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Sample records for activation energies calculated

  1. Calculating activation energies for temperature compensation in circadian rhythms

    NASA Astrophysics Data System (ADS)

    Bodenstein, C.; Heiland, I.; Schuster, S.

    2011-10-01

    Many biological species possess a circadian clock, which helps them anticipate daily variations in the environment. In the absence of external stimuli, the rhythm persists autonomously with a period of approximately 24 h. However, single pulses of light, nutrients, chemicals or temperature can shift the clock phase. In the case of light- and temperature-cycles, this allows entrainment of the clock to cycles of exactly 24 h. Circadian clocks have the remarkable property of temperature compensation, that is, the period of the circadian rhythm remains relatively constant within a physiological range of temperatures. For several organisms, temperature-regulated processes within the circadian clock have been identified in recent years. However, how these processes contribute to temperature compensation is not fully understood. Here, we theoretically investigate temperature compensation in general oscillatory systems. It is known that every oscillator can be locally temperature compensated around a reference temperature, if reactions are appropriately balanced. A balancing is always possible if the control coefficient with respect to the oscillation period of at least one reaction in the oscillator network is positive. However, for global temperature compensation, the whole physiological temperature range is relevant. Here, we use an approach which leads to an optimization problem subject to the local balancing principle. We use this approach to analyse different circadian clock models proposed in the literature and calculate activation energies that lead to temperature compensation.

  2. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  3. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  4. Calculation of activation energies for hydrogen-atom abstractions by radicals containing carbon triple bonds

    NASA Technical Reports Server (NTRS)

    Brown, R. L.; Laufer, A. H.

    1981-01-01

    Activation energies are calculated by the bond-energy-bond-order (BEBO) and the bond-strength-bond-length (BSBL) methods for the reactions of C2H radicals with H2, CH4, and C2H6 and for the reactions of CN radicals with H2 and CH4. The BSBL technique accurately predicts the activation energies for these reactions while the BEBO method yields energies averaging 9 kcal higher than those observed. A possible reason for the disagreement is considered.

  5. Density Functional Theory Calculations of Activation Energies for Carrier Capture by Defects in Semiconductors

    NASA Astrophysics Data System (ADS)

    Modine, N. A.; Wright, A. F.; Lee, S. R.

    The rate of defect-induced carrier recombination is determined by both defect levels and carrier capture cross-sections. Density functional theory (DFT) has been widely and successfully used to predict defect levels, but only recently has work begun to focus on using DFT to determine carrier capture cross-sections. Lang and Henry developed the theory of carrier-capture by multiphonon emission in the 1970s and showed that carrier-capture cross-sections differ between defects primarily due to differences in their carrier capture activation energies. We present an approach to using DFT to calculate carrier capture activation energies that does not depend on an assumed configuration coordinate and that fully accounts for anharmonic effects, which can substantially modify carrier activation energies. We demonstrate our approach for intrinisic defects in GaAs and GaN and discuss how our results depend on the choice of exchange-correlation functional and the treatment of spin polarization. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  6. Semi-empirical method for calculating the activation energies of the unimolecular thermal decomposition of vinyl ethers

    NASA Astrophysics Data System (ADS)

    Sargsyan, G. N.; Shakhrokh, B.; Harutyunyan, A. B.

    2015-02-01

    A semi-empirical method is proposed for calculating the activation energy of the unimolecular decomposition of complex compounds using the example of vinyl (ethyl, propyl, and butyl) ethers. The method is based on the concept of the formation of intramolecular hydrogen bonds and the possibility of calculating the energy of deformation of ether molecules upon activation, resulting in the potential surface of the transition state undergoing distortion and the transfer of a hydrogen atom from an alkyl group to a vinyl group. The energy of deformation is calculated using the Mathcad 2001i and MM2 computer programs.

  7. TI-73 Calculator Activities

    ERIC Educational Resources Information Center

    Phillips-Bey, Carol K.

