probability calculations. The former is realized over the fine SHEM mesh with Livolant-Jeanpierre self-shielded cross sections and the latter is performed with collapsed cross sections over the energy mesh being optimized. The optimization is done by the particle swarm algorithm implemented in the code AEMC and multigroup flux solutions are obtained from standard APOLLO2 solvers. By this new approach, a set of new optimized meshes which encompass from 10 to 50 groups has been defined for PWR and BWR calculations. This set will allow users to adapt the energy detail of the solution to the complexity of the calculation (assembly, multi-assembly, two-dimensional whole core). Some preliminary verifications, in which the accuracy of the new meshes is measured compared to a direct 281-group calculation, show that the 30-group optimized mesh offers a good compromise between simulation time and accuracy for a standard 17 x 17 UO 2 assembly with and without control rods. (author)

  15. A novel lattice energy calculation technique for simple inorganic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kaya, Cemal [Department of Chemistry, Faculty of Science, Cumhuriyet University, 58140 Sivas (Turkey); Kaya, Savaş, E-mail: savaskaya@cumhuriyet.edu.tr [Department of Chemistry, Faculty of Science, Cumhuriyet University, 58140 Sivas (Turkey); Banerjee, Priyabrata [Surface Engineering and Tribology Group, CSIR-Central Mechanical Engineering Research Institute, Mahatma Gandhi Avenue, Durgapur 713209 (India)

    2017-01-01

    In this pure theoretical study, a hitherto unexplored equation based on Shannon radii of the ions forming that crystal and chemical hardness of any crystal to calculate the lattice energies of simple inorganic ionic crystals has been presented. To prove the credibility of this equation, the results of the equation have been compared with experimental outcome obtained from Born-Fajans-Haber- cycle which is fundamentally enthalpy-based thermochemical cycle and prevalent theoretical approaches proposed for the calculation of lattice energies of ionic compounds. The results obtained and the comparisons made have demonstrated that the new equation is more useful compared to other theoretical approaches and allows to exceptionally accurate calculation of lattice energies of inorganic ionic crystals without doing any complex calculations.

  16. Increased Efficiency of Energy Calculation : Using .NET 4.0

    OpenAIRE

    Blommé, Carl

    2010-01-01

    The purpose of this thesis is to investigate if one is able to make the calculations that are performed in the calculation engine, in a program that calculates energy consumption, faster by using a multi-core based architecture. To do this the new multi-core functionalities in .Net 4.0 were examined, in order to determine if they are usable in the current system. A prototype for the calculation engine was made with parallel programming. An evaluation of this code was made and compared to the ...

  17. Performance calculation and simulation system of high energy laser weapon

    Science.gov (United States)

    Wang, Pei; Liu, Min; Su, Yu; Zhang, Ke

    2014-12-01

    High energy laser weapons are ready for some of today's most challenging military applications. Based on the analysis of the main tactical/technical index and combating process of high energy laser weapon, a performance calculation and simulation system of high energy laser weapon was established. Firstly, the index decomposition and workflow of high energy laser weapon was proposed. The entire system was composed of six parts, including classical target, platform of laser weapon, detect sensor, tracking and pointing control, laser atmosphere propagation and damage assessment module. Then, the index calculation modules were designed. Finally, anti-missile interception simulation was performed. The system can provide reference and basis for the analysis and evaluation of high energy laser weapon efficiency.

  18. Calculation of the surface free energy of fcc copper nanoparticles

    International Nuclear Information System (INIS)

    Jia Ming; Lai Yanqing; Tian Zhongliang; Liu Yexiang

    2009-01-01

    Using molecular dynamics simulations with the modified analytic embedded-atom method we calculate the Gibbs free energy and surface free energy for fcc Cu bulk, and further obtain the Gibbs free energy of nanoparticles. Based on the Gibbs free energy of nanoparticles, we have investigated the heat capacity of copper nanoparticles. Calculation results indicate that the Gibbs free energy and the heat capacity of nanoparticles can be divided into two parts: bulk quantity and surface quantity. The molar heat capacity of the bulk sample is lower compared with the molar heat capacity of nanoparticles, and this difference increases with the decrease in the particle size. It is also observed that the size effect on the thermodynamic properties of Cu nanoparticles is not really significant until the particle is less than about 20 nm. It is the surface atoms that decide the size effect on the thermodynamic properties of nanoparticles

  19. Calculation Tool for Determining the Net Energy Gain

    DEFF Research Database (Denmark)

    Laustsen, Jacob Birck; Svendsen, Svend

    2002-01-01

    for windows are presented. Based on these methods a program has been developed that determines the heat loss coefficient, U, and the total solar energy transmittance, g, for windows compounded of specific window components selected from a database. The program calculates the net energy gain for specific....... A proper and direct way to describe the energy performance of windows is by the net energy gain, E, which expresses the energy balance for the window. It is defined as the solar heat gain transmitted in minus the heat loss transmitted out through the window during the heating season. The net energy gain...... is dependent on both the U-values and the g-values. Beyond this it is dependent on the orientation of the windows and the climate and the actual period. This makes it difficult to choose the glazings and windows that are optimal with regard to energy performance in a given case. These facts have aroused a need...

  20. Developing a Decision Support Tool for Waste to Energy Calculations Using Energy Return on Investment

    Science.gov (United States)

    2016-12-01

    DECISION SUPPORT TOOL FOR WASTE -TO- ENERGY CALCULATIONS USING ENERGY RETURN ON INVESTMENT by Adam C. Haag December 2016 Thesis Advisor...SUPPORT TOOL FOR WASTE -TO- ENERGY CALCULATIONS USING ENERGY RETURN ON INVESTMENT 5. FUNDING NUMBERS 6. AUTHOR(S) Adam C. Haag 7. PERFORMING...economic viability of sites for waste -to- energy technologies, mirroring the current tool’s capabilities and expanding its use. This tool returns

  1. Calculation of transformers leakage reactance using electromagnetic energy technique

    International Nuclear Information System (INIS)

    Feiz, J.; Mohseni, H.; Sabet Marzooghi, S.; Naderian Jahromi, A.

    2004-01-01

    Determination of transformer leakage reactance using magnetic cores has long been an area of interest to engineers involved in the design of power and distribution transformers. This is required for predicting the performance of transformers before actual assembly of the transformers. In this paper a closed form solution technique applicable to the leakage reactance calculations for transformers is presented. An emphasis is on the development of a simple method to calculate the leakage reactance of the distribution transformers and smaller transformers. Energy technique procedure for computing the leakage reactances in distribution transformers is presented. This method is very efficient compared with the use of flux element and image technique and is also remarkably accurate. Examples of calculated leakage inductances and the short circuit impedance are given for illustration. For validation, the results are compared with the results obtained using test. This paper presents a novel technique for calculation of the leakage inductance in different parts of the transformer using the electromagnetic stored energy

  2. AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

    Science.gov (United States)

    Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

    2016-06-27

    Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection.

  3. Shielding calculation for treatment rooms of high energy linear accelerator

    International Nuclear Information System (INIS)

    Elleithy, M.A.

    2006-01-01

    A review of German Institute of Standardization (DIN) scheme of the shielding calculation and the essential data required has been done for X-rays and electron beam in the energy range from 1 MeV to 50 MeV. Shielding calculation was done for primary and secondary radiations generated during X-ray operation of Linac. In addition, shielding was done against X-rays generated (Bremsstrahlung) by useful electron beams. The calculations also covered the neutrons generated from the interactions of useful X-rays (at energies above 8 MeV) with the surrounding. The present application involved the computation of shielding against the double scattered components of X-rays and neutrons in the maze area and the thickness of the paraffin wax of the room door. A new developed computer program was designed to assist shielding thickness calculations for a new Linac installation or in replacing an existing machine. The program used a combination of published tables and figures in computing the shielding thickness at different locations for all possible radiation situations. The DIN published data of 40 MeV accelerator room was compared with the program calculations. It was found that there is good agreement between both calculations. The developed program improved the accuracy and speed of calculation

  4. On calculations of the ground state energy in quantum mechanics

    International Nuclear Information System (INIS)

    Efimov, G.V.

    1991-02-01

    In nonrelativistic quantum mechanics the Wick-ordering method called the oscillator representation suggested to calculate the ground-state energy for a wide class of potentials allowing the existence of a bound state. The following examples are considered: the orbital excitations of the ground-state in the Coulomb plus linear potential, the Schroedinger equation with a ''relativistic'' kinetic energy √p 2 +m 2 , the Coulomb three-body problem. (author). 22 refs, 2 tabs

  5. Experimental electron binding energies for thulium in different matrices

    Czech Academy of Sciences Publication Activity Database

    Inoyatov, A. K.; Kovalík, Alojz; Filosofov, D. V.; Ryšavý, Miloš; Perevoshchikov, L. L.; Yushkevich, Yu. V.; Zbořil, M.

    2015-01-01

    Roč. 202, JUL (2015), s. 46-55 ISSN 0368-2048 R&D Projects: GA MŠk LG14004; GA ČR(CZ) GAP203/12/1896 Institutional support: RVO:61389005 Keywords : Tm-169 * (169)yb * atomic environment * electron binding energy * chemical shift * natural atomic level width Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.561, year: 2015

  6. Effect of valence nucleons on nuclear binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Angeli, I. (Kossuth Lajos Tudomanyegyetem, Debrecen (HU))

    1991-10-01

    The nucleonic promiscuity factor P = N{sub p}N{sub n}/(N{sub p} + N{sub n}), where N{sub p}(N{sub n}) is the number of valence protons (neutrons) or holes, is shown to be a useful parameter in the description of the mass number dependence of nuclear binding energies. This means that most of the deviation from a smooth mass number dependence is caused by the isoscalar interaction between valence protons and neutrons.

  7. Calculation of energy spectrum of C isotope with modified Yukawa ...

    Indian Academy of Sciences (India)

    MS received 21 May 2015; revised 30 October 2015; accepted 16 December 2015; published online 12 September 2016. Abstract. In this paper, we have calculated the energy spectrum of 12C isotope in ... In 1937 [7], Wheeler [3] extended this work, and simi- lar models were suggested concurrently by Wefelmeier.

  8. Visual Method for Spectral Energy Distribution Calculation of ...

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. Visual Method for Spectral Energy Distribution Calculation of Blazars. Y. Huang1,3 & J. H. Fan2,3,∗. 1School of Computer Science and Education Software, Guangzhou University,. Guangzhou 510006, China. 2Centre for Astrophysics, Guangzhou University, Guangzhou 510006, China.

  9. Method for calculating annual energy efficiency improvement of TV sets

    International Nuclear Information System (INIS)

    Varman, M.; Mahlia, T.M.I.; Masjuki, H.H.

    2006-01-01

    The popularization of 24 h pay-TV, interactive video games, web-TV, VCD and DVD are poised to have a large impact on overall TV electricity consumption in the Malaysia. Following this increased consumption, energy efficiency standard present a highly effective measure for decreasing electricity consumption in the residential sector. The main problem in setting energy efficiency standard is identifying annual efficiency improvement, due to the lack of time series statistical data available in developing countries. This study attempts to present a method of calculating annual energy efficiency improvement for TV set, which can be used for implementing energy efficiency standard for TV sets in Malaysia and other developing countries. Although the presented result is only an approximation, definitely it is one of the ways of accomplishing energy standard. Furthermore, the method can be used for other appliances without any major modification

  10. Method for calculating annual energy efficiency improvement of TV sets

    Energy Technology Data Exchange (ETDEWEB)

    Varman, M. [Department of Mechanical Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur (Malaysia); Mahlia, T.M.I. [Department of Mechanical Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur (Malaysia)]. E-mail: indra@um.edu.my; Masjuki, H.H. [Department of Mechanical Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur (Malaysia)

    2006-10-15

    The popularization of 24 h pay-TV, interactive video games, web-TV, VCD and DVD are poised to have a large impact on overall TV electricity consumption in the Malaysia. Following this increased consumption, energy efficiency standard present a highly effective measure for decreasing electricity consumption in the residential sector. The main problem in setting energy efficiency standard is identifying annual efficiency improvement, due to the lack of time series statistical data available in developing countries. This study attempts to present a method of calculating annual energy efficiency improvement for TV set, which can be used for implementing energy efficiency standard for TV sets in Malaysia and other developing countries. Although the presented result is only an approximation, definitely it is one of the ways of accomplishing energy standard. Furthermore, the method can be used for other appliances without any major modification.

  11. Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems

    Science.gov (United States)

    Swinburne, Thomas D.; Marinica, Mihai-Cosmin

    2018-03-01

    The calculation of free energy differences for thermally activated mechanisms in the solid state are routinely hindered by the inability to define a set of collective variable functions that accurately describe the mechanism under study. Even when possible, the requirement of descriptors for each mechanism under study prevents implementation of free energy calculations in the growing range of automated material simulation schemes. We provide a solution, deriving a path-based, exact expression for free energy differences in the solid state which does not require a converged reaction pathway, collective variable functions, Gram matrix evaluations, or probability flux-based estimators. The generality and efficiency of our method is demonstrated on a complex transformation of C 15 interstitial defects in iron and double kink nucleation on a screw dislocation in tungsten, the latter system consisting of more than 120 000 atoms. Both cases exhibit significant anharmonicity under experimentally relevant temperatures.

  12. Calculations of vibration-rotation energy levels of HD+

    International Nuclear Information System (INIS)

    Balint-Kurti, G.G.; Moss, R.E.; Sadler, I.A.; Shapiro, M.

    1990-01-01

    An artificial-channels scattering method [M. Shapiro and G. G. Balint-Kurti, J. Chem. Phys. 71, 1461 (1979)] is used with a transformed Hamiltonian [R. E. Moss and I. A. Sadler, Molec. Phys. 66, 591 (1989)] to calculate the energies of vibration-rotation levels for the ground electronic state of HD + . All nonadiabatic effects, except for part of the coupling of rotational and electronic angular momenta, are accounted for. The results, which are for v=0--21, J=0,1, together with some other levels involved in observed transitions, are compared with previous calculations, particularly those of Wolniewicz and Poll [Molec. Phys. 59, 953 (1986)]. Inclusion of a correction to the energies of J≠0 levels to allow for the remaining contribution of Π electronic states permits comparison with experimental transition energies. The agreement is excellent

  13. Calculations of vibration-rotation energy levels of HD+

    Science.gov (United States)

    Balint-Kurti, G. G.; Moss, R. E.; Sadler, I. A.; Shapiro, M.

    1990-05-01

    An artificial-channels scattering method [M. Shapiro and G. G. Balint-Kurti, J. Chem. Phys. 71, 1461 (1979)] is used with a transformed Hamiltonian [R. E. Moss and I. A. Sadler, Molec. Phys. 66, 591 (1989)] to calculate the energies of vibration-rotation levels for the ground electronic state of HD+. All nonadiabatic effects, except for part of the coupling of rotational and electronic angular momenta, are accounted for. The results, which are for v=0-21, J=0,1, together with some other levels involved in observed transitions, are compared with previous calculations, particularly those of Wolniewicz and Poll [Molec. Phys. 59, 953 (1986)]. Inclusion of a correction to the energies of J≠0 levels to allow for the remaining contribution of Π electronic states permits comparison with experimental transition energies. The agreement is excellent.

  14. An ensemble docking calculation of lysozyme and HyHEL-10: Insight into the binding mechanism

    Science.gov (United States)

    Yamashita, Takefumi; Takamatsu, Yuichiro

    2017-11-01

    Although many computational methods have been proposed for predicting protein-protein complex structures, the prediction remains difficult at the atomic level. In this study, we applied a simple ensemble docking method to the complex of hen egg white lysozyme and its antibody (HyHEL-10). Although this method took into account the protein conformational ensemble, the result was not better than that of a typical rigid docking calculation. In the decomposition analysis, however, we found energetic minima near the crystal structure for a few conformation pairs. This may imply that conformational selection is essential during the early stage of binding.

  15. Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method.

    Science.gov (United States)

    Ngo, Son Tung; Mai, Binh Khanh; Hiep, Dinh Minh; Li, Mai Suan

    2015-10-01

    The binding mechanism of AC1NX476 to HIV-1 protease wild type and mutations was studied by the docking and molecular dynamics simulations. The binding free energy was calculated using the double-annihilation binding free energy method. It is shown that the binding affinity of AC1NX476 to wild type is higher than not only ritonavir but also darunavir, making AC1NX476 become attractive candidate for HIV treatment. Our theoretical results are in excellent agreement with the experimental data as the correlation coefficient between calculated and experimentally measured binding free energies R = 0.993. Residues Asp25-A, Asp29-A, Asp30-A, Ile47-A, Gly48-A, and Val50-A from chain A, and Asp25-B from chain B play a crucial role in the ligand binding. The mutations were found to reduce the receptor-ligand interaction by widening the binding cavity, and the binding propensity is mainly driven by the van der Waals interaction. Our finding may be useful for designing potential drugs to combat with HIV. © 2015 John Wiley & Sons A/S.

  16. Analysis of daylight calculated using the EnergyPlus programme

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Greici; Ghisi, Enedir [Universidade Federal de Santa Catarina, Departamento de Engenharia Civil, Laboratorio de Eficiencia Energetica em Edificacoes, Caixa Postal 476, Florianopolis - SC 88040-900 (Brazil)

    2010-09-15

    In order to properly evaluate the thermal energy performance of buildings it is also necessary to analyse the use of daylight, since this influences the thermal load of a building. In this context, the aim of this study was to evaluate the calculation of internal illuminances carried out using the EnergyPlus simulation programme. The analysis was carried out through a comparison of the Useful Daylight Illuminances (UDI) and the daylight factor (DF) estimated using the EnergyPlus programme with the results from another two programmes: Daysim/Radiance and TropLux. Also, the external horizontal illuminance estimated using EnergyPlus was compared with that measured in Florianopolis, Santa Catarina State, Brazil, between 2003 and 2005. The simulations were carried out for three different rooms: one square (5 m x 5 m x 3 m), one shallow rectangular (10 m x 5 m x 3 m) and one deep rectangular (5 m x 10 m x 3 m). From this analysis it was verified that the EnergyPlus programme has a problem related to both the DF and the external illuminance values. A comparison between the DF values calculated using the three programmes shows that there is a problem in EnergyPlus related to solving the internal reflection, such that the greater the importance of the portion of light reflected, the greater the difference found between the programmes. A comparison between the calculated and measured external horizontal illuminances shows differences greater than 100% both for the diffuse and direct illuminances indicating that the EnergyPlus programme overestimates these values. (author)

  17. Specific interactions and binding energies between thermolysin and potent inhibitors: molecular simulations based on ab initio molecular orbital method.

    Science.gov (United States)

    Hirakawa, Tatsuya; Fujita, Seiya; Ohyama, Tatsuya; Dedachi, Kenichi; Khan, Mahmud Tareq Hassan; Sylte, Ingebrigt; Kurita, Noriyuki

    2012-03-01

    Biochemical functions of the metalloprotease thermolysin (TLN) are controlled by various inhibitors. In a recent study we identified 12 compounds as TLN inhibitors by virtual screening and in vitro competitive binding assays. However, the specific interactions between TLN and these inhibitors have not been clarified. We here investigate stable structures of the solvated TLN-inhibitor complexes by classical molecular mechanics simulations and elucidate the specific interactions between TLN and these inhibitors at an electronic level by using ab initio fragment molecular orbital (FMO) calculations. The calculated binding energies between TLN and the inhibitors are qualitatively consistent with the experimental results, and the FMO results elucidate important amino acid residues of TLN for inhibitor binding. Based on the calculated results, we propose a novel potent inhibitor having a large binding affinity to TLN. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Application of Indenting Method for Calculation of Activation Energy

    International Nuclear Information System (INIS)

    Kim, Jong-Seog; Kim, Tae-Ryong

    2006-01-01

    For the calculation of activation energy of cable materials, we used to apply the break-elongation test in accordance with ASTM D412(Stand Test Methods for Rubber Properties in Tension). For the cable jacket and insulation which have regular thickness, break-elongation test had been preferred since it showed linear character in the activation energy curve. But, for the cable which has irregular thickness or rugged surface of cable inside, break-elongation test show scattered data which can not be used for the calculation of activation energy. It is not easy to prepare break-elongation specimen for the cable smaller than 13mm diameter in accordance with ASTM D412. In the cases of above, we sometime use TGA method which heat the specimen from 50 .deg. C to 700 .deg. C at heating rates of 10, 15, 20 .deg. C/min. But, TGA is suspected for the representative of natural aging in the plant since it measure the weight decreasing rate during burning which may have different aging mechanism with that of natural aging. To solve above problems, we investigated alternatives such as indenter test. Indenter test is very convenient since it does not ask for a special test specimen as the break-elongation test does. Regular surface of cable outside is the only requirement of indenter test. Experience of activation energy calculation by using the indenter test is described herein

  19. Binding energy and single–particle Energies in the 16 0 region ...

    African Journals Online (AJOL)

    ... single-particle energies in the oxygen region by folding together a Hamiltonian in the rest-frame of the nucleus with two-body correlation functions based on the Njimegen potential. We have found that the binding energies are very sensitive to the core radius rc and that the effects of tensor correlations are non-negligible.

  20. Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

    Directory of Open Access Journals (Sweden)

    Bodee Nutho

    2014-11-01

    Full Text Available In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.

  1. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.

    Directory of Open Access Journals (Sweden)

    Sharad Verma

    Full Text Available p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy have major contribution in binding free energy.

  2. A general intermolecular force field based on tight-binding quantum chemical calculations

    Science.gov (United States)

    Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

    2017-10-01

    A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

  3. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    Science.gov (United States)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  4. Impurities in semiconductors: total energy and infrared absorption calculations

    International Nuclear Information System (INIS)

    Yndurain, F.

    1987-01-01

    A new method to calculate the electronic structure of infinite nonperiodic system is discussed. The calculations are performed using atomic pseudopotentials and a basis of atomic Gaussiam wave functions. The Hartree-Fock self consistent equations are solved in the cluster-Bethe lattice system. Electron correlation is partially included in second order pertubation approximation. The formalism is applied to hydrogenated amorphous silicon. Total energy calculations of finite clusters of silicon atom in the presence of impurities, are also presented. The results show how atomic oxygen breaks the covalent silicon silicon bond forming a local configuration similar to that of SiO 2 . Calculations of the infrared absorption due to the presence of atomic oxygen in cristalline silicon are presented. The Born Hamiltonian to calculate the vibrational modes of the system and a simplied model to describe the infrared absorption mechanism are used. The interstitial and the the substitutional cases are considered and analysed. The position of the main infrared absorption peak, their intensities and their isotope shifts are calculated. The results are satisfactory agreement with the available data. (author) [pt

  5. EELOSS: the program for calculation of electron energy loss data

    International Nuclear Information System (INIS)

    Tanaka, Shun-ichi

    1980-10-01

    A computer code EELOSS has been developed to obtain the electron energy loss data required for shielding and dosimetry of beta- and gamma-rays in nuclear plants. With this code, the following data are obtainable for any energy from 0.01 to 15 MeV in any medium (metal, insulator, gas, compound, or mixture) composed of any choice of 69 elements with atomic number 1 -- 94: a) Collision stopping power, b) Restricted collision stopping power, c) Radiative stopping power, and d) Bremsstrahlung production cross section. The availability of bremsstrahlung production cross section data obtained by the EELOSS code is demonstrated by the comparison of calculated gamma-ray spectrum with measured one in Pb layer, where electron-photon cascade is included implicitly. As a result, it is concluded that the uncertainty in the bremsstrahlung production cross sections is negligible in the practical shielding calculations of gamma rays of energy less than 15 MeV, since the bremsstrahlung production cross sections increase with the gamma-ray energy and the uncertainty for them decreases with increasing the gamma-ray energy. Furthermore, the accuracy of output data of the EELOSS code is evaluated in comparison with experimental data, and satisfactory agreements are observed concerning the stopping power. (J.P.N.)

  6. Measurement of Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Chen, Xi; Zhu, Bairen; Cui, Xiaodong

    Excitonic effects are prominent in monolayer crystal of transition metal dichalcogenides (TMDCs) because of spatial confinement and reduced Coulomb screening. Here we use linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE) to measure the exciton binding energy of monolayer WS2. Peaks for excitonic absorptions of the direct gap located at K valley of the Brillouin zone and transitions from multiple points near Γ point of the Brillouin zone, as well as trion side band are shown in the linear absorption spectra of WS2. But there is no gap between distinct excitons and the continuum of the interband transitions. Strong electron-phonon scattering, overlap of excitons around Γ point and the transfer of the oscillator strength from interband continuum to exciton states make it difficult to resolve the electronic interband transition edge even down to 10K. The gap between excited states of the band-edge exciton and the single-particle band is probed by TP-PLE measurements. And the energy difference between 1s exciton and the single-particle gap gives the exciton binding energy of monolayer WS2 to be about 0.71eV. The work is supported by Area of excellency (AoE/P-04/08), CRF of Hong Kong Research Grant Council (HKU9/CRF/13G) and SRT on New Materials of The University of Hong Kong.

  7. Monte Carlo calculations for intermediate-energy standard neutron field

    International Nuclear Information System (INIS)

    Joneja, O.P.; Subbukutty, K.; Iyengar, S.B.D.; Navalkar, M.P.

    Intermediate-Energy Standard Neutron Field (ISNF) which produces a well characterised spectrum in the energy range of interest for fast reactors including breeders, has been set up at NBS using thin enriched 235 U fission sources. A proposal has been made for setting up a similar facility at BARC using however, easily available natural U instead of enriched U sources, to start with. In order to simulate the neutronics of such a facility Monte Carlo method of calculations has been adopted and developed. The results of these calculations have been compared with those of NBS and it is found that there may be a maximum difference of 10% in spectrum characteristics for the two cases of using thick and thin fission sources. (K.B.)

  8. Calculation of the energy of stacking faults in uranium dioxide

    International Nuclear Information System (INIS)

    Lefebvre, J.-M.; Soullard, J.

    1976-01-01

    Energy computations of some (100), (110) and (111), planar defects were performed using an ionic bond model for stoichiometric uranium dioxyde. The repulsive contribution to the fault was estimated in two different ways, i.e. using the Born-Mayer classical treatment, or potentials derived from shell model calculations. The stability of the various defect configurations has been studied; on the basis of the numerical values, it may be concluded that dislocation dissociation is unlikely in stoichiometric uranium dioxyde. (Auth.)

  9. Calculated surface-energy anomaly in the 3d metals

    DEFF Research Database (Denmark)

    Aldén, M.; Skriver, Hans Lomholt; Mirbt, S.

    1992-01-01

    Local-spin-density theory and a Green’s-function technique based on the linear muffin-tin orbitals method have been used to calculate the surface energy of the 3d metals. The theory explains the variation of the values derived from measurements of the surface tension of liquid metals including...... the pronounced anomaly occurring between vanadium and nickel in terms of a decrease in the d contribution caused by spin polarization....

  10. An energy dependent spatial approximation for transport deflection calculations

    International Nuclear Information System (INIS)

    Stankovski, Z.; Sanchez, R.; Roy, R.

    1989-01-01

    A model for transport depletion calculations based on an energy-dependent spatial representation of the fluxes has been developed. In the case of thermal absorbers, this model allows for regions in the fast range to be less discretized than in the thermal range. When depletion calculations are done to obtain the variation of the isotopic concentration vs. the burnup, the media where several spatial flux representations are used become heterogeneous. In the fast range, prehomogenization of the physical properties is done prior to each transport step. Even when taking into account this prehomogenization step, the computational cost of transport depleted calculations has been cut down significantly, while preserving the overall accuracy. Numerical results are given for a slab core and for a PWR poisoned assembly

  11. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  12. Energy difference space random walk to achieve fast free energy calculations.

    Science.gov (United States)

    Min, Donghong; Yang, Wei

    2008-05-21

    A method is proposed to efficiently obtain free energy differences. In the present algorithm, free energy calculations proceed by the realization of an energy difference space random walk. Thereby, this algorithm can greatly improve the sampling of the regions in phase space where target states overlap.

  13. CO dimer: new potential energy surface and rovibrational calculations.

    Science.gov (United States)

    Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker

    2013-08-15

    The spectrum of CO dimer was investigated by solving the rovibrational Schrödinger equation on a new potential energy surface constructed from coupled-cluster ab initio points. The Schrödinger equation was solved with a Lanczos algorithm. Several 4D (rigid monomer) global ab initio potential energy surfaces (PESs) were made using a previously reported interpolating moving least-squares (IMLS) fitting procedure specialized to describe the interaction of two linear fragments. The potential has two nonpolar minima giving rise to a complicated set of energy level stacks, which are very sensitive to the shapes and relative depths of the two wells. Although the CO dimer has defied previous attempts at an accurate purely ab initio description our best surface yields results in good agreement with experiment. Root-mean-square (rms) fitting errors of less than 0.1 cm(-1) were obtained for each of the fits using 2226 ab initio data at different levels. This allowed direct assessment of the quality of various levels of ab initio theory for prediction of spectra. Our tests indicate that standard CCSD(T) is slow to converge the interaction energy even when sextuple zeta bases as large as ACV6Z are used. The explicitly correlated CCSD(T)-F12b method was found to recover significantly more correlation energy (from singles and doubles) at the CBS limit. Correlation of the core-electrons was found to be important for this system. The best PES was obtained by extrapolation of calculations at the CCSD(T)(AE)-F12b/CVnZ-F12 (n = 3,4) levels. The calculated energy levels were compared to 105 J ≤ 10 levels from experiment. The rms error for 68 levels with J ≤ 6 is only 0.29 cm(-1). The calculated energy levels were assigned stack labels using several tools. New stacks were found. One of them, stack y1, has an energy lower than many previously known stacks and may be observable.

  14. Calculated intensity of high-energy neutron beams

    International Nuclear Information System (INIS)

    Mustapha, B.; Nolen, J.A.; Back, B.B.

    2004-01-01

    The flux, energy and angular distributions of high-energy neutrons produced by in-flight spallation and fission of a 400 MeV/A 238 U beam and by the break-up of a 400 MeV/A deuteron beam are calculated. In both cases very intense secondary neutron beams are produced, peaking at zero degrees, with a relatively narrow energy spread. Such secondary neutron beams can be produced with the primary beams from the proposed rare isotope accelerator driver linac. The break-up of a 400 kW deuteron beam on a liquid-lithium target can produce a neutron flux of >10 10 neutrons/cm 2 /s at a distance of 10 m from the target

  15. An Accurate Redetermination of the $^{118}Sn$ Binding Energy

    CERN Document Server

    Borzakov, S B; Faikow-Stanczyk, H; Grigoriev, Yu V; Panteleev, T; Pospísil, S; Smotritsky, L M; Telezhnikov, S A

    2001-01-01

    The energy of well-known strong {gamma}-line from {{^198}Au}, the "gold standard", has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, {B_n}, from complicated {(n , gamma)}-spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taking into account by a Monte Carlo simulation. The procedure was used in obtaining of {B_n} for {{^118}Sn} and {{^64}Cu}. The {gamma}-ray spectrum from thermal neutron radiative capture by {{^117}Sn} has been measured on the IBR-2 pulsed reactor. {gamma}-rays were detected by a 72 cm^3 HPGe-detector. {B_n} for {{^64}Cu} was obtained from two {gamma}-...

  16. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations.

    Science.gov (United States)

    Ullmann, R Thomas; Andrade, Susana L A; Ullmann, G Matthias

    2012-08-16

    Amt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting membrane proteins. The transport mode and the precise microscopic permeation mechanism utilized by these proteins are intensely debated. Open questions concern the identity of the transported substrate (ammonia and/or ammonium) and whether the transport is passive or active. To address these questions, we studied the overall thermodynamics of the different transport modes as a function of the environmental conditions. Then, we investigated the thermodynamics of the underlying microscopic transport mechanisms with free energy calculations within a continuum electrostatics model. The formalism developed for this purpose is of general utility in the calculation of binding free energies for ligands with multiple protonation forms or other binding forms. The results of our calculations are compared to the available experimental and theoretical data on Amt/Rh proteins and discussed in light of the current knowledge on the physiological conditions experienced by microorganisms and plants. We found that microscopic models of electroneutral and electrogenic transport modes are in principle thermodynamically viable. However, only the electrogenic variants have a net thermodynamic driving force under the physiological conditions experienced by microorganisms and plants. Thus, the transport mechanism of AfAmt-1 is most likely electrogenic.

  17. Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    2018-01-01

    Full Text Available DNA is the target of chemical compounds (drugs, pollutants, photosensitizers, etc., which bind through non-covalent interactions. Depending on their structure and their chemical properties, DNA binders can associate to the minor or to the major groove of double-stranded DNA. They can also intercalate between two adjacent base pairs, or even replace one or two base pairs within the DNA double helix. The subsequent biological effects are strongly dependent on the architecture of the binding motif. Discriminating between the different binding patterns is of paramount importance to predict and rationalize the effect of a given compound on DNA. The structural characterization of DNA complexes remains, however, cumbersome at the experimental level. In this contribution, we employed all-atom molecular dynamics simulations to determine the standard binding free energy of DNA with netropsin, a well-characterized antiviral and antimicrobial drug, which associates to the minor groove of double-stranded DNA. To overcome the sampling limitations of classical molecular dynamics simulations, which cannot capture the large change in configurational entropy that accompanies binding, we resort to a series of potentials of mean force calculations involving a set of geometrical restraints acting on collective variables.

  18. Graphical Calculation of Estimated Energy Expenditure in Burn Patients.

    Science.gov (United States)

    Egro, Francesco M; Manders, Ernest C; Manders, Ernest K

    2018-03-01

    Historically, estimated energy expenditure (EEE) has been related to the percent of body surface area burned. Subsequent evaluations of these estimates have indicated that the earlier formulas may overestimate the amount of caloric support necessary for burn-injured patients. Ireton-Jones et al derived 2 equations for determining the EEE required to support burn patients, 1 for ventilator-dependent patients and 1 for spontaneously breathing patients. Evidence has proved their reliability, but they remain challenging to apply in a clinical setting given the difficult and cumbersome mathematics involved. This study aims to introduce a graphical calculation of EEE in burn patients that can be easily used in the clinical setting. The multivariant linear regression analysis from Ireton-Jones et al yielded equations that were rearranged into the form of a simple linear equation of the type y = mx + b. By choosing an energy expenditure and the age of the subject, the weight was calculated. The endpoints were then calculated, and a graph was mapped by means of Adobe FrameMaker. A graphical representation of Ireton-Jones et al's equations was obtained by plotting the weight (kg) on the y axis, the age (years) on the x axis, and a series of parallel lines representing the EEE in burn patients. The EEE has been displayed graphically on a grid to allow rapid determination of the EEE needed for a given patient of a designated weight and age. Two graphs were plotted: 1 for ventilator-dependent patients and 1 for spontaneously breathing patients. Correction factors for sex, the presence of additional trauma, and obesity are indicated on the graphical calculators. We propose a graphical tool to calculate caloric requirements in a fast, easy, and portable manner.

  19. Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization.

    Science.gov (United States)

    Zhang, Haiyang; Tan, Tianwei; van der Spoel, David

    2015-11-10

    Evaluation of solvation (binding) free energies with implicit solvent models in different dielectric environments for biological simulations as well as high throughput ligand screening remain challenging endeavors. In order to address how well implicit solvent models approximate explicit ones we examined four generalized Born models (GB(Still), GB(HCT), GB(OBC)I, and GB(OBC)II) for determining the dimerization free energy (ΔG(0)) of β-cyclodextrin monomers in 17 implicit solvents with dielectric constants (D) ranging from 5 to 80 and compared the results to previous free energy calculations with explicit solvents ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 12684 - 12693 ). The comparison indicates that neglecting the environmental dependence of Born radii appears acceptable for such calculations involving cyclodextrin and that the GB(Still) and GB(OBC)I models yield a reasonable estimation of ΔG(0), although the details of binding are quite different from explicit solvents. Large discrepancies between implicit and explicit solvent models occur in high-dielectric media with strong hydrogen bond (HB) interruption properties. ΔG(0) with the GB models is shown to correlate strongly to 2(D-1)/(2D+1) (R(2) ∼ 0.90) in line with the Onsager reaction field ( Onsager J. Am. Chem. Soc. 1936 , 58 , 1486 - 1493 ) but to be very sensitive to D (D J. Chem. Inf. Model . 2015 , 55 , 1192 - 1201 ) reproduce the weak experimental correlations with 2(D-1)/(2D+1) very well.

  20. Uranium(VI) Binding Forms in Selected Human Body Fluids: Thermodynamic Calculations versus Spectroscopic Measurements.

    Science.gov (United States)

    Osman, Alfatih A A; Geipel, Gerhard; Barkleit, Astrid; Bernhard, Gert

    2015-02-16

    Human exposure to uranium increasingly becomes a subject of interest in many scientific disciplines such as environmental medicine, toxicology, and radiation protection. Knowledge about uranium chemical binding forms(speciation) in human body fluids can be of great importance to understand not only its biokinetics but also its relevance in risk assessment and in designing decorporation therapy in the case of accidental overexposure. In this study, thermodynamic calculations of uranium speciation in relevant simulated and original body fluids were compared with spectroscopic data after ex-situ uranium addition. For the first time, experimental data on U(VI) speciation in body fluids (saliva, sweat, urine) was obtained by means of cryogenic time-resolved laser-induced fluorescence spectroscopy (cryo-TRLFS) at 153 K. By using the time dependency of fluorescence decay and the band positions of the emission spectra, various uranyl complexes were demonstrated in the studied samples. The variations of the body fluids in terms of chemical composition, pH, and ionic strength resulted in different binding forms of U(VI). The speciation of U(VI) in saliva and in urine was affected by the presence of bioorganic ligands, whereas in sweat, the distribution depends mainly on inorganic ligands. We also elucidated the role of biological buffers, i.e., phosphate (H(2)PO(4−)/HPO(4)(2−)) on U(VI) distribution, and the system Ca(2+)/UO(2)(2+)/PO(4)(3−) was discussed in detail in both saliva and urine. The theoretical speciation calculations of the main U(VI) species in the investigated body fluids were significantly consistent with the spectroscopic data. Laser fluorescence spectroscopy showed success and reliability for direct determination of U(VI) in such biological matrices with the possibility for further improvement.

  1. Higher order energy transfer. Quantum electrodynamical calculations and graphical representation

    International Nuclear Information System (INIS)

    Jenkins, R.D.

    2000-01-01

    In Chapter 1, a novel method of calculating quantum electrodynamic amplitudes is formulated using combinatorial theory. This technique is used throughout instead of conventional time-ordered methods. A variety of hyperspaces are discussed to highlight isomorphism between a number of A generalisation of Pascal's triangle is shown to be beneficial in determining the form of hyperspace graphs. Chapter 2 describes laser assisted resonance energy transfer (LARET), a higher order perturbative contribution to the well-known process resonance energy transfer, accommodating an off resonance auxiliary laser field to stimulate the migration. Interest focuses on energy exchanges between two uncorrelated molecular species, as in a system where molecules are randomly oriented. Both phase-weighted and standard isotropic averaging are required for the calculations. Results are discussed in terms of a laser intensity-dependent mechanism. Identifying the applied field regime where LARET should prove experimentally significant, transfer rate increases of up to 30% are predicted. General results for three-center energy transfer are elucidated in chapter 3. Cooperative and accretive mechanistic pathways are identified with theory formulated to elicit their role in a variety of energy transfer phenomena and their relative dominance. In multichromophoric the interplay of such factors is analysed with regard to molecular architectures. The alignments and magnitudes of donor and acceptor transition moments and polarisabilities prove to have profound effects on achievable pooling efficiency for linear configurations. Also optimum configurations are offered. In ionic lattices, although both mechanisms play significant roles in pooling and cutting processes, only the accretive is responsible for sensitisation. The local, microscopic level results are used to gauge the lattice response, encompassing concentration and structural effects. (author)

  2. Calculation steps. Building integrated energy supply; Beregningsgang. Bygningsintegreret energiforsyning

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Rasmus L.; Noergaard, J.; Daniels, O.; Justesen, R.O.

    2011-08-15

    In the future, buildings will not only act as consumers of energy but as producers as well. For these ''prosumers'', energy production by use of solar panels, photovoltaics and heat pumps etc will be essential. The objective of this project was to find the most optimal combinations of building insulation and use of renewable energy sources in existing buildings in terms of economics and climate impacts. Five houses were analyzed based on different personal load, consumption profiles, solar orientation and proposed building envelope improvements and use of combinations of renewable energy systems. The analysis was conducted by making a large number of simulations. The present report describes the applied simulation models, and explains the results and computer codes. The parameter variations are described for each house as well as the common calculation steps for each house. The results are presented in case sheets, as performance graphs, and top-50 lists for the best cases regarding CO{sub 2} emission, energy consumption and economics. (ln)

  3. Atom probe tomography simulations and density functional theory calculations of bonding energies in Cu3Au

    KAUST Repository

    Boll, Torben

    2012-10-01

    In this article the Cu-Au binding energy in Cu3Au is determined by comparing experimental atom probe tomography (APT) results to simulations. The resulting bonding energy is supported by density functional theory calculations. The APT simulations are based on the Müller-Schottky equation, which is modified to include different atomic neighborhoods and their characteristic bonds. The local environment is considered up to the fifth next nearest neighbors. To compare the experimental with simulated APT data, the AtomVicinity algorithm, which provides statistical information about the positions of the neighboring atoms, is applied. The quality of this information is influenced by the field evaporation behavior of the different species, which is connected to the bonding energies. © Microscopy Society of America 2012.

  4. Binding energies of hypernuclei and Λ-nuclear interactions

    International Nuclear Information System (INIS)

    Bodmer, A.R.; Usmani, Q.N.

    1985-01-01

    Variational Monte Carlo calculations have been made for the s-shell hypernuclei and also of 9 Be hypernuclei with a 2α + Λ model. The well depth is calculated variationally with the Fermi hypernetted chain method. A satisfactory description of all the relevant experimental Λ separation energies and also of the Λp scattering can be obtained with reasonable TPE ΛN and ΛNN forces and strongly repulsive dispersive ΛNN forces which are preferred to be spin dependent. We discuss variational calculations for 6 He and 10 Be hypernuclei with α + 2Λ and 2α + 2Λ models, and the results obtained for the ΛΛ interaction and for 6 He hypernuclei from analysis of 10 Be hypernuclei Coulomb effects and charge symmetry breaking in the A = 4 hypernuclei are discussed. 24 refs., 5 figs

  5. Binding energies of hypernuclei and. lambda. -nuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R.; Usmani, Q.N.

    1985-01-01

    Variational Monte Carlo calculations have been made for the s-shell hypernuclei and also of /sup 9/Be hypernuclei with a 2..cap alpha.. + ..lambda.. model. The well depth is calculated variationally with the Fermi hypernetted chain method. A satisfactory description of all the relevant experimental ..lambda.. separation energies and also of the ..lambda..p scattering can be obtained with reasonable TPE ..lambda..N and ..lambda..NN forces and strongly repulsive dispersive ..lambda..NN forces which are preferred to be spin dependent. We discuss variational calculations for /sup 6/He and /sup 10/Be hypernuclei with ..cap alpha.. + 2..lambda.. and 2..cap alpha.. + 2..lambda.. models, and the results obtained for the ..lambda lambda.. interaction and for /sup 6/He hypernuclei from analysis of /sup 10/Be hypernuclei Coulomb effects and charge symmetry breaking in the A = 4 hypernuclei are discussed. 24 refs., 5 figs.

  6. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

    Science.gov (United States)

    Deng, Nanjie; Forli, Stefano; He, Peng; Perryman, Alex; Wickstrom, Lauren; Vijayan, R S K; Tiefenbrunn, Theresa; Stout, David; Gallicchio, Emilio; Olson, Arthur J; Levy, Ronald M

    2015-01-22

    Molecular docking is a powerful tool used in drug discovery and structural biology for predicting the structures of ligand-receptor complexes. However, the accuracy of docking calculations can be limited by factors such as the neglect of protein reorganization in the scoring function; as a result, ligand screening can produce a high rate of false positive hits. Although absolute binding free energy methods still have difficulty in accurately rank-ordering binders, we believe that they can be fruitfully employed to distinguish binders from nonbinders and reduce the false positive rate. Here we study a set of ligands that dock favorably to a newly discovered, potentially allosteric site on the flap of HIV-1 protease. Fragment binding to this site stabilizes a closed form of protease, which could be exploited for the design of allosteric inhibitors. Twenty-three top-ranked protein-ligand complexes from AutoDock were subject to the free energy screening using two methods, the recently developed binding energy analysis method (BEDAM) and the standard double decoupling method (DDM). Free energy calculations correctly identified most of the false positives (≥83%) and recovered all the confirmed binders. The results show a gap averaging ≥3.7 kcal/mol, separating the binders and the false positives. We present a formula that decomposes the binding free energy into contributions from the receptor conformational macrostates, which provides insights into the roles of different binding modes. Our binding free energy component analysis further suggests that improving the treatment for the desolvation penalty associated with the unfulfilled polar groups could reduce the rate of false positive hits in docking. The current study demonstrates that the combination of docking with free energy methods can be very useful for more accurate ligand screening against valuable drug targets.

  7. Binding energy of a hydrogenic impurity in a coaxial quantum wire with an insulator layer

    Science.gov (United States)

    Kes, H.; Bilekkaya, A.; Aktas, S.; Okan, S. E.

    2017-11-01

    The electronic properties of a coaxial cylindrical quantum well-barrier system constituted about an central insulating wire were determined under an external electric field. The model wire, inside to outside, was considered to be layered as AlAs / GaAs / Alx1 Ga1 -x1 As / GaAs / Alx2 Ga1 -x2 As. Within the framework of the effective mass-approximation, the binding energy of a hydrogenic impurity is calculated by using the combination of the fourth-order Runge-Kutta method and variational approaches. The binding energy exhibits sharp changes depending on the impurity position and the geometrical parameters of the structure such as the well widths of the GaAs wires and the height and thickness of the barrier constituted by Alx1 Ga1 -x1 As . The binding energy of the electron was found to be independent from the impurity position for the specific widths of the well wires. Also, the barrier properties appeared as very effective parameters in controlling the probability distribution of the electron.

  8. Development of nuclear models for higher energy calculations

    International Nuclear Information System (INIS)

    Bozoian, M.; Siciliano, E.R.; Smith, R.D.

    1988-01-01

    Two nuclear models for higher energy calculations have been developed in the regions of high and low energy transfer, respectively. In the former, a relativistic hybrid-type preequilibrium model is compared with data ranging from 60 to 800 MeV. Also, the GNASH exciton preequilibrium-model code with higher energy improvements is compared with data at 200 and 318 MeV. In the region of low energy transfer, nucleon-nucleus scattering is predominately a direct reaction involving quasi-elastic collisions with one or more target nucleons. We discuss various aspects of quasi-elastic scattering which are important in understanding features of cross sections and spin observables. These include (1) contributions from multi-step processes; (2) damping of the continuum response from 2p-2h excitations; (3) the ''optimal'' choice of frame in which to evaluate the nucleon-nucleon amplitudes; and (4) the effect of optical and spin-orbit distortions, which are included in a model based on the RPA the DWIA and the eikonal approximation. 33 refs., 15 figs

  9. Ab initio calculations of free-energy reaction barriers

    International Nuclear Information System (INIS)

    Bucko, T

    2008-01-01

    The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion

  10. Double binding energy differences: Mean-field or pairing effect?

    Science.gov (United States)

    Qi, Chong

    2012-10-01

    In this Letter we present a systematic analysis on the average interaction between the last protons and neutrons in atomic nuclei, which can be extracted from the double differences of nuclear binding energies. The empirical average proton-neutron interaction Vpn thus derived from experimental data can be described in a very simple form as the interplay of the nuclear mean field and the pairing interaction. It is found that the smooth behavior as well as the local fluctuations of the Vpn in even-even nuclei with N ≠ Z are dominated by the contribution from the proton-neutron monopole interactions. A strong additional contribution from the isoscalar monopole interaction and isovector proton-neutron pairing interaction is seen in the Vpn for even-even N = Z nuclei and for the adjacent odd-A nuclei with one neutron or proton being subtracted.

  11. Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.

    Science.gov (United States)

    Steinbrecher, Thomas; Abel, Robert; Clark, Anthony; Friesner, Richard

    2017-04-07

    Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations. Free energy perturbation theory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-based approach for calculating thermodynamic effects of, for example, protein side-chain mutations. Over the past several years, we have initiated an investigation of the ability of our most recent free energy perturbation methodology to model the thermodynamics of protein mutation for two specific problems: protein-protein binding affinities and protein thermal stability. We highlight recent advances in the field and outline current and future challenges. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Calculations of molecular ionization energies using a self-consistent-charge Hartree-Fock-Slater method

    Science.gov (United States)

    Rosen, A.; Ellis, D. E.; Adachi, H.; Averill, F. W.

    1976-01-01

    A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.

  13. Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study

    Science.gov (United States)

    Yang, Zhiwei; Yang, Gang; Zhou, Lijun

    2013-11-01

    A systematic study has been performed on neuraminidase (NA) mutations and NA-inhibitor docked complexes, with the aim to understand protein-ligand interactions and design broad-spectrum antiviral drugs with minimal resistances. The catalytic D151 residue is likely to mutate while others are relatively conserved. The NA active-site conformations are altered by mutations, but more alterations do not necessarily result in larger deviations to the binding properties. The effects of all related mutations have been discussed; e.g., for the arginine triad (R118, R292 and R371), it is found that residue R118 plays the most significant role during ligand binding. Generally, the calculated binding free energies agree well with the experimental observations. Susceptibility of influenza virus to NA inhibitors can be reinforced by some mutations; e.g., the binding free energies of ligands with N2 subtype increase from -18.0 to -42.1 kcal mol-1 by the E119D mutation. Mutations of the various NA subtypes often cause similar conformational and binding changes, explaining the occurrence of cross resistances; nonetheless, differences can be detected in some cases that correspond to subtype-specific resistances. For all NA subtypes, the electrostatic contributions are the major driving force for ligand binding and largely responsible for the binding differences between the wild-type and mutated NA proteins.

  14. Kaempferol-human serum albumin interaction: Characterization of the induced chirality upon binding by experimental circular dichroism and TDDFT calculations

    Science.gov (United States)

    Matei, Iulia; Ionescu, Sorana; Hillebrand, Mihaela

    2012-10-01

    The experimental induced circular dichroism (ICD) and absorption spectra of the achiral flavonoid kaempferol upon binding to human serum albumin (HSA) were correlated to electronic CD and UV-vis spectra theoretically predicted by time-dependent density functional theory (TDDFT). The neutral and four anionic species of kaempferol in various conformations were considered in the calculations. The appearance of the experimental ICD signal was rationalized in terms of kaempferol binding to HSA in a distorted, chiral, rigid conformation. The comparison between the experimental and simulated spectra allowed for the identification of the kaempferol species that binds to HSA, namely the anion generated by deprotonation of the hydroxyl group in position 7. This approach constitutes a convenient method for evidencing the binding species and for determining its conformation in the binding pocket of the protein. Its main advantage over the UV-vis absorption method lays in the fact that only the bound ligand species gives an ICD signal.

  15. An exploration of possible design options for a binding energy savings target in Europe

    NARCIS (Netherlands)

    Harmsen, Robert; Eichhammer, Wolfgang; Wesselink, Bart

    2014-01-01

    As Europe is not on track in meeting its 2020 energy savings target, there has been quite some debate to make the energy savings target binding instead of indicative. Although the final draft text of the Energy Efficiency Directive left the option of a binding target explicitly open for the period

  16. Calculation of Bremsstrahlung energy spectrum induced by beta ray

    CERN Document Server

    Fukano, S

    2003-01-01

    Bremsstrahlung energy spectra induced by beta ray from radionuclides sup 3 H, sup 6 sup 3 Ni, sup 1 sup 4 C, sup 1 sup 4 sup 7 Pm, sup 9 sup 0 Sr, sup 3 sup 2 P and sup 9 sup 0 Y are calculated by using numerical data of radiation yield published by Berger et. al. and compared with those obtained from classical approximate expressions of Wu and Segre. The results for sup 3 H, sup 6 sup 3 Ni, sup 1 sup 4 C and sup 1 sup 4 sup 7 Pm are in good agreement with those from Segre's, while spectra from such as sup 3 sup 2 P and sup 9 sup 0 Y are similar to those obtained by using Wu's expression. The result for sup 9 sup 0 Sr is in fair agreement with those from Wu's and Segre's.

  17. Variationally Optimized Free-Energy Flooding for Rate Calculation

    Science.gov (United States)

    McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

    2015-08-01

    We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

  18. Hypernuclear interactions and the binding energies of and hypernuclei

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R.; Usmani, Q.N.

    1988-01-01

    By use of variational calculations a reasonable hadronic description is obtained of the s-shell hypernuclei, of /sub /ZBe, and of the well depth, with N forces which are consistent with p scattering and which are quite strongly spin-dependent, with reasonable TPE NN forces with strongly repulsive dispersive-type NN forces. For the latter we also consider a spin-dependent version which is somewhat favored by our analysis. /sub /ZBe is treated as a 2ed + system and is significantly overbound, approx. =1 MeV, if only ed ed and ed potentials are used. An ed ed potential obtained from the NN forces nicely accounts for this overbinding. The hypernuclei /sub /WHe and /sub / Be are treated as ed + 2 and 2ed + 2 systems. Use of the /sub / Be event gives approx. =1.5 MeV too little binding for /sub /WHe. The S0 potential obtained from /sub / Be is quite strongly attractive, comparable to the N and also to the NN potential without OPE. 18 refs.

  19. Research on energy transmission calculation problem on laser detecting submarine

    Science.gov (United States)

    Fu, Qiang; Li, Yingchao; Zhang, Lizhong; Wang, Chao; An, Yan

    2014-12-01

    The laser detection and identification is based on the method of using laser as the source of signal to scan the surface of ocean. If the laser detection equipment finds out the target, it will immediately reflect the returning signal, and then through receiving and disposing the returning signal by the receiving system, to realize the function of detection and identification. Two mediums channels should be though in the process of laser detection transmission, which are the atmosphere and the seawater. The energy loss in the process of water transport, mainly considering the surface reflection and scattering attenuation and internal attenuation factors such as seawater. The energy consumption though atmospheric transmission, mainly considering the absorption of atmospheric and the attenuation causing by scattering, the energy consumption though seawater transmission, mainly considering the element such as surface reflection, the attenuation of scattering and internal attenuation of seawater. On the basis of the analysis and research, through the mode of establishment of atmospheric scattering, the model of sea surface reflection and the model of internal attenuation of seawater, determine the power dissipation of emitting lasers system, calculates the signal strength that reaches the receiver. Under certain conditions, the total attenuation of -98.92 dB by calculation, and put forward the related experiment scheme by the use of Atmospheric analog channel, seawater analog channel. In the experiment of the theory, we use the simulation pool of the atmosphere and the sea to replace the real environment where the laser detection system works in this kind of situation. To start with, we need to put the target in the simulating seawater pool of 10 meters large and then control the depth of the target in the sea level. We, putting the laser detection system in position where it is 2 kilometers far from one side, secondly use the equipment to aim at the target in some

  20. Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 1: free energy of binding to a binding site.

    Science.gov (United States)

    Chunsrivirot, Surasak; Diao, Ying; Trout, Bernhardt L

    2011-10-18

    Crystallization is commonly used in a separation and purification process in the production of a wide range of materials in various industries. In industry, crystallization usually starts with heterogeneous nucleation on a foreign surface. The complicated mechanism of heterogeneous nucleation is not well understood; however, we hypothesize that there might be a possible correlation between binding affinity to a surface and enhancement of nucleation. Recent studies show that amorphous polymers can be used to control crystallization, selectively produce pharmaceutical polymorphs, and discover novel pharmaceutical polymorphs. To investigate the possible correlation between the binding affinity of one molecule to key binding sites (local binding) and heterogeneous nucleation activity as well as the possibility of using this binding affinity to help guide the selection of polymers that promote heterogeneous nucleation, we computed the free energy of binding of aspirin to four nonporous cross-linked polymers in an ethanol-water 38 v% mixture. These cross-linked polymers are poly(4-acryloylmorpholine) (PAM), poly(2-carboxyethyl acrylate) (PCEA), poly(4-hydroxylbutyl acrylate) (PHBA), and polystyrene (PS); all of them were cross-linked with divinylbenzene (DVB). These systems were used because their heterogeneous nucleation activities are available in literature, and the ranking is PAM > PCEA > PHBA ≈ PS. We generated three independent surfaces for each polymer and computed the free energy of binding of aspirin to the best binding site that we found on each surface. The average free energies of binding to the best sites of PAM, PCEA, PHBA, and PS are -20.4 ± 1.0, -16.7 ± 1.0, -14.4 ± 1.1, and -13.6 ± 1.1 kcal/mol, respectively. We found that the trend of the magnitudes of the average free energies of binding to the best sites is PAM > PCEA > PHBA ≈ PS. This trend is very similar to that of heterogeneous nucleation activity. Our results suggest the importance of the

  1. First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO.

    Science.gov (United States)

    Lábas, Anikó; Menyhárd, Dóra K; Harvey, Jeremy N; Oláh, Julianna

    2017-12-28

    Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O 2 , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

    Science.gov (United States)

    Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

    2015-01-01

    A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

  3. An Energy Conservation Approach to Adsorbate-Induced Surface Stress and the Extraction of Binding Energy Using Nanomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Pinnaduwage, Lal A [ORNL; Boiadjiev, Vassil I [ORNL; Fernando, G. W. [University of Connecticut, Storrs; Hawk, J. E. [Oak Ridge National Laboratory (ORNL); Wijewardhana, L.C. R. [University of Cincinnati; Gehl, Anthony C [ORNL

    2008-01-01

    Microcantilevers are ideally-suited for the study of surface phenomena due to their large surface-to-volume ratios, which amplify surface effects. We show that when guest molecules bind to atoms/molecules on a microcantilever surface, the released binding energy is retained in the host surface, leading to a metastable state where the excess energy on the surface is manifested as an increase in surface stress leading to the bending of the microcantilever. When the excess energy is released, the microcantilever relaxes back to the original state, and the relaxation time depends on the particular binding process involved. Such experiments were conducted for three binding processes in vapor phase experiments: physisorption, hydrogen bonding, and chemisorption. To our knowledge, such an energy conservation approach has not been taken into account in adsorbate-induced surface effect investigations. Furthermore, these experiments illustrate that detailed molecular-level information on binding energies can be extracted from this simple micromechanical sensor.

  4. Assessing the stability of free-energy perturbation calculations by performing variations in the method

    Science.gov (United States)

    Manzoni, Francesco; Ryde, Ulf

    2018-03-01

    We have calculated relative binding affinities for eight tetrafluorophenyl-triazole-thiogalactoside inhibitors of galectin-3 with the alchemical free-energy perturbation approach. We obtain a mean absolute deviation from experimental estimates of only 2-3 kJ/mol and a correlation coefficient (R 2) of 0.5-0.8 for seven relative affinities spanning a range of up to 11 kJ/mol. We also studied the effect of using different methods to calculate the charges of the inhibitor and different sizes of the perturbed group (the atoms that are described by soft-core potentials and are allowed to have differing coordinates). However, the various approaches gave rather similar results and it is not possible to point out one approach as consistently and significantly better than the others. Instead, we suggest that such small and reasonable variations in the computational method can be used to check how stable the calculated results are and to obtain a more accurate estimate of the uncertainty than if performing only one calculation with a single computational setup.

  5. An energy conservation approach to adsorbate-induced surface stress and the extraction of binding energy using nanomechanics

    Science.gov (United States)

    Pinnaduwage, Lal A.; Boiadjiev, Vassil I.; Hawk, John E.; Gehl, Anthony C.; Fernando, Gayanath W.; Rohana Wijewardhana, L. C.

    2008-03-01

    Surface stress induced by molecular adsorption in three different binding processes has been studied experimentally using a microcantilever sensor. A comprehensive free-energy analysis based on an energy conservation approach is proposed to explain the experimental observations. We show that when guest molecules bind to atoms/molecules on a microcantilever surface, the released binding energy is retained in the host surface, leading to a metastable state where the excess energy on the surface is manifested as an increase in surface stress leading to the bending of the microcantilever. The released binding energy appears to be almost exclusively channeled to the surface energy, and energy distribution to other channels, including heat, appears to be inactive for this micromechanical system. When this excess surface energy is released, the microcantilever relaxes back to the original state, and the relaxation time depends on the particular binding process involved. Such vapor phase experiments were conducted for three binding processes: physisorption, hydrogen bonding, and chemisorption. Binding energies for these three processes were also estimated.

  6. An energy conservation approach to adsorbate-induced surface stress and the extraction of binding energy using nanomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Pinnaduwage, Lal A; Boiadjiev, Vassil I; Hawk, John E; Gehl, Anthony C [Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6122 (United States); Fernando, Gayanath W [Physics Department, University of Connecticut, Storrs, CT 06269 (United States); Wijewardhana, L C Rohana [Physics Department, University of Cincinnati, Cincinnati, OH 45221 (United States)

    2008-03-12

    Surface stress induced by molecular adsorption in three different binding processes has been studied experimentally using a microcantilever sensor. A comprehensive free-energy analysis based on an energy conservation approach is proposed to explain the experimental observations. We show that when guest molecules bind to atoms/molecules on a microcantilever surface, the released binding energy is retained in the host surface, leading to a metastable state where the excess energy on the surface is manifested as an increase in surface stress leading to the bending of the microcantilever. The released binding energy appears to be almost exclusively channeled to the surface energy, and energy distribution to other channels, including heat, appears to be inactive for this micromechanical system. When this excess surface energy is released, the microcantilever relaxes back to the original state, and the relaxation time depends on the particular binding process involved. Such vapor phase experiments were conducted for three binding processes: physisorption, hydrogen bonding, and chemisorption. Binding energies for these three processes were also estimated.

  7. Caveat Emptor: Calculating All the Costs of Energy.

    Science.gov (United States)

    Zinberg, Dorothy S.

    This paper examines the energy problem. Specific topics discussed include the recent history of oil and gas consumption in the United States, conservation, coal, solar energy, and nuclear energy. While solutions to the energy problem differ, there is an urgent need for broad, public debate. Ultimately, the decisions made regarding energy will be…

  8. Resonance energy transfer study on the proximity relationship between the GTP binding site and the rifampicin binding site of Escherichia coli RNA polymerase

    International Nuclear Information System (INIS)

    Kumar, K.P.; Chatterji, D.

    1990-01-01

    Terbium(III) upon complexation with guanosine 5'-triphosphate showed remarkable enhancement of fluorescence emission at 488 and 545 nm when excited at 295 nm. Analysis of the binding data yielded a value for the mean K d between Tb(III) and GTP of 0.2 μM, with three binding sites for TB(III) on GTP. 31 P and 1 H NMR measurements revealed that Tb(III) mainly binds the phosphate moiety of GTP. Fluorescence titration of the emission signals of the TbGTP complex with varying concentrations of Escherichia coli RNA polymerase resulted in a K d values of 4 μM between the TbGTP and the enzyme. It was observed that TbGTP can be incorporated in the place of GTP during E. coli RNA polymerase catalyzed abortive synthesis of dinucleotide tetraphosphate at T7A2 promoter. Both the substrate TbGTP and the inhibitor of the initiation of transcription rifampicin bind to the β-subunit of E. coli RNA polymerase. This allows the measurement of the fluorescence excited-state energy transfer from the donor TbGTP-RNA polymerase to the acceptor rifampicin. Both emission bands of Tb(III) overlap with the rifampicin absorption, and the distances at 50% efficiency of energy transfer were calculated to be 28 and 24 angstrom for the 488- and 545-nm emission bands, respectively. The distance between the substrate binding site and the rifampicin binding site on the β-subunit of E. coli RNA polymerase was measured to be around 30 angstrom. This suggest that the nature of inhibition of transcription by rifampicin is essentially noncompetitive with the substrate

  9. Calculation of almost all energy levels of baryons

    Directory of Open Access Journals (Sweden)

    Mario Everaldo de Souza

    2011-03-01

    Full Text Available It is considered that the effective  interaction between any two quarks of a baryon can be approximately described by a simple harmonic potential. The problem is firstly solved in Cartesian coordinates in order to find the energy levels irrespective of their angular momenta. Then, the problem is also solved in polar cylindrical coordinates in order to take into account the angular momenta of the levels. Comparing the two solutions, a correspondence is made between the angular momenta and parities for almost all experimentally determined levels. The agreement with the experimental data is quite impressive and, in general, the discrepancy between calculated and experimental values is below 5%. A couple of levels of $Delta$, $N$, $Sigma^{pm}$, and $Omega$ present discrepacies between 6.7% and 12.5% ($N(1655$, $N(1440$, $N(1675$, $N(1685$, $N(1700$, $N(1710$, $N(1720$, $N(1990$, $N(2600$, $Delta(1700$, $Delta(2000$, $Delta(2300$, $Sigma^{pm}(1189$, $Lambda(1520$, $Omega(1672$ and $Omega(2250$.Received: 6 June 2011, Accepted: 13 July 2011; Edited by: D. Restrepo; Reviewed by: J. H. Muñoz, Universidad del Tolima, Ibagué, Colombia and Centro Brasileiro de Pesquisas Fisica; DOI: http://dx.doi.org/10.4279/PIP.030003Cite as: M. E. de Souza, Papers in Physics 3, 030003 (2011

  10. Biexciton binding energy in ZnSe quantum wells and quantum wires

    DEFF Research Database (Denmark)

    Wagner, Hans-Peter; Langbein, Wolfgang; Hvam, Jørn Märcher

    2002-01-01

    The biexciton binding energy E-XX is investigated in ZnSe/ZnMgSe quantum wells and quantum wires as a function of the lateral confinement by transient four-wave mixing. In the quantum wells one observes for decreasing well width a significant increase in the relative binding energy, saturating fo...

  11. Calculation of the yearly energy performance of heating systems based on the European Building Energy Directive and related CEN Standards

    DEFF Research Database (Denmark)

    Olesen, Bjarne W.; de Carli, Michele

    2011-01-01

    According to the Energy Performance of Buildings Directive (EPBD) all new European buildings (residential, commercial, industrial, etc.) must since 2006 have an energy declaration based on the calculated energy performance of the building, including heating, ventilating, cooling and lighting syst......–20% of the building energy demand. The additional loss depends on the type of heat emitter, type of control, pump and boiler. Keywords: Heating systems; CEN standards; Energy performance; Calculation methods......According to the Energy Performance of Buildings Directive (EPBD) all new European buildings (residential, commercial, industrial, etc.) must since 2006 have an energy declaration based on the calculated energy performance of the building, including heating, ventilating, cooling and lighting...

  12. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.

    Directory of Open Access Journals (Sweden)

    Marharyta Petukh

    2015-07-01

    Full Text Available A new methodology termed Single Amino Acid Mutation based change in Binding free Energy (SAAMBE was developed to predict the changes of the binding free energy caused by mutations. The method utilizes 3D structures of the corresponding protein-protein complexes and takes advantage of both approaches: sequence- and structure-based methods. The method has two components: a MM/PBSA-based component, and an additional set of statistical terms delivered from statistical investigation of physico-chemical properties of protein complexes. While the approach is rigid body approach and does not explicitly consider plausible conformational changes caused by the binding, the effect of conformational changes, including changes away from binding interface, on electrostatics are mimicked with amino acid specific dielectric constants. This provides significant improvement of SAAMBE predictions as indicated by better match against experimentally determined binding free energy changes over 1300 mutations in 43 proteins. The final benchmarking resulted in a very good agreement with experimental data (correlation coefficient 0.624 while the algorithm being fast enough to allow for large-scale calculations (the average time is less than a minute per mutation.

  13. High level theoretical study of binding and of the potential energy surface in benzene-hydride system

    Energy Technology Data Exchange (ETDEWEB)

    Coletti, Cecilia, E-mail: ccoletti@unich.it [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy); Re, Nazzareno [Dipartimento di Scienze del Farmaco, Universita ' G. d' Annunzio' Chieti-Pescara, Via dei Vestini 31, 66100 Chieti (Italy)

    2012-04-04

    Graphical abstract: In-plane minimum geometries for benzene-H{sup -} non-covalent adducts: linear adduct (left) with the hydride ion hydrogen bonded to one aromatic hydrogen; bifurcated adduct (right), with the hydride ion hydrogen bonded to two adjacent aromatic hydrogens. Highlights: Black-Right-Pointing-Pointer Theoretical study on covalent and non-covalent binding in benzene-hydride. Black-Right-Pointing-Pointer Two non-covalent stable adducts were characterized in the in-plane geometry. Black-Right-Pointing-Pointer Significant sections of the potential energy surface were determined. Black-Right-Pointing-Pointer Formation of a very stable C{sub 6}H{sub 7}{sup -} anion upon covalent binding to carbon. - Abstract: High level ab initio calculations were performed on the interaction of the hydride anion with benzene, a system of potential interest for modelling the interactions occurring in hydrogen rich planetary atmospheres. We investigated both non-covalent and covalent binding, exploring the complete basis set limit using highly correlated MP2 and CCSD(T) levels of theory. Two non-covalent minima on the potential energy surface have been characterized, and found to correspond to moderately strong hydrogen bonding interactions. To gain further insight on the nature of binding, the total interaction energy was decomposed into its physically meaningful components and selected sections of the potential energy surface were calculated. Moreover, we found that H{sup -} can easily covalently bind to one of the carbon atoms of benzene to form a stable C{sub 6}H{sub 7}{sup -} anion, a global minimum on the potential energy surface, characterized by a puckered geometry, with a carbon atom bending out of the benzene plane. A slightly less stable planar C{sub 6}H{sub 7}{sup -} structure was also identified, corresponding to the transition state for the flipping motion of the puckered species.

  14. Interband absorption and exciton binding energy in an inverse parabolic quantum well under the magnetic field

    International Nuclear Information System (INIS)

    Kasapoglu, E.; Soekmen, I.

    2007-01-01

    We have investigated the effects of the magnetic field which is applied perpendicular to the growth direction of the well on the interband absorption and on the binding energy of the excitons in an GaAs/Ga 1-x Al x As inverse parabolic quantum well (IPQW) with different widths as well as different Al concentrations at the well center. The calculations were performed within the effective mass approximation, using a variational method. We observe that IPQW structure turns into parabolic quantum well with the inversion effect of the magnetic field and the effective band gap of the system can be modified by changing Al concentration at the well center, the strength of the magnetic field and well dimensions. This case directly influences the nature of electronic and optical properties in this structure

  15. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  16. Scaling Universality between Band Gap and Exciton Binding Energy of Two-Dimensional Semiconductors

    Science.gov (United States)

    Jiang, Zeyu; Liu, Zhirong; Li, Yuanchang; Duan, Wenhui

    2017-06-01

    Using first-principles G W Bethe-Salpeter equation calculations and the k .p theory, we unambiguously show that for two-dimensional (2D) semiconductors, there exists a robust linear scaling law between the quasiparticle band gap (Eg) and the exciton binding energy (Eb), namely, Eb≈Eg/4 , regardless of their lattice configuration, bonding characteristic, as well as the topological property. Such a parameter-free universality is never observed in their three-dimensional counterparts. By deriving a simple expression for the 2D polarizability merely with respect to Eg, and adopting the screened hydrogen model for Eb, the linear scaling law can be deduced analytically. This work provides an opportunity to better understand the fantastic consequence of the 2D nature for materials, and thus offers valuable guidance for their property modulation and performance control.

  17. Binding energy of one [sup 4]He impurity in liquid [sup 3]He

    Energy Technology Data Exchange (ETDEWEB)

    Boronat, J. (Universitat Politecnica de Catalunya, Barcelona (Spain)); Saavedra, F.A. de; Buendia, E. (Universidad de Granola (Spain)); Polls, A. (Universitat de Barcelona (Spain))

    1994-02-01

    A variational microscopic calculation of the binding energy of a [sup 4]He impurity ([mu][sub I]) in homogeneous liquid [sup 3]He at zero temperature is presented. Starting on an extended Jastrow-Slater wave function including three-body correlations, the expression for [mu][sub I] is derived and the appropriated FHNC formalism for this problem is reviewed. In the framework of the Average Correlation Approximation (ACA), it is proved that it is possible to obtain the chemical potential of the impurity only from liquid [sup 3]He magnitudes with a good accuracy. The results are consistent with both a recent experimental determination of [mu][sub I] at zero pressure and the non-solubility of [sup 4]He in [sup 3]He. However, numerical uncertainties preclude a firm conclusion about the latter property.

  18. Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

    Science.gov (United States)

    Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L

    2017-06-13

    λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.

  19. Total energy calculation of perovskite, BaTiO3, by self-consistent ...

    Indian Academy of Sciences (India)

    Unknown

    ods were applied for calculation of BaTiO3. Among them are the first-principle calculations based on the local den- sity approximation (LDA, see for example, ... It is also interpreted as occupation numbers of one-electron orbital. ψλ(r о. ) can be expanded in the series of tight binding orthogonal orbital, ν, localized at site i,. )(r.

  20. Variations in first principles calculated defect energies in GaAs and ...

    Indian Academy of Sciences (India)

    functional theory and first principles non-local pseudo- potential of the same type as Jansen and Sankey. In both these calculations, however, relaxations were not included. It is important to relax the ions while performing elec- tronic structure calculations. There have been such theo- retical studies using tight binding (TB) ...

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

    Science.gov (United States)

    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.

  2. Magnetoelastic energy calculations for finite element analysis of superconductors

    International Nuclear Information System (INIS)

    Akin, J.E.; Stoddart, W.C.T.

    1977-01-01

    It has been shown that the high current density and magnetic flux density associated with superconductors can make the magnetoelastic energy a significant portion of the total energy in a structural system. The present work presents a procedure for evaluating this magnetoelastic energy for use in the finite element analysis of the structural dynamics and stability of the superconductor. A simple, special case of the element matrices is illustrated

  3. Electron momentum distributions and binding energies for the valence orbitals of hydrogen bromide and hydrogen iodide

    International Nuclear Information System (INIS)

    Brion, C.E.; McCarthy, I.E.; Suzuki, I.H.; Weigold, E.; Williams, G.R.J.; Bedford, K.L.; Kunz, A.B.; Weidman, R.

    1981-12-01

    The electron binding energy spectra and momentum distributions have been obtained for the valence orbitals of HBr and HI using noncoplanar symmetric electron coincidence spectroscopy at 1200eV. The weakly bonding inner valence ns orbitals, which have not been previously observed, have their spectroscopic (pole) strength severely split among a number of ion states. For HBr the strength of the main inner valence (ns) transition is 0.42 0.03 whereas for HI it is 0.37 0.04, in close agreement with that observed for the valence s orbitals of the corresponding isoelectronic inert gas atoms. The spectroscopic strength for the two outermost orbitals is found to be close to unity, in agreement with many body Green's function calculations. The measured momentum distributions are compared with several spherically averaged MO momentum distributions, as well as (for HBr) with a Green's function calculation of the generalized overlap amplitude (GOA). The GOA momentum distributions are in excellent agreement with the HBr data, both in shape and relative magnitude. Not all of the MO momentum distributions are in reasonable agreement with the data. Comparison is also made with the calculated momentum distributions for Kr, Br, Xe and I

  4. Practical ambiguities during calculation of energy ratios and their impacts on life cycle assessment calculations

    International Nuclear Information System (INIS)

    Zhang, Yongli; Colosi, Lisa M.

    2013-01-01

    The energy ratio metrics are increasingly important means of assessing the efficiency of energy production for emerging biofuels platforms, making comparisons among multiple alternatives, and formulating policies to foster commercialization of sustainable energy systems. However, these metrics are susceptible to inadvertent or meaningful mathematical manipulation, whereby the same dataset can be used to compute dramatically different values of energy return on investment (EROI). In this study, previously published life cycle assessment (LCA) data for algal biofuels, corn ethanol, and switchgrass ethanol are used to demonstrate how seven seemingly reasonable EROI formulations give rise to a wide range of output values. It is then demonstrated that production of bioelectricity, and to a lesser extent, other co-products, significantly increases EROI ambiguity. Overall, the EROI results are used to illustrate how EROI ambiguity makes it difficult to properly assess the energetic favorability of a particular energy system or to make accurate comparisons among multiple systems. It is then recommended that all future biofuels studies restrict themselves to usage of “EROI 1 ”, which documents all input and outputs as explicit terms, to mitigate EROI ambiguity and improve policy decision-making. - Highlights: ► Energy ratios are appealing but potentially ambiguous sustainability metrics. ► Various ratio formulations can give different metrics for the same dataset. ► Production of electricity or other co-products exacerbates ratio ambiguity

  5. Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

    Science.gov (United States)

    Fukunishi, Yoshifumi; Hongo, Saki; Lintuluoto, Masami; Matsuo, Hiroshi

    2012-01-01

    The human APOBEC3G protein (A3G) is a single-stranded DNA deaminase that inhibits the replication of retrotransposons and retroviruses, including HIV-1. Atomic details of A3G’s catalytic mechanism have started to emerge, as the structure of its catalytic domain (A3Gctd) has been revealed by NMR and X-ray crystallography. The NMR and crystal structures are similar overall; however, differences are apparent for β2 strand (β2) and loops close to the catalytic site. To add some insight into these differences and to better characterize A3Gctd dynamics, we calculated its free energy profile by using the Generalized-Born surface area (GBSA) method accompanied with a molecular dynamics simulation. The GBSA method yielded an enthalpy term for A3Gctd’s free energy, and we developed a new method that takes into account the distribution of the protein’s dihedral angles to calculate its entropy term. The structure solved by NMR was found to have a lower energy than that of the crystal structure, suggesting that this conformation is dominant in solution. In addition, β2-loop-β2’ configuration was stable throughout a 20-ns molecular dynamics (MD) simulation. This finding suggests that in solution A3Gctd is not likely to adopt the continuous β2 strand configuration present in the APOBEC2 crystal structure. In the NMR structure, the solvent water accessibility of the catalytic Zn2+ was limited throughout the 20-ns MD simulation. This result explains previous observations in which A3G did not bind or catalyze single cytosine nucleotide, even when at excessive concentrations. PMID:24832225

  6. Subsite binding energies of an exo-polygalacturonase using isothermal titration calorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Mertens, Jeffrey A., E-mail: Jeffrey.Mertens@ars.usda.gov [Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604 (United States); Hector, Ronald E.; Bowman, Michael J. [Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604 (United States)

    2012-01-10

    Highlights: Black-Right-Pointing-Pointer Thermodynamics of (GalpA){sub n} oligomers binding to an exo-polygalacturonase. Black-Right-Pointing-Pointer Energetics of binding (GalpA){sub n} were determined by ITC. Black-Right-Pointing-Pointer Thermodynamic parameters attributable to individual subsites were determined. - Abstract: Thermodynamic parameters for binding of a series of galacturonic acid oligomers to an exo-polygalacturonase, RPG16 from Rhizopus oryzae, were determined by isothermal titration calorimetry. Binding of oligomers varying in chain length from two to five galacturonic acid residues is an exothermic process that is enthalpically driven and results in extremely tight binding of the substrate to RPG16. Binding energies in combination with prior biochemical data suggests that RPG16 has the potential for five subsites, -1 to +4, with the greatest contribution to binding energies arising from subsite -1/+1. While the enthalpic contribution to binding decreases substantially for subsites +2 to +4, beneficial entropic effects occur in subsites +3 and +4 leading to increased total free energy as the length of oligomer increases. This information will be useful for additional studies in determining the binding contributions of specific amino acids with mutant enzymes.

  7. Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations

    DEFF Research Database (Denmark)

    Capoferri, Luigi; Leth, Rasmus; Ter Haar, Ernst

    2016-01-01

    of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way...... of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD...... and binding free-energy calculation is useful for studying biocatalysis in those cases in which enzyme binding is a critical event in determining the selective metabolism of a substrate. Proteins 2016; 84:383-396. © 2016 Wiley Periodicals, Inc....