    2004-01-01

    This article describes TI-73 calculator activities appropriate for middle school students. It was found that the use of the calculator allowed for higher-level thinking and a richer exploration of mathematical ideas by students. [Included with this article are "Dice Roll Worksheet" and "Transforming Tree Worksheet".] (Contains 9 figures.)

  8. Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.

    PubMed

    Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S

    2016-03-01

    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. PMID:26958888

  9. CALCULATING SEPARATE MAGNETIC FREE ENERGY ESTIMATES FOR ACTIVE REGIONS PRODUCING MULTIPLE FLARES: NOAA AR11158

    SciTech Connect

    Tarr, Lucas; Longcope, Dana; Millhouse, Margaret

    2013-06-10

    It is well known that photospheric flux emergence is an important process for stressing coronal fields and storing magnetic free energy, which may then be released during a flare. The Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) captured the entire emergence of NOAA AR 11158. This region emerged as two distinct bipoles, possibly connected underneath the photosphere, yet characterized by different photospheric field evolutions and fluxes. The combined active region complex produced 15 GOES C-class, two M-class, and the X2.2 Valentine's Day Flare during the four days after initial emergence on 2011 February 12. The M and X class flares are of particular interest because they are nonhomologous, involving different subregions of the active region. We use a Magnetic Charge Topology together with the Minimum Current Corona model of the coronal field to model field evolution of the complex. Combining this with observations of flare ribbons in the 1600 A channel of the Atmospheric Imaging Assembly on board SDO, we propose a minimization algorithm for estimating the amount of reconnected flux and resulting drop in magnetic free energy during a flare. For the M6.6, M2.2, and X2.2 flares, we find a flux exchange of 4.2 Multiplication-Sign 10{sup 20} Mx, 2.0 Multiplication-Sign 10{sup 20} Mx, and 21.0 Multiplication-Sign 10{sup 20} Mx, respectively, resulting in free energy drops of 3.89 Multiplication-Sign 10{sup 30} erg, 2.62 Multiplication-Sign 10{sup 30} erg, and 1.68 Multiplication-Sign 10{sup 32} erg.

  10. Activation Energy Calculations for the Portevin-Le Chatelier Effect in Nimonic 263 Superalloy

    NASA Astrophysics Data System (ADS)

    Han, G. M.; Tian, C. G.; Chu, Z. K.; Cui, C. Y.; Hu, Z. Q.; Sun, X. F.

    2015-10-01

    The Portevin-Le Chatelier (PLC) effect in the Nimonic 263 superalloy was investigated by tensile test in a wide temperature range, from room temperature to 1033 K (760 °C), and at strain rates between 0.1 and 4 × 10-4 s-1. Types A, B, and C serrations were observed depending upon the test temperatures and strain rates. The activation energy ( Q) for serrated flow was determined by employing various methodologies for T < 723 K (450 °C), where a normal PLC effect was observed. The value of Q was found to be independent of the method employed. The average Q value of 70 KJ/mol was found to be in agreement with that for diffusion of substitutional solutes such as Cr and Mo in a Ni matrix by pipe diffusion. At temperatures ranging from 723 K to 923 K (450 °C to 650 °C), type C serrations and an inverse PLC effect were noticed, which may be caused by unlocking process.

  11. Activation Energy Calculations for Formamide–TiO2 and Formamide–Pt Interactions in the Presence of Water

    PubMed Central

    Dushanov, E; Kholmurodov, Kh; Yasuoka, K

    2013-01-01

    Formamide contains the four elements (C, H, O, and N) most required for life and it is attractive as a potential prebiotic starting material for nucleobase synthesis. In the presence of catalysts (for example, TiO2) and with moderate heating, formamide can pass surface energy barriers, yielding a complete set of nucleic bases and acyclonucleosides, and favoring both phosphorylations and transphosphorylations necessary for life. In the reaction mechanism, interaction with water seems to be an essential factor for the formamide molecule to function. In this paper, a formamide–water solution on a TiO$_2$ (anatase) surface is simulated using the molecular dynamics method, and activation energy calculations are performed for the temperature range of T = 250 K to T = 400 K. A correlation is established between the diffusion and density profiles for the formamide and water molecules on an anatase surface. Also, the calculated activation energies of the formamide–water–anatase and formamide–water–platinum systems are compared. A comparative analysis is performed of the behavior of formamide–water and ethanol–water interaction on the same (anatase and platinum) surfaces. PMID:23802018