  8. How to shape a binding energy savings target for Europe that allows for effective evaluation

    NARCIS (Netherlands)

    Harmsen, R.; Wesselink, B.; Eichhammer, W.

    2012-01-01

    This paper considers which design of a binding energy savings target for the EU is the most feasible to both make it work and to ensure it can be evaluated in an efficient and transparent manner. We look at four possible design options. We conclude that a binding target at Member State level

  9. Variations in first principles calculated defect energies in GaAs and ...

    Indian Academy of Sciences (India)

    Abstract. There is an abundant literature on calculations of formation and ionization energies of point defects in GaAs. Since most of these energies, especially the formation energies, are difficult to measure, the calculations are primary means of obtaining their values. However, based on the assumptions of the calcula-.

  10. Full charge-density calculation of the surface energy of metals

    DEFF Research Database (Denmark)

    Vitos, Levente; Kollár, J..; Skriver, Hans Lomholt

    1994-01-01

    We have calculated the surface energy and the work function of the 4d metals by means of an energy functional based on a self-consistent, spherically symmetric atomic-sphere potential. In this approach the kinetic energy is calculated completely within the atomic-sphere approximation (ASA) by mea...

  11. Expansion and Automation of the Energy Conserving Orientational Force for Calculation of Grain Boundary Mobility

    Science.gov (United States)

    2018-02-21

    ARL-TR-8302 ● FEB 2018 US Army Research Laboratory Expansion and Automation of the Energy Conserving Orientational Force for...US Army Research Laboratory Expansion and Automation of the Energy Conserving Orientational Force for Calculation of Grain Boundary...TITLE AND SUBTITLE Expansion and Automation of the Energy Conserving Orientational Force for Calculation of Grain Boundary Mobility 5a. CONTRACT

  12. Radiated energy calculation in free electron lasers without inversion

    International Nuclear Information System (INIS)

    Oganesyan, K.B.

    2017-01-01

    The equations of particle motion in the free electron lasers without inversion are derived using the Hamiltonian formalism. In small signal regime the uncoupled one dimensional phase equation is derived in the form of pendulum equation. For the practical estimations the same equation along with the equation of particle energy change are solved using perturbation theory and the expressions for gain in FEL regime and particle angle dependence of energy at the exit of first undulator are obtained. Results for gain, particle phase and energy change depending on beam parameters and device are presented

  13. Stored energy in transformers: calculation by a computer program. [Computer code TFORMR calculates and prints the stored energy in a transformer with an iron core

    Energy Technology Data Exchange (ETDEWEB)

    Willmann, P.A.; Hooper, E.B. Jr.

    1977-02-01

    A computer program was written to calculate the stored energy in a transformer. This result easily yields the inductance and leakage reactance of the transformer and is estimated to be accurate to better than 5 percent. The program was used to calculate the leakage reactance of the main transformer for the LLL neutral beam High Voltage Test Stand.

  14. Calculation of energy spectrum of 12 C isotope with modified ...

    Indian Academy of Sciences (India)

    Then, we increase the accuracy by adding spin-orbit coupling and tensor force and solve them by perturbationtheory in both models. Finally, the calculated results for both models are compared with each other and with the experimental data. The results show that the isotope 12 C should be considered as a three- α cluster ...

  15. Application of the step-wise regression procedure to the semi-empirical formulae of the nuclear binding energy

    International Nuclear Information System (INIS)

    Eissa, E.A.; Ayad, M.; Gashier, F.A.B.

    1984-01-01

    Most of the binding energy semi-empirical terms without the deformation corrections used by P.A. Seeger are arranged in a multiple linear regression form. The stepwise regression procedure with 95% confidence levels for acceptance and rejection of variables is applied for seeking a model for calculating binding energies of even-even (E-E) nuclei through a significance testing of each basic term. Partial F-values are taken as estimates for the significance of each term. The residual standard deviation and the overall F-value are used for selecting the best linear regression model. (E-E) nuclei are taken into sets lying between two successive proton and neutron magic numbers. The present work is in favour of the magic number 126 followed by 164 for the neutrons and indecisive in supporting the recently predicted proton magic number 114 rather than the previous one, 126. (author)

  16. Lowest excited-state impurity binding energy in InGaN/GaN parabolic QWW: magnetic field effect

    International Nuclear Information System (INIS)

    Haddou El Ghazi; Anouar Jorio; Izeddine Zorkani

    2013-01-01

    In this paper, we have investigated the magnetic field effect on the lowest excited-state binding energy of hydrogenic shallow-donor impurity in wurtzite (In,Ga)N/GaN parabolic transversal-section quantum-well wire (PQWW) using the finite-difference method within the quasi-one-dimensional effective potential model. The calculations are performed within the framework of the effective mass approximation. A cylindrical QWW effective radius is taken into account to describe the lateral confinement strength. The numerical results show that: (i) the probability density is the largest on a circularity whose radius is the effective radius and (ii) the lowest excited-state binding energy is the largest when an impurity is located on this circularity while it starts to decrease as the impurity is away from the circularity. (author)

  17. Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

    International Nuclear Information System (INIS)

    El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

    2013-01-01

    Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN (core|well|shell) spherical quantum dot–quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities

  18. Development and validation of continuous energy adjoint-weighted calculations

    International Nuclear Information System (INIS)

    Truchet, Guillaume

    2015-01-01

    A key issue in nowadays Reactor Physics is to propagate input data uncertainties (e.g. nuclear data, manufacturing tolerances, etc.) to nuclear codes final results (e.g. k(eff), reaction rate, etc.). In order to propagate uncertainties, one typically assumes small variations around a reference and evaluates at first sensitivity profiles. Problem is that nuclear Monte Carlo codes are not - or were not until very recently - able to straightforwardly process such sensitivity profiles, even thought they are considered as reference codes. First goal of this PhD thesis is to implement a method to calculate k(eff)-sensitivity profiles to nuclear data or any perturbations in TRIPOLI-4, the CEA Monte Carlo neutrons transport code. To achieve such a goal, a method has first been developed to calculate the adjoint flux using the Iterated Fission Probability (IFP) principle that states that the adjoint flux at a given phase space point is proportional to the neutron importance in a just critical core after several power iterations. Thanks to our developments, it has been made possible, for the fist time, to calculate the continuous adjoint flux for an actual and complete reactor core configuration. From that new feature, we have elaborated a new method able to forwardly apply the exact perturbation theory in Monte Carlo codes. Exact perturbation theory does not rely on small variations which makes possible to calculate very complex experiments. Finally and after a deep analysis of the IFP method, this PhD thesis also reproduces and improves an already used method to calculate adjoint weighted kinetic parameters as well as reference migrations areas. (author) [fr

  19. Classical calculation of the total ionization energy of helium-like atoms

    International Nuclear Information System (INIS)

    Karastoyanov, A.

    1990-01-01

    Quantum mechanics rejects the classical modelling of microworld. One of the reasons is that the Bohr's rules can not be applied for many-electron atoms and molecules. But the many-body problem in classical mechanics has no analytical solution even for 3 particles. Numerical solutions should be used. The quantum Bohr's rule expressing the moment of momentum conservation for two particles is invalid in more complicated cases. Yet Bohr reached some success for helium-like atoms. The Bohr's formula concerning helim-like atoms is deduced again in this paper and its practical reliability is analyzed with contemporary data. The binding energy of the system is obtained in the simple form E=(Z-1/4) 2 α 2 mc 2 , where Z is the atomic number, α - the fine structure constant, M - the electron mass and c - the light speed in vacuum. The calculated values are compared with experimental data on the total ionization energy of the helium-like atoms from 2 He 4 to 29 Cu 64 . The error decreases quickly with the increasing of atomic mass, reaching zero for Cu. This indicated that the main source of error is the nucleus motion. The role of other possible causes is analyzed and proves negligible. (author). 1 tab, 4 refs

  20. Energy benchmarks for methane-water systems from quantum Monte Carlo and second-order Møller-Plesset calculations

    International Nuclear Information System (INIS)

    Gillan, M. J.; Alfè, D.; Manby, F. R.

    2015-01-01

    The quantum Monte Carlo (QMC) technique is used to generate accurate energy benchmarks for methane-water clusters containing a single methane monomer and up to 20 water monomers. The benchmarks for each type of cluster are computed for a set of geometries drawn from molecular dynamics simulations. The accuracy of QMC is expected to be comparable with that of coupled-cluster calculations, and this is confirmed by comparisons for the CH 4 -H 2 O dimer. The benchmarks are used to assess the accuracy of the second-order Møller-Plesset (MP2) approximation close to the complete basis-set limit. A recently developed embedded many-body technique is shown to give an efficient procedure for computing basis-set converged MP2 energies for the large clusters. It is found that MP2 values for the methane binding energies and the cohesive energies of the water clusters without methane are in close agreement with the QMC benchmarks, but the agreement is aided by partial cancelation between 2-body and beyond-2-body errors of MP2. The embedding approach allows MP2 to be applied without loss of accuracy to the methane hydrate crystal, and it is shown that the resulting methane binding energy and the cohesive energy of the water lattice agree almost exactly with recently reported QMC values

  1. A Variational Approach to Enhanced Sampling and Free Energy Calculations

    Science.gov (United States)

    Parrinello, Michele

    2015-03-01

    The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.

  2. Variational Approach to Enhanced Sampling and Free Energy Calculations

    Science.gov (United States)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

  3. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.

    Science.gov (United States)

    Petukh, Marharyta; Dai, Luogeng; Alexov, Emil

    2016-04-12

    Predicting the effect of amino acid substitutions on protein-protein affinity (typically evaluated via the change of protein binding free energy) is important for both understanding the disease-causing mechanism of missense mutations and guiding protein engineering. In addition, researchers are also interested in understanding which energy components are mostly affected by the mutation and how the mutation affects the overall structure of the corresponding protein. Here we report a webserver, the Single Amino Acid Mutation based change in Binding free Energy (SAAMBE) webserver, which addresses the demand for tools for predicting the change of protein binding free energy. SAAMBE is an easy to use webserver, which only requires that a coordinate file be inputted and the user is provided with various, but easy to navigate, options. The user specifies the mutation position, wild type residue and type of mutation to be made. The server predicts the binding free energy change, the changes of the corresponding energy components and provides the energy minimized 3D structure of the wild type and mutant proteins for download. The SAAMBE protocol performance was tested by benchmarking the predictions against over 1300 experimentally determined changes of binding free energy and a Pearson correlation coefficient of 0.62 was obtained. How the predictions can be used for discriminating disease-causing from harmless mutations is discussed. The webserver can be accessed via http://compbio.clemson.edu/saambe_webserver/.

  4. Incipient localization and tight-binding superconductivity: Tsub(c) calculation

    International Nuclear Information System (INIS)

    Kolley, E.; Kolley, W.

    1984-01-01

    Localization effects on the superconducting transition temperature Tsub(c) are examined in strongly disordered three-dimensional systems. A tight-binding formulation of strong-coupling superconductivity is combined, after configuration averaging, with the self-consistent treatment of Anderson localization developed by Vollhardt and Woelfle. The Coulomb interaction becomes retarded via the joint local local density of states, giving rise to an enhancement of the pseudopotential. Numerical Tsub(c) results as a function of disorder are compared with another theoretical work and experimental values for some high-Tsub(c) materials. (orig.)

  5. Quantum computing applied to calculations of molecular energies

    Czech Academy of Sciences Publication Activity Database

    Pittner, Jiří; Veis, L.

    2011-01-01

    Roč. 241, - (2011), 151-phys ISSN 0065-7727. [National Meeting and Exposition of the American-Chemical-Society (ACS) /241./. 27.03.2011-31.03.2011, Anaheim] Institutional research plan: CEZ:AV0Z40400503 Keywords : molecular energie * quantum computers Subject RIV: CF - Physical ; Theoretical Chemistry

  6. A practical method to calculate the R1 index of waste-to-energy facilities.

    Science.gov (United States)

    Viganò, Federico

    2018-03-01

    According to Directive 98/2008/EC, the operation carried out by an incinerator of Municipal Solid Waste (MSW) is classified either as energy recovery (R1) or as disposal (D10) depending on the result achieved by the application of the R1 formula. In 2011 the DG Environment of the European Commission (EC) issued some non-binding guidelines on the interpretation of such a formula that clarified many aspects related to its application. A point not fully clarified by the EC guidelines is the determination of the energy contained in the treated waste (E W ). For this term of the formula, reference is made to the indirect method for the calculation of boiler thermal efficiency, as defined by the norm EN 12952-15. However, the application of such a norm to an entire year of operation of a Waste-to-Energy (WtE) boiler is not immediate. Therefore, a practical method for the calculation of the E W term has been developed in the framework of a collaboration between the MatER Study Centre and the Lombardy Region (Italy). The method is based on: (i) the identification of the most reliable data available from the Distributed Control System (DCS) of the plant; (ii) the definition of a control volume around the boiler(s) also based on the availability of data; (iii) the closure of the mass balance for such a control volume; (iv) the energy balance of the same control volume that gives, thus, the E W term of the R1 formula. The method has been applied in 2015-2016 to nine plants, generating a number of interesting data reported and discussed in this work, such as R1 index values, Lower Heating Values (LHV) of the treated wastes, main sources of energy losses in WtE boilers, etc. For one case study, discussed in detail in this work, the law of propagation of uncertainties has been applied according to the ISO/IEC Guide 98-3, leading to the assessment of the accuracy of the method, which resulted in ±2.4% with a confidence level of circa 95%. Copyright © 2017 Elsevier Ltd. All

  7. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

    Science.gov (United States)

    Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

    2014-11-20

    Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  8. The Suppression of Energy Discretization Errors in Multigroup Transport Calculations

    International Nuclear Information System (INIS)

    Larsen, Edward

    2013-01-01

    The Objective of this project is to develop, implement, and test new deterministric methods to solve, as efficiently as possible, multigroup neutron transport problems having an extremely large number of groups. Our approach was to (i) use the standard CMFD method to 'coarsen' the space-angle grid, yielding a multigroup diffusion equation, and (ii) use a new multigrid-in-space-and-energy technique to efficiently solve the multigroup diffusion problem. The overall strategy of (i) how to coarsen the spatial an energy grids, and (ii) how to navigate through the various grids, has the goal of minimizing the overall computational effort. This approach yields not only the fine-grid solution, but also coarse-group flux-weighted cross sections that can be used for other related problems.

  9. Visual Method for Spectral Energy Distribution Calculation of ...

    Indian Academy of Sciences (India)

    Abstract. In this work, we propose to use 'The Geometer's Sketchpad' to the fitting of a spectral energy distribution of blazar based on three effective spectral indices, αRO, αOX, and αRX and the flux density in the radio band. It can make us to see the fitting in detail with both the peak frequency and peak luminosity given ...

  10. Using Electronic Energy Derivative Information in Automated Potential Energy Surface Construction for Vibrational Calculations.

    Science.gov (United States)

    Sparta, Manuel; Hansen, Mikkel B; Matito, Eduard; Toffoli, Daniele; Christiansen, Ove

    2010-10-12

    The availability of an accurate representation of the potential energy surface (PES) is an essential prerequisite in an anharmonic vibrational calculation. At the same time, the high dimensionality of the fully coupled PES and the adverse scaling properties with respect to the molecular size make the construction of an accurate PES a computationally demanding task. In the past few years, our group tested and developed a series of tools and techniques aimed at defining computationally efficient, black-box protocols for the construction of PESs for use in vibrational calculations. This includes the definition of an adaptive density-guided approach (ADGA) for the construction of PESs from an automatically generated set of evaluation points. Another separate aspect has been the exploration of the use of derivative information through modified Shepard (MS) interpolation/extrapolation procedures. With this article, we present an assembled machinery where these methods are embedded in an efficient way to provide both a general machinery as well as concrete computational protocols. In this framework we introduce and discuss the accuracy and computational efficiency of two methods, called ADGA[2gx3M] and ADGA[2hx3M], where the ADGA recipe is used (with MS interpolation) to automatically define modest sized grids for up to two-mode couplings, while MS extrapolation based on, respectively, gradients only and gradients and Hessians from the ADGA determined points provides access to sufficiently accurate three-mode couplings. The performance of the resulting potentials is investigated in vibrational coupled cluster (VCC) calculations. Three molecular systems serve as benchmarks: a trisubstituted methane (CHFClBr), methanimine (CH2NH), and oxazole (C3H3NO). Furthermore, methanimine and oxazole are addressed in accurate calculations aiming to reproduce experimental results.

  11. Impact of dietary fiber energy on the calculation of food total energy value in the Brazilian Food Composition Database.

    Science.gov (United States)

    Menezes, Elizabete Wenzel de; Grande, Fernanda; Giuntini, Eliana Bistriche; Lopes, Tássia do Vale Cardoso; Dan, Milana Cara Tanasov; Prado, Samira Bernardino Ramos do; Franco, Bernadette Dora Gombossy de Melo; Charrondière, U Ruth; Lajolo, Franco Maria

    2016-02-15

    Dietary fiber (DF) contributes to the energy value of foods and including it in the calculation of total food energy has been recommended for food composition databases. The present study aimed to investigate the impact of including energy provided by the DF fermentation in the calculation of food energy. Total energy values of 1753 foods from the Brazilian Food Composition Database were calculated with or without the inclusion of DF energy. The energy values were compared, through the use of percentage difference (D%), in individual foods and in daily menus. Appreciable energy D% (⩾10) was observed in 321 foods, mainly in the group of vegetables, legumes and fruits. However, in the Brazilian typical menus containing foods from all groups, only D%foods, when individually considered. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Selective binding of pyrene in subdomain IB of human serum albumin: Combining energy transfer spectroscopy and molecular modelling to understand protein binding flexibility

    Science.gov (United States)

    Ling, Irene; Taha, Mohamed; Al-Sharji, Nada A.; Abou-Zied, Osama K.

    2018-04-01

    The ability of human serum albumin (HSA) to bind medium-sized hydrophobic molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, the interaction between pyrene, a hydrophobic fluorescent probe, and HSA was thoroughly investigated using steady-state and time-resolved fluorescence techniques, ligand docking, and molecular dynamics (MD) simulations. A slight quenching of the fluorescence signal from Trp214 (the sole tryptophan residue in the protein) in the presence of pyrene was used to determine the ligand binding site in the protein, using Förster's resonance energy transfer (FRET) theory. The estimated FRET apparent distance between pyrene and Trp214 was 27 Å, which was closely reproduced by the docking analysis (29 Å) and MD simulation (32 Å). The highest affinity site for pyrene was found to be in subdomain IB from the docking results. The calculated equilibrium structure of the complex using MD simulation shows that the ligand is largely stabilized by hydrophobic interaction with Phe165, Phe127, and the nonpolar moieties of Tyr138 and Tyr161. The fluorescence vibronic peak ratio I1/I3 of bound pyrene inside HSA indicates the presence of polar effect in the local environment of pyrene which is less than that of free pyrene in buffer. This was clarified by the MD simulation results in which an average of 5.7 water molecules were found within 0.5 nm of pyrene in the binding site. Comparing the fluorescence signals and lifetimes of pyrene inside HSA to that free in buffer, the high tendency of pyrene to form dimer was almost completely suppressed inside HSA, indicating a high selectivity of the binding pocket toward pyrene monomer. The current results emphasize the ability of HSA, as a major carrier of several drugs and ligands in blood, to bind hydrophobic molecules in cavities other than subdomain IIA which is known to bind most hydrophobic drugs. This ability stems from the nature of the amino acids forming the binding

  13. Calculations for Adjusting Endogenous Biomarker Levels During Analytical Recovery Assessments for Ligand-Binding Assay Bioanalytical Method Validation.

    Science.gov (United States)

    Marcelletti, John F; Evans, Cindy L; Saxena, Manju; Lopez, Adriana E

    2015-07-01

    It is often necessary to adjust for detectable endogenous biomarker levels in spiked validation samples (VS) and in selectivity determinations during bioanalytical method validation for ligand-binding assays (LBA) with a matrix like normal human serum (NHS). Described herein are case studies of biomarker analyses using multiplex LBA which highlight the challenges associated with such adjustments when calculating percent analytical recovery (%AR). The LBA test methods were the Meso Scale Discovery V-PLEX® proinflammatory and cytokine panels with NHS as test matrix. The NHS matrix blank exhibited varied endogenous content of the 20 individual cytokines before spiking, ranging from undetectable to readily quantifiable. Addition and subtraction methods for adjusting endogenous cytokine levels in %AR calculations are both used in the bioanalytical field. The two methods were compared in %AR calculations following spiking and analysis of VS for cytokines having detectable endogenous levels in NHS. Calculations for %AR obtained by subtracting quantifiable endogenous biomarker concentrations from the respective total analytical VS values yielded reproducible and credible conclusions. The addition method, in contrast, yielded %AR conclusions that were frequently unreliable and discordant with values obtained with the subtraction adjustment method. It is shown that subtraction of assay signal attributable to matrix is a feasible alternative when endogenous biomarkers levels are below the limit of quantitation, but above the limit of detection. These analyses confirm that the subtraction method is preferable over that using addition to adjust for detectable endogenous biomarker levels when calculating %AR for biomarker LBA.

  14. Use of an expert system for energy cost calculations in the pulp and paper industry

    International Nuclear Information System (INIS)

    Viinikainen, S.; Malinen, H.

    1991-12-01

    In this paper, an application for the calculation of energy prices and product energy costs in the pulp and paper industry by using the Xi Plus expert system is presented. The use of expert systems in the energy field and also the Xi Plus expert system and its general features are also discussed. The application has been made after collecting data from several sources. It runs in an IBM AT compatible microcomputer therefore being easily used in mills. The name of the application is PRODUCT ENERGY COST. It has a three level structure: the mill level, the department level and the main equipment level. Currently, the mill level and, in the energy production area, the department level (power plant) and the equipment level (boilers, turbines) are used. The application consists of four knowledge base groups. Altogether there are 52 separate knowledge bases having 534 rules or demons. The knowledge base groups are: BASIC DATA, ENERGY USE, ENERGY PRODUCTION and ENERGY COSTS. The application can be used for various heat and electrical energy price calculations or for energy cost calculations for different pulp and paper products. In this study, the energy prices for kraft pulp, TMP, newsprint and fine paper in different operating conditions and the associated energy costs of the products are calculated. Also, in some cases a sensitivity analysis is done. The expert system is quite suitable for this type of calculation and the method could be further developed for specific industrial needs, e.g. to enhance the energy management systems

  15. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

    Science.gov (United States)

    Gao, Kaifu; Yin, Jian; Henriksen, Niel M; Fenley, Andrew T; Gilson, Michael K

    2015-10-13

    Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.

  16. Free-energy calculation methods for collective phenomena in membranes

    Science.gov (United States)

    Smirnova, Yuliya G.; Fuhrmans, Marc; Barragan Vidal, Israel A.; Müller, Marcus

    2015-09-01

    Collective phenomena in membranes are those which involve the co-operative reorganization of many molecules. Examples of these are membrane fusion, pore formation, bending, adhesion or fission. The time and length scales, on which these processes occur, pose a challenge for atomistic simulations. Therefore, in order to solve the length scale problem it is popular to introduce a coarse-grained representation. To facilitate sampling of the relevant states additional computational techniques, which encourage the system to explore the free-energy landscape far from equilibrium and visit transition states, are needed. These computational techniques provide insights about the free-energy changes involved in collective transformations of membranes, yielding information about the rate limiting states, the transformation mechanism and the influence of architectural, compositional and interaction parameters. A common approach is to identify an order parameter (or reaction coordinate), which characterizes the pathway of membrane reorganization. However, no general strategy exists to define such an order parameter that can properly describe cooperative reorganizations in membranes. Recently developed methods can overcome this problem of the order-parameter choice and allow us to study collective phenomena in membranes. We will discuss such methods as thermodynamic integration, umbrella sampling, and the string method and results provided by their applications to particle-based simulations, particularly focusing on membrane fusion and pore formation.

  17. Parallel implementation of electronic structure energy, gradient, and Hessian calculations

    Science.gov (United States)

    Lotrich, V.; Flocke, N.; Ponton, M.; Yau, A. D.; Perera, A.; Deumens, E.; Bartlett, R. J.

    2008-05-01

    ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.

  18. Sensitivity Analysis of Grain Surface Chemistry to Binding Energies of Ice Species

    Science.gov (United States)

    Penteado, E. M.; Walsh, C.; Cuppen, H. M.

    2017-07-01

    Advanced telescopes, such as ALMA and the James Webb Space Telescope, are likely to show that the chemical universe may be even more complex than currently observed, requiring astrochemical modelers to improve their models to account for the impact of new data. However, essential input information for gas-grain models, such as binding energies of molecules to the surface, have been derived experimentally only for a handful of species, leaving hundreds of species with highly uncertain estimates. We present in this paper a systematic study of the effect of uncertainties in the binding energies on an astrochemical two-phase model of a dark molecular cloud, using the rate equations approach. A list of recommended binding energy values based on a literature search of published data is presented. Thousands of simulations of dark cloud models were run, and in each simulation a value for the binding energy of hundreds of species was randomly chosen from a normal distribution. Our results show that the binding energy of H2 is critical for the surface chemistry. For high binding energies, H2 freezes out on the grain forming an H2 ice. This is not physically realistic, and we suggest a change in the rate equations. The abundance ranges found are in reasonable agreement with astronomical ice observations. Pearson correlation coefficients revealed that the binding energy of HCO, HNO, CH2, and C correlate most strongly with the abundance of dominant ice species. Finally, the formation route of complex organic molecules was found to be sensitive to the branching ratios of H2CO hydrogenation.

  19. Segmentation of the Striatum from MR Brain Images to Calculate the -TRODAT-1 Binding Ratio in SPECT Images

    Directory of Open Access Journals (Sweden)

    Ching-Fen Jiang

    2013-01-01

    Full Text Available Quantification of regional -TRODAT-1 binding ratio in the striatum regions in SPECT images is essential for differential diagnosis between Alzheimer's and Parkinson's diseases. Defining the region of the striatum in the SPECT image is the first step toward success in the quantification of the TRODAT-1 binding ratio. However, because SPECT images reveal insufficient information regarding the anatomical structure of the brain, correct delineation of the striatum directly from the SPECT image is almost impossible. We present a method integrating the active contour model and the hybrid registration technique to extract regions from MR T1-weighted images and map them into the corresponding SPECT images. Results from three normal subjects suggest that the segmentation accuracy using the proposed method was compatible with the expert decision but has a higher efficiency and reproducibility than manual delineation. The binding ratio derived by this method correlated well (R2 = 0.76 with those values calculated by commercial software, suggesting the feasibility of the proposed method.

  20. Halide Binding and Inhibition of Laccase Copper Clusters: The Role of Reorganization Energy

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2015-01-01

    complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters...

  1. Accelerating activity coefficient calculations using multicore platforms, and profiling the energy use resulting from such calculations.

    Science.gov (United States)

    Topping, David; Alibay, Irfan; Bane, Michael

    2017-04-01

    To predict the evolving concentration, chemical composition and ability of aerosol particles to act as cloud droplets, we rely on numerical modeling. Mechanistic models attempt to account for the movement of compounds between the gaseous and condensed phases at a molecular level. This 'bottom up' approach is designed to increase our fundamental understanding. However, such models rely on predicting the properties of molecules and subsequent mixtures. For partitioning between the gaseous and condensed phases this includes: saturation vapour pressures; Henrys law coefficients; activity coefficients; diffusion coefficients and reaction rates. Current gas phase chemical mechanisms predict the existence of potentially millions of individual species. Within a dynamic ensemble model, this can often be used as justification for neglecting computationally expensive process descriptions. Indeed, on whether we can quantify the true sensitivity to uncertainties in molecular properties, even at the single aerosol particle level it has been impossible to embed fully coupled representations of process level knowledge with all possible compounds, typically relying on heavily parameterised descriptions. Relying on emerging numerical frameworks, and designed for the changing landscape of high-performance computing (HPC), in this study we focus specifically on the ability to capture activity coefficients in liquid solutions using the UNIFAC method. Activity coefficients are often neglected with the largely untested hypothesis that they are simply too computationally expensive to include in dynamic frameworks. We present results demonstrating increased computational efficiency for a range of typical scenarios, including a profiling of the energy use resulting from reliance on such computations. As the landscape of HPC changes, the latter aspect is important to consider in future applications.

  2. Effect of magnetic field on the impurity binding energy of the excited ...

    Indian Academy of Sciences (India)

    Keywords. Impurity energy; turning point; binding energy. PACS Nos 73.20.Dx; 73.20.Hb; 71.55.-i; 71.55.Eq. 1. Introduction. Because of the recent advances in nanofabrication technology, it is possible to pro- duce quantum dots whose characteristic dimensions are comparable with the elec- tronic de Broglie wavelengths.

  3. Analysis of binding energy activity of TIBO and HIV-RT based on ...

    African Journals Online (AJOL)

    KEN

    2007-02-05

    Feb 5, 2007 ... the structure of TIBO-HIV-RT complex (Ren et al., 1995,. 1999). In this theoretical research, the energy change corresponding to the conformational change within TIBO was investigated. It was observed that change in the beta dihedral angle conformation critically affects the binding energy. Decreased ...

  4. New directions in low energy electron molecule collision calculations

    International Nuclear Information System (INIS)

    Burke, P.G.; Noble, C.J.

    1982-01-01

    New theoretical and computational methods for studying low energy electron molecule collisions are discussed. Having considered the fixed-nuclei approximation and the form of the expansion of the total collision wavefunction, the various approximations which have been made are examined, including the static plus model exchange approximation, the static exchange approximation and the close coupling approximation, particular attention being paid to methods of including the molecular charge polarisation. Various ways which have been developed to solve the resultant equations are discussed and it is found that there is increasing emphasis being given to methods which combine the advantages of discrete multi-centre analytic bases with single centre numerical bases. (U.K.)

  5. Electron self-energy calculation using a general multi-pole approximation

    CERN Document Server

    Soininen, J A; Shirley, E L

    2003-01-01

    We present a method for calculating the inverse of the dielectric matrix in a solid using a band Lanczos algorithm. The method produces a multi-pole approximation for the inverse dielectric matrix with an arbitrary number of poles. We discuss how this approximation can be used to calculate the screened Coulomb interaction needed for electron self-energy calculations in solids.

  6. A calculation of Zsub(eff) for low-energy positron-hydrogen-molecule scattering

    International Nuclear Information System (INIS)

    Armour, E.A.G.; Baker, D.J.

    1985-01-01

    The value of Zsub(eff), the effective number of electrons per molecule available to the positron for annihilation, is calculated for low-energy positron-hydrogen-molecule scattering using the scattering wavefunctions obtained in recent detailed ab initio calculations. The results are higher than those obtained in previous calculations but much lower than the experimental value. (author)

  7. A New Approach for Offshore Wind Farm Energy Yields Calculation with Mixed Hub Height Wind Turbines

    DEFF Research Database (Denmark)

    Hou, Peng; Hu, Weihao; Soltani, Mohsen

    2016-01-01

    In this paper, a mathematical model for calculating the energy yields of offshore wind farm with mixed types of wind turbines is proposed. The Jensen model is selected as the base and developed to a three dimension wake model to estimate the energy yields. Since the wind turbines are with differe...... hub heights, the wind shear effect is also taken into consideration. The results show that the proposed wake model is effective in calculating the wind speed deficit. The calculation framework is applicable for energy yields calculation in offshore wind farms.......In this paper, a mathematical model for calculating the energy yields of offshore wind farm with mixed types of wind turbines is proposed. The Jensen model is selected as the base and developed to a three dimension wake model to estimate the energy yields. Since the wind turbines are with different...

  8. Calculations for nuclear data evaluation for Nb, Zr and W in the high energy region

    Energy Technology Data Exchange (ETDEWEB)

    Kitsuki, Hirohiko; Maruyama, Shin-ichi; Ishibashi, Kenji [Kyushu Univ., Fukuoka (Japan)

    1998-03-01

    Neutron total cross sections on Nb, Zr and W were calculated in the high energy region. In this calculation, we used the neutron optical-model potentials derived from those for proton incidence with introducing the symmetry term. Proton-induced activation yields for Nb and Zr was calculated by means of HETC/KFA2 and QMD plus SDM at incident energies up to 5 GeV. (author)

  9. The structure and binding energy of K+endash ether complexes: A comparison of MP2, RI-MP2, and density functional methods

    International Nuclear Information System (INIS)

    Feller, D.; Apra, E.; Nichols, J.A.; Bernholdt, D.E.

    1996-01-01

    The structures and binding energies of several cation:ether complexes (K + :dimethyl ether, K + :dimethoxyethane, K + :12-crown-4 and K + :18-crown-6) were determined with second and fourth order perturbation theory using correlation consistent basis sets. Several of these are the largest correlated calculations yet attempted on crown ethers. The observed systematic convergence to the complete basis set limit provides a standard by which the accuracy of previous studies can be measured and facilitates the calibration of density functional methods. Recent Fouier transform ion cyclotron resonance experiments predicted K + :18-crown-6 binding energies which were significantly smaller than ab initio calculations. None of the potential sources of error examined in the present study were large enough to explain this difference. Although the 6-31+G* basis set used in an earlier theoretical study was smaller than the smallest of the correlation consistent basis sets, with suitable correction for basis set superposition error, it appears capable of yielding binding energies within several kcal/mol of the basis set limit. Perturbation theory calculations exploiting the open-quote open-quote resolution of the identity close-quote close-quote approximation were found to faithfully reproduce binding energies and conformational differences. Although the cation endash ether interaction is dominated by classical electrostatics, the accuracy of density functional techniques was found to be quite sensitive to the choice of functionals. The local density SVWN procedure performed well for binding energies and conformational differences, while underestimating K + O distances by up to 0.08 A. The gradient-corrected Becke endash Lee endash Yang endash Parr functional underestimated the K + :12c4 binding energy by 4 endash 7 kcal/mol or 15%. copyright 1996 American Institute of Physics

  10. Theoretical analysis of the time-resolved binary (e, 2e) binding energy spectra on three-body photodissociation of acetone at 195 nm

    Science.gov (United States)

    Yamazaki, M.; Nakayama, S.; Zhu, C. Y.; Takahashi, M.

    2017-11-01

    We report on theoretical progress in time-resolved (e, 2e) electron momentum spectroscopy of photodissociation dynamics of the deuterated acetone molecule at 195 nm. We have examined the predicted minimum energy reaction path to investigate whether associated (e, 2e) calculations meet the experimental results. A noticeable difference between the experiment and calculations has been found at around binding energy of 10 eV, suggesting that the observed difference may originate, at least partly, in ever-unconsidered non-minimum energy paths.

  11. Assessment of Density-Functional Tight-Binding Ionization Potentials and Electron Affinities of Molecules of Interest for Organic Solar Cells Against First-Principles GW Calculations

    Directory of Open Access Journals (Sweden)

    Ala Aldin M. H. M. Darghouth

    2015-12-01

    Full Text Available Ionization potentials (IPs and electron affinities (EAs are important quantities input into most models for calculating the open-circuit voltage (Voc of organic solar cells. We assess the semi-empirical density-functional tight-binding (DFTB method with the third-order self-consistent charge (SCC correction and the 3ob parameter set (the third-order DFTB (DFTB3 organic and biochemistry parameter set against experiments (for smaller molecules and against first-principles GW (Green’s function, G, times the screened potential, W calculations (for larger molecules of interest in organic electronics for the calculation of IPs and EAs. Since GW calculations are relatively new for molecules of this size, we have also taken care to validate these calculations against experiments. As expected, DFTB is found to behave very much like density-functional theory (DFT, but with some loss of accuracy in predicting IPs and EAs. For small molecules, the best results were found with ΔSCF (Δ self-consistent field SCC-DFTB calculations for first IPs (good to ± 0.649 eV. When considering several IPs of the same molecule, it is convenient to use the negative of the orbital energies (which we refer to as Koopmans’ theorem (KT IPs as an indication of trends. Linear regression analysis shows that KT SCC-DFTB IPs are nearly as accurate as ΔSCF SCC-DFTB eigenvalues (± 0.852 eV for first IPs, but ± 0.706 eV for all of the IPs considered here for small molecules. For larger molecules, SCC-DFTB was also the ideal choice with IP/EA errors of ± 0.489/0.740 eV from ΔSCF calculations and of ± 0.326/0.458 eV from (KT orbital energies. Interestingly, the linear least squares fit for the KT IPs of the larger molecules also proves to have good predictive value for the lower energy KT IPs of smaller molecules, with significant deviations appearing only for IPs of 15–20 eV or larger. We believe that this quantitative analysis of errors in SCC-DFTB IPs and EAs may be of

  12. Tight-binding calculations of structural energetics of transition metal-carbides. [TiC; ZrC; HfC; VC; NbC; TaC

    Energy Technology Data Exchange (ETDEWEB)

    Le, D.H.; Colinet, C.; Pasturel, A. (Lab. de Thermodynamique et Physico-Chimie Metallurgiques, ENSEEG, 38 - Saint-Martin-d' Heres (France))

    1991-05-01

    A tight-binding recursion method is used to study the electronic and cohesive properties of stoichiometric and substoichiometric transition metal-carbides crystallizing with the NaCl structure. The electronic structure is analyzed in terms of a p-d interaction between the p orbitals of C and the d orbitals of the transition metal. Concerning the cohesive properties of these compounds, we have calculated the energies of formation of stoichiometric (Ti, Zr, Hf, V, Nb, Ta)-C compounds and compared with the experimental values. We have also studied the stability of vacancy-ordered compounds with a vacancy concentration of 50% on the carbon sublattice, i.e. M{sub 2}C compounds. (orig.).

  13. Calculations of energy levels and lifetimes of low-lying states of barium and radium

    International Nuclear Information System (INIS)

    Dzuba, V. A.; Ginges, J. S. M.

    2006-01-01

    We use the configuration-interaction method and many-body perturbation theory to perform accurate calculations of energy levels, transition amplitudes, and lifetimes of low-lying states of barium and radium. Calculations for radium are needed for the planning of measurements of parity- and time-invariance-violating effects which are strongly enhanced in this atom. Calculations for barium are used to control the accuracy of the calculations

  14. Application of wavelet scaling function expansion continuous-energy resonance calculation method to MOX fuel problem

    International Nuclear Information System (INIS)

    Yang, W.; Wu, H.; Cao, L.

    2012-01-01

    More and more MOX fuels are used in all over the world in the past several decades. Compared with UO 2 fuel, it contains some new features. For example, the neutron spectrum is harder and more resonance interference effects within the resonance energy range are introduced because of more resonant nuclides contained in the MOX fuel. In this paper, the wavelets scaling function expansion method is applied to study the resonance behavior of plutonium isotopes within MOX fuel. Wavelets scaling function expansion continuous-energy self-shielding method is developed recently. It has been validated and verified by comparison to Monte Carlo calculations. In this method, the continuous-energy cross-sections are utilized within resonance energy, which means that it's capable to solve problems with serious resonance interference effects without iteration calculations. Therefore, this method adapts to treat the MOX fuel resonance calculation problem natively. Furthermore, plutonium isotopes have fierce oscillations of total cross-section within thermal energy range, especially for 240 Pu and 242 Pu. To take thermal resonance effect of plutonium isotopes into consideration the wavelet scaling function expansion continuous-energy resonance calculation code WAVERESON is enhanced by applying the free gas scattering kernel to obtain the continuous-energy scattering source within thermal energy range (2.1 eV to 4.0 eV) contrasting against the resonance energy range in which the elastic scattering kernel is utilized. Finally, all of the calculation results of WAVERESON are compared with MCNP calculation. (authors)

  15. Calculating free energy profiles using entropy as a reaction coordinate: Application to water nucleation

    Science.gov (United States)

    Desgranges, Caroline; Delhommelle, Jerome

    2018-03-01

    We identify the nucleation pathway for a liquid droplet of a water-like system. In order to calculate the free energy barrier associated with the droplet formation, we use the recently developed μVT- S simulation method to unravel the nucleation process. We analyze the interdependence between droplet size, entropy and free energy of nucleation. Three key features emerge: the droplet size increases as entropy decreases during the process, the nucleation free energy increases as supersaturation decreases, and the nucleation free energy increases as T decreases. This method can be readily applied to calculate free energy barriers of activated events with entropy as the reaction coordinate.