  12. Biogas - the calculable energy

    NASA Astrophysics Data System (ADS)

    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

  13. Activities: More Calculator Capers.

    ERIC Educational Resources Information Center

    Schmalz, Rosemary

    1983-01-01

    Provided is an activity designed to give grades 7-12 students opportunities to discover numerical patterns and to derive general conclusions from observing data. The activity focuses attention on patterns in products such as 33x34, 333x334, and 3333x3334. Three worksheets and answers are included. (JN)

  14. Density-functional calculations of prefactors and activation energies for H diffusion in BaZrO3

    NASA Astrophysics Data System (ADS)

    Sundell, Per G.; Björketun, Mårten E.; Wahnström, Göran

    2007-09-01

    Density-functional calculations are used to investigate hydrogen diffusion in the solid-state proton conductor BaZrO3 . Activation energies and prefactors for the rate of proton transfer and reorientation are evaluated for a defect-free region of this simple cubic perovskite-structured oxide. Both semiclassical over-barrier jumps and phonon-assisted tunneling transitions between sites are considered. It is found that the classical barriers for the elementary transfer and reorientation steps are both of the order of 0.2eV . The quantum-mechanical zero-point motion effects are found to be sizable, to effectively reduce the barrier heights, and to make the prefactors similar for the transfer and reorientation steps. The Flynn-Stoneham model [Phys. Rev. B 1, 3966 (1970)] of phonon-assisted tunneling yields an activation energy of around 0.2eV and a very small prefactor for proton transfer, whereas the corresponding adiabatic model gives a similar activation energy but a much larger prefactor. It is suggested that the effect of other defects such as dopants has to be included for a proper description of hydrogen diffusion in this material.

  15. The impact of pulsed irradiation upon neutron activation calculations for inertial and magnetic fusion energy power plants

    SciTech Connect

    Latkowski, J.F.; Sanz, J.; Vujic, J.L.

    1996-06-26

    Inertial fusion energy (IFE) and magnetic fusion energy (MFE) power plants will probably operate in a pulsed mode. The two different schemes, however, will have quite different time periods. Typical repetition rates for IFE power plants will be 1-5 Hz. MFE power plants will ramp up in current for about 1 hour, shut down for several minutes, and repeat the process. Traditionally, activation calculations for IFE and MFE power plants have assumed continuous operation and used either the ``steady state`` (SS) or ``equivalent steady state`` (ESS) approximations. It has been suggested recently that the SS and ESS methods may not yield accurate results for all radionuclides of interest. The present work expands that of Sisolak, et al. by applying their formulae to conditions which might be experienced in typical IFE and MFE power plants. In addition, complicated, multi-step reaction/decay chains are analyzed using an upgraded version of the ACAB radionuclide generation/depletion code. Our results indicate that the SS method is suitable for application to MFE power plant conditions. We also find that the ESS method generates acceptable results for radionuclides with half-lives more than a factor of three greater than the time between pulses. For components that are subject to 0.05 Hz (or more frequent) irradiation (such as coolant), use of the ESS method is recommended. For components or materials that are subject to less frequent irradiation (such as high-Z target materials), pulsed irradiation calculations should be used.

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

    PubMed

    Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris

    2016-01-01

    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. PMID:27092480

  17. Neutron and deuteron activation calculations for IFMIF

    NASA Astrophysics Data System (ADS)

    Forrest, R. A.; Loughlin, M. J.

    2007-08-01

    The materials for future fusion devices such as DEMO require testing to high neutron fluence. Such testing is planned to be carried out in IFMIF, an accelerator based facility where the neutrons will have maximum energy of about 55 MeV, but with a broad peak near 14 MeV. In order that activation calculations for IFMIF can be carried out, the nuclear data must contain cross sections covering a similar energy range. A description of the EASY-2005 system is given and it is noted that a new library has been added to EASY to cover another significant source of activation from deuteron-induced reactions. Calculations of the neutron activation of materials in many regions of IFMIF have been carried out. These calculations are reported, and the contribution of neutrons above 20 MeV to the activation is discussed. Preliminary calculations using the deuteron library have been made and the activation from deuterons is discussed.

  18. Calculation of activation energies for transport and recombination in mesoporous TiO2/dye/electrolyte films--taking into account surface charge shifts with temperature.

    PubMed

    O'Regan, Brian C; Durrant, James R

    2006-05-01

    Transient photovoltage and photocurrent measurements have been employed to determine the recombination and transport kinetics in operating dye-sensitized photovoltaic cells as a function of potential and temperature. Photocurrent transients have been taken at the open circuit potential, as opposed to the standard measurement at short circuit. Kinetic results have been used to calculate the activation energy as function of the Fermi level position in the TiO(2). In the calculation of activation energies, we have explicitly taken into account the temperature dependence of the offset between the electrolyte redox potential and the conduction band edge. This new method gives activation energies that decrease linearly as the Fermi level position moves toward the conduction band edge, as expected, but not found in previous studies. The results are consistent with the presence of a distribution of traps below the TiO(2) conduction band, the detrapping from which limits both the transport and the recombination of electrons. PMID:16640403

  19. Light Pipe Energy Savings Calculator

    NASA Astrophysics Data System (ADS)

    Owens, Erin; Behringer, Ernest R.

    2009-04-01

    Dependence on fossil fuels is unsustainable and therefore a shift to renewable energy sources such as sunlight is required. Light pipes provide a way to utilize sunlight for interior lighting, and can reduce the need for fossil fuel-generated electrical energy. Because consumers considering light pipe installation may be more strongly motivated by cost considerations than by sustainability arguments, an easy means to examine the corresponding costs and benefits is needed to facilitate informed decision-making. The purpose of this American Physical Society Physics and Society Fellowship project is to create a Web-based calculator to allow users to quantify the possible cost savings for their specific light pipe application. Initial calculations show that the illumination provided by light pipes can replace electric light use during the day, and in many cases can supply greater illumination levels than those typically given by electric lighting. While the installation cost of a light pipe is significantly greater than the avoided cost of electricity over the lifetime of the light pipe at current prices, savings may be realized if electricity prices increase.

  20. ACTIVE: a program to calculate and plot reaction rates from ANISN calculated fluxes

    SciTech Connect

    Judd, J.L.

    1981-12-01

    The ACTIVE code calculates spatial heating rates, tritium production rates, neutron reaction rates, and energy spectra from particle fluxes calculated by ANISN. ACTIVE has a variety of input options including the capability to plot all calculated spatial distributions. The code was primarily designed for use with fusion first wall/blanket systems, but could be applied to any one-dimensional problem.

  1. Benchmark test of neutron transport calculations: indium, nickel, gold, europium, and cobalt activation with and without energy moderated fission neutrons by iron simulating the Hiroshima atomic bomb casing.