  16. Binding energies: New values and impact on the efficiency of chemical desorption

    Science.gov (United States)

    Wakelam, V.; Loison, J.-C.; Mereau, R.; Ruaud, M.

    2017-03-01

    Recent laboratory measurements have confirmed that chemical desorption (desorption of products due to exothermic surface reactions) can be an efficient process. The impact of including this process into gas-grain chemical models entirely depends on the formalism used and the associated parameters. Among these parameters, binding energies are probably the most uncertain ones for the moment. We propose a new model to compute binding energy of species to water ice surfaces. We have also compared the model results using either the new chemical desorption model proposed by Minissale et al. (2016) or the one of Garrod et al. (2007). The new binding energies have a strong impact on the formation of complex organic molecules. In addition, the new chemical desorption model from Minissale produces a much smaller desorption of these species and also of methanol. Combining the two effects, the abundances of CH3OH and COMs observed in cold cores cannot be reproduced by astrochemical models anymore.

  17. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    Energy Technology Data Exchange (ETDEWEB)

    Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

    2008-01-01

    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  18. Simulations of hydrogen sorption in rht-MOF-1: identifying the binding sites through explicit polarization and quantum rotation calculations

    KAUST Repository

    Pham, Tony

    2014-01-01

    Grand canonical Monte Carlo (GCMC) simulations of hydrogen sorption were performed in rht-MOF-1, a metal-organic framework (MOF) that consists of isophthalate groups joined by copper paddlewheel clusters and Cu3O trimers through tetrazolate moeities. This is a charged rht-MOF that contains extra-framework nitrate counterions within the material. For the simulations performed herein, excellent agreement with experiment was achieved for the simulated hydrogen sorption isotherms and calculated isosteric heat of adsorption, Qst, values only when using a polarizable potential. Thermodynamic agreement is demonstrated via comparing to experimental isotherms and binding sites are revealed by combining simulation and inelastic neutron scattering (INS) data. Simulations involving explicit many-body polarization interactions assisted in the determination of the binding sites in rht-MOF-1 through the distribution of the induced dipoles that led to strong adsorbate interactions. Four distinct hydrogen sorption sites were determined from the polarization distribution: the nitrate ions located in the corners of the truncated tetrahedral cages, the Cu2+ ions of the paddlewheels that project into the truncated tetrahedral and truncated octahedral cages (Cu1 ions), the Cu2+ ions of the Cu3O trimers (Cu3 ions), and the sides of the paddlewheels in the cuboctahedral cage. The simulations revealed that the initial sorption sites for hydrogen in rht-MOF-1 are the nitrate ions; this site corresponds to the high initial Qst value for hydrogen (9.5 kJ mol-1) in the MOF. The radial distribution functions, g(r), about the Cu2+ ions at various loadings revealed that the Cu1 ions are the preferred open-metal sorption sites for hydrogen at low loading, while the Cu3 ions become occupied at higher loadings. The validation of the aforementioned sorption sites in rht-MOF-1 was confirmed by calculating the two-dimensional quantum rotational levels about each site and comparing the levels to the

  19. Verification of the DUCT-III for calculation of high energy neutron streaming

    Energy Technology Data Exchange (ETDEWEB)

    Masukawa, Fumihiro; Nakano, Hideo; Nakashima, Hiroshi; Sasamoto, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Tayama, Ryu-ichi; Handa, Hiroyuki; Hayashi, Katsumi [Hitachi Engineering Co., Ltd., Hitachi, Ibaraki (Japan); Hirayama, Hideo [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Shin, Kazuo [Kyoto Univ., Kyoto (Japan)

    2003-03-01

    A large number of radiation streaming calculations under a variety of conditions are required as a part of shielding design for a high energy proton accelerator facility. Since sophisticated methods are very time consuming, simplified methods are employed in many cases. For accuracy evaluation of a simplified code DUCT-III for high energy neutron streaming calculations, two kinds of benchmark problems based on the experiments were analyzed. Through comparison of the DUCT-III calculations with both the measurements and the sophisticated Monte Carlo calculations, DUCT-III was seen reliable enough for applying to the shielding design for the Intense Proton Accelerator Facility. (author)

  20. CONTINUOUS-ENERGY MONTE CARLO METHODS FOR CALCULATING GENERALIZED RESPONSE SENSITIVITIES USING TSUNAMI-3D

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, Christopher M [ORNL; Rearden, Bradley T [ORNL

    2014-01-01

    This work introduces a new approach for calculating sensitivity coefficients for generalized neutronic responses to nuclear data uncertainties using continuous-energy Monte Carlo methods. The approach presented in this paper, known as the GEAR-MC method, allows for the calculation of generalized sensitivity coefficients for multiple responses in a single Monte Carlo calculation with no nuclear data perturbations or knowledge of nuclear covariance data. The theory behind the GEAR-MC method is presented here, and proof of principle is demonstrated by using the GEAR-MC method to calculate sensitivity coefficients for responses in several 3D, continuous-energy Monte Carlo applications.

  1. The influence of gravitational binding energy on cosmic expansion dynamics: new perspectives for cosmology

    Science.gov (United States)

    Fahr, Hans-Jörg; Sokaliwska, Michael

    2012-06-01

    Confronted with microwave background observations by WMAP and with consternating supernova locations in the magnitude-redshift diagram modern cosmology feels enforced to call for cosmic vacuum energy as a necessary cosmological ingredient. Most often this vacuum energy is associated with Einstein's cosmological constant Λ or with so-called "dark energy". A positive value of Λ describes an inflationary action on cosmic dynamics which in view of recent cosmological data appears as an absolute need. In this article, however, we question the hypothesis of a constant vacuum energy density since not justifiable on physical grounds. Instead we show that gravitational binding energy of cosmic matter, connected with ongoing structure formation during cosmic expansion, acts similar to vacuum energy, since it reduces the effective gravitating proper mass density. Thus one may be encouraged to believe that actions of cosmic vacuum energy and gravitational binding energy concerning their cosmological effects are closely related to each other, perhaps in some respects even have identical phenomenologies. Based on results presented in this article we propose that the generally wanted action of vacuum energy on cosmic spacetime dynamics inevitably leads to a decay of vacuum energy density. Connected with this decay is a decrease of cosmic binding energy and the generation of new effective gravitating mass in the universe. If this all is adequately taken into account by the energy-momentum tensor of the GR field equations, one is then led to non-standard cosmologies which for the first time can guarantee the conservation of the total energy both in static and expanding universes. We describe the structuring of cosmic matter by a change in time of the 2-point correlation-function. We do show here that cosmic structure formation drives accelerated cosmic expansion and feigns the action of vacuum energy density.

  2. Atomic structure calculation of energy levels and oscillator strenghts in Fe ion, 1

    International Nuclear Information System (INIS)

    Ishii, Keishi; Kubo, Hirotaka; Ozawa, Kunio.

    1984-01-01

    Energy levels and oscillator strengths were calculated for 3s-3p and 3p-3d transition arrays in Fe XV, isoelectronic to Mg I. The energy levels are obtained by the Slater-Condon theory of atomic structure, including explicitly the strong configuration interactions. The calculated wavelengths are presented for electric dipole transition with gf>= 0.0001. The calculated energy levels are given in diagrams, too. The theoretical spectra are also shown in graphical representation, where the gf is plotted as a function of the wavelength. The results are compared with experimental data, where available. (author)

  3. Efficiency of free-energy calculations of spin lattices by spectral quantum algorithms

    International Nuclear Information System (INIS)

    Master, Cyrus P.; Yamaguchi, Fumiko; Yamamoto, Yoshihisa

    2003-01-01

    Ensemble quantum algorithms are well suited to calculate estimates of the energy spectra for spin-lattice systems. Based on the phase estimation algorithm, these algorithms efficiently estimate discrete Fourier coefficients of the density of states. Their efficiency in calculating the free energy per spin of general spin lattices to bounded error is examined. We find that the number of Fourier components required to bound the error in the free energy due to the broadening of the density of states scales polynomially with the number of spins in the lattice. However, the precision with which the Fourier components must be calculated is found to be an exponential function of the system size

  4. Total energy calculation of perovskite, BaTiO3, by self-consistent ...

    Indian Academy of Sciences (India)

    We present results of numerical computation on some characteristics of BaTiO3 such as total energy, lattice constant, density of states, band structure etc using self-consistent tight binding method. Besides strong Ti–O bond between 3 on titanium and 2 orbital on oxygen states, we also include weak hybridization ...

  5. Total energy calculation of perovskite, BaTiO 3 , by self-consistent ...

    Indian Academy of Sciences (India)

    We present results of numerical computation on some characteristics of BaTiO3 such as total energy, lattice constant, density of states, band structure etc using self-consistent tight binding method. Besides strong Ti–O bond between 3 on titanium and 2 orbital on oxygen states, we also include weak hybridization ...

  6. Pressure-dependent shallow donor binding energy in InGaN/GaN square QWWs

    International Nuclear Information System (INIS)

    Ghazi, Haddou El; Jorio, Anouar; Zorkani, Izeddine

    2013-01-01

    Using a variational approach, we perform a theoretical study of hydrostatic pressure effect on the ground-state of axial hydrogenic shallow-donor impurity binding energy in InGaN/GaN square quantum well wire (SQWWs) as a function of the side length within the effective-mass scheme and finite potential barrier. The pressure dependence of wire length, effective mass, dielectric constant and potential barrier are taken into account. Numerical results show that: (i) the binding energy is strongly affected by the wire length and the external applied pressure and (ii) its maximum moves to the narrow wire in particular for height pressure.

  7. Experimental Support for Desolvation Energy Term in Governing Equations for Binding Equilibria

    OpenAIRE

    Castellano, Brian M.; Eggers, Daryl K.

    2013-01-01

    This study introduces a new thermodynamic framework for aqueous reaction equilibria that treats water as a co-reactant in the development of a general binding equation. The approach features an explicit consideration for the change in hydration that occurs when two solvated surfaces come into contact. As an outcome of this framework, the standard state free energy of binding is defined by the summation of two terms, the traditional term (−RTlnKi) plus a desolvation free energy term that is we...

  8. The calculation of surface free energy based on embedded atom method for solid nickel

    International Nuclear Information System (INIS)

    Luo Wenhua; Hu Wangyu; Su Kalin; Liu Fusheng

    2013-01-01

    Highlights: ► A new solution for accurate prediction of surface free energy based on embedded atom method was proposed. ► The temperature dependent anisotropic surface energy of solid nickel was obtained. ► In isotropic environment, the approach does not change most predictions of bulk material properties. - Abstract: Accurate prediction of surface free energy of crystalline metals is a challenging task. The theory calculations based on embedded atom method potentials often underestimate surface free energy of metals. With an analytical charge density correction to the argument of the embedding energy of embedded atom method, an approach to improve the prediction for surface free energy is presented. This approach is applied to calculate the temperature dependent anisotropic surface energy of bulk nickel and surface energies of nickel nanoparticles, and the obtained results are in good agreement with available experimental data.

  9. Sustainable manufacturing by calculating the energy demand during turning of AISI 1045 steel

    Science.gov (United States)

    Nur, R.; Nasrullah, B.; Suyuti, M. A.; Apollo

    2018-01-01

    Sustainable development will become important issues for many fields, including production, industry, and manufacturing. In order to achieve sustainable development, industry should be able to perform of sustainable production processes and environmentally friendly. Therefore, there is need to minimize the energy demand in the machining process. This paper presents a calculation method of energy consumption in the machining process, especially turning process which calculated by summing the number of energy consumption, such as the electric energy consumed during the machining preparation, the electrical energy during the cutting processes, and the electrical energy to produce a cutting tool. A case study was performed on dry turning of mild carbon steel using coated carbide. This approach can be used to determine the total amount of electrical energy consumed in the specific machining process. It concluded that the energy consumption will be an increase for using the high cutting speed as well as for the feed rate was increased.

  10. Identification of potential inhibitors of Fasciola gigantica thioredoxin1: computational screening, molecular dynamics simulation, and binding free energy studies.

    Science.gov (United States)

    Shukla, Rohit; Shukla, Harish; Kalita, Parismita; Sonkar, Amit; Pandey, Tripti; Singh, Dev Bukhsh; Kumar, Awanish; Tripathi, Timir

    2017-07-04

    Fasciola gigantica is the causative organism of fascioliasis and is responsible for major economic losses in livestock production globally. F. gigantica thioredoxin1 (FgTrx1) is an important redox-active enzyme involved in maintaining the redox homeostasis in the cell. To identify a potential anti-fasciolid compound, we conducted a structure-based virtual screening of natural compounds from the ZINC database (n = 1,67,740) against the FgTrx1 structure. The ligands were docked against FgTrx1 and 309 ligands were found to have better docking score. These compounds were evaluated for Lipinski and ADMET prediction, and 30 compounds were found to fit well for re-docking studies. After refinement by molecular docking and drug-likeness analysis, three potential inhibitors (ZINC15970091, ZINC9312362, and ZINC9312661) were identified. These three ligands were further subjected to molecular dynamics simulation (MDS) to compare the dynamics and stability of the protein structure after binding of the ligands. The binding free energy analyses were calculated to determine the intermolecular interactions. The results suggested that the two compounds had a binding free energy of -82.237, and -109.52 kJ.mol -1 for compounds with IDs ZINC9312362 and ZINC9312661, respectively. These predicted compounds displayed considerable pharmacological and structural properties to be drug candidates. We concluded that these two compounds could be potential drug candidates to fight against F. gigantica parasites.

  11. New mixed ligand palladium(II) complexes based on the antiepileptic drug sodium valproate and bioactive nitrogen-donor ligands: Synthesis, structural characterization, binding interactions with DNA and BSA, in vitro cytotoxicity studies and DFT calculations

    Science.gov (United States)

    Tabrizi, Leila; Chiniforoshan, Hossein; Tavakol, Hossein

    2015-04-01

    The complexes [Pd(valp)2(imidazole)2] (1), [Pd(valp)2(pyrazine)2] (2) (valp is sodium valproate) have been synthesized and characterized using IR, 1H NMR, 13C{1H} NMR and UV-Vis spectrometry. The interaction of complexes with CT-DNA has been investigated using spectroscopic tools and viscosity measurement. In each case, the association constant (Kb) was deduced from the absorption spectral study and the number of binding sites (n) and the binding constant (K) were calculated from relevant fluorescence quenching data. As a result, a non-covalent interaction between the metal complex and DNA was suggested, which could be assigned to an intercalative binding. In addition, the interaction of 1 and 2 was ventured with bovine serum albumin (BSA) with the help of absorption and fluorescence spectroscopy measurements. Through these techniques, the apparent association constant (Kapp) and the binding constant (K) could be calculated for each complex. Evaluation of cytotoxic activity of the complexes against four different cancer cell lines proved that the complexes exhibited cytotoxic specificity and significant cancer cell inhibitory rate. Moreover, density functional theory (DFT) calculations were employed to provide more evidence about the observed data. The majority of trans isomers were supported not only by energies, but also by the similarity of its calculated IR frequencies, UV adsorptions and NMR chemical shifts to the experimental values.

  12. Calculating systems-scale energy efficiency and net energy returns: A bottom-up matrix-based approach

    International Nuclear Information System (INIS)

    Brandt, Adam R.; Dale, Michael; Barnhart, Charles J.

    2013-01-01

    In this paper we expand the work of Brandt and Dale (2011) on ERRs (energy return ratios) such as EROI (energy return on investment). This paper describes a “bottom-up” mathematical formulation which uses matrix-based computations adapted from the LCA (life cycle assessment) literature. The framework allows multiple energy pathways and flexible inclusion of non-energy sectors. This framework is then used to define a variety of ERRs that measure the amount of energy supplied by an energy extraction and processing pathway compared to the amount of energy consumed in producing the energy. ERRs that were previously defined in the literature are cast in our framework for calculation and comparison. For illustration, our framework is applied to include oil production and processing and generation of electricity from PV (photovoltaic) systems. Results show that ERR values will decline as system boundaries expand to include more processes. NERs (net energy return ratios) tend to be lower than GERs (gross energy return ratios). External energy return ratios (such as net external energy return, or NEER (net external energy ratio)) tend to be higher than their equivalent total energy return ratios. - Highlights: • An improved bottom-up mathematical method for computing net energy return metrics is developed. • Our methodology allows arbitrary numbers of interacting processes acting as an energy system. • Our methodology allows much more specific and rigorous definition of energy return ratios such as EROI or NER

  13. On the Surface Free Energy of PVC/EVA Polymer Blends: Comparison of Different Calculation Methods.

    Science.gov (United States)

    Michalski; Hardy; Saramago

    1998-12-01

    The surface free energy of polymeric films of polyvinylchloride (PVC) + poly(ethylene-co-vinylacetate) (EVA) blends was calculated using the van Oss treatment (Lifshitz and electron donor-electron acceptor components of surface free energy) and the Owens-Wendt treatment (dispersive and nondispersive components of surface free energy). Surface free energy results were found to be greatly dependent on the calculation method and on the number of standard liquids used for contact angle measurements. The nondispersive/donor-acceptor surface free energy component and the total surface free energy of polymeric films were always higher when the van Oss treatment was used compared to the Owens-Wendt treatment. Conversely, both methods led to similar apolar/Lifshitz components. All the calculation methods were in good agreement for the surface free energy of PVC; however, a discrepancy between the methods arose as EVA content in the blends increased. It seems that there is not yet a definite solution for the calculation of solid surface free energy. Further developments of existing models are needed in order to gain consistency when calculating this important physicochemical quantity. Copyright 1998 Academic Press.

  14. Accurate lattice energies of organic molecular crystals from periodic turbomole calculations.

    Science.gov (United States)

    Buchholz, Hannes Konrad; Stein, Matthias

    2018-03-05

    Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom-centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non-covalently bound organic molecular crystals. The accuracy and convergence of results with basis set size and k-space sampling from periodic calculations is evaluated for the two reference molecules benzoic acid and naphthalene. For the X23 benchmark set of small molecular crystals accurate lattice energies are obtained using the PBE-D3 functional. In particular for hydrogen-bonded systems, a sufficiently large basis set is required. The calculated lattice energy differences between enantiopure and racemic crystal forms for a prototype set of chiral molecules are in good agreement with experimental results and allow the rationalization and computer-aided design of chiral separation processes. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  15. Calculation of Electrochemical Reorganization Energies for Redox Molecules at Self-Assembled Monolayer Modified Electrodes.

    Science.gov (United States)

    Ghosh, Soumya; Hammes-Schiffer, Sharon

    2015-01-02

    Electrochemical electron transfer reactions play an important role in energy conversion processes with many technological applications. Electrodes modified by self-assembled monolayers (SAMs) exhibit reduced double layer effects and are used in molecular electronics. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in the solute geometry and the environment. In this Letter, an approach for calculating the electrochemical reorganization energy for a redox molecule attached to or near a SAM modified electrode is presented. This integral equations formalism polarizable continuum model (IEF-PCM) approach accounts for the detailed electronic structure of the molecule, as well as the contributions from the electrode, SAM, and electronic and inertial solvent responses. The calculated total reorganization energies are in good agreement with experimental data for a series of metal complexes in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts.

  16. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

    Science.gov (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

    2015-01-22

    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  17. Energy density calculations for ball-lightning-like luminous silicon balls

    Energy Technology Data Exchange (ETDEWEB)

    Paiva, Gerson S; Ferreira, Joacy V; Bastos, Cristiano C; Dos Santos, Marcus V; Pavao, Antonio C [Departamento de Quimica Fundamental, Universidade Federal de Pernambuco, Pernambuco (Brazil)

    2010-05-11

    The energy density of a luminous silicon ball [Phys. Rev. Lett. 98 048501 (2007)] is calculated for a model with a metal core surrounded by an atmosphere of silicon oxides. Experimental data combined with the molecular orbital calculations of the oxidation enthalpy lead to a mean energy density of 3.9 MJ m{sup -3}, which is within the range of estimates from other ball lightning models. This result provides good evidence to support the silicon-based model. (methodological notes)

  18. METHODOLOGICAL NOTES: Energy density calculations for ball-lightning-like luminous silicon balls

    Science.gov (United States)

    Paiva, Gerson S.; Ferreira, Joacy V.; Bastos, Cristiano C.; dos Santos, Marcus V.; Pavão, Antonio C.

    2010-05-01

    The energy density of a luminous silicon ball [Phys. Rev. Lett. 98 048501 (2007)] is calculated for a model with a metal core surrounded by an atmosphere of silicon oxides. Experimental data combined with the molecular orbital calculations of the oxidation enthalpy lead to a mean energy density of 3.9 MJ m-3, which is within the range of estimates from other ball lightning models. This result provides good evidence to support the silicon-based model.

  19. Window Energy Rating System and Calculation of Energy Performance of Windows

    DEFF Research Database (Denmark)

    Laustsen, Jacob Birck; Svendsen, Svend

    The goal of reducing the energy consumption in buildings is the background for the introduction of an energy rating system of fenestration products in Denmark. The energy rating system requires that producers declare, among other things, the heat loss coefficient, U, and the total solar energy...

  20. Calculation of the neutron W value for neutron dosimetry below the MeV energy region

    International Nuclear Information System (INIS)

    Endo, S.; Shizuma, K.; Goodhead, D.T.

    2000-01-01

    The effective neutron W value for tissue-equivalent gas in the energy region from 5 keV to 5.7 MeV has been calculated using W values for recoil particles (protons, alpha particles, oxygen, carbon and nitrogen ions), which are produced by incident neutrons. The W value is assumed to be an energy-fluence-average over the W values of the recoil particles. The energy fluence spectra for the recoil particles are calculated by using a continuous slowing-down approximation (CSDA). For the W values of recoil particles in the low-energy region, the recently evaluated data by Siebert et al and Taylor et al were used. Results are presented which show that the effective neutron W value depends strongly on energy in the low-energy region. This result indicates that neutron dose measurements using ionization chambers need a considerable correction of the W value in the low-energy region. (author)

  1. Incremental binding free energies of aluminum (III) vs. magnesium (II) complexes

    International Nuclear Information System (INIS)

    Mercero, Jose M.; Mujika, Jon I.; Matxain, Jon M.; Lopez, Xabier; Ugalde, Jesus M.

    2003-01-01

    A sequential ligand addition to the aluminum (III) cation has been studied using the B3LYP functional and a combined all-electron/pseudopotentials basis set. The aluminum complexes are compared with analogous magnesium (II) complexes. Different thermodynamical data, such as incremental binding energies, enthalpies, entropies and free energies, are presented for these addition reactions. While the magnesium (II) cation can only accommodate three negatively charged ligands, aluminum (III) accommodates four even after including bulk solvent effects. The main differences between both cations complexing with the neutral ligands, is that aluminum (III) is not able to form complexes with methanol until the number of methanol ligands is equal to 3. Magnesium (II) prefers to bind methanol and formamide when the number of ligands is small, while aluminum prefers formamide. For the largest complexes both cations prefer to bind water

  2. Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

    Science.gov (United States)

    Cappel, Daniel; Sherman, Woody; Beuming, Thijs

    2017-01-01

    The ability to accurately characterize the solvation properties (water locations and thermodynamics) of biomolecules is of great importance to drug discovery. While crystallography, NMR, and other experimental techniques can assist in determining the structure of water networks in proteins and protein-ligand complexes, most water molecules are not fully resolved and accurately placed. Furthermore, understanding the energetic effects of solvation and desolvation on binding requires an analysis of the thermodynamic properties of solvent involved in the interaction between ligands and proteins. WaterMap is a molecular dynamics-based computational method that uses statistical mechanics to describe the thermodynamic properties (entropy, enthalpy, and free energy) of water molecules at the surface of proteins. This method can be used to assess the solvent contributions to ligand binding affinity and to guide lead optimization. In this review, we provide a comprehensive summary of published uses of WaterMap, including applications to lead optimization, virtual screening, selectivity analysis, ligand pose prediction, and druggability assessment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  3. First-principles calculations of the vacancy formation energy in transition and noble metals

    DEFF Research Database (Denmark)

    Korzhavyi, P.A.; Abrikosov, Igor A.; Johansson, Börje

    1999-01-01

    Abstract: The vacancy formation energy and the vacancy formation volume of the 3d, 4d, and 5d transition and noble metals have been calculated within the local-density approximation. The calculations employ the order-N locally self-consistent Green's-function method in conjunction with a supercel...

  4. Gamma-point lattice free energy estimates from O(1) force calculations

    DEFF Research Database (Denmark)

    Voss, Johannes; Vegge, Tejs

    2008-01-01

    We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum...

  5. Continuous Energy, Multi-Dimensional Transport Calculations for Problem Dependent Resonance Self-Shielding

    Energy Technology Data Exchange (ETDEWEB)

    T. Downar

    2009-03-31

    The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system.

  6. Calculating the energy spectrum of neutrons from tritium target of the NG-150 type generator

    International Nuclear Information System (INIS)

    Bortash, A.I.; Kuznetsov, V.S.

    1987-01-01

    Calculation procedure of neutron spectra yielding from the NG-150 generator target chamber with regard to deutron moderation is suggested. Using the suggested procedure, neutron spectra for different escape angles formed in the tritium target are calculated. The spectrum of neutrons scattered in cooling water is calculated. The mean energy of neutrons escaping at the angle of 0 deg equalling 14.5 MeV is obtained

  7. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Juanjuan [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); Kara, Abdelkader, E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Pasquali, Luca [Dipartimento di Ingegneria “E. Ferrari,” Università di Modena e Reggio Emilia, Via Vignolese 905, 41125 Modena (Italy); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa); Bendounan, Azzedine; Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex (France); Esaulov, Vladimir A., E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy)

    2015-09-14

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

  8. Analysis of binding energy activity of TIBO and HIV-RT based on ...

    African Journals Online (AJOL)

    Tetrahydro-imidazo[4,5,l-jk][1,4]-benzodiazepin-2 (1 H)one (TIBO) is a noncompetitive non nucleotide antiretroviral drug with a specific allosteric binding site of HIV-1 RT. The conformational analysis shows that the effect of the drug depends on the potential energy which varied due to the beta rotatable dihedral angles (N6 ...

  9. Calculation of embodied energy in Sino-USA trade: 1997–2011

    International Nuclear Information System (INIS)

    Yang, Ranran; Long, Ruyin; Yue, Ting; Shi, Haihong

    2014-01-01

    In order to find efficient trade measures to reduce China's energy consumption and to provide theoretical support for the climate talks between China and America, we investigate the impact of Sino-USA trade on energy consumption from the perspective of embodied energy. An Environmental Input–Output Life Cycle Assessment (EIO-LCA) model was established to calculate the total energy consumption coefficient, the direct consumption coefficient and the complete consumption coefficient of the sectors of the national economies of China and America. After taking into consideration the data of every sector of the national economy in Sino-USA trade, energy embodied in the import and export trade between China and America was calculated to verify the real energy flows in Sino-USA trade. The research results suggest the following: China is the net exporter of embodied energy in Sino-USA trade, and coal, crude oil and natural gas are the major components. In 1997–2011, the net exports of China's embodied energy totaled 1523,082,200 t of standard coal, the amount of China's energy consumption increased by 895,527,900 t of standard coal, and America's energy consumption decreased by 11,871,200 t of standard coal as a result of Sino-USA trade. On this basis, corresponding policies and recommendations are proposed. - Highlights: • An EIO-LCA model is established to examine China's embodied energy in Sino-USA trade. • Embodied energy is calculated from the perspective of energy sources. • China is found to be the net exporter of embodied energy in Sino-USA trade. • Coal, crude oil and natural gas are the major components of China's net embodied energy exports. • China's energy consumption has increased and America's has shifted to China in Sino-USA trade

  10. Substitutional disorder, random dipoles and the binding energy of orthorhombic La2-xSrxCuO4

    International Nuclear Information System (INIS)

    Birkholz, M.; Rudert, R.

    1995-01-01

    This study investigates the effect of heterovalent, substitutional disorder on the binding energy of La 2-x Sr x CuO 4 . First, disorder has been found to create crystal electric fields that fluctuate over different lattice sites and induce ionic dipole moments of varying strength and orientation. The strength of these random dipoles will be presented for increasing x. Second, disorder may slightly displace the ions from their average lattice sites. The large thermal parameters obtained from diffraction experiments are discussed in this context. Finally, the polarization energy related to random dipoles was calculated to be on the order of eV and favourizes the positive charge carriers introduced by Sr doping to be associated with the copper ions. It is concluded that the solid exists in a state containing mixed copper valencies (Cu 2+ /Cu 3+ ). (orig.)

  11. Continuous-energy eigenvalue sensitivity coefficient calculations in TSUNAMI-3D

    International Nuclear Information System (INIS)

    Perfetti, C. M.; Rearden, B. T.

    2013-01-01

    Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several test problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and a low memory footprint, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations. (authors)

  12. Continuous-energy eigenvalue sensitivity coefficient calculations in TSUNAMI-3D

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, C. M.; Rearden, B. T. [Oak Ridge National Laboratory, Reactor and Nuclear Systems Division, P.O. Box 2008, Oak Ridge, TN 37831-6170 (United States)

    2013-07-01

    Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several test problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and a low memory footprint, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations. (authors)

  13. Development of a SCALE Tool for Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, Christopher M [ORNL; Rearden, Bradley T [ORNL

    2013-01-01

    Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several criticality safety problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and low memory requirements, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations.

  14. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    International Nuclear Information System (INIS)

    Narayan, Monishka Rita; Singh, Jai

    2012-01-01

    The influence of binding energy and diffusion length on the dissociation of excitons in organic solids is studied. The binding energy and excitonic Bohr radius of singlet and triplet excitons are calculated and compared using the dissociation energy of 0.3 eV, which is provided by the lowest unoccupied molecular orbital offset in heterojunction organic solar cells. A relation between the diffusion coefficient and diffusion length of singlet and triplet excitons is derived using the Foerster and Dexter transfer processes and are plotted as a function of the donor-acceptor separation. The diffusion length reduces nearly to a zero if the distance between donor and acceptor is increased to more than 1.5 nm. It is found that the donor-acceptor separation needs to be ≤ 1.5 nm for easy dissociation on singlet excitons leading to better conversion efficiency in heterojunction organic solar cells. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  15. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Narayan, Monishka Rita [Centre for Renewable Energy and Low Emission Technology, Charles Darwin University, Darwin, NT 0909 (Australia); Singh, Jai [School of Engineering and IT, Charles Darwin University, Darwin, NT 0909 (Australia)

    2012-12-15

    The influence of binding energy and diffusion length on the dissociation of excitons in organic solids is studied. The binding energy and excitonic Bohr radius of singlet and triplet excitons are calculated and compared using the dissociation energy of 0.3 eV, which is provided by the lowest unoccupied molecular orbital offset in heterojunction organic solar cells. A relation between the diffusion coefficient and diffusion length of singlet and triplet excitons is derived using the Foerster and Dexter transfer processes and are plotted as a function of the donor-acceptor separation. The diffusion length reduces nearly to a zero if the distance between donor and acceptor is increased to more than 1.5 nm. It is found that the donor-acceptor separation needs to be {<=} 1.5 nm for easy dissociation on singlet excitons leading to better conversion efficiency in heterojunction organic solar cells. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Computational Chemistry Laboratory: Calculating the Energy Content of Food Applied to a Real-Life Problem

    Science.gov (United States)

    Barbiric, Dora; Tribe, Lorena; Soriano, Rosario

    2015-01-01

    In this laboratory, students calculated the nutritional value of common foods to assess the energy content needed to answer an everyday life application; for example, how many kilometers can an average person run with the energy provided by 100 g (3.5 oz) of beef? The optimized geometries and the formation enthalpies of the nutritional components…

  17. Variations in first principles calculated defect energies in GaAs and ...

    Indian Academy of Sciences (India)

    In particular, we have compared a large set of computed energies and selected the most appropriate values. Then, in the context of GaAs material quality, we investigated the impact of errors in calculation of formation energies on the performance of the GaAs substrate for device fabrication. We find that in spite of the errors ...

  18. REFINED ALGORITHMS OF ELECTRICAL ENERGY LOSSES CALCULATION IN 0,38 KV NETWORKS IN REAL TIME

    Directory of Open Access Journals (Sweden)

    Miroshnyk A.

    2010-08-01

    Full Text Available An approach for closer definition of electrical energy losses size in air lines due to the accounting of environment temperature influence and flowing current size on the wire resistance is offered. Multifunctional microprocessor devices for energy losses calculation are elaborated.

  19. Calculation of isotopic mass and energy production by a matrix operator method

    International Nuclear Information System (INIS)

    Lee, C.E.

    1976-08-01

    The Volterra method of the multiplicative integral is used to determine the isotopic density, mass, and energy production in linear systems. The solution method, assumptions, and limitations are discussed. The method allows a rapid accurate calculation of the change in isotopic density, mass, and energy production independent of the magnitude of the time steps, production or decay rates, or flux levels

  20. Estimating the energy of intramolecular hydrogen bonds from1H NMR and QTAIM calculations.

    Science.gov (United States)

    Afonin, Andrei V; Vashchenko, Alexander V; Sigalov, Mark V

    2016-11-29

    The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρ BCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the 1 H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρ BCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρ BCP and V parameters and the hydrogen bond energies obtained from empirical 1 H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.

  1. Amine-hydrogen halide complexes: experimental electric dipole moments and a theoretical decomposition of dipole moments and binding energies.

    Science.gov (United States)

    Brauer, Carolyn S; Craddock, Matthew B; Kilian, Jacob; Grumstrup, Erik M; Orilall, M Christopher; Mo, Yirong; Gao, Jiali; Leopold, Kenneth R

    2006-08-24

    The Stark effect has been observed in the rotational spectra of several gas-phase amine-hydrogen halide complexes and the following electric dipole moments have been determined: H(3)(15)N-H(35)Cl (4.05865 +/- 0.00095 D), (CH(3))(3)(15)N-H(35)Cl (7.128 +/- 0.012 D), H(3)(15)N-H(79)Br (4.2577 +/- 0.0022 D), and (CH(3))(3)(15)N-H(79)Br (8.397 +/- 0.014 D). Calculations of the binding energies and electric dipole moments for the full set of complexes R(n)()(CH(3))(3)(-)(n)()N-HX (n = 0-3; X = F, Cl, Br) at the MP2/aug-cc-pVDZ level are also reported. The block localized wave function (BLW) energy decomposition method has been used to partition the binding energies into contributions from electrostatic, exchange, distortion, polarization, and charge-transfer terms. Similarly, the calculated dipole moments have been decomposed into distortion, polarization, and charge-transfer components. The complexes studied range from hydrogen-bonded systems to proton-transferred ion pairs, and the total interaction energies vary from 7 to 17 kcal/mol across the series. The individual energy components show a much wider variation than this, but cancellation of terms accounts for the relatively narrow range of net binding energies. For both the hydrogen-bonded complexes and the proton-transferred ion pairs, the electrostatic and exchange terms have magnitudes that increase with the degree of proton transfer but are of opposite sign, leaving most of the net stabilization to arise from polarization and charge transfer. In all of the systems studied, the polarization terms contribute the most to the induced dipole moment, followed by smaller but still significant contributions from charge transfer. A significant contribution to the induced moment of the ion pairs also arises from distortion of the HX monomer.

  2. Wave packet methods for the direct calculation of energy-transfer moments in molecular collisions

    International Nuclear Information System (INIS)

    Bradley, K.S.; Schatz, G.C.; Balint-Kurti, G.G.

    1999-01-01

    The authors present a new wave packet based theory for the direct calculation of energy-transfer moments in molecular collision processes. This theory does not contain any explicit reference to final state information associated with the collision dynamics, thereby avoiding the need for determining vibration-rotation bound states (other than the initial state) for the molecules undergoing collision and also avoiding the calculation of state-to-state transition probabilities. The theory applies to energy-transfer moments of any order, and it generates moments for a wide range of translational energies in a single calculation. Two applications of the theory are made that demonstrate its viability; one is to collinear He + H 2 and the other to collinear He + CS 2 (with two active vibrational modes in CS 2 ). The results of these applications agree well with earlier results based on explicit calculation of transition probabilities

  3. Possible explanations for the gap between calculated and measured energy consumption of new houses

    DEFF Research Database (Denmark)

    Kragh, Jesper; Rose, Jørgen; Knudsen, Henrik N.

    2017-01-01

    The overall aim to reduce CO2 emissions has brought the energy requirements for new houses into focus. The question is whether the stepwise tightening of the energy requirements for new houses has had the expected impact on the actual realized energy consumption. In the news media, headlines......’s “careless” energy behavior. However, this may not be the full explanation and there may be other reasons for the difference. Or more specifically: Does the theoretical calculated energy demand, based on standard assumptions and without taking into account the effect of variations in e.g. hot water...

  4. Age dependence of specific effective energy in calculation of internal dose

    International Nuclear Information System (INIS)

    Zheng Wenzhong

    1986-01-01

    Based on the relationship between specific effective energy (SEE) and other physical parameters (energy and type of radiation emitted, mass, size and shape of organs, and between source organs and target distance organs), the method used for the calculation of age dependent values of specific effective energy was described for several types of radiation. In order to assess their significance of SEE in calculation of internal dose for the general public, the mean ratios of SEE for persons of less than 20 years of age to those for the adult were given

  5. Calculating energy and labor impacts of capital readjustments due to changes in personal consumption. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Pleszkun, A.R.

    1979-05-01

    Previous work on the energy and labor impacts of energy-consumption policies has included the effect of respending of money saved, but not the capital implications of this respending. Here the capital effects are fully accounted for, and turn out to be negligible for a specified conservation scenario and a specified capital expansion model (..delta..C = kC). The robustness of this conclusion is discussed. The implication is that inclusion of only the respending effect is adequate for calculating energy and labor impacts and provides an accuracy to within +- 1% of the total impacts. Operationally, this result obviates the requirement for detailed and expensive calculations.

  6. Self-consistent Hartree energy band calculation for manganese oxide (MnO)

    International Nuclear Information System (INIS)

    Bakhshai, A.

    1982-01-01

    A self-consistent Hartree energy band calculation was done for the MnO crystal using the linear combination of atomic orbitals (LCAO) method. Gaussian type atomic orbitals were used in the LCAO method. This calculation was done for paramagnetic MnO with the NaCl lattice structure. The results show that the energy bands around the Fermi level of MnO are unusually flat, meaning that the electrons in this region are strongly localized. Therefore short range correlation was added to the results of this band calculation. The short range correlation effects were added by calculating atomic type corrections to the original band structure. The results of this correlation calculation show that a large amount of energy is required to excite an electron from the Mn 3d band. Therefore the lowest excitation (the one that requires the least energy) is an excitation from the top of the O 2p band to the Fermi level. This yields a fundamental band gap of 4.8 eV which is in good agreement with optical absorption experiments. This fundamental band gap of 4.8 eV implies that MnO is an insulator, in agreement with conductivity experiments. The Hartree results for the valence bands of MnO agree very well with the results of photoemission experiments. In comparison to the photoemission data, the results of the self-consistent Hartree calculation are an order of magnitude better than the results of the only other band calculation for MnO. Comparison with band calculations for other transition metal oxides (other than MnO) imply that with a good self-consistent Hartree energy band calculation for MnO can be superior

  7. Dzyaloshinskii-Moriya interaction and chiral magnetism in 3d-5d zigzag chains: Tight-binding model and ab initio calculations

    Science.gov (United States)

    Kashid, Vikas; Schena, Timo; Zimmermann, Bernd; Mokrousov, Yuriy; Blügel, Stefan; Shah, Vaishali; Salunke, H. G.

    2014-08-01

    We investigate the chiral magnetic order in freestanding planar 3d-5d biatomic metallic chains (3d: Fe, Co; 5d: Ir, Pt, Au) using first-principles calculations based on density functional theory. We find that the antisymmetric exchange interaction, commonly known as the Dzyaloshinskii-Moriya interaction (DMI), contributes significantly to the energetics of the magnetic structure. For the Fe-Pt and Co-Pt chains, the DMI can compete with the isotropic Heisenberg-type exchange interaction and the magnetocrystalline anisotropy energy, and for both cases a homogeneous left-rotating cycloidal chiral spin-spiral with a wavelength of 51 Å and 36 Å, respectively, was found. The sign of the DMI, which determines the handedness of the magnetic structure, changes in the sequence of the 5d atoms Ir(+), Pt(-), Au(+). We use the full-potential linearized augmented plane wave method and perform self-consistent calculations of homogeneous spin spirals, calculating the DMI by treating the effect of spin-orbit interaction in the basis of the spin-spiral states in first-order perturbation theory. To gain insight into the DMI results of our ab initio calculations, we develop a minimal tight-binding model of three atoms and four orbitals that contains all essential features: the spin canting between the magnetic 3d atoms, the spin-orbit interaction at the 5d atoms, and the structure inversion asymmetry facilitated by the triangular geometry. We find that spin canting can lead to spin-orbit active eigenstates that split in energy due to the spin-orbit interaction at the 5d atom. We show that the sign and strength of the hybridization, the bonding or antibonding character between d orbitals of the magnetic and nonmagnetic sites, the bandwidth, and the energy difference between occupied and unoccupied states of different spin projection determine the sign and strength of the DMI. The key features observed in the trimer model are also found in the first-principles results.

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

    Energy Technology Data Exchange (ETDEWEB)

    McKechnie, Scott [Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Booth, George H. [Theory and Simulation of Condensed Matter, King’s College London, The Strand, London WC2R 2LS (United Kingdom); Cohen, Aron J. [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Cole, Jacqueline M., E-mail: jmc61@cam.ac.uk [Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Argonne National Laboratory, 9700 S Cass Avenue, Argonne, Illinois 60439 (United States)

    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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

  10. Monte Carlo calculation of the energy response characteristics of a RadFET radiation detector

    Science.gov (United States)

    Belicev, P.; Spasic Jokic, V.; Mayer, S.; Milosevic, M.; Ilic, R.; Pesic, M.

    2010-07-01

    The Metal -Oxide Semiconductor Field-Effect-Transistor (MOSFET, RadFET) is frequently used as a sensor of ionizing radiation in nuclear-medicine, diagnostic-radiology, radiotherapy quality-assurance and in the nuclear and space industries. We focused our investigations on calculating the energy response of a p-type RadFET to low-energy photons in range from 12 keV to 2 MeV and on understanding the influence of uncertainties in the composition and geometry of the device in calculating the energy response function. All results were normalized to unit air kerma incident on the RadFET for incident photon energy of 1.1 MeV. The calculations of the energy response characteristics of a RadFET radiation detector were performed via Monte Carlo simulations using the MCNPX code and for a limited number of incident photon energies the FOTELP code was also used for the sake of comparison. The geometry of the RadFET was modeled as a simple stack of appropriate materials. Our goal was to obtain results with statistical uncertainties better than 1% (fulfilled in MCNPX calculations for all incident energies which resulted in simulations with 1 - 2×109 histories.

  11. Communication: regularizing binding energy distributions and thermodynamics of hydration: theory and application to water modeled with classical and ab initio simulations.

    Science.gov (United States)

    Weber, Valéry; Merchant, Safir; Asthagiri, D

    2011-11-14

    The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce external fields centered on the solute to modulate the short-range repulsive interaction between the solute and solvent. This regularizes the binding energy distribution and makes it easy to calculate the free energy of the solute with the field. Together with the work done to apply the field in the presence and absence of the solute, we calculate the excess chemical potential of the solute. We present the formal development of this idea and apply it to study liquid water. © 2011 American Institute of Physics

  12. Free Energy Minimization Calculation of Complex Chemical Equilibria. Reduction of Silicon Dioxide with Carbon at High Temperature.

    Science.gov (United States)

    Wai, C. M.; Hutchinson, S. G.

    1989-01-01

    Discusses the calculation of free energy in reactions between silicon dioxide and carbon. Describes several computer programs for calculating the free energy minimization and their uses in chemistry classrooms. Lists 16 references. (YP)

  13. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    Science.gov (United States)

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  14. Extended wave-packet model to calculate energy-loss moments of protons in matter

    Science.gov (United States)

    Archubi, C. D.; Arista, N. R.

    2017-12-01

    In this work we introduce modifications to the wave-packet method proposed by Kaneko to calculate the energy-loss moments of a projectile traversing a target which is represented in terms of Gaussian functions for the momentum distributions of electrons in the atomic shells. These modifications are introduced using the Levine and Louie technique to take into account the energy gaps corresponding to the different atomic levels of the target. We use the extended wave-packet model to evaluate the stopping power, the energy straggling, the inverse mean free path, and the ionization cross sections for protons in several targets, obtaining good agreements for all these quantities on an extensive energy range that covers low-, intermediate-, and high-energy regions. The extended wave-packet model proposed here provides a method to calculate in a very straightforward way all the significant terms of the inelastic interaction of light ions with any element of the periodic table.

  15. Effects of an Intense Laser Field and Hydrostatic Pressure on the Intersubband Transitions and Binding Energy of Shallow Donor Impurities in a Quantum Well

    International Nuclear Information System (INIS)

    Yesilgul, U.; Ungan, F.; Kasapoglu, E.; Sari, H.; Sökmen, I.

    2011-01-01

    We have calculated the intersubband transitions and the ground-state binding energies of a hydrogenic donor impurity in a quantum well in the presence of a high-frequency laser field and hydrostatic pressure. The calculations are performed within the effective mass approximation, using a variational method. We conclude that the laser field amplitude and the hydrostatic pressure provide an important effect on the electronic and optical properties of the quantum wells. According to the results obtained from the present work, it is deduced that (i) the binding energies of donor impurity decrease as the laser field increase, (ii) the binding energies of donor impurity increase as the hydrostatic pressure increase, (iii) the intersubband absorption coefficients shift toward lower energies as the hydrostatic pressure increases, (iv) the magnitude of absorption coefficients decrease and also shift toward higher energies as the laser field increase. It is hopeful that the obtained results will provide important improvements in device applications. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  16. Binding energy and optical properties of an off-center hydrogenic donor impurity in a spherical quantum dot placed at the center of a cylindrical nano-wire

    International Nuclear Information System (INIS)

    Safarpour, Gh.; Barati, M.; Zamani, A.; Niknam, E.

    2014-01-01

    The binding energy as well as the linear, third-order nonlinear and total optical absorption coefficient and refractive index changes of an off-center hydrogenic donor impurity in an InAs spherical quantum dot placed at the center of a GaAs cylindrical nano-wire have been investigated. In this regard, the effective-mass approximation approach is considered and eigenvalues and corresponding eigenfunctions are calculated via the finite element method. The binding energy is plotted as a function of the dot size and impurity position along with optical properties as a function of photon energy. In this study two different directions have been considered for impurity position, along the nano-wire axis and perpendicular to it. It has been found that the binding energy, absorption coefficient and refractive index changes are impressively affected not only by the dot radius but also by the position of the impurity and its direction. Additionally, the optical saturation can be tuned by the direction of the impurity and incident optical intensity. -- Highlights: • We consider spherical quantum dot located at the center of a cylindrical nano-wire. • An off-center hydrogenic donor impurity is considered in the system. • Binding energy is affected by orientation of impurity and its distance from center. • Saturation depends on the orientation of impurity position. • By shifting impurity position, orientation and dot radius blue- and red-shifts appear

  17. Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems.

    Science.gov (United States)

    Isaksen, Geir Villy; Andberg, Tor Arne Heim; Åqvist, Johan; Brandsdal, Bjørn Olav

    2015-07-01

    Structural information and activity data has increased rapidly for many protein targets during the last decades. In this paper, we present a high-throughput interface (Qgui) for automated free energy and empirical valence bond (EVB) calculations that use molecular dynamics (MD) simulations for conformational sampling. Applications to ligand binding using both the linear interaction energy (LIE) method and the free energy perturbation (FEP) technique are given using the estrogen receptor (ERα) as a model system. Examples of free energy profiles obtained using the EVB method for the rate-limiting step of the enzymatic reaction catalyzed by trypsin are also shown. In addition, we present calculation of high-precision Arrhenius plots to obtain the thermodynamic activation enthalpy and entropy with Qgui from running a large number of EVB simulations. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

    Science.gov (United States)

    Chen, Changjun

    2016-03-31

    The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

  19. Experimental support for a desolvation energy term in governing equations for binding equilibria.

    Science.gov (United States)

    Castellano, Brian M; Eggers, Daryl K

    2013-07-11

    This study introduces a new thermodynamic framework for aqueous reaction equilibria that treats water as a coreactant in the development of a general binding equation. The approach features an explicit consideration for the change in hydration that occurs when two solvated surfaces come into contact. As an outcome of this framework, the standard-state free energy of binding is defined by the summation of two terms: the traditional term (-RT ln Ki) plus a desolvation free-energy term that is weighted by the number of complexes formed at equilibrium. The new formalism suggests that the equilibrium ratio, Ki, is not a constant and that the observed concentration dependence of Ki may be used to obtain the molar desolvation energy and the standard-state free energy at infinite dilution. The governing equation is supported by results from isothermal titration calorimetry using the chelation of calcium(II) by EDTA as a model binding reaction. This work may have far-reaching implications for solution thermodynamics, including an explanation for the oft-noted discrepancy between the enthalpy values obtained by calorimetry and those from the van't Hoff approach.

  20. Experimental Support for Desolvation Energy Term in Governing Equations for Binding Equilibria

    Science.gov (United States)

    Castellano, Brian M.; Eggers, Daryl K.

    2013-01-01

    This study introduces a new thermodynamic framework for aqueous reaction equilibria that treats water as a co-reactant in the development of a general binding equation. The approach features an explicit consideration for the change in hydration that occurs when two solvated surfaces come into contact. As an outcome of this framework, the standard state free energy of binding is defined by the summation of two terms, the traditional term (−RTlnKi) plus a desolvation free energy term that is weighted by the number of complexes formed at equilibrium. The new formalism suggests that the equilibrium ratio, Ki, is not a constant and that the observed concentration dependence of Ki may be used to obtain the molar desolvation energy and the standard state free energy at infinite dilution. The governing equation is supported by results from isothermal titration calorimetry using the chelation of calcium(II) by EDTA as a model binding reaction. This work may have far-reaching implications for solution thermodynamics, including an explanation for the oft-noted discrepancy between enthalpy values obtained by calorimetry and the van’t Hoff approach. PMID:23773139

  1. Influence of simulation assumptions and input parameters on energy balance calculations of residential buildings

    International Nuclear Information System (INIS)

    Dodoo, Ambrose; Tettey, Uniben Yao Ayikoe; Gustavsson, Leif

    2017-01-01

    In this study, we modelled the influence of different simulation assumptions on energy balances of two variants of a residential building, comprising the building in its existing state and with energy-efficient improvements. We explored how selected parameter combinations and variations affect the energy balances of the building configurations. The selected parameters encompass outdoor microclimate, building thermal envelope and household electrical equipment including technical installations. Our modelling takes into account hourly as well as seasonal profiles of different internal heat gains. The results suggest that the impact of parameter interactions on calculated space heating of buildings is somewhat small and relatively more noticeable for an energy-efficient building in contrast to a conventional building. We find that the influence of parameters combinations is more apparent as more individual parameters are varied. The simulations show that a building's calculated space heating demand is significantly influenced by how heat gains from electrical equipment are modelled. For the analyzed building versions, calculated final energy for space heating differs by 9–14 kWh/m 2 depending on the assumed energy efficiency level for electrical equipment. The influence of electrical equipment on calculated final space heating is proportionally more significant for an energy-efficient building compared to a conventional building. This study shows the influence of different simulation assumptions and parameter combinations when varied simultaneously. - Highlights: • Energy balances are modelled for conventional and efficient variants of a building. • Influence of assumptions and parameter combinations and variations are explored. • Parameter interactions influence is apparent as more single parameters are varied. • Calculated space heating demand is notably affected by how heat gains are modelled.

  2. Calculation of the magnetic anisotropy energy and finite-temperature magnetic properties of transition-metal films

    International Nuclear Information System (INIS)

    Garibay-Alonso, R; Villasenor-Gonzalez, P; Dorantes-Davila, J; Pastor, G M

    2004-01-01

    The magnetic anisotropy energy at the interface (IMAE) of Co films deposited on the Pd(111) surface are determined in the framework of a self-consistent, real-space tight-binding method at zero temperature. Significant spin moments are induced at the Pd atoms at the interface which have an important influence on the observed reorientation transitions as a function of Co film thickness. Film-substrate hybridizations are therefore crucial for the magneto-anisotropic behaviour of thin transition-metal films deposited on metallic non-magnetic substrates. Furthermore, using a real-space recursive expansion of the local Green function and within the virtual-crystal approximation we calculate the magnetization curves and the Curie temperature T C for free-standing Fe films

  3. Calculation of the magnetic anisotropy energy and finite-temperature magnetic properties of transition-metal films

    Energy Technology Data Exchange (ETDEWEB)

    Garibay-Alonso, R [Instituto de Fisica, Universidad Autonoma de San Luis Potosi, San Luis Potosi (Mexico); Villasenor-Gonzalez, P [Instituto de Fisica, Universidad Autonoma de San Luis Potosi, San Luis Potosi (Mexico); Dorantes-Davila, J [Instituto de Fisica, Universidad Autonoma de San Luis Potosi, San Luis Potosi (Mexico); Pastor, G M [Laboratoire de Physique Quantique, UMR 5626 du CNRS, Universite Paul Sabatier, Toulouse (France)

    2004-06-09

    The magnetic anisotropy energy at the interface (IMAE) of Co films deposited on the Pd(111) surface are determined in the framework of a self-consistent, real-space tight-binding method at zero temperature. Significant spin moments are induced at the Pd atoms at the interface which have an important influence on the observed reorientation transitions as a function of Co film thickness. Film-substrate hybridizations are therefore crucial for the magneto-anisotropic behaviour of thin transition-metal films deposited on metallic non-magnetic substrates. Furthermore, using a real-space recursive expansion of the local Green function and within the virtual-crystal approximation we calculate the magnetization curves and the Curie temperature T{sub C} for free-standing Fe films.

  4. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

    Science.gov (United States)

    Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

    2016-11-25

    The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  5. Interaction of C2H with molecular hydrogen: Ab initio potential energy surface and scattering calculations

    Science.gov (United States)

    Dagdigian, Paul J.

    2018-01-01

    The potential energy surface (PES) describing the interaction of the ethynyl (C2H) radical in its ground X˜ 2Σ+ electronic state with molecular hydrogen has been computed through restricted coupled cluster calculations including single, double, and (perturbative) triple excitations [RCCSD(T)], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants. A representative set of energy dependent state-to-state cross sections is presented and discussed. The PES and cross sections for collisions of H2(j = 0) are compared with a previous study [F. Najar et al., Chem. Phys. Lett. 614, 251 (2014)] of collisions of C2H with H2 treated as a spherical collision partner. Good agreement is found between the two sets of calculations when the H2 molecule in the present calculation is spherically averaged.

  6. Vibrational frequencies via total-energy calculations. Applications to transition metals

    International Nuclear Information System (INIS)

    Ho, K.; Fu, C.L.; Harmon, B.N.

    1984-01-01

    The important longitudinal ((2/3),(2/3),(2/3)) vibrational modes in Mo, Nb, and bcc Zr as well as the H-point modes in Mo and Nb have been studied using the frozen-phonon approach. These entirely first-principles calculations involve the precise evaluation of the total crystalline energy as a function of lattice displacement and yield calculated phonon frequencies to within a few percent of the experimental values. Anharmonic terms are readily obtained and are found to be very important for causing the tendency toward the ω-phase instability in bcc Zr. The charge densities and single-particle energies obtained in the course of the calculations allow a detailed analysis of the electronic response to lattice distortions and the mechanisms causing phonon anomalies. The calculations also provide first-principles benchmarks at a few wave vectors where the validity of phenomenological models can be tested or their parameters determined

  7. Annotated references on shielding experiment and calculation of high energy particles

    International Nuclear Information System (INIS)

    Hirayama, H.; Ban, S.; Nakamura, T.

    1990-12-01

    The literature on shielding experiment and calculation of high energy particles above 20 MeV has been surveyed. The survey covers thirteen journals, from 1965 up to 1989. For each paper, applicable information is listed on type and energy of the projectile, the accelerator used, composition and thickness of the target and shielding materials, shielding geometry, the experimental and calculational methods, and the quantities obtained. The references on shielding experiment and on shielding calculation are accessed through two indices which list the projectile-target and shielding material combination, shielding geometry and the projectile energy range. The literature on neutron, photon and hadron production from thick target bombarded by charged particles has been surveyed mainly from 1984 as a complement of the previous work. (author)

  8. Reformulated tight binding calculation for band discontinuity at CdTe/Hg xCd1-xTe heterointerfaces and their type I-type III transitions

    International Nuclear Information System (INIS)

    Ekpunobi, A.J.

    2005-01-01

    A recently reformulated tight binding method is used to calculate the valence band discontinuity at the CdTe/Hg x Cd 1-x Te interface in the s 2 p 2 configuration. The calculated valence band discontinuity of 0.31 eV at CdTe/HgTe interface is in good agreement with self-consistent calculation and accepted experimental value. Calculations were extended to alloy interfaces, which enabled the investigation of the band-offset problem at the transition point. Both valence band discontinuity ratio and conduction band discontinuity ratio show inflexions at the transition point

  9. Precision measurements of high-energy conversion electron lines and determination of neutron binding energies

    International Nuclear Information System (INIS)

    Braumandl, F.

    1979-01-01

    The paper first discusses the energy accuracy of the BILL conversion electron spectrometer at the Grenoble high flux reactor. With an improved temperature stabilisation of the magnets, an energy accuracy of ΔE/E -5 can be reached. After this, highly exact measurements of high-energy conversion electron lines of the 200 Hg, 114 Cd, 165 Dy, 168 Er, 239 U nuclei and the 13 C, 28 Al 3 H and 92 Zr photoelectron lines were carried out. Energy calibration of the spectrometer was carried out in the 1.5 MeV to 6.5 MeV range with intensive high-energy transitions of the 200 Hg nucleus. Systematic calibration errors could be investigated by means of combinations between the calibration lines. A calibration for absolute energies was obtained by comparing low-energy gamma transitions of 200 Hg with the 411.8 keV gold standard. (orig.) [de

  10. Calculating economy-wide energy intensity decline rate: The role of sectoral output and energy shares

    International Nuclear Information System (INIS)

    Baksi, Soham; Green, Chris

    2007-01-01

    We specify formulas for computing the rate of decline in economy-wide energy intensity by aggregating its two determinants-technical efficiency improvements in the various sectors of the economy, and shifts in economic activity among these sectors. The formulas incorporate the interdependence between sectoral shares, and establish a one-to-one relation between sectoral output and energy shares. This helps to eliminate future energy intensity decline scenarios which involve implausible values of either sectoral share. An illustrative application of the formulas is provided, using within-sector efficiency improvement estimates suggested by Lightfoot-Green and Harvey

  11. Development of Continuous-Energy Eigenvalue Sensitivity Coefficient Calculation Methods in the Shift Monte Carlo Code

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, Christopher M [ORNL; Martin, William R [University of Michigan; Rearden, Bradley T [ORNL; Williams, Mark L [ORNL

    2012-01-01

    Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the SHIFT Monte Carlo code within the Scale code package. The methods were used for several simple test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods.

  12. Calculation of intensity of high energy muon groups observed deep underground

    Science.gov (United States)

    Vavilov, Y. N.; Dedenko, L. G.

    1985-01-01

    The intensity of narrow muon groups observed in Kolar Gold Field (KGF) at the depth of 3375 m.w.e. was calculated in terms of quark-gluon strings model for high energy hadron - air nuclei interactions by the method of direct modeling of nuclear cascade in the air and muon propagation in the ground for normal primary cosmic ray composition. The calculated intensity has been found to be approx. 10 to the 4 times less than one observed experimentally.

  13. Binding energy and momentum distribution of nuclear matter using Green's function methods

    International Nuclear Information System (INIS)

    Ramos, A.; Dickhoff, W.H.; Polls, A.

    1991-01-01

    The influence of hole-hole (h-h) propagation in addition to the conventional particle-particle (p-p) propagation, on the energy per particle and the momentum distribution is investigated for the v 2 central interaction which is derived from Reid's soft-core potential. The results are compared to Brueckner-Hartree-Fock calculations with a continuous choice for the single-particle (SP) spectrum. Calculation of the energy from a self-consistently determined SP spectrum leads to a lower saturation density. This result is not corroborated by calculating the energy from the hole spectral function, which is, however, not self-consistent. A generalization of previous calculations of the momentum distribution, based on a Goldstone diagram expansion, is introduced that allows the inclusion of h-h contributions to all orders. From this result an alternative calculation of the kinetic energy is obtained. In addition, a direct calculation of the potential energy is presented which is obtained from a solution of the ladder equation containing p-p and h-h propagation to all orders. These results can be considered as the contributions of selected Goldstone diagrams (including p-p and h-h terms on the same footing) to the kinetic and potential energy in which the SP energy is given by the quasiparticle energy. The results for the summation of Goldstone diagrams leads to a different momentum distribution than the one obtained from integrating the hole spectral function which in general gives less depletion of the Fermi sea. Various arguments, based partly on the results that are obtained, are put forward that a self-consistent determination of the spectral functions including the p-p and h-h ladder contributions (using a realistic interaction) will shed light on the question of nuclear saturation at a nonrelativistic level that is consistent with the observed depletion of SP orbitals in finite nuclei

  14. Binding energy and momentum distribution of nuclear matter using Green's function methods

    International Nuclear Information System (INIS)

    Ramos, A.; Dickhoff, W.H.; Polls, A.

    1990-07-01

    The influence of hole-hole (hh) propagation in addition to the conventional particle-particle (pp) propagation on the energy per particle and the momentum distribution is investigated for two central interactions (v 2 and v 2 l=0 ) which are derived from Reid's soft core potential. The results are compared to Brueckner-Hartree-Fock calculations with a continuous choice for the single-particle (sp) spectrum. Calculation of the energy from a self-consistently determined sp spectrum leads to a lower saturation density. This result is not corroborated by calculating the energy from the hole spectral function which is, however, not self-consistent. A generalization of previous calculations of the momentum distribution based on a Goldstone diagram expansion is introduced which allows the inclusion of hh contributions to all orders. From this result an alternative calculation of the kinetic energy is obtained. In addition, a direct calculation of the potential energy is presented which is obtained from a solution of the ladder equation containing pp and hh propagation to all orders. These results can be considered as the contributions of selected Goldstone diagrams (including pp and hh terms on the same footing) to the kinetic and potential energy in which the sp energy is given by the quasi-article energy. The results for the summation of Goldstone diagrams leads to a different momentum distribution than the one obtained from integrating the hole spectral function which in general gives less depletion of the Fermi sea. Various arguments, based partly on the results that are obtained, are put forward that a self-consistent determination of the spectral functions including the pp and hh ladder contributions (using a realistic interaction) will shed light on the question of nuclear saturation at a non-relativistic level which is consistent with the observed depletion of sp orbitals in finite nuclei. (Author) (51 refs., 3 tabs., 15 figs)

  15. Calculation of Zeeman splitting and Zeeman transition energies of spherical quantum dot in uniform magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Çakır, Bekir; Atav, Ülfet [Physics Department, Faculty of Sciences, Selcuk University, Campus 42031 Konya (Turkey); Yakar, Yusuf, E-mail: yuyakar@yahoo.com [Physics Department, Faculty of Arts and Sciences, Aksaray University, Campus 68100 Aksaray (Turkey); Özmen, Ayhan [Physics Department, Faculty of Sciences, Selcuk University, Campus 42031 Konya (Turkey)

    2016-08-22

    Highlights: • The magnetic field effects on the ground and excited energy states of QD are investigated. • The Zeeman transition energies between energy states are calculated. • Wave functions and the energy eigenvalues are computed by using Quantum Genetic Algorithm and Hartree–Fock Roothaan method. - Abstract: In this study we report a detailed theoretical investigation of the effect of an external magnetic field on the 1s-, 2p-, 3d- and 4f-energy states of a spherical quantum dot. We treat the contribution of the diamagnetic term as a perturbation and discuss the effect of the diamagnetic term on the 1s-, 2p-, 3d- and 4f-energy states. We also have calculated the Zeeman transition energies between 2p → 1s and 3d → 2p states with m = 0, ±1 and 0, ±1, ±2 as a function of dot radius and the magnetic field strength. The results show that the magnetic field, impurity charge and dot radius have a strong influence on the energy states and the Zeeman transitions. It is found that the energies of the electronic states with m < 0 addition of the diamagnetic term firstly decrease toward a minimum, and then increase with the increasing magnetic field strength. We have seen that as magnetic field intensity is adjusted, frequency of the emitted light can be changed for Zeeman transitions.

  16. Quantum confinement effect and exciton binding energy of layered perovskite nanoplatelets

    Directory of Open Access Journals (Sweden)

    Qiang Wang

    2018-02-01

    Full Text Available We report the preparation of monolayer (n = 1, few-layer (n = 2–5 and 3D (n = ∞ organic lead bromide perovskite nanoplatelets (NPLs by tuning the molar ratio of methylammonium bromide (MABr and hexadecammonium bromide (HABr. The absorption spectrum of the monolayer (HA2PbBr4 perovskite NPLs shows about 138 nm blue shift from that of 3D MAPbBr3 perovskites, which is attributed to strong quantum confinement effect. We further investigate the two-photon photoluminescence (PL of the NPLs and measure the exciton binding energy of monolayer perovskite NPLs using linear absorption and two-photon PL excitation spectroscopy. The exciton binding energy of monolayer perovskite NPLs is about 218 meV, which is far larger than tens of meV in 3D lead halide perovskites.

  17. Atomic structure calculation of energy levels and oscillator strengths in Ti ion, 2

    International Nuclear Information System (INIS)

    Ishii, Keishi

    1983-10-01

    Energy levels and oscillator strengths are calculated for 3s-3p and 3p-3d transition arrays in Ti X, isoelectronic to Al I. The energy levels are obtained by the Slater-Condon theory of atomic structure, including explicitly the strong configuration interactions. The results are presented both in numerical tables and in diagrams. In the tables, the observed data are included for comparison, where available. The calculated weighted oscillator strengths (gf-value) are also displayed in figures, where the weighted oscillator strengths are plotted as a function of wavelength. (author)

  18. An efficient method for energy levels calculation using full symmetry and exact kinetic energy operator: Tetrahedral molecules

    Science.gov (United States)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2015-03-01

    A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)-2 type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.

  19. Valence proton-neutron interaction strengths from double binding energy differences

    International Nuclear Information System (INIS)

    Brenner, D.S.; Foy, B.D.; Warner, D.D.; Zamfir, N.V.; Casten, R.F.

    1996-01-01

    Empirical p-n interaction strengths have been extracted from experimental mass data using double-difference binding energy equations. The especially strong interactions for self-conjugate nuclei will be discussed as well as microstructure found for deformed and in doubly magic regions. Valence correlation Schemes provide a basis to comment on the stability of medium mass near-drip-line nuclei and superheavy elements

  20. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores

    Science.gov (United States)

    Benson, Mark L.; Faver, John C.; Ucisik, Melek N.; Dashti, Danial S.; Zheng, Zheng; Merz, Kenneth M.

    2012-05-01

    Two families of binding affinity estimation methodologies are described which were utilized in the SAMPL3 trypsin/fragment binding affinity challenge. The first is a free energy decomposition scheme based on a thermodynamic cycle, which included separate contributions from enthalpy and entropy of binding as well as a solvent contribution. Enthalpic contributions were estimated with PM6-DH2 semiempirical quantum mechanical interaction energies, which were modified with a statistical error correction procedure. Entropic contributions were estimated with the rigid-rotor harmonic approximation, and solvent contributions to the free energy were estimated with several different methods. The second general methodology is the empirical score LISA, which contains several physics-based terms trained with the large PDBBind database of protein/ligand complexes. Here we also introduce LISA+, an updated version of LISA which, prior to scoring, classifies systems into one of four classes based on a ligand's hydrophobicity and molecular weight. Each version of the two methodologies (a total of 11 methods) was trained against a compiled set of known trypsin binders available in the Protein Data Bank to yield scaling parameters for linear regression models. Both raw and scaled scores were submitted to SAMPL3. Variants of LISA showed relatively low absolute errors but also low correlation with experiment, while the free energy decomposition methods had modest success when scaling factors were included. Nonetheless, re-scaled LISA yielded the best predictions in the challenge in terms of RMS error, and six of these models placed in the top ten best predictions by RMS error. This work highlights some of the difficulties of predicting binding affinities of small molecular fragments to protein receptors as well as the benefit of using training data.

  1. Methodology for calculating the impact of distributed generation on energy losses in a distribution network

    Directory of Open Access Journals (Sweden)

    Perić Jelena

    2013-01-01

    Full Text Available This paper is the result of the Master's final project 'Methodology for calculating the impact of distributed generation on energy losses in distribution network'. The question is whether, for estimation of the impact of the power plant on energy losses in the distribution network, it is necessary to analyze each hour value of small power plant engagement and its effect, or it is sufficient to analyze a small number of states, and the extent to which it is possible to reduce the number of states that will be analyzed in order to review adequately the impact of the power plant on the change of energy losses in the network. To answer this question, an algorithm consisting of two steps is performed, annual production diagrams are obtained and, on the basis of calculated specific discrete values, the impact of the small power plant on energy losses in the distribution network to which it is connected is evaluated.

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

    Science.gov (United States)

    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.

  3. Hot-electron-mediated desorption rates calculated from excited-state potential energy surfaces

    DEFF Research Database (Denmark)

    Olsen, Thomas; Gavnholt, Jeppe; Schiøtz, Jakob

    2009-01-01

    We present a model for desorption induced by (multiple) electronic transitions [DIET (DIMET)] based on potential energy surfaces calculated with the delta self-consistent field extension of density-functional theory. We calculate potential energy surfaces of CO and NO molecules adsorbed on various...... transition-metal surfaces and show that classical nuclear dynamics does not suffice for propagation in the excited state. We present a simple Hamiltonian describing the system with parameters obtained from the excited-state potential energy surface and show that this model can describe desorption dynamics...... in both the DIET and DIMET regimes and reproduce the power-law behavior observed experimentally. We observe that the internal stretch degree of freedom in the molecules is crucial for the energy transfer between the hot electrons and the molecule when the coupling to the surface is strong....

  4. R-matrix calculation of low-energy electron collisions with phosphoric acid

    Energy Technology Data Exchange (ETDEWEB)

    Bryjko, Lilianna; Van Mourik, Tanja [School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST (United Kingdom); Dora, Amar; Tennyson, Jonathan, E-mail: j.tennyson@ucl.ac.u [Department of Physics and Astronomy, University College London, Gower St, London WC1E 6BT (United Kingdom)

    2010-12-14

    Electron collision calculations are performed on two conformers of H{sub 3}PO{sub 4}, a weakly dipolar form with all OH groups pointing up and a strongly dipolar form where one OH group points down. Strong evidence is found for a broad shape resonance at about 7 eV for both conformers, although the precise parameters of this resonance are sensitive to the details of the target wavefunction used. Ten-state close-coupling calculations suggest the presence of very narrow Feshbach resonances in a similar energy region. Again both conformers behave similarly. Elastic and electronically inelastic cross sections are calculated for both conformers.

  5. Line Tension and Interaction Energies of Membrane Rafts Calculated from Lipid Splay and Tilt

    OpenAIRE

    Kuzmin, Peter I.; Akimov, Sergey A.; Chizmadzhev, Yuri A.; Zimmerberg, Joshua; Cohen, Fredric S.

    2004-01-01

    Membrane domains known as rafts are rich in cholesterol and sphingolipids, and are thought to be thicker than the surrounding membrane. If so, monolayers should elastically deform so as to avoid exposure of hydrophobic surfaces to water at the raft boundary. We calculated the energy of splay and tilt deformations necessary to avoid such hydrophobic exposure. The derived value of energy per unit length, the line tension γ, depends on the elastic moduli of the raft and the surrounding membrane;...

  6. Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

    Directory of Open Access Journals (Sweden)

    Nan eZhao

    2013-08-01

    Full Text Available Previously we have shown that ONIOM type (QM/MM calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and 18O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0, 2,3,5,6-tetramethyl-1,4-benzoquinone (duroquinone, DQ, and 2,3-dimethyl-l,4-naphthoquinone (DMNQ incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites.The normal modes that contribute to the bands in the calculated spectra, their composition, frequency and intensity, and how these quantities are modified upon 18O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10-13 cm-1 separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are tail-less. Spectra were also calculated for reaction centers with corresponding tail containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated s

  7. Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dan; Han, Ju-Guang; Chen, Hang; Li, Liang; Zhao, Run-Ning Zhao; Liu, Guang; Duan, Yuhua

    2012-05-01

    The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap region (residues 38-58) and the active site region (residues 23-32) in HIV-1 protease contribute 63.72% of the protease to the binding of the inhibitor. In particular, the mechanisms for the interactions of key residues of these species are fully explored and analyzed. Interestingly, the regression analyses show that both CAS and BFED based on the generalized Born model yield similar results, with a correlation coefficient of 0.94. However, compared to CAS, BFED is faster and can decompose the per-residue binding free-energy contributions into backbone and sidechain contributions. The results obtained in this study are useful for studying the binding mechanism between receptor and ligand and for designing potent inhibitors that can combat diseases.

  8. Definition of the G protein-coupled receptor transmembrane bundle binding pocket and calculation of receptor similarities for drug design

    DEFF Research Database (Denmark)

    Gloriam, David Erik Immanuel; Foord, Steven M; Blaney, Frank E

    2009-01-01

    Recent advances in structural biology for G-protein-coupled receptors (GPCRs) have provided new opportunities to improve the definition of the transmembrane binding pocket. Here a reference set of 44 residue positions accessible for ligand binding was defined through detailed analysis of all...... to endogenous ligand types, although it revealed subdivision of certain classes, notably peptide and lipid receptors. The transmembrane binding site reference set, particularly when coupled with a means of identifying the subset of ligand binding residues, provides a general paradigm for understanding...

  9. Methods of Calculating Ionization Energies of Multielectron (Five or More Isoelectronic Atomic Ions

    Directory of Open Access Journals (Sweden)

    Peter F. Lang

    2013-01-01

    Full Text Available We have previously used simple empirical equations to reproduce the literature values of the ionization energies of isoelectronic sequences of up to four electrons which gave very good agreement. We reproduce here a kinetic energy expression with corrections for relativity and Lamb shift effects which give excellent agreement with the literature values. These equations become more complex as the number of electrons in the system increases. Alternative simple quadratic expressions for calculating ionization energies of multielectron ions are discussed. A set of coefficients when substituted into a simple expression produces very good agreement with the literature values. Our work shows that Slater's rules are not appropriate for predicting trends or screening constants. This work provides very strong evidence that ionization energies are not functions of complete squares, and when calculating ionization energies electron transition/relaxation has to be taken into account. We demonstrate clearly that for particular isoelectronic sequences, the ionizing electrons may occupy different orbitals and in such cases more than one set of constants are needed to calculate the ionization energies.

  10. The importance of geospatial data to calculate the optimal distribution of renewable energies

    Science.gov (United States)

    Díaz, Paula; Masó, Joan

    2013-04-01

    Specially during last three years, the renewable energies are revolutionizing the international trade while they are geographically diversifying markets. Renewables are experiencing a rapid growth in power generation. According to REN21 (2012), during last six years, the total renewables capacity installed grew at record rates. In 2011, the EU raised its share of global new renewables capacity till 44%. The BRICS nations (Brazil, Russia, India and China) accounted for about 26% of the total global. Moreover, almost twenty countries in the Middle East, North Africa, and sub-Saharan Africa have currently active markets in renewables. The energy return ratios are commonly used to calculate the efficiency of the traditional energy sources. The Energy Return On Investment (EROI) compares the energy returned for a certain source and the energy used to get it (explore, find, develop, produce, extract, transform, harvest, grow, process, etc.). These energy return ratios have demonstrated a general decrease of efficiency of the fossil fuels and gas. When considering the limitations of the quantity of energy produced by some sources, the energy invested to obtain them and the difficulties of finding optimal locations for the establishment of renewables farms (e.g. due to an ever increasing scarce of appropriate land) the EROI becomes relevant in renewables. A spatialized EROI, which uses variables with spatial distribution, enables the optimal position in terms of both energy production and associated costs. It is important to note that the spatialized EROI can be mathematically formalized and calculated the same way for different locations in a reproducible way. This means that having established a concrete EROI methodology it is possible to generate a continuous map that will highlight the best productive zones for renewable energies in terms of maximum energy return at minimum cost. Relevant variables to calculate the real energy invested are the grid connections between

  11. Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

    Science.gov (United States)

    Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

    2016-01-01

    While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.

  12. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces.

    Science.gov (United States)

    Simões, Inês C M; Costa, Inês P D; Coimbra, João T S; Ramos, Maria J; Fernandes, Pedro A

    2017-01-23

    Knowing how proteins make stable complexes enables the development of inhibitors to preclude protein-protein (P:P) binding. The identification of the specific interfacial residues that mostly contribute to protein binding, denominated as hot spots, is thus critical. Here, we refine an in silico alanine scanning mutagenesis protocol, based on a residue-dependent dielectric constant version of the Molecular Mechanics/Poisson-Boltzmann Surface Area method. We have used a large data set of structurally diverse P:P complexes to redefine the residue-dependent dielectric constants used in the determination of binding free energies. The accuracy of the method was validated through comparison with experimental data, considering the per-residue P:P binding free energy (ΔΔG binding ) differences upon alanine mutation. Different protocols were tested, i.e., a geometry optimization protocol and three molecular dynamics (MD) protocols: (1) one using explicit water molecules, (2) another with an implicit solvation model, and (3) a third where we have carried out an accelerated MD with explicit water molecules. Using a set of protein dielectric constants (within the range from 1 to 20) we showed that the dielectric constants of 7 for nonpolar and polar residues and 11 for charged residues (and histidine) provide optimal ΔΔG binding predictions. An overall mean unsigned error (MUE) of 1.4 kcal mol -1 relative to the experiment was achieved in 210 mutations only with geometry optimization, which was further reduced with MD simulations (MUE of 1.1 kcal mol -1 for the MD employing explicit solvent). This recalibrated method allows for a better computational identification of hot spots, avoiding expensive and time-consuming experiments or thermodynamic integration/ free energy perturbation/ uBAR calculations, and will hopefully help new drug discovery campaigns in their quest of searching spots of interest for binding small drug-like molecules at P:P interfaces.

  13. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  14. Evaluation of the HTTR criticality and burnup calculations with continuous-energy and multigroup cross sections

    International Nuclear Information System (INIS)

    Chiang, Min-Han; Wang, Jui-Yu; Sheu, Rong-Jiun; Liu, Yen-Wan Hsueh

    2014-01-01

    The High Temperature Engineering Test Reactor (HTTR) in Japan is a helium-cooled graphite-moderated reactor designed and operated for the future development of high-temperature gas-cooled reactors. Two detailed full-core models of HTTR have been established by using SCALE6 and MCNP5/X, respectively, to study its neutronic properties. Several benchmark problems were repeated first to validate the calculation models. Careful code-to-code comparisons were made to ensure that two calculation models are both correct and equivalent. Compared with experimental data, the two models show a consistent bias of approximately 20–30 mk overestimation in effective multiplication factor for a wide range of core states. Most of the bias could be related to the ENDF/B-VII.0 cross-section library or incomplete modeling of impurities in graphite. After that, a series of systematic analyses was performed to investigate the effects of cross sections on the HTTR criticality and burnup calculations, with special interest in the comparison between continuous-energy and multigroup results. Multigroup calculations in this study were carried out in 238-group structure and adopted the SCALE double-heterogeneity treatment for resonance self-shielding. The results show that multigroup calculations tend to underestimate the system eigenvalue by a constant amount of ∼5 mk compared to their continuous-energy counterparts. Further sensitivity studies suggest the differences between multigroup and continuous-energy results appear to be temperature independent and also insensitive to burnup effects

  15. Evaluation of the HTTR criticality and burnup calculations with continuous-energy and multigroup cross sections

    Energy Technology Data Exchange (ETDEWEB)

    Chiang, Min-Han; Wang, Jui-Yu [Institute of Nuclear Engineering and Science, National Tsing Hua University, 101, Section 2, Kung-Fu Road, Hsinchu 30013, Taiwan (China); Sheu, Rong-Jiun, E-mail: rjsheu@mx.nthu.edu.tw [Institute of Nuclear Engineering and Science, National Tsing Hua University, 101, Section 2, Kung-Fu Road, Hsinchu 30013, Taiwan (China); Department of Engineering System and Science, National Tsing Hua University, 101, Section 2, Kung-Fu Road, Hsinchu 30013, Taiwan (China); Liu, Yen-Wan Hsueh [Institute of Nuclear Engineering and Science, National Tsing Hua University, 101, Section 2, Kung-Fu Road, Hsinchu 30013, Taiwan (China); Department of Engineering System and Science, National Tsing Hua University, 101, Section 2, Kung-Fu Road, Hsinchu 30013, Taiwan (China)

    2014-05-01

    The High Temperature Engineering Test Reactor (HTTR) in Japan is a helium-cooled graphite-moderated reactor designed and operated for the future development of high-temperature gas-cooled reactors. Two detailed full-core models of HTTR have been established by using SCALE6 and MCNP5/X, respectively, to study its neutronic properties. Several benchmark problems were repeated first to validate the calculation models. Careful code-to-code comparisons were made to ensure that two calculation models are both correct and equivalent. Compared with experimental data, the two models show a consistent bias of approximately 20–30 mk overestimation in effective multiplication factor for a wide range of core states. Most of the bias could be related to the ENDF/B-VII.0 cross-section library or incomplete modeling of impurities in graphite. After that, a series of systematic analyses was performed to investigate the effects of cross sections on the HTTR criticality and burnup calculations, with special interest in the comparison between continuous-energy and multigroup results. Multigroup calculations in this study were carried out in 238-group structure and adopted the SCALE double-heterogeneity treatment for resonance self-shielding. The results show that multigroup calculations tend to underestimate the system eigenvalue by a constant amount of ∼5 mk compared to their continuous-energy counterparts. Further sensitivity studies suggest the differences between multigroup and continuous-energy results appear to be temperature independent and also insensitive to burnup effects.

  16. Comparison of Measured Dark Current Distributions with Calculated Damage Energy Distributions in HgCdTe

    Science.gov (United States)

    Marshall, C. J.; Marshall, P. W.; Howe, C. L.; Reed, R. A.; Weller, R. A.; Mendenhall, M.; Waczynski, A.; Ladbury, R.; Jordan, T. M.

    2007-01-01

    This paper presents a combined Monte Carlo and analytic approach to the calculation of the pixel-to-pixel distribution of proton-induced damage in a HgCdTe sensor array and compares the results to measured dark current distributions after damage by 63 MeV protons. The moments of the Coulombic, nuclear elastic and nuclear inelastic damage distributions were extracted from Monte Carlo simulations and combined to form a damage distribution using the analytic techniques first described in [1]. The calculations show that the high energy recoils from the nuclear inelastic reactions (calculated using the Monte Carlo code MCNPX [2]) produce a pronounced skewing of the damage energy distribution. While the nuclear elastic component (also calculated using the MCNPX) contributes only a small fraction of the total nonionizing damage energy, its inclusion in the shape of the damage across the array is significant. The Coulombic contribution was calculated using MRED [3-5], a Geant4 [4,6] application. The comparison with the dark current distribution strongly suggests that mechanisms which are not linearly correlated with nonionizing damage produced according to collision kinematics are responsible for the observed dark current increases. This has important implications for the process of predicting the on-orbit dark current response of the HgCdTe sensor array.

  17. Three-dimensional dynamic calculation in the low energy region of an electron linac

    International Nuclear Information System (INIS)

    Song Zhongheng; Wang Xiaomin

    1990-09-01

    The model of charge discs with variable radius and the model of charge rings are used in the three-dimensional dynamic calculation at the low energy region of an electron linac. The charged particles displacement, rate of displacement and trajectories are computed. The RMS emittance and pictures of beam emittance on different phase planes are also given

  18. Marginal cost calculation of energy production in hydro thermoelectric systems considering the transmission system

    International Nuclear Information System (INIS)

    Pereira, M.V.F.; Gorenstin, B.G.; Alvarenga Filho, S.

    1989-01-01

    The alternatives for calculation of energy marginal cost in hydroelectric systems, considering the transmission one, was analysed, including fundamental concepts; generation/transmission systems, represented by linear power flow model; production marginal costs in hydrothermal systems and computation aspects. (C.G.C.). 11 refs, 5 figs

  19. A Novel Energy Yields Calculation Method for Irregular Wind Farm Layout

    DEFF Research Database (Denmark)

    Hou, Peng; Hu, Weihao; Soltani, Mohsen

    2015-01-01

    Due to the increasing size of offshore wind farm, the impact of the wake effect on energy yields become more and more evident. The Seafloor topography would limit the layout of the wind farm so that irregular layout is usually adopted inlarge scale offshore wind farm. However, the calculation...

  20. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Science.gov (United States)

    2010-01-01

    ... cost indexes? 591.220 Section 591.220 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ALLOWANCES AND DIFFERENTIALS Cost-of-Living Allowance and Post Differential-Nonforeign Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM...

  1. Calculation of the Stabilization Energies of Oxidatively Damaged Guanine Base Pairs with Guanine

    Directory of Open Access Journals (Sweden)

    Hiroshi Miyazawa

    2012-06-01

    Full Text Available DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H-oxazolone (Oz, guanidinohydantoin (Gh/iminoallantoin (Ia and spiro-imino-dihydantoin (Sp are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.

  2. Performance of SOPPA-based methods in the calculation of vertical excitation energies and oscillator strengths

    DEFF Research Database (Denmark)

    Sauer, Stephan P. A.; Pitzner-Frydendahl, Henrik Frank; Buse, Mogens

    2015-01-01

    methods, the original SOPPA method as well as SOPPA(CCSD) and RPA(D) in the calculation of vertical electronic excitation energies and oscillator strengths is investigated for a large benchmark set of 28 medium-size molecules with 139 singlet and 71 triplet excited states. The results are compared...

  3. A Simple Method to Calculate the Temperature Dependence of the Gibbs Energy and Chemical Equilibrium Constants

    Science.gov (United States)

    Vargas, Francisco M.

    2014-01-01

    The temperature dependence of the Gibbs energy and important quantities such as Henry's law constants, activity coefficients, and chemical equilibrium constants is usually calculated by using the Gibbs-Helmholtz equation. Although, this is a well-known approach and traditionally covered as part of any physical chemistry course, the required…

  4. User guide - COE calculation tool for wave energy converters. Draft version 1

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Chozas, J.; Kofoed, J.P. [Aalborg Univ., Aalborg (Denmark); Helstrup Jensen, N.E. [Energinet.dk, Fredericia (Denmark)

    2013-08-15

    Aalborg University together with Energinet.dk and Julia F. Chozas Consulting Engineer, have released a freely available online spreadsheet to evaluate the Levelised Cost of Energy (LCOE) for wave energy projects. The open-access tool calculates the LCOE based on the power production of a Wave Energy Converter (WEC) at a particular location. Production data may derive from laboratory testing, numerical modelling or from sea trials. The tool has been developed as a transparent and simple model that evaluates WEC's economic feasibility in a range of locations, while scaling WEC's features to the selected site. (Author)

  5. A calculation program for harvesting and transportation costs of energy wood; Energiapuun korjuun ja kuljetuksen kustannuslaskentaohjelmisto

    Energy Technology Data Exchange (ETDEWEB)

    Kuitto, P.J.

    1996-12-31

    VTT Energy is compiling a large and versatile calculation program for harvesting and transportation costs of energy wood. The work has been designed and will be carried out in cooperation with Metsaeteho and Finntech Ltd. The program has been realised in Windows surroundings using SQLWindows graphical database application development system, using the SQLBase relational database management system. The objective of the research is to intensify and create new possibilities for comparison of the utilization costs and the profitability of integrated energy wood production chains with each other inside the chains

  6. Steric effect studies on solar energy storage of norbornadiene-quadracyclane system: DFT calculations

    Directory of Open Access Journals (Sweden)

    E. Vessally

    2009-08-01

    Full Text Available The aim of this research is to determine the possible solar energy storage in the norbornadiene (1 / quadricyclane (2 system, through involving steric effects on various position of carbon C1, C2 or C7 for 1 and 2; calculating the corresponding energies at B3LYP/6-311G** level of theory. The extent of the solar energy storage is the least for 11-i-Pr (-21.018, 12-t-Bu (-22.525 and 17-i-Pr (-17.753 when the bulk substituents (X were occured at C1, C2 and C7, respectively.

  7. Practical methodologies for the calculation of capacity in electricity markets for wind energy

    International Nuclear Information System (INIS)

    Botero B, Sergio; Giraldo V, Luis Alfonso; Isaza C, Felipe

    2008-01-01

    Determining the real capacity of the generators in a power market is an essential task in order to estimate the actual system reliability, and to estimate the reward for generators due to their capacity in the firm energy market. In the wind power case, which is an intermittent resource, several methodologies have been proposed to estimate the capacity of a wind power emplacement, not only for planning but also for firm energy remuneration purposes. This paper presents some methodologies that have been proposed or implemented around the world in order to calculate the capacity of this energy resource.

  8. Relativistic many-body calculations of energies for n=3 states in aluminiumlike ions

    Energy Technology Data Exchange (ETDEWEB)

    Safronova, U.I.; Namba, C. [National Inst. for Fusion Science, Toki, Gifu (Japan); Johnson, W.R.; Safronova, M.S. [Department of Physics, Univ. of Notre Dame, Notre Dame, IN (United States)

    2001-01-01

    Energies of the 148 (3l3l'3l'') states for aluminiumlike ions with Z =14-100 are evaluated to second order in relativistic many-body perturbation theory. Second-order Coulomb and Breit-Coulomb interactions are included. Corrections are made to lowest order for the frequency-dependent Breit interaction and for the Lamb shift. A detailed discussion of the various contributions to the energy levels is given for aluminiumlike germanium (Z=32). Comparisons of the calculated energy levels with available experimental data are made for the entire sequence. (author)

  9. Automated calculation of surface energy fluxes with high-frequency lake buoy data

    Science.gov (United States)

    Woolway, R. Iestyn; Jones, Ian D; Hamilton, David P.; Maberly, Stephen C; Muroaka, Kohji; Read, Jordan S.; Smyth, Robyn L; Winslow, Luke A.

    2015-01-01

    Lake Heat Flux Analyzer is a program used for calculating the surface energy fluxes in lakes according to established literature methodologies. The program was developed in MATLAB for the rapid analysis of high-frequency data from instrumented lake buoys in support of the emerging field of aquatic sensor network science. To calculate the surface energy fluxes, the program requires a number of input variables, such as air and water temperature, relative humidity, wind speed, and short-wave radiation. Available outputs for Lake Heat Flux Analyzer include the surface fluxes of momentum, sensible heat and latent heat and their corresponding transfer coefficients, incoming and outgoing long-wave radiation. Lake Heat Flux Analyzer is open source and can be used to process data from multiple lakes rapidly. It provides a means of calculating the surface fluxes using a consistent method, thereby facilitating global comparisons of high-frequency data from lake buoys.

  10. Locating Temporal Functional Dynamics of Visual Short-Term Memory Binding using Graph Modular Dirichlet Energy

    Science.gov (United States)

    Smith, Keith; Ricaud, Benjamin; Shahid, Nauman; Rhodes, Stephen; Starr, John M.; Ibáñez, Augustin; Parra, Mario A.; Escudero, Javier; Vandergheynst, Pierre

    2017-02-01

    Visual short-term memory binding tasks are a promising early marker for Alzheimer’s disease (AD). To uncover functional deficits of AD in these tasks it is meaningful to first study unimpaired brain function. Electroencephalogram recordings were obtained from encoding and maintenance periods of tasks performed by healthy young volunteers. We probe the task’s transient physiological underpinnings by contrasting shape only (Shape) and shape-colour binding (Bind) conditions, displayed in the left and right sides of the screen, separately. Particularly, we introduce and implement a novel technique named Modular Dirichlet Energy (MDE) which allows robust and flexible analysis of the functional network with unprecedented temporal precision. We find that connectivity in the Bind condition is less integrated with the global network than in the Shape condition in occipital and frontal modules during the encoding period of the right screen condition. Using MDE we are able to discern driving effects in the occipital module between 100-140 ms, coinciding with the P100 visually evoked potential, followed by a driving effect in the frontal module between 140-180 ms, suggesting that the differences found constitute an information processing difference between these modules. This provides temporally precise information over a heterogeneous population in promising tasks for the detection of AD.

  11. Observation of core-level binding energy shifts between (100) surface and bulk atoms of epitaxial CuInSe{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, A.J. [Colorado School of Mines, Golden, CO (United States); Berry, G.; Rockett, A. [Univ. of Illinois, Urbana-Champaign, IL (United States)] [and others

    1997-04-01

    Core-level and valence band photoemission from semiconductors has been shown to exhibit binding energy differences between surface atoms and bulk atoms, thus allowing one to unambiguously distinguish between the two atomic positions. Quite clearly, surface atoms experience a potential different from the bulk due to the lower coordination number - a characteristic feature of any surface is the incomplete atomic coordination. Theoretical accounts of this phenomena are well documented in the literature for III-V and II-VI semiconductors. However, surface state energies corresponding to the equilibrium geometry of (100) and (111) surfaces of Cu-based ternary chalcopyrite semiconductors have not been calculated or experimental determined. These compounds are generating great interest for optoelectronic and photovoltaic applications, and are an isoelectronic analog of the II-VI binary compound semiconductors. Surface core-level binding energy shifts depend on the surface cohesive energies, and surface cohesive energies are related to surface structure. For ternary compound semiconductor surfaces, such as CuInSe{sub 2}, one has the possibility of variations in surface stoichiometry. Applying standard thermodynamical calculations which consider the number of individual surface atoms and their respective chemical potentials should allow one to qualitatively determine the magnitude of surface core-level shifts and, consequently, surface state energies.

  12. Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants.

    Science.gov (United States)

    Feenstra, K Anton; Starikov, Eugene B; Urlacher, Vlada B; Commandeur, Jan N M; Vermeulen, Nico P E

    2007-03-01

    Hydroxylations of octane and lauric acid by Cytochrome P450-BM3 (CYP102A1) wild-type and three active site mutants--F87A, L188Q/A74G, and F87V/L188Q/A74G--were rationalized using a combination of substrate orientation from docking, substrate binding statistics from molecular dynamics simulations, and barrier energies for hydrogen atom abstraction from quantum mechanical calculations. Wild-type BM3 typically hydroxylates medium- to long-chain fatty acids on subterminal (omega-1, omega-2, omega-3) but not the terminal (omega) positions. The known carboxylic anchoring site Y51/R47 for lauric acid, and hydrophobic interactions and steric exclusion, mainly by F87, for octane as well as lauric acid, play a role in the binding modes of the substrates. Electrostatic interactions between the protein and the substrate strongly modulate the substrate's regiodependent activation barriers. A combination of the binding statistics and the activation barriers of hydrogen-atom abstraction in the substrates is proposed to determine the product formation. Trends observed in experimental product formation for octane and lauric acid by wild-type BM3 and the three active site mutants were qualitatively explained. It is concluded that the combination of substrate binding statistics and hydrogen-atom abstraction barrier energies is a valuable tool to rationalize substrate binding and product formation and constitutes an important step toward prediction of product ratios.

  13. Calculated distance distributions of energy transfer events in irradiated liquid water

    International Nuclear Information System (INIS)

    Hamm, R.N.; Turner, J.E.; Wright, H.A.; Ritchie, R.H.

    1980-01-01

    Histories from a Monte Carlo electron transport calculation in liquid water are analyzed to obtain the distance distribution functions, t(x) and T(x), of energy transfer events. These functions, which give the average energy transferred within a distance x from an arbitrary transfer event, are presented for irradiation by monoenergetic electrons of several energies between 500 eV and 1 MeV, for monoenergetic photons of 10, 50, and 200 keV energy and for 65 kVp and 200 kVp x rays and 60 Coγ rays. The dose average lineal energy in spherical sites as a function of site radius is also presented for these same photon spectra

  14. Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.

    Science.gov (United States)

    Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S

    2016-03-08

    We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. Learning Approach on the Ground State Energy Calculation of Helium Atom

    Science.gov (United States)

    Shah, Syed Naseem Hussain

    2010-07-01

    This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function. The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.

  16. Calculation of energy costs of composite biomass stirring at biogas stations

    Science.gov (United States)

    Suslov, D. Yu; Temnikov, D. O.

    2018-03-01

    The paper is devoted to the study of the equipment to produce biogas fuel from organic wastes. The bioreactor equipped with a combined stirring system ensuring mechanical and bubbling stirring is designed. The method of energy cost calculation of the combined stirring system with original design is suggested. The received expressions were used in the calculation of the stirring system installed in the 10 m3 bioreactor: power consumed by the mixer during the start-up period made Nz =9.03 kW, operating power of the mixer made NE =1.406 kW, compressor power for bubbling stirring made NC =18.5 kW. Taking into account the operating mode of single elements of the stirring system, the energy cost made 4.38% of the total energy received by the biogas station.

  17. Learning Approach on the Ground State Energy Calculation of Helium Atom

    International Nuclear Information System (INIS)

    Shah, Syed Naseem Hussain

    2010-01-01

    This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function.The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.

  18. Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening?

    Directory of Open Access Journals (Sweden)

    Arsen V Grigoryan

    Full Text Available The ranking of scores of individual chemicals within a large screening library is a crucial step in virtual screening (VS for drug discovery. Previous studies showed that the quality of protein-ligand recognition can be improved using spectrum properties and the shape of the binding energy landscape. Here, we investigate whether the energy gap, defined as the difference between the lowest energy pose generated by a docking experiment and the average energy of all other generated poses and inferred to be a measure of the binding energy landscape sharpness, can improve the separation power between true binders and decoys with respect to the use of the best docking score. We performed retrospective single- and multiple-receptor conformation VS experiments in a diverse benchmark of 40 domains from 38 therapeutically relevant protein targets. Also, we tested the performance of the energy gap on 36 protein targets from the Directory of Useful Decoys (DUD. The results indicate that the energy gap outperforms the best docking score in its ability to discriminate between true binders and decoys, and true binders tend to have larger energy gaps than decoys. Furthermore, we used the energy gap as a descriptor to measure the height of the native binding phase and obtained a significant increase in the success rate of near native binding pose identification when the ligand binding conformations within the boundaries of the native binding phase were considered. The performance of the energy gap was also evaluated on an independent test case of VS-identified PKR-like ER-localized eIF2α kinase (PERK inhibitors. We found that the energy gap was superior to the best docking score in its ability to more highly rank active compounds from inactive ones. These results suggest that the energy gap of the protein-ligand binding energy landscape is a valuable descriptor for use in VS.

  19. Toward understanding as photosynthetic biosignatures: light harvesting and energy transfer calculation

    Science.gov (United States)

    Komatsu, Y.; Umemura, M.; Shoji, M.; Shiraishi, K.; Kayanuma, M.; Yabana, K.

    2014-03-01

    Among several proposed biosignatures, red edge is a direct evidence of photosynthetic life if it is detected (Kiang et al 2007). Red edge is a sharp change in reflectance spectra of vegetation in NIR region (about 700-750 nm). The sign of red edge is observed by Earthshine or remote sensing (Wolstencroft & Raven 2002, Woolf et al 2002). But, why around 700-750 nm? The photosynthetic organisms on Earth have evolved to optimize the sunlight condition. However, if we consider about photosynthetic organism on extrasolar planets, they should have developed to utilize the spectra of its principal star. Thus, it is not strange even if it shows different vegetation spectra. In this study, we focused on the light absorption mechanism of photosynthetic organisms on Earth and investigated the fundamental properties of the light harvesting mechanisms, which is the first stage for the light absorption. Light harvesting complexes contain photosynthetic pigments like chlorophylls. Effective light absorption and the energy transfer are accomplished by the electronic excitations of collective photosynthetic pigments. In order to investigate this mechanism, we constructed an energy transfer model by using a dipole-dipole approximation for the interactions between electronic excitations. Transition moments and transition energies of each pigment are calculated at the time-dependent density functional theory (TDDFT) level (Marques & Gross 2004). Quantum dynamics simulation for the excitation energy transfer was calculated by the Liouvelle's equation. We adopted the model to purple bacteria, which has been studied experimentally and known to absorb lower energy. It is meaningful to focus on the mechanism of this bacteria, since in the future mission, M planets will become a important target. We calculated the oscillator strengths in one light harvesting complex and confirmed the validity by comparing to the experimental data. This complex is made of an inner and an outer ring. The

  20. Comparison of calculated energy flux of internal tides with microstructure measurements

    Directory of Open Access Journals (Sweden)

    Saeed Falahat

    2014-10-01

    Full Text Available Vertical mixing caused by breaking of internal tides plays a major role in maintaining the deep-ocean stratification. This study compares observations of dissipation from microstructure measurements to calculations of the vertical energy flux from barotropic to internal tides, taking into account the temporal variation due to the spring-neap tidal cycle. The dissipation data originate from two surveys in the Brazil Basin Tracer Release Experiment (BBTRE, and one over the LArval Dispersal along the Deep East Pacific Rise (LADDER3, supplemented with a few stations above the North-Atlantic Ridge (GRAVILUCK and in the western Pacific (IZU. A good correlation is found between logarithmic values of energy flux and local dissipation in BBTRE, suggesting that the theory is able to predict energy fluxes. For the LADDER3, the local dissipation is much smaller than the calculated energy flux, which is very likely due to the different topographic features of BBTRE and LADDER3. The East Pacific Rise consists of a few isolated seamounts, so that most of the internal wave energy can radiate away from the generation site, whereas the Brazil Basin is characterised by extended rough bathymetry, leading to a more local dissipation. The results from all four field surveys support the general conclusion that the fraction of the internal-tide energy flux that is dissipated locally is very different in different regions.

  1. First-Principle Framework for Total Charging Energies in Electrocatalytic Materials and Charge-Responsive Molecular Binding at Gas-Surface Interfaces.

    Science.gov (United States)

    Tan, Xin; Tahini, Hassan A; Seal, Prasenjit; Smith, Sean C

    2016-05-04

    Heterogeneous charge-responsive molecular binding to electrocatalytic materials has been predicted in several recent works. This phenomenon offers the possibility of using voltage to manipulate the strength of the binding interaction with the target gas molecule and thereby circumvent thermochemistry constraints, which inhibit achieving both efficient binding and facile release of important targets such as CO2 and H2. Stability analysis of such charge-induced molecular adsorption has been beyond the reach of existing first-principle approaches. Here, we draw on concepts from semiconductor physics and density functional theory to develop a first principle theoretical approach that allows calculation of the change in total energy of the supercell due to charging. Coupled with the calculated adsorption energy of gas molecules at any given charge, this allows a complete description of the energetics of the charge-induced molecular adsorption process. Using CO2 molecular adsorption onto negatively charged h-BN (wide-gap semiconductor) and g-C4N3 (half metal) as example cases, our analysis reveals that - while adsorption is exothermic after charge is introduced - the overall adsorption processes are not intrinsically spontaneous due to the energetic cost of charging the materials. The energies needed to overcome the barriers of these processes are 2.10 and 0.43 eV for h-BN and g-C4N3, respectively. This first principle approach opens up new pathways for a more complete description of charge-induced and electrocatalytic processes.

  2. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach.

    Science.gov (United States)

    Sanusi, Z K; Govender, T; Maguire, G E M; Maseko, S B; Lin, J; Kruger, H G; Honarparvar, B

    2017-09-01

    Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?G bind ) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Quantum complex rotation and uniform semiclassical calculations of complex energy eigenvalues

    International Nuclear Information System (INIS)

    Connor, J.N.L.; Smith, A.D.

    1983-01-01

    Quantum and semiclassical calculations of complex energy eigenvalues have been carried out for an exponential potential of the form V 0 r 2 exp(-r) and Lennard-Jones (12,6) potential. A straightforward method, based on the complex coordinate rotation technique, is described for the quantum calculation of complex eigenenergies. For singular potentials, the method involves an inward and outward integration of the radial Schroedinger equation, followed by matching of the logarithmic derivatives of the wave functions at an intermediate point. For regular potentials, the method is simpler, as only an inward integration is required. Attention is drawn to the World War II researches of Hartree and co-workers who anticipated later quantum mechanical work on the complex rotation method. Complex eigenenergies are also calculated from a uniform semiclassical three turning point quantization formula, which allows for the proximity of the outer pair of complex turning points. Limiting cases of this formula, which are valid for very narrow or very broad widths, are also used in the calculations. We obtain good agreement between the semiclassical and quantum results. For the Lennard-Jones (12,6) potential, we compare resonance energies and widths from the complex energy definition of a resonance with those obtained from the time delay definition

  4. Constraining the gravitational binding energy of PSR J0737-3039B using terrestrial nuclear data

    International Nuclear Information System (INIS)

    Newton, W. G.; Li Baoan

    2009-01-01

    We show that the gravitational binding energy of a neutron star of a given mass is correlated with the slope of the nuclear symmetry energy at 1-2 times nuclear saturation density for equations of state without significant softening (i.e., those that predict maximum masses M max >1.44M · in line with the largest accurately measured neutron star mass). Applying recent laboratory constraints on the slope of the symmetry energy to this correlation we extract a constraint on the baryon mass of the lower mass member of the double pulsar binary system, PSR J0737-3039B. We compare with independent constraints derived from modeling the progenitor star of J0737-3039B up to and through its collapse under the assumption that it formed in an electron capture supernova. The two sets of constraints are consistent only if L < or approx. 70 MeV.

  5. Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations.

    Science.gov (United States)

    Sun, Dong-Ru; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2017-03-01

    Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation and binding free energy studies were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase. The binding free energies predicted by MM/GBSA methods are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. The key residues responsible for achieving strong binding have been identified by the MM/GBSA free energy decomposition analysis. Especially, Trp215 and Phe99 had an important impact on active site architecture and ligand binding. The results clearly identify the two class inhibitors exist different binding modes. Through summarizing the two different modes, we have mastered some important and favorable interaction patterns between matriptase and inhibitors. Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.

  6. Solute-vacancy binding in aluminum

    International Nuclear Information System (INIS)

    Wolverton, C.

    2007-01-01

    Previous efforts to understand solute-vacancy binding in aluminum alloys have been hampered by a scarcity of reliable, quantitative experimental measurements. Here, we report a large database of solute-vacancy binding energies determined from first-principles density functional calculations. The calculated binding energies agree well with accurate measurements where available, and provide an accurate predictor of solute-vacancy binding in other systems. We find: (i) some common solutes in commercial Al alloys (e.g., Cu and Mg) possess either very weak (Cu), or even repulsive (Mg), binding energies. Hence, we assert that some previously reported large binding energies for these solutes are erroneous. (ii) Large binding energies are found for Sn, Cd and In, confirming the proposed mechanism for the reduced natural aging in Al-Cu alloys containing microalloying additions of these solutes. (iii) In addition, we predict that similar reduction in natural aging should occur with additions of Si, Ge and Au. (iv) Even larger binding energies are found for other solutes (e.g., Pb, Bi, Sr, Ba), but these solutes possess essentially no solubility in Al. (v) We have explored the physical effects controlling solute-vacancy binding in Al. We find that there is a strong correlation between binding energy and solute size, with larger solute atoms possessing a stronger binding with vacancies. (vi) Most transition-metal 3d solutes do not bind strongly with vacancies, and some are even energetically strongly repelled from vacancies, particularly for the early 3d solutes, Ti and V

  7. Alternative Approaches to Calculate Benefits of an Energy Imbalance Market With Wind and Solar Energy: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Kirby, B.; King, J.; Milligan, M.

    2012-06-01

    The anticipated increase in variable generation in the Western Interconnection over the next several years has raised concerns about how to maintain system balance, especially in smaller Balancing Authority Areas (BAAs). Given renewable portfolio standards in the West, it is possible that more than 50 gigawatts of wind capacity will be installed by 2020. Significant quantities of solar generation are likely to be added as well. The consequent increase in variability and uncertainty that must be managed by the conventional generation fleet and responsive loads has resulted in a proposal for an Energy Imbalance Market (EIM). This paper extends prior work to estimate the reserve requirements for regulation, spinning, and non-spinning reserves with and without the EIM. We also discuss alternative approaches to allocating reserve requirements and show that some apparently attractive allocation methods have undesired consequences.

  8. Development of continuous-energy eigenvalue sensitivity coefficient calculation methods in the shift Monte Carlo Code

    International Nuclear Information System (INIS)

    Perfetti, C.; Martin, W.; Rearden, B.; Williams, M.

    2012-01-01

    Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the Shift Monte Carlo code within the SCALE code package. The methods were used for two small-scale test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods. (authors)

  9. Development of continuous-energy eigenvalue sensitivity coefficient calculation methods in the shift Monte Carlo Code

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, C.; Martin, W. [Univ. of Michigan, Dept. of Nuclear Engineering and Radiological Sciences, 2355 Bonisteel Boulevard, Ann Arbor, MI 48109-2104 (United States); Rearden, B.; Williams, M. [Oak Ridge National Laboratory, Reactor and Nuclear Systems Div., Bldg. 5700, P.O. Box 2008, Oak Ridge, TN 37831-6170 (United States)

    2012-07-01

    Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the Shift Monte Carlo code within the SCALE code package. The methods were used for two small-scale test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods. (authors)

  10. An Exact Calculation of Electron-Ion Energy Splitting in a Hot Plasma

    Energy Technology Data Exchange (ETDEWEB)

    Singleton, Robert L [Los Alamos National Laboratory

    2012-09-10

    In this brief report, I summarize the rather involved recent work of Brown, Preston, and Singleton (BPS). In Refs. [2] and [3], BPS calculate the energy partition into ions and electrons as a charged particle traverses a non-equilibrium two-temperature plasma. These results are exact to leading and next-to-leading order in the plasma coupling g, and are therefore extremely accurate in a weakly coupled plasma. The new BPS calculations are compared with the more standard work of Fraley et al. [12]. The results differ substantially at higher temperature when T{sub I} {ne} T{sub e}.

  11. Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

    Science.gov (United States)

    Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong

    2018-04-10

    Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.

  12. Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

    Science.gov (United States)

    Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

    2018-03-01

    We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.

  13. Efficient First-Principles Calculation of the Quantum Kinetic Energy and Momentum Distribution of Nuclei

    Science.gov (United States)

    Ceriotti, Michele; Manolopoulos, David E.

    2012-09-01

    Light nuclei at room temperature and below exhibit a kinetic energy which significantly deviates from the predictions of classical statistical mechanics. This quantum kinetic energy is responsible for a wide variety of isotope effects of interest in fields ranging from chemistry to climatology. It also furnishes the second moment of the nuclear momentum distribution, which contains subtle information about the chemical environment and has recently become accessible to deep inelastic neutron scattering experiments. Here, we show how, by combining imaginary time path integral dynamics with a carefully designed generalized Langevin equation, it is possible to dramatically reduce the expense of computing the quantum kinetic energy. We also introduce a transient anisotropic Gaussian approximation to the nuclear momentum distribution which can be calculated with negligible additional effort. As an example, we evaluate the structural properties, the quantum kinetic energy, and the nuclear momentum distribution for a first-principles simulation of liquid water.

  14. Binding energy of donor impurity states and optical absorption in the Tietz-Hua quantum well under an applied electric field

    Science.gov (United States)

    Al, E. B.; Kasapoglu, E.; Sakiroglu, S.; Duque, C. A.; Sökmen, I.

    2018-04-01

    For a quantum well which has the Tietz-Hua potential, the ground and some excited donor impurity binding energies and the total absorption coefficients, including linear and third order nonlinear terms for the transitions between the related impurity states with respect to the structure parameters and the impurity position as well as the electric field strength are investigated. The binding energies were obtained using the effective-mass approximation within a variational scheme and the optical transitions between any two impurity states were calculated by using the density matrix formalism and the perturbation expansion method. Our results show that the effects of the electric field and the structure parameters on the optical transitions are more pronounced. So we can adjust the red or blue shift in the peak position of the absorption coefficient by changing the strength of the electric field as well as the structure parameters.

  15. Anisotropic Lithium Insertion Behavior in Silicon Nanowires: Binding Energy, Diffusion Barrier, and Strain Effect

    KAUST Repository

    Zhang, Qianfan

    2011-05-19

    Silicon nanowires (SiNWs) have recently been shown to be promising as high capacity lithium battery anodes. SiNWs can be grown with their long axis along several different crystallographic directions. Due to distinct atomic configuration and electronic structure of SiNWs with different axial orientations, their lithium insertion behavior could be different. This paper focuses on the characteristics of single Li defects, including binding energy, diffusion barriers, and dependence on uniaxial strain in [110], [100], [111], and [112] SiNWs. Our systematic ab initio study suggests that the Si-Li interaction is weaker when the Si-Li bond direction is aligned close to the SiNW long axis. This results in the [110] and [111] SiNWs having the highest and lowest Li binding energy, respectively, and it makes the diffusion barrier along the SiNW axis lower than other pathways. Under external strain, it was found that [110] and [001] SiNWs are the most and least sensitive, respectively. For diffusion along the axial direction, the barrier increases (decreases) under tension (compression). This feature results in a considerable difference in the magnitude of the energy barrier along different diffusion pathways. © 2011 American Chemical Society.

  16. EnergyPlus Analysis Capabilities for Use in California Building Energy Efficiency Standards Development and Compliance Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Tianzhen; Buhl, Fred; Haves, Philip

    2008-03-28

    California has been using DOE-2 as the main building energy analysis tool in the development of building energy efficiency standards (Title 24) and the code compliance calculations. However, DOE-2.1E is a mature program that is no longer supported by LBNL on contract to the USDOE, or by any other public or private entity. With no more significant updates in the modeling capabilities of DOE-2.1E during recent years, DOE-2.1E lacks the ability to model, with the necessary accuracy, a number of building technologies that have the potential to reduce significantly the energy consumption of buildings in California. DOE-2's legacy software code makes it difficult and time consuming to add new or enhance existing modeling features in DOE-2. Therefore the USDOE proposed to develop a new tool, EnergyPlus, which is intended to replace DOE-2 as the next generation building simulation tool. EnergyPlus inherited most of the useful features from DOE-2 and BLAST, and more significantly added new modeling capabilities far beyond DOE-2, BLAST, and other simulations tools currently available. With California's net zero energy goals for new residential buildings in 2020 and for new commercial buildings in 2030, California needs to evaluate and promote currently available best practice and emerging technologies to significantly reduce energy use of buildings for space cooling and heating, ventilating, refrigerating, lighting, and water heating. The California Energy Commission (CEC) needs to adopt a new building energy simulation program for developing and maintaining future versions of Title 24. Therefore, EnergyPlus became a good candidate to CEC for its use in developing and complying with future Title 24 upgrades. In 2004, the Pacific Gas and Electric Company contracted with ArchitecturalEnergy Corporation (AEC), Taylor Engineering, and GARD Analytics to evaluate EnergyPlus in its ability to model those energy efficiency measures specified in both the residential and

  17. Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

    Science.gov (United States)

    Mondal, Abhisek; Datta, Saumen

    2017-06-01

    Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. An optimized ultra-fine energy group structure for neutron transport calculations

    International Nuclear Information System (INIS)

    Huria, Harish; Ouisloumen, Mohamed

    2008-01-01

    This paper describes an optimized energy group structure that was developed for neutron transport calculations in lattices using the Westinghouse lattice physics code PARAGON. The currently used 70-energy group structure results in significant discrepancies when the predictions are compared with those from the continuous energy Monte Carlo methods. The main source of the differences is the approximations employed in the resonance self-shielding methodology. This, in turn, leads to ambiguous adjustments in the resonance range cross-sections. The main goal of developing this group structure was to bypass the self-shielding methodology altogether thereby reducing the neutronic calculation errors. The proposed optimized energy mesh has 6064 points with 5877 points spanning the resonance range. The group boundaries in the resonance range were selected so that the micro group cross-sections matched reasonably well with those derived from reaction tallies of MCNP for a number of resonance absorbers of interest in reactor lattices. At the same time, however, the fast and thermal energy range boundaries were also adjusted to match the MCNP reaction rates in the relevant ranges. The resulting multi-group library was used to obtain eigenvalues for a wide variety of reactor lattice numerical benchmarks and also the Doppler reactivity defect benchmarks to establish its adequacy. (authors)

  19. Calculating the X-Ray Fluorescence from the Planet Mercury Due to High-Energy Electrons

    Science.gov (United States)

    Burbine, T. H.; Trombka, J. I.; Bergstrom, P. M., Jr.; Christon, S. P.

    2005-01-01

    The least-studied terrestrial planet is Mercury due to its proximity to the Sun, which makes telescopic observations and spacecraft encounters difficult. Our lack of knowledge about Mercury should change in the near future due to the recent launching of MESSENGER, a Mercury orbiter. Another mission (BepiColombo) is currently being planned. The x-ray spectrometer on MESSENGER (and planned for BepiColombo) can characterize the elemental composition of a planetary surface by measuring emitted fluorescent x-rays. If electrons are ejected from an atom s inner shell by interaction with energetic particles such as photons, electrons, or ions, electrons from an outer shell can transfer to the inner shell. Characteristic x-rays are then emitted with energies that are the difference between the binding energy of the ion in its excited state and that of the ion in its ground state. Because each element has a unique set of energy levels, each element emits x-rays at a unique set of energies. Electrons and ions usually do not have the needed flux at high energies to cause significant x-ray fluorescence on most planetary bodies. This is not the case for Mercury where high-energy particles were detected during the Mariner 10 flybys. Mercury has an intrinsic magnetic field that deflects the solar wind, resulting in a bow shock in the solar wind and a magnetospheric cavity. Electrons and ions accelerated in the magnetosphere tend to follow its magnetic field lines and can impact the surface on Mercury s dark side Modeling has been done to determine if x-ray fluorescence resulting from the impact of high-energy electrons accelerated in Mercury's magnetosphere can be detected by MESSENGER. Our goal is to understand how much bulk chemical information can be obtained from x-ray fluorescence measurements on the dark side of Mercury.

  20. Calculation of Reaction Free Energies in Solution: A Comparison of Current Approaches.

    Science.gov (United States)

    Besora, Maria; Vidossich, Pietro; Lledós, Agustí; Ujaque, Gregori; Maseras, Feliu

    2018-02-08

    The result of the application of different approaches based on the ideal gas/rigid rotor/harmonic oscillator (IGRRHO) model, commonly used in popular software packages, for the calculation of free energies in solution is compared with that of ab initio molecular dynamics for a process involving ligand exchange in palladium complexes. The IGRRHO-based approaches considered differ in most cases in the extent to which the rotational and translational contributions are included in the correction. Our study supports the use the free energy values directly obtained from dispersion-corrected DFT functionals without any correction or with minor corrections at most.

  1. Fabrication of CuCl quantum dots and the size dependence of the biexciton binding energy

    CERN Document Server

    Park, S T; Kim, H Y; Kim, I G

    2000-01-01

    We fabricated CuCl quantum dots (QDs) in an aluminoborosilicate glass matrix. The photoluminescence of the CuCl QDs was surveyed by using the band-to-band excitation and the site selective luminescence methods. The excitation density dependence of the exciton and the biexciton luminescence was measured, and the saturation effects of the luminescence intensities were observed. The biexciton binding energies measured using the site selective luminescence method increased with decreasing QD size. The data were well fitted by a function resulting from the numerical matrix-diagonalization method.

  2. High-throughput DFT calculations of formation energy, stability and oxygen vacancy formation energy of ABO3 perovskites

    Science.gov (United States)

    Emery, Antoine A.; Wolverton, Chris

    2017-10-01

    ABO3 perovskites are oxide materials that are used for a variety of applications such as solid oxide fuel cells, piezo-, ferro-electricity and water splitting. Due to their remarkable stability with respect to cation substitution, new compounds for such applications potentially await discovery. In this work, we present an exhaustive dataset of formation energies of 5,329 cubic and distorted perovskites that were calculated using first-principles density functional theory. In addition to formation energies, several additional properties such as oxidation states, band gap, oxygen vacancy formation energy, and thermodynamic stability with respect to all phases in the Open Quantum Materials Database are also made publicly available. This large dataset for this ubiquitous crystal structure type contains 395 perovskites that are predicted to be thermodynamically stable, of which many have not yet been experimentally reported, and therefore represent theoretical predictions. The dataset thus opens avenues for future use, including materials discovery in many research-active areas.

  3. Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes.

    Science.gov (United States)

    Ruan, Chunhai; Yang, Zhibo; Hallowita, Nuwan; Rodgers, M T

    2005-12-22

    Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

  4. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

    Science.gov (United States)

    Koppisetty, Chaitanya A K; Frank, Martin; Kemp, Graham J L; Nyholm, Per-Georg

    2013-10-28

    Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

  5. Radial dose distributions from carbon ions of therapeutic energies calculated with Geant4-DNA.

    Science.gov (United States)

    Wang, He; Vassiliev, Oleg N

    2017-05-21

    We report on radial dose distributions [Formula: see text] for carbon ions calculated with Geant4-DNA code. These distributions characterize ion tracks on a nanoscale and are important for understanding the biological effects of ion beams. We present data for carbon ion beams in the energy range from 20 to 400 MeV u -1 . To approximate the Monte Carlo results, we developed a simple formula that combines the well-known inverse square distance dependence with a factor correcting [Formula: see text] for small [Formula: see text]. The proposed formula can be used to calculate [Formula: see text] for any energy within the above range and for distances [Formula: see text] from 1 nm to 2 μm with a maximum error not exceeding 14%. This range of distances corresponds to a dose range of over seven orders of magnitude. Differences between our results and those of previously published analytical models are discussed.

  6. S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence

    Energy Technology Data Exchange (ETDEWEB)

    sapirstein, J; Cheng, K T

    2010-11-02

    A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.

  7. Calculating alpha Eigenvalues in a Continuous-Energy Infinite Medium with Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Betzler, Benjamin R. [Los Alamos National Laboratory; Kiedrowski, Brian C. [Los Alamos National Laboratory; Brown, Forrest B. [Los Alamos National Laboratory; Martin, William R. [Los Alamos National Laboratory

    2012-09-04

    The {alpha} eigenvalue has implications for time-dependent problems where the system is sub- or supercritical. We present methods and results from calculating the {alpha}-eigenvalue spectrum for a continuous-energy infinite medium with a simplified Monte Carlo transport code. We formulate the {alpha}-eigenvalue problem, detail the Monte Carlo code physics, and provide verification and results. We have a method for calculating the {alpha}-eigenvalue spectrum in a continuous-energy infinite-medium. The continuous-time Markov process described by the transition rate matrix provides a way of obtaining the {alpha}-eigenvalue spectrum and kinetic modes. These are useful for the approximation of the time dependence of the system.

  8. Krylov subspace method for evaluating the self-energy matrices in electron transport calculations

    DEFF Research Database (Denmark)

    Sørensen, Hans Henrik Brandenborg; Hansen, Per Christian; Petersen, D. E.

    2008-01-01

    We present a Krylov subspace method for evaluating the self-energy matrices used in the Green's function formulation of electron transport in nanoscale devices. A procedure based on the Arnoldi method is employed to obtain solutions of the quadratic eigenvalue problem associated with the infinite...... calculations. Numerical tests within a density functional theory framework are provided to validate the accuracy and robustness of the proposed method, which in most cases is an order of magnitude faster than conventional methods....

  9. Calculations of energy levels and electromagnetic properties for tellurium pair isotopes, by unified method

    International Nuclear Information System (INIS)

    Teixeira, R.R.P.

    1988-01-01

    Calculations with the Unified Model (vibrator coupled to two particles), of the energy levels and the eletromagnetic properties have been performed and compared with the twelve pair isotopes from tellurium with A between 112 and 134. The results were analysed using as particles interaction: pairing and SDI (Surface Delta Interaction). The SDI and 3 fonons collective states were used in the fittings, and a syntematic comparison between the theoretical and experimental results was made. The dependence of the results with the model parameters was determined, through large variation sof them. Calculations using 4 fonons have been made, and the importance of the introduced variations in the results was discussed. Calculations have been made in the VAX Computer of the Pelletron at IFUSP. (author) [pt

  10. Precise calculations in simulations of the interaction of low energy neutrons with nano-dispersed media

    Energy Technology Data Exchange (ETDEWEB)

    Artem’ev, V. A., E-mail: niitm@inbox.ru [Research Institute of Materials Technology (Russian Federation); Nezvanov, A. Yu. [Moscow State Industrial University (Russian Federation); Nesvizhevsky, V. V. [Institut Max von Laue—Paul Langevin (France)

    2016-01-15

    We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2–5 nm and for neutron energies 3 × 10{sup -7}–10{sup -3} eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.

  11. Theoretical calculations of magnetic order and anisotropy energies in molecular magnets

    International Nuclear Information System (INIS)

    Pederson, M. R.; Porezag, D. V.; Kortus, J.; Khanna, S. N.

    2000-01-01

    We present theoretical electronic structure calculations on the nature of electronic states and the magnetic coupling in the Mn 12 O 12 free cluster and the Mn 12 O 12 (RCOO) 16 (H 2 O) 4 molecular magnetic crystal. The calculations have been performed with the all-electron full-potential NRLMOL code. We find that the free Mn 12 O 12 cluster relaxes to an antiferromagnetic cluster with no net moment. However, when coordinated by sixteen HCOO ligands and four H 2 O groups, as it is in the molecular crystal, we find that the ferrimagnetic ordering and geometrical and magnetic structure observed in the experiments is restored. Local Mn moments for the free and ligandated molecular magnets are presented and compared to experiment. We identify the occupied and unoccupied electronic states that are most responsible for the formation of the large anisotropy barrier and use a recently developed full-space and full-potential method for calculating the spin-orbit coupling interaction and anisotropy energies. Our calculated second-order anisotropy energy is in excellent agreement with experiment. (c) 2000 American Institute of Physics

  12. Weather data for simplified energy calculation methods. Volume IV. United States: WYEC data

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, A.R.; Moreno, S.; Deringer, J.; Watson, C.R.

    1984-08-01

    The objective of this report is to provide a source of weather data for direct use with a number of simplified energy calculation methods available today. Complete weather data for a number of cities in the United States are provided for use in the following methods: degree hour, modified degree hour, bin, modified bin, and variable degree day. This report contains sets of weather data for 23 cities using Weather Year for Energy Calculations (WYEC) source weather data. Considerable overlap is present in cities (21) covered by both the TRY and WYEC data. The weather data at each city has been summarized in a number of ways to provide differing levels of detail necessary for alternative simplified energy calculation methods. Weather variables summarized include dry bulb and wet bulb temperature, percent relative humidity, humidity ratio, wind speed, percent possible sunshine, percent diffuse solar radiation, total solar radiation on horizontal and vertical surfaces, and solar heat gain through standard DSA glass. Monthly and annual summaries, in some cases by time of day, are available. These summaries are produced in a series of nine computer generated tables.

  13. Relativistic many-body calculation of energies, lifetimes, hyperfine constants, and polarizabilities in 7Li

    International Nuclear Information System (INIS)

    Johnson, W. R.; Safronova, U. I.; Derevianko, A.; Safronova, M. S.

    2008-01-01

    The excitation energies of ns, np, nd, and nf (n≤6) states in neutral lithium are evaluated within the framework of relativistic many-body theory. First-, second-, third-, and all-order Coulomb energies and first- and second-order Breit corrections to energies are calculated. All-order calculations of reduced matrix elements, oscillator strengths, transition rates, and lifetimes are given for levels up to n=4. Electric-dipole (2s-np), electric-quadrupole (2s-nd), and electric-octupole (2s-nf), matrix elements are evaluated to obtain the corresponding ground-state multipole polarizabilities using the sum-over-states approach. Scalar and tensor polarizabilities for the 2p 1/2 and 2p 3/2 states are also calculated. Magnetic-dipole hyperfine constants A are determined for low-lying levels up to n=4. The quadratic Stark shift for the (F=2 M=0)↔(F=1 M=0) ground-state hyperfine transition is found to be -0.0582 Hz/(kV/cm) 2 , in slight disagreement with the experimental value -0.061±0.002 Hz/(kV/cm) 2 . Matrix elements used in evaluating polarizabilities, hyperfine constants, and the quadratic Stark shift are obtained using the all-order method

  14. Use of SCALE Continuous-Energy Monte Carlo Tools for Eigenvalue Sensitivity Coefficient Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, Christopher M [ORNL; Rearden, Bradley T [ORNL

    2013-01-01

    The TSUNAMI code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, such as quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The CLUTCH and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE KENO framework to generate the capability for TSUNAMI-3D to perform eigenvalue sensitivity calculations in continuous-energy applications. This work explores the improvements in accuracy that can be gained in eigenvalue and eigenvalue sensitivity calculations through the use of the SCALE CE KENO and CE TSUNAMI continuous-energy Monte Carlo tools as compared to multigroup tools. The CE KENO and CE TSUNAMI tools were used to analyze two difficult models of critical benchmarks, and produced eigenvalue and eigenvalue sensitivity coefficient results that showed a marked improvement in accuracy. The CLUTCH sensitivity method in particular excelled in terms of efficiency and computational memory requirements.

  15. Embodied Energy Calculation in Mitigating Environmental Impact of Low-Cost Housing Construction

    Directory of Open Access Journals (Sweden)

    Larasati ZR Dewi

    2017-01-01

    Full Text Available Reduction of the negative impacts of building construction, or mitigation, should be done in the early phase of a project. Particular method that can be used to reduce the negative impact is Embodied Energy (EE calculation. This research develops a method to calculate the total EE of materials used in building construction by using the Material Selection Analysis (MSA based on Indonesia’s Construction Work Unit Price Analysis (WUPA. MSA breaks down the types, its unit, and total volume of materials within an object. Using the EE data from Inventory Carbon and Energy (ICE Bath, in the UK, this research calculate the embodied energy in three small house types in Indonesia: Type 21 M2, Type 36 M2, and Type 45 M2. The result reveals a negative correlation between building’s area and EE value. Nonetheless, the EE value is positively related to the volume of material used. Proposed strategies to decrease the value of EE in low cost housing construction manly; a design approach in improving the efficiency of material usage, b materials substitution to material with lower value of EE, especially on material on large volume of usage, c socialization of EE value to stakeholders as consideration in determining the choice of materials used, thus, environmental mitigation is expected to be an important aspect in determining the design decisions and the choice of materials used.

  16. Stabilization energies of charged multiexciton complexes calculated at configuration interaction level

    Science.gov (United States)

    Corni, S.; Braskén, M.; Lindberg, M.; Olsen, J.; Sundholm, D.

    2003-06-01

    Recombination and stabilization energies of multiexcitons confined in positively and negatively charged semiconductor InGaAs/GaAs quantum dot (QD) samples have been studied by employing large-scale configuration interaction (CI) calculations. The CI calculations show that at most six electrons or two holes can be confined in the QD. Multiply charged multiexciton complexes with up to five excess electrons or two excess holes are also found to be stable, even when a few electron-hole pairs are present in the QD. The chemical potential functions for charged QD samples do not possess the pronounced stepped form as obtained for the corresponding neutral multiexciton complexes. The negatively and the positively charged excitons (negative and positive trions) lie lower in energy as compared to a neutral exciton and a single non-interacting charge carrier in the lowest single-particle state of another quantum dot. The other charged multiexciton complexes studied are not confined with respect to the corresponding neutral multiexciton and a non-interacting charge carrier. To include the contributions from the heavy-hole light-hole (HH-LH) coupling, a perturbative treatment of the band-mixing effects was implemented. The perturbation-theory calculations show that the HH-LH coupling does not shift the energies in the present InGaAs/GaAs QD sample.

  17. Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent

    Science.gov (United States)

    Nakano, Hiroshi; Yamamoto, Takeshi

    2012-04-01

    Quantum mechanical/molecular mechanical (QM/MM) free energy calculation presents a significant challenge due to an excessive number of QM calculations. A useful approach for reducing the computational cost is that based on the mean field approximation to the QM subsystem. Here, we describe such a mean-field QM/MM theory for electronically polarizable systems by starting from the Hartree product ansatz for the total system and invoking a variational principle of free energy. The MM part is then recast to a classical polarizable model by introducing the charge response kernel. Numerical test shows that the potential of mean force (PMF) thus obtained agrees quantitatively with that obtained from a direct QM/MM calculation, indicating the utility of self-consistent mean-field approximation. Next, we apply the obtained method to prototypical reactions in several qualitatively different solvents and make a systematic comparison of polarization effects. The results show that in aqueous solution the PMF does not depend very much on the water models employed, while in nonaqueous solutions the PMF is significantly affected by explicit polarization. For example, the free energy barrier for a phosphoryl dissociation reaction in acetone and cyclohexane is found to increase by more than 10 kcal/mol when switching the solvent model from an empirical to explicitly polarizable one. The reason for this is discussed based on the parametrization of empirical nonpolarizable models.

  18. GEDAE-LaB: A Free Software to Calculate the Energy System Contributions during Exercise.

    Science.gov (United States)

    Bertuzzi, Rômulo; Melegati, Jorge; Bueno, Salomão; Ghiarone, Thaysa; Pasqua, Leonardo A; Gáspari, Arthur Fernandes; Lima-Silva, Adriano E; Goldman, Alfredo

    2016-01-01

    The aim of the current study is to describe the functionality of free software developed for energy system contributions and energy expenditure calculation during exercise, namely GEDAE-LaB. Eleven participants performed the following tests: 1) a maximal cycling incremental test to measure the ventilatory threshold and maximal oxygen uptake (V̇O2max); 2) a cycling workload constant test at moderate domain (90% ventilatory threshold); 3) a cycling workload constant test at severe domain (110% V̇O2max). Oxygen uptake and plasma lactate were measured during the tests. The contributions of the aerobic (AMET), anaerobic lactic (LAMET), and anaerobic alactic (ALMET) systems were calculated based on the oxygen uptake during exercise, the oxygen energy equivalents provided by lactate accumulation, and the fast component of excess post-exercise oxygen consumption, respectively. In order to assess the intra-investigator variation, four different investigators performed the analyses independently using GEDAE-LaB. A direct comparison with commercial software was also provided. All subjects completed 10 min of exercise at moderate domain, while the time to exhaustion at severe domain was 144 ± 65 s. The AMET, LAMET, and ALMET contributions during moderate domain were about 93, 2, and 5%, respectively. The AMET, LAMET, and ALMET contributions during severe domain were about 66, 21, and 13%, respectively. No statistical differences were found between the energy system contributions and energy expenditure obtained by GEDAE-LaB and commercial software for both moderate and severe domains (P > 0.05). The ICC revealed that these estimates were highly reliable among the four investigators for both moderate and severe domains (all ICC ≥ 0.94). These findings suggest that GEDAE-LaB is a free software easily comprehended by users minimally familiarized with adopted procedures for calculations of energetic profile using oxygen uptake and lactate accumulation during exercise. By

  19. Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.

    Science.gov (United States)

    Boulougouris, Georgios C

    2014-05-15

    The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be

  20. An accurate redetermination of the sup 1 sup 1 sup 8 Sn binding energy

    CERN Document Server

    Borzakov, S B; Faikow-Stanczyk, H; Grigoriev, Y V; Panteleev, T; Pospísil, S; Smotritsky, L M; Telezhnikov, S A

    2002-01-01

    The energy of well-known strong gamma line from sup 1 sup 9 sup 8 Au, the 'gold standard', has been modified in the light of new adjustments in the fundamental constants and the value of 411.80176(12) keV was determined, which is 0.29 eV lower than the latest 1999 value. An energy calibration procedure for determining the neutron binding energy, B sub n , from complicated (n, gamma) spectra has been developed. A mathematically simple minimization function consisting only of terms having as parameters the coefficients of the energy calibration curve (polynomial) is used. A priori information about the relationships among the energies of different peaks on the spectrum is taken into account by a Monte-Carlo simulation. The procedure was used in obtaining B sub n for sup 1 sup 1 sup 8 Sn. The gamma-ray spectrum from thermal neutron radiative capture by sup 1 sup 1 sup 7 Sn has been measured on the IBR-2 pulsed reactor. gamma-rays were detected by a 72 cm sup 3 HPGe detector. For a better determination of B sub n...

  1. Energy spectrum of two-dimensional tight-binding electrons in a spatially varying magnetic field

    International Nuclear Information System (INIS)

    Oh, G.Y.; Lee, M.H.

    1996-01-01

    The electronic energy spectrum of a two-dimensional lattice in a spatially varying magnetic field is studied within the framework of the tight-binding model by using the scheme of the transfer matrix. It is found that, in comparison with the case of a uniform magnetic field, the energy spectrum exhibits more complicated behavior; band broadening (or gap closing) and band splitting (or gap opening) occur depending on characteristic parameters of the lattice. The origin of these phenomena lies in the existence of direct touching and indirect overlapping between neighboring subbands. Dependence of direct touching and indirect overlapping, and thus the electronic band structure together with the density of states, on characteristic parameters of the lattice is elucidated in detail. copyright 1996 The American Physical Society

  2. Dependence of single-walled carbon nanotube adsorption kinetics on temperature and binding energy.

    Science.gov (United States)

    Rawat, D S; Krungleviciute, V; Heroux, L; Bulut, M; Calbi, M M; Migone, A D

    2008-12-02

    We present results for the isothermal adsorption kinetics of methane, hydrogen, and tetrafluoromethane on closed-ended single-walled carbon nanotubes. In these experiments, we monitor the pressure decrease as a function of time as equilibrium is approached, after a dose of gas is added to the cell containing the nanotubes. The measurements were performed at different fractional coverages limited to the first layer. The results indicate that, for a given coverage and temperature, the equilibration time is an increasing function of E/(k(B)T), where E is the binding energy of the adsorbate and k(B)T is the thermal energy. These findings are consistent with recent theoretical predictions and computer simulations results that we use to interpret the experimental measurements.

  3. The COOLER Code: A Novel Analytical Approach to Calculate Subcellular Energy Deposition by Internal Electron Emitters.

    Science.gov (United States)

    Siragusa, Mattia; Baiocco, Giorgio; Fredericia, Pil M; Friedland, Werner; Groesser, Torsten; Ottolenghi, Andrea; Jensen, Mikael

    2017-08-01

    COmputation Of Local Electron Release (COOLER), a software program has been designed for dosimetry assessment at the cellular/subcellular scale, with a given distribution of administered low-energy electron-emitting radionuclides in cellular compartments, which remains a critical step in risk/benefit analysis for advancements in internal radiotherapy. The software is intended to overcome the main limitations of the medical internal radiation dose (MIRD) formalism for calculations of cellular S-values (i.e., dose to a target region in the cell per decay in a given source region), namely, the use of the continuous slowing down approximation (CSDA) and the assumption of a spherical cell geometry. To this aim, we developed an analytical approach, entrusted to a MATLAB-based program, using as input simulated data for electron spatial energy deposition directly derived from full Monte Carlo track structure calculations with PARTRAC. Results from PARTRAC calculations on electron range, stopping power and residual energy versus traveled distance curves are presented and, when useful for implementation in COOLER, analytical fit functions are given. Example configurations for cells in different culture conditions (V79 cells in suspension or adherent culture) with realistic geometrical parameters are implemented for use in the tool. Finally, cellular S-value predictions by the newly developed code are presented for different cellular geometries and activity distributions (uniform activity in the nucleus, in the entire cell or on the cell surface), validated against full Monte Carlo calculations with PARTRAC, and compared to MIRD standards, as well as results based on different track structure calculations (Geant4-DNA). The largest discrepancies between COOLER and MIRD predictions were generally found for electrons between 25 and 30 keV, where the magnitude of disagreement in S-values can vary from 50 to 100%, depending on the activity distribution. In calculations for

  4. Evaluated Nuclear Data Library for Transport Calculations at Energies up to 150 MeV

    International Nuclear Information System (INIS)

    Korovin, Yu.A.; Konobeyev, A.Yu.; Pilnov, G.B.; Stankovskiy, A.Yu.

    2005-01-01

    A new evaluated nuclear data library has been created. The library consists of two sub-libraries for neutron and proton incident particles. The first version of neutron sub-library has been completed and described in the present paper. The library contains nuclear data for transport, heating, and shielding applications for 242 nuclides ranging in atomic number from 8 to 82 in the energy region of primary neutrons from 10-5 eV to 150 MeV. Data below 20 MeV are taken mainly from ENDF/B-VI (Revision 8) and for some nuclides, from the JENDL-3.3 and JEFF-3.0 libraries. The evaluation of emitted particle energy and angular distributions at the energies above 20 MeV was performed with the help of the ALICE/ASH code and the analysis of available experimental data. The total cross sections, elastic cross sections, and elastic scattering angular distributions were calculated with the help of the coupled channel model. The results of the calculation were adjusted to the data from ENDF/B-VI, JENDL-3.3m or JEFF-3.0 at the neutron energy equal to 20 MeV. The library is written in ENDF/B-VI format using the MF=3/MT=5 and MF=6/MT=5 representations

  5. Monte Carlo dose calculation improvements for low energy electron beams using eMC

    International Nuclear Information System (INIS)

    Fix, Michael K; Frei, Daniel; Volken, Werner; Born, Ernst J; Manser, Peter; Neuenschwander, Hans

    2010-01-01

    The electron Monte Carlo (eMC) dose calculation algorithm in Eclipse (Varian Medical Systems) is based on the macro MC method and is able to predict dose distributions for high energy electron beams with high accuracy. However, there are limitations for low energy electron beams. This work aims to improve the accuracy of the dose calculation using eMC for 4 and 6 MeV electron beams of Varian linear accelerators. Improvements implemented into the eMC include (1) improved determination of the initial electron energy spectrum by increased resolution of mono-energetic depth dose curves used during beam configuration; (2) inclusion of all the scrapers of the applicator in the beam model; (3) reduction of the maximum size of the sphere to be selected within the macro MC transport when the energy of the incident electron is below certain thresholds. The impact of these changes in eMC is investigated by comparing calculated dose distributions for 4 and 6 MeV electron beams at source to surface distance (SSD) of 100 and 110 cm with applicators ranging from 6 x 6 to 25 x 25 cm 2 of a Varian Clinac 2300C/D with the corresponding measurements. Dose differences between calculated and measured absolute depth dose curves are reduced from 6% to less than 1.5% for both energies and all applicators considered at SSD of 100 cm. Using the original eMC implementation, absolute dose profiles at depths of 1 cm, d max and R50 in water lead to dose differences of up to 8% for applicators larger than 15 x 15 cm 2 at SSD 100 cm. Those differences are now reduced to less than 2% for all dose profiles investigated when the improved version of eMC is used. At SSD of 110 cm the dose difference for the original eMC version is even more pronounced and can be larger than 10%. Those differences are reduced to within 2% or 2 mm with the improved version of eMC. In this work several enhancements were made in the eMC algorithm leading to significant improvements in the accuracy of the dose calculation

  6. Monte Carlo dose calculation improvements for low energy electron beams using eMC.

    Science.gov (United States)

    Fix, Michael K; Frei, Daniel; Volken, Werner; Neuenschwander, Hans; Born, Ernst J; Manser, Peter

    2010-08-21

    The electron Monte Carlo (eMC) dose calculation algorithm in Eclipse (Varian Medical Systems) is based on the macro MC method and is able to predict dose distributions for high energy electron beams with high accuracy. However, there are limitations for low energy electron beams. This work aims to improve the accuracy of the dose calculation using eMC for 4 and 6 MeV electron beams of Varian linear accelerators. Improvements implemented into the eMC include (1) improved determination of the initial electron energy spectrum by increased resolution of mono-energetic depth dose curves used during beam configuration; (2) inclusion of all the scrapers of the applicator in the beam model; (3) reduction of the maximum size of the sphere to be selected within the macro MC transport when the energy of the incident electron is below certain thresholds. The impact of these changes in eMC is investigated by comparing calculated dose distributions for 4 and 6 MeV electron beams at source to surface distance (SSD) of 100 and 110 cm with applicators ranging from 6 x 6 to 25 x 25 cm(2) of a Varian Clinac 2300C/D with the corresponding measurements. Dose differences between calculated and measured absolute depth dose curves are reduced from 6% to less than 1.5% for both energies and all applicators considered at SSD of 100 cm. Using the original eMC implementation, absolute dose profiles at depths of 1 cm, d(max) and R50 in water lead to dose differences of up to 8% for applicators larger than 15 x 15 cm(2) at SSD 100 cm. Those differences are now reduced to less than 2% for all dose profiles investigated when the improved version of eMC is used. At SSD of 110 cm the dose difference for the original eMC version is even more pronounced and can be larger than 10%. Those differences are reduced to within 2% or 2 mm with the improved version of eMC. In this work several enhancements were made in the eMC algorithm leading to significant improvements in the accuracy of the dose

  7. Photoelectron binding energy shifts observed during oxidation of group IIA, IIIA and IVA elemental surfaces

    International Nuclear Information System (INIS)

    Heide, P.A.W. van der

    2006-01-01

    An extensive re-evaluation of XPS binding energies (BE's) and binding energy shifts (ΔBE's) from metals, oxides and the carbonates of the group II, III and IVA elements (exceptions are Be, Mg and Hf) has been carried out using a substrate specific BE referencing approach. From this, O-1s BE's are found to fall into surface oxide, bulk oxide and carbonate groupings, with bulk oxides showing the lowest BE's followed by surface oxides (+∼1.5 eV) and then carbonates (+∼3.0 eV). The O-1s BE's from the bulk oxides also appear to scale with 1/d, where d is inter-atomic distance. The same is noted in the ΔBE's observed from the metallic counterparts during oxidation of the elemental surfaces. This, and the decreasing BE exhibited by Ca, Sr and Ba on oxidation is explained within the charge potential model as resulting from competing inter- and intra-atomic effects, and is shown to be consistent with partial covalency arguments utilizing Madulung potentials. The ΔBE's also fall into groups according to the elements location in the periodic table, i.e. s, p or d block. These trends open up the possibility of approximating ΔBE's arising from initial and final state effects, and bond distances

  8. Calculation of Hamilton energy and control of dynamical systems with different types of attractors.

    Science.gov (United States)

    Ma, Jun; Wu, Fuqiang; Jin, Wuyin; Zhou, Ping; Hayat, Tasawar

    2017-05-01

    Strange attractors can be observed in chaotic and hyperchaotic systems. Most of the dynamical systems hold a finite number of attractors, while some chaotic systems can be controlled to present an infinite number of attractors by generating infinite equilibria. Chaos can also be triggered in some dynamical systems that can present hidden attractors, and the attractors in these dynamical systems find no equilibria and the basin of attraction is not connected with any equilibrium (the equilibria position meets certain restriction function). In this paper, Hamilton energy is calculated on the chaotic systems with different types of attractors, and energy modulation is used to control the chaos in these systems. The potential mechanism could be that negative feedback in energy can suppress the phase space and oscillating behaviors, and thus, the chaotic, periodical oscillators can be controlled. It could be effective to control other chaotic, hyperchaotic and even periodical oscillating systems as well.

  9. Absolute Hydration Free Energy of Proton from First Principles Electronic Structure Calculations

    International Nuclear Information System (INIS)

    Zhan, Chang-Guo; Dixon, David A.

    2001-01-01

    The absolute hydration free energy of the proton, DGhyd298(H+), is one of the fundamental quantities for the thermodynamics of aqueous systems. Its exact value remains unknown despite extensive experimental and computational efforts. We report a first-principles determination of DGhyd298(H+) by using the latest developments in electronic structure theory and massively parallel computers. DGhyd298(H+) is accurately predicted to be -262.4 kcal/mol based on high-level, first-principles solvation-included electronic structure calculations. The absolute hydration free energies of other cations can be obtained by using appropriate available thermodynamic data in combination with this value. The high accuracy of the predicted absolute hydration free energy of proton is confirmed by applying the same protocol to predict DGhyd298(Li+)

  10. Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.

    Science.gov (United States)

    Meirovitch, Hagai

    2010-01-01

    , HSMD is being extended for calculating the absolute and relative free energies of ligand-enzyme binding. We describe the whole approach and discuss future directions. 2009 John Wiley & Sons, Ltd.

  11. The fifth Atomic Energy Research dynamic benchmark calculation with HEXTRAN-SMABRE

    International Nuclear Information System (INIS)

    Haenaelaeinen, Anitta

    1998-01-01

    The fifth Atomic Energy Research dynamic benchmark is the first Atomic Energy Research benchmark for coupling of the thermohydraulic codes and three-dimensional reactor dynamic core models. In VTT HEXTRAN 2.7 is used for the core dynamics and SMABRE 4.6 as a thermohydraulic model for the primary and secondary loops. The plant model for SMABRE is based mainly on two input models. the Loviisa model and standard WWER-440/213 plant model. The primary circuit includes six separate loops, totally 505 nodes and 652 junctions. The reactor pressure vessel is divided into six parallel channels. In HEXTRAN calculation 176 symmetry is used in the core. In the sequence of main steam header break at the hot standby state, the liquid temperature is decreased symmetrically in the core inlet which leads to return to power. In the benchmark, no isolations of the steam generators are assumed and the maximum core power is about 38 % of the nominal power at four minutes after the break opening in the HEXTRAN-SMABRE calculation. Due to boric acid in the high pressure safety injection water, the power finally starts to decrease. The break flow is pure steam in the HEXTRAN-SMABRE calculation during the whole transient even in the swell levels in the steam generators are very high due to flashing. Because of sudden peaks in the preliminary results of the steam generator heat transfer, the SMABRE drift-flux model was modified. The new model is a simplified version of the EPRI correlation based on test data. The modified correlation behaves smoothly. In the calculations nuclear data is based on the ENDF/B-IV library and it has been evaluated with the CASMO-HEX code. The importance of the nuclear data was illustrated by repeating the benchmark calculation with using three different data sets. Optimal extensive data valid from hot to cold conditions were not available for all types of fuel enrichments needed in this benchmark.(Author)

  12. TASK 2.5.4 DEVELOPMENT OF AN ENERGY SAVINGS CALCULATOR

    Energy Technology Data Exchange (ETDEWEB)

    Miller, William A [ORNL; New, Joshua Ryan [ORNL; Desjarlais, Andre Omer [ORNL; Huang, Joe [Lawrence Berkeley National Laboratory (LBNL); Erdem, Ender [Lawrence Berkeley National Laboratory (LBNL); Ronnen, Levinson [Lawrence Berkeley National Laboratory (LBNL)

    2010-03-01

    California s major energy utilities and the California Energy Commission (CEC) are seeking to allocate capital that yields the greatest return on investment for energy infrastructure that meets any part of the need for reliable supplies of energy. The utilities are keenly interested in knowing the amount of electrical energy savings that would occur if cool roof color materials are adopted in the building market. To meet this need the Oak Ridge National Laboratory and the Lawrence Berkeley National Laboratory (LBNL) have been collaborating on a Public Interest Energy Research (PIER) project to develop an industry-consensus energy-savings calculator. The task was coordinated with an ongoing effort supported by the DOE to develop one calculator to achieve both the DOE and the EPA objectives for deployment of cool roof products. Recent emphasis on domestic building energy use has made the work a top priority by the Department of Energy s (DOE) Building Technologies Program. The Roof Savings Calculator (RSC) tool is designed to help building owners, manufacturers, distributors, contractors and practitioners easily run complex simulations. The latest web technologies and usability design were employed to provide an easy input interface to an annual simulation of hour-by-hour, whole-building performance using the world-class simulation tools DOE-2.1E and AtticSim. Building defaults were assigned based on the best available statistical evidence and can provide energy and cost savings after the user selects nothing more than the building location. A key goal for the tool is to promote the energy benefits of cool color tile, metal and asphalt shingle roof products and other energy saving systems. The RSC tool focuses on applications for the roof and attic; however, the code conducts a whole building simulation that puts the energy and heat flows of the roof and attic into the perspective of the whole house. An annual simulation runs in about 30 sec. In addition to cool

  13. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.

    Science.gov (United States)

    Peddi, Saikiran Reddy; Sivan, Sree Kanth; Manga, Vijjulatha

    2018-02-01

    The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔG bind and experimental pIC 50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC 50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC 50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.

  14. Insights into the complex formed by matrix metalloproteinase-2 and alloxan inhibitors: molecular dynamics simulations and free energy calculations.

    Directory of Open Access Journals (Sweden)

    Ilenia Giangreco

    Full Text Available Matrix metalloproteinases (MMP are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. Hence, the development of potent and selective inhibitors targeting these enzymes continues to be eagerly sought. In this paper, a number of alloxan-based compounds, initially conceived to bias other therapeutically relevant enzymes, were rationally modified and successfully repurposed to inhibit MMP-2 (also named gelatinase A in the nanomolar range. Importantly, the alloxan core makes its debut as zinc binding group since it ensures a stable tetrahedral coordination of the catalytic zinc ion in concert with the three histidines of the HExxHxxGxxH metzincin signature motif, further stabilized by a hydrogen bond with the glutamate residue belonging to the same motif. The molecular decoration of the alloxan core with a biphenyl privileged structure allowed to sample the deep S(1' specificity pocket of MMP-2 and to relate the high affinity towards this enzyme with the chance of forming a hydrogen bond network with the backbone of Leu116 and Asn147 and the side chains of Tyr144, Thr145 and Arg149 at the bottom of the pocket. The effect of even slight structural changes in determining the interaction at the S(1' subsite of MMP-2 as well as the nature and strength of the binding is elucidated via molecular dynamics simulations and free energy calculations. Among the herein presented compounds, the highest affinity (pIC(50 = 7.06 is found for BAM, a compound exhibiting also selectivity (>20 towards MMP-2, as compared to MMP-9, the other member of the gelatinases.

  15. Insights into the complex formed by matrix metalloproteinase-2 and alloxan inhibitors: molecular dynamics simulations and free energy calculations.

    Science.gov (United States)

    Giangreco, Ilenia; Lattanzi, Gianluca; Nicolotti, Orazio; Catto, Marco; Laghezza, Antonio; Leonetti, Francesco; Stefanachi, Angela; Carotti, Angelo

    2011-01-01

    Matrix metalloproteinases (MMP) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. Hence, the development of potent and selective inhibitors targeting these enzymes continues to be eagerly sought. In this paper, a number of alloxan-based compounds, initially conceived to bias other therapeutically relevant enzymes, were rationally modified and successfully repurposed to inhibit MMP-2 (also named gelatinase A) in the nanomolar range. Importantly, the alloxan core makes its debut as zinc binding group since it ensures a stable tetrahedral coordination of the catalytic zinc ion in concert with the three histidines of the HExxHxxGxxH metzincin signature motif, further stabilized by a hydrogen bond with the glutamate residue belonging to the same motif. The molecular decoration of the alloxan core with a biphenyl privileged structure allowed to sample the deep S(1)' specificity pocket of MMP-2 and to relate the high affinity towards this enzyme with the chance of forming a hydrogen bond network with the backbone of Leu116 and Asn147 and the side chains of Tyr144, Thr145 and Arg149 at the bottom of the pocket. The effect of even slight structural changes in determining the interaction at the S(1)' subsite of MMP-2 as well as the nature and strength of the binding is elucidated via molecular dynamics simulations and free energy calculations. Among the herein presented compounds, the highest affinity (pIC(50) = 7.06) is found for BAM, a compound exhibiting also selectivity (>20) towards MMP-2, as compared to MMP-9, the other member of the gelatinases.

  16. High energy nuclear reactions ('Spallation') and their application in calculation of the Acceleration Driven Systems (ADS)

    International Nuclear Information System (INIS)

    Rossi, Pedro Carlos Russo

    2011-01-01

    This work presents a study of high energy nuclear reactions which are fundamental to dene the source term in accelerator driven systems. These nuclear reactions, also known as spallation, consist in the interaction of high energetic hadrons with nucleons in the atomic nucleus. The phenomenology of these reactions consist in two step. In the rst, the proton interacts through multiple scattering in a process called intra-nuclear cascade. It is followed by a step in which the excited nucleus, coming from the intranuclear cascade, could either, evaporates particles to achieve a moderate energy state or fission. This process is known as competition between evaporation and fission. In this work the main nuclear models, Bertini and Cugnon are reviewed, since these models are fundamental for design purposes of the source term in ADS, due to lack of evaluated nuclear data for these reactions. The implementation and validation of the calculation methods for the design of the source is carried out to implement the methodology of source design using the program MCNPX (Monte Carlo N-Particle eXtended), devoted to calculation of transport of these particles and the validation performed by an international cooperation together with a Coordinated Research Project (CRP) of the International Atomic Energy Agency and available jobs, in order to qualify the calculations on nuclear reactions and the de-excitation channels involved, providing a state of the art of design and methodology for calculating external sources of spallation for source driven systems. The CRISP, is a brazilian code for the phenomenological description of the reactions involved and the models implemented in the code were reviewed and improved to continue the qualification process. Due to failure of the main models in describing the production of light nuclides, the multifragmentation reaction model was studied. Because the discrepancies in the calculations of production of these nuclides are attributes to the

  17. DEVELOPMENT OF METHODS OF CALCULATION OF TRACTION POWER SUPPLY SYSTEMS AND ENERGY SYSTEMS FEEDING THEM

    Directory of Open Access Journals (Sweden)

    I.V. Domanskyi

    2015-08-01

    Full Text Available Currently, the cause deterioration of quality rating of electricity on tire traction substations AC can be either how mode of operation of power systems, industrial loads so and the impact of electric traction. The experience of energy surveys show that the loss from flow potential equalization currents in each the third plot between traction substations AC is amount to not less than 250 thousand kW∙h per year. To select the optimum power and places location of the device longitudinal capacitive of compensation and decision other tasks it is necessary methodology of systems of calculation that takes into account the complex nature of the mutual influence of the quality of the electricity coming from the energy system of and the transportation process. In the paper proposed three options for calculation algorithms modes work of existing and perspective systems, traction power supply AC jointly with power supply their by energy systems, including the algorithm for calculating networks of different nominal voltages using the transformations; decomposition and synthesis of networks with different voltage levels; the iterations and probabilistic assessment of the impact of power mains. Developed the schemes formalization of graphs and the matrices of portions of the outer and traction power supply and method of selecting parameters and places location of the devices longitudinal capacitive of compensation, which are based on direct methods solving systems of linear algebraic equations with a dense banded and profile-sparse the matrix. Are generalized ways of formation and transformation of graphs of schemes traction power supply and feeding them energy systems and proposed the method of calculation the complex the moment of schemes, which increases the accuracy of calculating of flows power on traction networks to 1-2 % and allows you to select the optimal parameters and places location of the devices longitudinal capacitive of compensation

  18. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy.

    Science.gov (United States)

    Sheng, Wenchao; Zhuang, Zhongbin; Gao, Minrui; Zheng, Jie; Chen, Jingguang G; Yan, Yushan

    2015-01-08

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  19. Development of a SCALE tool for continuous-energy eigenvalue sensitivity coefficient calculations

    International Nuclear Information System (INIS)

    Perfetti, C.M.; Rearden, B.T.

    2013-01-01

    Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several criticality safety problems. The 2 methods are: the Iterated Fission Probability (IFP) method and the newly developed Contribution-Linked eigenvalue sensitivity/Uncertainty estimation via Track-length importance Characterization (CLUTCH) method. Unlike MG TSUNAMI, the IFP and CLUTCH methods avoid directly simulating adjoint particle histories by instead storing additional information about each particle that is later used to determine the importance of the particle during its lifetime. The IFP method uses this information to estimate the importance of events according to the concept that the importance of an event is proportional to the population of neutrons present in the system during some future generation. The CLUTCH method calculates the importance of events during a particle's lifetime by examining how many fission neutrons are created by that particle after those events occur. Both methods have produced sensitivity coefficients that agreed well with reference direct perturbation sensitivity coefficients although some differences were observed around energies corresponding to large neutron capture resonances. The CLUTCH method has been consistently more efficient than the IFP method and has required less memory that the IFP and MG TSUNAMI methods

  20. High-accuracy water potential energy surface for the calculation of infrared spectra

    Science.gov (United States)

    Mizus, Irina I.; Kyuberis, Aleksandra A.; Zobov, Nikolai F.; Makhnev, Vladimir Yu.; Polyansky, Oleg L.; Tennyson, Jonathan

    2018-03-01

    Transition intensities for small molecules such as water and CO2 can now be computed with such high accuracy that they are being used to systematically replace measurements in standard databases. These calculations use high-accuracy ab initio dipole moment surfaces and wave functions from spectroscopically determined potential energy surfaces (PESs). Here, an extra high-accuracy PES of the water molecule (H216O) is produced starting from an ab initio PES which is then refined to empirical rovibrational energy levels. Variational nuclear motion calculations using this PES reproduce the fitted energy levels with a standard deviation of 0.011 cm-1, approximately three times their stated uncertainty. The use of wave functions computed with this refined PES is found to improve the predicted transition intensities for selected (problematic) transitions. A new room temperature line list for H216O is presented. It is suggested that the associated set of line intensities is the most accurate available to date for this species. This article is part of the theme issue `Modern theoretical chemistry'.

  1. A DFT based method for calculating the surface energies of asymmetric MoP facets

    Science.gov (United States)

    Tian, Xinxin; Wang, Tao; Fan, Lifang; Wang, Yuekui; Lu, Haigang; Mu, Yuewen

    2018-01-01

    MoP is a promising catalyst in heterogeneous catalysis. Understanding its surface stability and morphology is the first and essential step in exploring its catalytic properties. However, traditional surface energy calculation method does not work for the asymmetric termination of MoP. In this work, we reported a useful DFT based method to get the surface energies of asymmetric MoP facets. Under ideal condition, the (101) surface with mixed Mo/P termination is most stable, followed by the (100) surface, while the (001) surface is least stable. Wulff construction reveals the exposure of six surfaces on the MoP nanoparticle, where the (101) has the largest contribution. Atomistic thermodynamics results reveal the changes in surface stability orders with experimental conditions, and the (001)-P termination becomes more and more stable with increasing P chemical potential, which indicates its exposure is possible at defined conditions. Our results agree well with the previous experimental XRD and TEM data. We believe the reported method for surface energy calculation could be extended to other similar systems with asymmetric surface terminations.

  2. High-accuracy water potential energy surface for the calculation of infrared spectra.

    Science.gov (United States)

    Mizus, Irina I; Kyuberis, Aleksandra A; Zobov, Nikolai F; Makhnev, Vladimir Yu; Polyansky, Oleg L; Tennyson, Jonathan

    2018-03-13

    Transition intensities for small molecules such as water and CO 2 can now be computed with such high accuracy that they are being used to systematically replace measurements in standard databases. These calculations use high-accuracy ab initio dipole moment surfaces and wave functions from spectroscopically determined potential energy surfaces (PESs). Here, an extra high-accuracy PES of the water molecule (H 2 16 O) is produced starting from an ab initio PES which is then refined to empirical rovibrational energy levels. Variational nuclear motion calculations using this PES reproduce the fitted energy levels with a standard deviation of 0.011 cm -1 , approximately three times their stated uncertainty. The use of wave functions computed with this refined PES is found to improve the predicted transition intensities for selected (problematic) transitions. A new room temperature line list for H 2 16 O is presented. It is suggested that the associated set of line intensities is the most accurate available to date for this species.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

  3. Analysis on Binding Energy and Auger Parameter for Estimating Size and Stoichiometry of ZnO Nanorods

    Directory of Open Access Journals (Sweden)

    Santanu Bera

    2012-01-01

    Full Text Available ZnO nanorods prepared through chemical vapor deposition technique are characterized by microscopic and X-ray photoelectron spectroscopy (XPS techniques to correlate the effects of size on the binding energy of Zn 2p3/2 photoelectrons. A positive shift in Zn 2p3/2-binding energy as compared to that in bulk ZnO is assumed to be the effect of size of ZnO tips. The shift in binding energy has been explained in terms of relaxation energy in the photoemission process. Simultaneously, Auger parameter of the nanorods is evaluated for stoichiometric composition. The extra peak in O1s spectrum of nanorods is explained as adsorbed O-bearing species or surface contaminants.

  4. Relation between heat of vaporization, ion transport, molar volume, and cation-anion binding energy for ionic liquids.

    Science.gov (United States)

    Borodin, Oleg

    2009-09-10

    A number of correlations between heat of vaporization (H(vap)), cation-anion binding energy (E(+/-)), molar volume (V(m)), self-diffusion coefficient (D), and ionic conductivity for 29 ionic liquids have been investigated using molecular dynamics (MD) simulations that employed accurate and validated many-body polarizable force fields. A significant correlation between D and H(vap) has been found, while the best correlation was found for -log(DV(m)) vs H(vap) + 0.28E(+/-). A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids. A deviation of some ILs from the reported master curve is explained based upon ion packing and proposed diffusion pathways. No general correlations were found between the ion diffusion coefficient and molecular volume or the diffusion coefficient and cation/anion binding energy.

  5. Conventional method for the calculation of the global energy cost of buildings; Methode conventionnelle de calcul du cout global energetique des batiments

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-05-01

    A working group driven by Electricite de France (EdF), Chauffage Fioul and Gaz de France (GdF) companies has been built with the sustain of several building engineering companies in order to clarify the use of the method of calculation of the global energy cost of buildings. This global cost is an economical decision help criterion among others. This press kit presents, first, the content of the method (input data, calculation of annual expenses, calculation of the global energy cost, display of results and limitations of the method). Then it fully describes the method and its appendixes necessary for its implementation: economical and financial context, general data of the project in progress, environmental data, occupation and comfort level, variants, investment cost of energy systems, investment cost for the structure linked with the energy system, investment cost for other invariant elements of the structure, calculation of consumptions (space heating, hot water, ventilation), maintenance costs (energy systems, structure), operation and exploitation costs, tariffs and consumption costs and taxes, actualized global cost, annualized global cost, comparison between variants. The method is applied to a council building of 23 flats taken as an example. (J.S.)

  6. Monte Carlo calculation of scattered radiation from applicators in low energy clinical electron beams

    International Nuclear Information System (INIS)

    Jabbari, N.; Hashemi-Malayeri, B.; Farajollahi, A. R.; Kazemnejad, A.

    2007-01-01

    In radiotherapy with electron beams, scattered radiation from an electron applicator influences the dose distribution in the patient. The contribution of this radiation to the patient dose is significant, even in modern accelerators. In most of radiotherapy treatment planning systems, this component is not explicitly included. In addition, the scattered radiation produced by applicators varies based on the applicator design as well as the field size and distance from the applicators. The aim of this study was to calculate the amount of scattered dose contribution from applicators. We also tried to provide an extensive set of calculated data that could be used as input or benchmark data for advanced treatment planning systems that use Monte Carlo algorithms for dose distribution calculations. Electron beams produced by a NEPTUN 10PC medical linac were modeled using the BEAMnrc system. Central axis depth dose curves of the electron beams were measured and calculated, with and without the applicators in place, for different field sizes and energies. The scattered radiation from the applicators was determined by subtracting the central axis depth dose curves obtained without the applicators from that with the applicator. The results of this study indicated that the scattered radiation from the electron applicators of the NEPTUN 10PC is significant and cannot be neglected in advanced treatment planning systems. Furthermore, our results showed that the scattered radiation depends on the field size and decreases almost linearly with depth. (author)

  7. A simplified analytical dose calculation algorithm accounting for tissue heterogeneity for low-energy brachytherapy sources

    Science.gov (United States)

    Mashouf, Shahram; Lechtman, Eli; Beaulieu, Luc; Verhaegen, Frank; Keller, Brian M.; Ravi, Ananth; Pignol, Jean-Philippe

    2013-09-01

    The American Association of Physicists in Medicine Task Group No. 43 (AAPM TG-43) formalism is the standard for seeds brachytherapy dose calculation. But for breast seed implants, Monte Carlo simulations reveal large errors due to tissue heterogeneity. Since TG-43 includes several factors to account for source geometry, anisotropy and strength, we propose an additional correction factor, called the inhomogeneity correction factor (ICF), accounting for tissue heterogeneity for Pd-103 brachytherapy. This correction factor is calculated as a function of the media linear attenuation coefficient and mass energy absorption coefficient, and it is independent of the source internal structure. Ultimately the dose in heterogeneous media can be calculated as a product of dose in water as calculated by TG-43 protocol times the ICF. To validate the ICF methodology, dose absorbed in spherical phantoms with large tissue heterogeneities was compared using the TG-43 formalism corrected for heterogeneity versus Monte Carlo simulations. The agreement between Monte Carlo simulations and the ICF method remained within 5% in soft tissues up to several centimeters from a Pd-103 source. Compared to Monte Carlo, the ICF methods can easily be integrated into a clinical treatment planning system and it does not require the detailed internal structure of the source or the photon phase-space.

  8. CASSCF/CI calculations of electronic states and potential energy surfaces of PtH2

    International Nuclear Information System (INIS)

    Balasubramanian, K.

    1987-01-01

    Complete active space MCSCF followed by MRSDCI (multireference singles and doubles configuration interaction) calculations are carried out on the electronic states of PtH 2 . Spin--orbit interaction is introduced using a relativistic configuration interaction scheme on PtH + whose d orbital Mulliken population is close to that of the d population of PtH 2 and thus enables calculation of spin--orbit splittings for the electronic states of PtH 2 . The bending potential energy surfaces of the 1 A 1 and 3 A 1 states are obtained. The 1 A 1 surface has a bent minimum and dissociates almost without a barrier into Pt( 1 S 0 ) and H 2 , while the 3 A 1 state has a large (--55 kcal/mol) barrier to dissociation into Pt( 3 D 3 )+H 2 . The ground state of PtH 2 is a bent 1 A 1 state (θ = 85 0 )

  9. A practical approach for the calculation of the activation energy of the sintering

    Directory of Open Access Journals (Sweden)

    Pouchly Vaclav

    2016-01-01

    Full Text Available Newly developed software for calculation of activation energy (Qs in the following of sintering using the Wang and Raj model is presented. To demonstrate the practical potential of the software and to evaluate the behaviour of the Qs during the sintering process, alumina and cubic zirconia ceramic compacts were prepared from nanometric powders. The results obtained with both materials are in agreement with previously published data calculated by different approaches. In the interval of interest (relative densities from 60 % to almost 100 % of theoretical density, both materials show similar behaviour. Three distinct regions can be seen: the initial constant values of Qs 868 kJ/mol and 762 kJ/mol for alumina and cubic zirconia, respectively; a region containing linear drop of Qs and the final region of constant Qs values 625 kJ/mol and 645 kJ/mol for alumina and cubic zirconia, respectively.

  10. Energy-efficient and preservable windows. Measurements and calculations; Energieffektive bevaringsverdige vinduer. Maalinger og beregninger

    Energy Technology Data Exchange (ETDEWEB)

    Homb, Anders; Uvsloekk, Sivert

    2012-11-01

    SINTEF has carried out a project for Cultural Heritage and Enova to document specific qualities of energy-efficient and preservable windows. The work has been based on an older type two-rams window with simple frames and one glass divided into three squares of horizontal crossbars. There were produced two kinds of commodity window, respectively, with single glazing with Insulating. Measurements and calculations have been performed with two different distances from the outer glass to the last frame. The project had the following contents: Measurements of the U-value, Calculation of U-value of accurate and simplified method, Measurements of air density and drying ability, Measurement and evaluation of sound insulation, Estimation of the heat balance (eb)

  11. Calculation of nuclear data for incident energies to 200 MeV with the FKK-GNASH code system

    International Nuclear Information System (INIS)

    Chadwick, M.B.; Young, P.G.

    1993-02-01

    We describe how the FKK-GNASH code system has been extended to calculate nucleon-induced reactions up to 200 MeV, and used to predict (p,xn) and (p,xp) cross sections on 208 Pb at incident energies of 25, 45, 80 and 160 MeV, for an intermediate energy code intercomparison. Details of the reaction mechanisms calculated by FKK-GNASH are given, and the calculational procedure is described

  12. Dislocation dissociation and stacking-fault energy calculation in strontium titanate

    International Nuclear Information System (INIS)

    Castillo-Rodriguez, M.; Sigle, W.

    2010-01-01

    The dislocation microstructure of strontium titanate plastically deformed below room temperature shows dipolar configurations of a screw dislocations. The dipole height is so small that dipole annihilation is expected. Here we show why this is inhibited. By high-resolution transmission electron microscopy observations we find that in such dipoles each dislocation is dissociated into two collinear a/2 partials on a {1 1 0} plane. Elasticity theory calculations provide a stacking-fault energy value of 340 ± 90 mJ m -2 . Finally, we discuss the effects of this dissociation process on the mechanical behaviour.

  13. Note on isotopic effects in range calculations of high-energy ion beams

    International Nuclear Information System (INIS)

    Dominguez-Vazquez, Javier; Perez-Martin, A.M.C.; Jimenez-Rodriguez, J.J.; Konoplev, Vladimir; Gras-Marti, Albert; Castella-Mayor, Javier

    1995-01-01

    A simple analytical model that allows the calculation of the percent-level differences of the average ranges of isotopic ion beams slowing down in solid targets is extended to energies in the MeV region and to investigate isotopic effects due to small variations in the mass of the target species. The various contributions to the range in terms of ion stopping, both nuclear and electronic, and angular scattering, can be investigated separately. The model agrees with available experimental data, and predictions are made for a range of cases of interest. (orig.)

  14. Approximate albedo boundary conditions for energy multigroup X,Y-geometry discrete ordinates nuclear global calculations

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Davi J.M.; Nunes, Carlos E.A.; Alves Filho, Hermes; Barros, Ricardo C., E-mail: davijmsilva@yahoo.com.br, E-mail: ceanunes@yahoo.com.br, E-mail: rcbarros@pq.cnpq.br [Secretaria Municipal de Educacao de Itaborai, RJ (Brazil); Universidade Estacio de Sa (UNESA), Rio de Janeiro, RJ (Brazil); Universidade do Estado do Rio de Janeiro (UERJ), Novra Friburgo, RJ (Brazil). Instituto Politecnico. Departamento de Modelagem Computacional

    2017-11-01

    Discussed here is the accuracy of approximate albedo boundary conditions for energy multigroup discrete ordinates (S{sub N}) eigenvalue problems in two-dimensional rectangular geometry for criticality calculations in neutron fission reacting systems, such as nuclear reactors. The multigroup (S{sub N}) albedo matrix substitutes approximately the non-multiplying media around the core, e.g., baffle and reflector, as we neglect the transverse leakage terms within these non-multiplying regions. Numerical results to a typical model problem are given to illustrate the accuracy versus the computer running time. (author)

  15. Calculation of energy relaxation rates of fast particles by phonons in crystals

    Energy Technology Data Exchange (ETDEWEB)

    Prange, Micah P.; Campbell, Luke W.; Wu, Dangxin; Gao, Fei; Kerisit, Sebastien N.

    2015-03-01

    We present ab initio calculations of the temperature-dependent exchange of energy between a classical charged point-particle and the phonons of a crystalline material. The phonons, which are computed using density functional perturbation theory (DFPT) methods, interact with the mov- ing particle via the Coulomb interaction between the density induced in the material by phonon excitation and the charge of the classical particle. Energy relaxation rates are computed using time- dependent perturbation theory. The method, which is applicable wherever DFPT is, is illustrated with results for CsI, an important scintillator whose performance is affected by electron thermal- ization. We discuss the influence of the form assumed for quasiparticle dispersion on theoretical estimates of electron cooling rates.

  16. Spectral characterization, optical band gap calculations and DNA binding of some binuclear Schiff-base metal complexes derived from 2-amino-ethanoic acid and acetylacetone

    Science.gov (United States)

    Hussien, Mostafa A.; Nawar, Nagwa; Radwan, Fatima M.; Hosny, Nasser Mohammed

    2015-01-01

    Bi-nuclear metal complexes derived from the reaction of Cu(II), Co(II), Ni(II) and Zn(II) acetates with the Schiff-base ligand (H2L) resulted from the condensation of 2-amino-ethanoic acid (glycine) and acetylacetone have been synthesized and characterized by elemental analyses, Raman spectra, FT-IR, ES-MS, UV-Vis., 1H NMR, ESR, thermal analyses (TG, DTG and DTA) and magnetic measurements. The results showed that, the Schiff base ligand can bind two metal ions in the same time. It coordinates to the first metal ion as mono-negative bi-dentate through azomethine nitrogen and enolic carbonyl after deprotonation. At the same time, it binds to the second metal ion via carboxylate oxygen after deprotonation. The thermodynamic parameters E∗, ΔH∗, ΔG∗ and ΔS∗ have been calculated by Coats-Redfern (CR) and Horowitz-Metzger (HM) methods. The optical band gaps of the isolated complexes have been calculated from absorption spectra and the results indicated semi-conducting nature of the investigated complexes. The interactions between the copper (II) complex and calf thymus DNA (CT-DNA) have been studied by UV spectra. The results confirm that the Cu(II) complex binds to CT-DNA.

  17. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

    Directory of Open Access Journals (Sweden)

    Nicolas Panel

    2017-09-01

    Full Text Available PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or “PB/LIE” free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo. The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

  18. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.

    Science.gov (United States)

    Panel, Nicolas; Sun, Young Joo; Fuentes, Ernesto J; Simonson, Thomas

    2017-01-01

    PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or "PB/LIE" free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α 2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo . The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

  19. Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

    Science.gov (United States)

    Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

    2016-07-14

    We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  20. Glucose Sensors Based on Microcapsules Containing an Orange/Red Competitive Binding Resonance Energy Transfer Assay

    Science.gov (United States)

    CHINNAYELKA, SWETHA; McSHANE, and MICHAEL J.

    2015-01-01

    Fluorescent sensing systems offer the potential for noninvasive monitoring with implantable devices, but they require carrier technologies that provide suitable immobilization, accessibility, and biocompatibility while maintaining adequate response characteristics. A recent development towards this goal is a highly specific and sensitive competitive binding assay for glucose using apo-glucose oxidase (apo-GOx) as the recognition element and dextran as the competing ligand; this has been demonstrated as a glucose sensor system by encapsulating the competitive binding assay in semipermeable microcapsule carriers. This paper describes the extension of this sensor design to longer wavelengths in an attempt to increase the applicability to in vivo monitoring. The glucose sensitivity of the tetramethylrhodamine isothiocyanate-dextran (TD) and cyanine Cy5-apo-GOx (CAG) complexes showed five to 10 times greater specificity for β-D-glucose over other sugars. Microcapsules loaded with TD/CAG complexes exhibited a linear, totally reversible response in the range of 0–720 mg/dL, with a sensitivity (percent change in intensity ratio) of 0.06%/(mg/dL). The decrease in sensitivity observed with the use of longer-wavelength dyes is most likely to be compensated with the deeper penetration of light and reduced tissue scattering. These findings imply that the encapsulation of sensing assay elements in microcapsules is a simple and translatable method for the fabrication of stable biosensors, and optimization of resonance energy transfer pairs and assay component preparation will further improve the response to approach clinically relevant performance. PMID:16800748

  1. First-Principles Calculations of Electronic, Optical, and Transport Properties of Materials for Energy Applications

    Science.gov (United States)

    Shi, Guangsha

    Solar electricity is a reliable and environmentally friendly method of sustainable energy production and a realistic alternative to conventional fossil fuels. Moreover, thermoelectric energy conversion is a promising technology for solid-state refrigeration and efficient waste-heat recovery. Predicting and optimizing new photovoltaic and thermoelectric materials composed of Earth-abundant elements that exceed the current state of the art, and understanding how nanoscale structuring and ordering improves their energy conversion efficiency pose a challenge for materials scientists. I approach this challenge by developing and applying predictive high-performance computing methods to guide research and development of new materials for energy-conversion applications. Advances in computer-simulation algorithms and high-performance computing resources promise to speed up the development of new compounds with desirable properties and significantly shorten the time delay between the discovery of new materials and their commercial deployment. I present my calculated results on the extraordinary properties of nanostructured semiconductor materials, including strong visible-light absorbance in nanoporous silicon and few-layer SnSe and GeSe. These findings highlight the capability of nanoscale structuring and ordering to improve the performance of Earth-abundant materials compared to their bulk counterparts for solar-cell applications. I also successfully identified the dominant mechanisms contributing to free-carrier absorption in n-type silicon. My findings help evaluate the impact of the energy loss from this absorption mechanism in doped silicon and are thus important for the design of silicon solar cells. In addition, I calculated the thermoelectric transport properties of p-type SnSe, a bulk material with a record thermoelectric figure of merit. I predicted the optimal temperatures and free-carrier concentrations for thermoelectric energy conversion, as well the

  2. Estimating Parameter Uncertainty in Binding-Energy Models by the Frequency-Domain Bootstrap

    Science.gov (United States)

    Bertsch, G. F.; Bingham, Derek

    2017-12-01

    We propose using the frequency-domain bootstrap (FDB) to estimate errors of modeling parameters when the modeling error is itself a major source of uncertainty. Unlike the usual bootstrap or the simple χ2 analysis, the FDB can take into account correlations between errors. It is also very fast compared to the Gaussian process Bayesian estimate as often implemented for computer model calibration. The method is illustrated with a simple example, the liquid drop model of nuclear binding energies. We find that the FDB gives a more conservative estimate of the uncertainty in liquid drop parameters than the χ2 method, and is in fair accord with more empirical estimates. For the nuclear physics application, there are no apparent obstacles to apply the method to the more accurate and detailed models based on density-functional theory.

  3. Spin assignments of nuclear levels above the neutron binding energy in $^{88}$Sr

    CERN Multimedia

    Neutron resonances reveal nuclear levels in the highly excited region of the nucleus around the neutron binding energy. Nuclear level density models are therefore usually calibrated to the number of observed levels in neutron-induced reactions. The gamma-ray cascade from the decay of the highly excited compound nucleus state to the ground state show dierences dependent on the initial spin. This results in a dierence in the multiplicity distribution which can be exploited. We propose to use the 4${\\pi}$ total absorption calorimeter (TAC) at the n TOF facility to determine the spins of resonances formed by neutrons incident on a metallic $^{87}$Sr sample by measuring the gamma multiplicity distributions for the resolved resonances. In addition we would like to use the available enriched $^{87}$Sr target for cross section measurements with the C$\\scriptscriptstyle{6}$D$\\scriptscriptstyle{6}$ detector setup.

  4. Energy gap of extended states in SiC-doped graphene nanoribbon: Ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xiaoshi; Wu, Yong [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Shanghai Key Lab of Modern Optical System, Shanghai 200093 (China); Li, Zhongyao, E-mail: lizyusst@gmail.com [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Shanghai Key Lab of Modern Optical System, Shanghai 200093 (China); Gao, Yong [School of Science, Shanghai Second Polytechnic University, Shanghai 201209 (China)

    2017-04-01

    Highlights: • The gap of isolated ribbon is inversely proportional to the width of ribbon. • The gap of doped ribbon cannot be modeled by effective width approximation. • The fitted energy gap can match the experimental observations. • The doping results in a spin-polarized metallic-like band structure. - Abstract: The energy gap of extended states in zigzag graphene nanoribbons (ZGNRs) was examined on the basis of density-functional theory. In isolated ZGNRs, the energy gap is inversely proportional to the width of ribbon. It agrees well with the results from the Dirac equation in spin-unpolarized ZGNRs, although the considered ZGNRs have spin-polarized edges. However, the energy gap in SiC-doped ZGNRs cannot be modeled by effective width approximation. The doping also lifts the spin-degenerate of edge states and results in a metallic-like band structure near the Fermi level in SiC-doped ZGNRs. Our calculations may be helpful for understanding the origin of the reported single-channel ballistic transport in epitaxial graphene nanoribbons.

  5. Density Functional Theory Calculations of Activation Energies for Carrier Capture by Defects in Semiconductors

    Science.gov (United States)

    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.

  6. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    Science.gov (United States)

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Efficient elimination of response parameters in molecular property calculations for variational and nonvariational energies.

    Science.gov (United States)

    Kristensen, Kasper; Jørgensen, Poul; Thorvaldsen, Andreas J; Helgaker, Trygve

    2008-12-07

    A general method is presented for the efficient elimination of response parameters in molecular property calculations for variational and nonvariational energies. For variational energies, Wigner's 2n+1 rule is obtained as a special case of the more general k(2n+1) rule, which states that for a subset of k perturbations within a total set of z>or=k perturbations, response parameters may be eliminated according to the 2n+1 rule (normally applied to the full set of perturbations). Nonvariational energies may be treated by introducing Lagrange multipliers that satisfy the stronger 2n+2 rule for the k perturbations, while the wave-function parameters still satisfy the 2n+1 rule for the k perturbations. The corresponding rule for nonvariational energies is referred to as the k(2n+1,2n+2) rule. For k=z, the well-known 2n+2 rule for the multipliers is reproduced, while the wave-function parameters satisfy the 2n+1 rule. The application of the k(2n+1) and k(2n+1,2n+2) rules minimizes the total number of response equations to be solved when the molecular property contains k extensive perturbations (e.g., geometrical derivatives) and z-k intensive perturbations (e.g., electric fields).

  8. Methods for calculating energy and current requirements for industrial electron beam processing

    International Nuclear Information System (INIS)

    Cleland, M.R.; Farrell, J.P.

    1976-01-01

    The practical problems of determining electron beam parameters for industrial irradiation processes are discussed. To assist the radiation engineer in this task, the physical aspects of electron beam absorption are briefly described. Formulas are derived for calculating the surface dose in the treated material using the electron energy, beam current and the area thruput rate of the conveyor. For thick absorbers electron transport results are used to obtain the depth-dose distributions. From these the average dose in the material, anti D, and the beam power utilization efficiency, F/sub p/, can be found by integration over the distributions. These concepts can be used to relate the electron beam power to the mass thruput rate. Qualitatively, the thickness of the material determines the beam energy, the area thruput rate and surface dose determine the beam current while the mass thruput rate and average depth-dose determine the beam power requirements. Graphs are presented showing these relationships as a function of electron energy from 0.2 to 4.0 MeV for polystyrene. With this information, the determination of electron energy and current requirements is a relatively simple procedure

  9. Free energy calculation of water addition coupled to reduction of aqueous RuO4-

    International Nuclear Information System (INIS)

    Tateyama, Yoshitaka; Blumberger, Jochen; Ohno, Takahisa; Sprik, Michiel

    2007-01-01

    Free energy calculations were carried out for water addition coupled reduction of aqueous ruthenate, RuO 4 - +H 2 O+e - →[RuO 3 (OH) 2 ] 2- , using Car-Parrinello molecular dynamics simulations. The full reaction is divided into the reduction of the tetrahedral monoanion, RuO 4 - +e - →RuO 4 2- , followed by water addition, RuO 4 2- +H 2 O→[RuO 3 (OH) 2 ] 2- . The free energy of reduction is computed from the fluctuations of the vertical energy gap using the MnO 4 - +e - →MnO 4 2- reaction as reference. The free energy for water addition is estimated using constrained molecular dynamics methods. While the description of this complex reaction, in principle, involves multiple reaction coordinates, we found that reversible transformation of the reactant into the product can be achieved by control of a single reaction coordinate consisting of a suitable linear combination of atomic distances. The free energy difference of the full reaction is computed to be -0.62 eV relative to the normal hydrogen electrode. This is in good agreement with the experimental value of -0.59 eV, lending further support to the hypothesis that, contrary to the ruthenate monoanion, the dianion is not tetrahedral but forms a trigonal-bipyramidal dihydroxo complex in aqueous solution. We construct an approximate two-dimensional free energy surface using the coupling parameter for reduction and the mechanical constraint for water addition as variables. Analyzing this surface we find that in the most favorable reaction pathway the reduction reaction precedes water addition. The latter takes place via the protonated complex [RuO 3 (OH)] - and subsequent transport of the created hydroxide ion to the fifth coordination site of Ru

  10. Affinity capillary electrophoresis and quantum mechanical calculations applied to the investigation of hexaarylbenzene-based receptor binding with lithium ion

    Czech Academy of Sciences Publication Activity Database

    Ehala, Sille; Toman, Petr; Rathore, R.; Makrlík, E.; Kašička, Václav

    2011-01-01

    Roč. 34, č. 18 (2011), s. 2433-2440 ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA203/08/1428; GA ČR(CZ) GA203/09/0675; GA AV ČR 1ET400500402 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40500505 Keywords : affinity capillary electrophoresis * binding constant * hexaarylbenzene-based receptor Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.733, year: 2011

  11. High Accuracy Potential Energy Surface, Dipole Moment Surface, Rovibrational Energies and Line List Calculations for ^{14}NH_3

    Science.gov (United States)

    Coles, Phillip; Yurchenko, Sergei N.; Polyansky, Oleg; Kyuberis, Aleksandra; Ovsyannikov, Roman I.; Zobov, Nikolay Fedorovich; Tennyson, Jonathan

    2017-06-01

    We present a new spectroscopic potential energy surface (PES) for ^{14}NH_3, produced by refining a high accuracy ab initio PES to experimental energy levels taken predominantly from MARVEL. The PES reproduces 1722 matched J=0-8 experimental energies with a root-mean-square error of 0.035 cm-1 under 6000 cm^{-1} and 0.059 under 7200 cm^{-1}. In conjunction with a new DMS calculated using multi reference configuration interaction (MRCI) and H=aug-cc-pVQZ, N=aug-cc-pWCVQZ basis sets, an infrared (IR) line list has been computed which is suitable for use up to 2000 K. The line list is used to assign experimental lines in the 7500 - 10,500 cm^{-1} region and previously unassigned lines in HITRAN in the 6000-7000 cm^{-1} region. Oleg L. Polyansky, Roman I. Ovsyannikov, Aleksandra A. Kyuberis, Lorenzo Lodi, Jonathan Tennyson, Andrey Yachmenev, Sergei N. Yurchenko, Nikolai F. Zobov, J. Mol. Spec., 327 (2016) 21-30 Afaf R. Al Derzia, Tibor Furtenbacher, Jonathan Tennyson, Sergei N. Yurchenko, Attila G. Császár, J. Quant. Spectrosc. Rad. Trans., 161 (2015) 117-130

  12. Ab initio calculation of reaction energies. III. Basis set dependence of relative energies on the FH2 and H2CO potential energy surfaces

    International Nuclear Information System (INIS)

    Frisch, M.J.; Binkley, J.S.; Schaefer, H.F. III

    1984-01-01

    The relative energies of the stationary points on the FH 2 and H 2 CO nuclear potential energy surfaces relevant to the hydrogen atom abstraction, H 2 elimination and 1,2-hydrogen shift reactions have been examined using fourth-order Moller--Plesset perturbation theory and a variety of basis sets. The theoretical absolute zero activation energy for the F+H 2 →FH+H reaction is in better agreement with experiment than previous theoretical studies, and part of the disagreement between earlier theoretical calculations and experiment is found to result from the use of assumed rather than calculated zero-point vibrational energies. The fourth-order reaction energy for the elimination of hydrogen from formaldehyde is within 2 kcal mol -1 of the experimental value using the largest basis set considered. The qualitative features of the H 2 CO surface are unchanged by expansion of the basis set beyond the polarized triple-zeta level, but diffuse functions and several sets of polarization functions are found to be necessary for quantitative accuracy in predicted reaction and activation energies. Basis sets and levels of perturbation theory which represent good compromises between computational efficiency and accuracy are recommended

  13. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes

    Science.gov (United States)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali

    2015-05-01

    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  14. Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

    Directory of Open Access Journals (Sweden)

    Adrien Nicolaï

    Full Text Available ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD of Hsp70 propagates a signal to its substrate-binding domain (SBD. Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in

  15. Potential energy surface and binding energy in the presence of an external electric field: modulation of anion-π interactions for graphene-based receptors.

    Science.gov (United States)

    Foroutan-Nejad, Cina; Marek, Radek

    2014-02-14

    Measuring the binding energy or scanning the potential energy surface (PES) of the charged molecular systems in the presence of an external electric field (EEF) requires a careful evaluation of the origin-dependency of the energy of the system and references. Scanning the PES for charged or purely ionic systems for obtaining the intrinsic energy barriers needs careful analysis of the electric work applied on ions by the EEF. The binding energy in the presence of an EEF is different from that in the absence of an electric field as the binding energy is an anisotropic characteristic which depends on the orientation of molecules with respect to the EEF. In this contribution we discuss various aspects of the PES and the concept of binding energy in the presence of an EEF. In addition, we demonstrate that the anion-π bonding properties can be modulated by applying a uniform EEF, which has a more pronounced effect on the larger, more polarizable π-systems. An analogous behavior is presumed for cation-π systems. We predict that understanding the phenomenon introduced in the present account has enormous potential, for example, for separating charged species on the surface of polarizable two-dimensional materials such as graphene or the surface of carbon nanotubes, in desalination of water.

  16. Energy Savings Calculations for Heat Island Reduction Strategies in Baton Rouge, Sacramento and Salt Lake City

    Energy Technology Data Exchange (ETDEWEB)

    Konopacki, S.; Akbari, H.

    2000-03-01

    In 1997, the US Environmental Protection Agency (EPA) established the ''Heat Island Reduction Initiative'', to quantify the potential benefits of Heat Island Reduction (HIR) strategies (i.e., shade trees, reflective roofs, reflective pavements and urban vegetation) to reduce cooling energy use in buildings, lower the ambient air temperature and improve urban air quality in cities, and reduce CO2 emissions from power plants. Under this initiative, the Urban Heat Island Pilot Project (UHIPP) was created with the objective to investigate the potential of HIR strategies in residential and commercial buildings in three initial UHIPP cities: Baton Rouge, Sacramento and Salt Lake City. This paper summarizes our efforts to calculate the annual energy savings, peak power avoidance and annual C02 reduction of HIR strategies in the three initial cities. In this analysis, we focused on three building types that offer most savings potential: single-family residence, office and retail store. Each building type was characterized in detail by old or new construction and with a gas furnace or an electric heat pump. We defined prototypical building characteristics for each building type and simulated the impact of HIR strategies on building cooling and heating energy use and peak power demand using the DOE-2.IE model. Our simulations included the impact of (1) strategically-placed shade trees near buildings [direct effect], (2) use of high-albedo roofing material on building [direct effect], (3) combined strategies I and 2 [direct effect], (4) urban reforestation with high-albedo pavements and building surfaces [indirect effect] and (5) combined strategies 1, 2 and 4 [direct and indirect effects]. We then estimated the total roof area of air-conditioned buildings in each city using readily obtainable data to calculate the metropolitan-wide impact of HIR strategies. The results show, that in Baton Rouge, potential annual energy savings of $15M could be realized by

  17. Cost optimal and nearly zero-energy buildings (nZEB) definitions, calculation principles and case studies

    CERN Document Server

    Kurnitski, Jarek

    2013-01-01

    This book introduces technical definitions, system boundaries, energy calculation methods and input data for setting primary energy based minimum/cost optimal and nZEB requirements in national energy frames. Offers five case studies of nZEB office buildings.

  18. The Development and Calculation of an Energy-saving Plant for Obtaining Water from Atmospheric Air

    Science.gov (United States)

    Uglanov, D. A.; Zheleznyak, K. E.; Chertykovsev, P. A.

    2018-01-01

    The article shows the calculation of characteristics of energy-efficient water generator from atmospheric air. This installation or the atmospheric water generator is the unique mechanism which produces safe drinking water by extraction it from air. The existing atmospheric generators allow to receive safe drinking water by means of process of condensation at air humidity at least equal to 35% and are capable to give to 25 liters of water in per day, and work from electricity. Authors offer to use instead of the condenser in the scheme of installation for increase volume of produced water by generator in per day, the following refrigerating machines: the vapor compression refrigerating machines (VCRM), the thermoelectric refrigerating machines (TRM) and the Stirling-cycle refrigerating machines (SRM). The paper describes calculation methods for each of refrigerating systems. Calculation of technical-and-economic indexes for the atmospheric water generator was carried out and the optimum system with the maximum volume of received water in per day was picked up. The atmospheric water generator which is considered in article will work from autonomous solar power station.

  19. First-principles calculations of the magnetic anisotropy energy of Fe-V multilayers

    International Nuclear Information System (INIS)

    Le Bacq, O.; Eriksson, O.; Johansson, B.; James, P.; Delin, A.

    2002-06-01

    The magnetic anisotropy energy (MAE) of Fe 2 V-6, Fe 3 , and Fe 4 V 4 multilayers are investigated using first-principles spin-polarized and relativistic band-structure calculations based upon the full-potential linearized muffin-tin-orbital method. A strong difference in the MAE and the easy axis of magnetization (calculated for the experimental lattice parameters) is observed between the three studied multilayer systems, with easy axes of (001), (110), and (100) for Fe 2 V 6 , Fe 3 V 5 , and Fe-4V 4 , respectively. The MAE of the Fe 2 V6 and Fe 4 V 4 multilayers agrees well with the experimental data. The origin of this difference of behavior is analyzed, via a study of the influence of the atomic volume as well as a relaxation study of the multilayers with respect to the tetragonal deformation. The important role played by the c/a axial ratio, imposed by the alloying effects, is outlined. The magnetic anisotropy coefficients entering the expression of the MAE, as a function of the directional cosines, are extracted from a series of calculations for four independent spin directions. Finally, the band-filling effects on the MAE are analyzed as well as the different contributions in reciprocal space. (author)

  20. Ion induced dipole clusters H(n)- (3 ≤ n-odd ≤ 13): density functional theory calculations of structure and energy.

    Science.gov (United States)

    Huang, Lulu; Matta, Chérif F; Massa, Lou

    2011-11-17

    We investigate anew the possible equilibrium geometries of ion induced dipole clusters of hydrogen molecular ions, of molecular formula H(n)(-) (3 ≤ n-odd ≤ 13). Our previous publications [Sapse, A. M.; et al. Nature 1979, 278, 332; Rayez, J. C.; et al., J. Chem. Phys. 1981, 75, 5393] indicated these molecules would have a shallow minimum and adopt symmetrical geometries that accord with the valence shell electron pair repulsion (VSEPR) rules for geometries defined by electron pairs surrounding a central point of attraction. These earlier calculations were all based upon Hartree-Fock (HF) calculations with a fairly small basis of atomic functions, except for the H3(-) ion for which configuration interaction (CI) calculations were carried out. A related paper [Hirao, K.; et al., Chem. Phys. 1983, 80, 237] carried out similar calculations on the same clusters, finding geometries similar to our earlier calculations. However, although that paper argued that the stabilization energy of negative ion clusters H(n)(-) is small, vibration frequencies for the whole set of clusters was not reported, and so a definitive assertion of a true equilibrium was not present. In this paper we recalculate the energetics of the ion induced dipole clusters using density function theory (DFT) B3LYP method calculations in a basis of functions (6-311++G(d,p)). By calculating the vibration frequencies of the VSEPR geometries, we prove that in general they are not true minima because not all the resulting frequencies correspond to real values. By searching the energy surface of the B3LYP calculations, we find the true minimum geometries, which are surprising configurations and are perhaps counterintuitive. We calculate the total energy and binding energy of the new geometries. We also calculate the bond paths associated with the quantum theory of atoms in molecules (QTAIM). The B3LYP/6-311++G(d,p) results, for each molecule, deliver bond paths that radiate between each polarized H2