    PubMed

    Iwatani, K; Hoshi, M; Shizuma, K; Hiraoka, M; Hayakawa, N; Oka, T; Hasai, H

    1994-10-01

    A benchmark test of the Monte Carlo neutron and photon transport code system (MCNP) was performed using a bare- and energy-moderated 252Cf fission neutron source which was obtained by transmission through 10-cm-thick iron. An iron plate was used to simulate the effect of the Hiroshima atomic bomb casing. This test includes the activation of indium and nickel for fast neutrons and gold, europium, and cobalt for thermal and epithermal neutrons, which were inserted in the moderators. The latter two activations are also to validate 152Eu and 60Co activity data obtained from the atomic bomb-exposed specimens collected at Hiroshima and Nagasaki, Japan. The neutron moderators used were Lucite and Nylon 6 and the total thickness of each moderator was 60 cm or 65 cm. Measured activity data (reaction yield) of the neutron-irradiated detectors in these moderators decreased to about 1/1,000th or 1/10,000th, which corresponds to about 1,500 m ground distance from the hypocenter in Hiroshima. For all of the indium, nickel, and gold activity data, the measured and calculated values agreed within 25%, and the corresponding values for europium and cobalt were within 40%. From this study, the MCNP code was found to be accurate enough for the bare- and energy-moderated 252Cf neutron activation calculations of these elements using moderators containing hydrogen, carbon, nitrogen, and oxygen. PMID:8083048

  2. Benchmark test of neutron transport calculations: Indium, nickel, gold, europium, and cobalt activation with and without energy moderated fission neutrons by iron simulating the Hiroshima atomic bomb casing

    SciTech Connect

    Iwatani, Kazuo; Shizuma, Kiyoshi; Hasai, Hiromi; Hoshi, Masaharu; Hiraoka, Masayuki; Hayakawa, Norihiko; Oka, Takamitsu

    1994-10-01

    A benchmark test of the Monte Carlo neutron and photon transport code system (MCNP) was performed using a bare- and energy-moderated {sup 252}Cf fission neutron source which was obtained by transmission through 10-cm-thick iron. An iron plate was used to simulate the effect of the Hiroshima atomic bomb casing. This test includes the activation of indium and nickel for fast neutrons and gold, europium, and cobalt for thermal and epithermal neutrons, which were inserted in the moderators. The latter two activations are also to validate {sup 152}Eu and {sup 60}Co activity data obtained from the atomic bomb-exposed specimens collected at Hiroshima and Nagasaki, Japan. The neutron moderators used were Lucite and Nylon 6 and the total thickness of each moderator was 60 cm or 65 cm. Measured activity data (reaction yield) of the neutron-irradiated detectors in these moderators decreased to about 1/1,000th or 1/10,000th, which corresponds to about 1,500 m ground distance from the hypocenter in Hiroshima. For all of the indium, nickel, and gold activity data, the measured and calculated values agreed within 25%, and the corresponding values for europium and cobalt were within 40%. From this study, the MCNP code was found to be accurate enough for the bare- and energy-moderated {sup 252}Cf neutron activation calculations of these elements using moderators containing hydrogen, carbon, nitrogen, and oxygen. 18 refs., 10 figs., 4 tabs.

  3. Calculation of water activation for the LHC

    NASA Astrophysics Data System (ADS)

    Vollaire, Joachim; Brugger, Markus; Forkel-Wirth, Doris; Roesler, Stefan; Vojtyla, Pavol

    2006-06-01

    The management of activated water in the Large Hadron Collider (LHC) at CERN is a key concern for radiation protection. For this reason, the induced radioactivity of the different water circuits is calculated using the Monte-Carlo (MC) code FLUKA. The results lead to the definition of procedures to be taken into account during the repair and maintenance of the machine, as well as to measures being necessary for a release of water into the environment. In order to assess the validity of the applied methods, a benchmark experiment was carried out at the CERN-EU High Energy Reference Field (CERF) facility, where a hadron beam (120 GeV) is impinging on a copper target. Four samples of water, as used at the LHC, and different in their chemical compositions, were irradiated near the copper target. In addition to the tritium activity measured with a liquid scintillation counter, the samples were also analyzed using gamma spectroscopy in order to determine the activity of the gamma emitting isotopes such as Be7 and Na24. While for the latter an excellent agreement between simulation and measurement was found, for the calculation of tritium a correction factor is derived to be applied for future LHC calculations in which the activity is calculated by direct scoring of produced nuclei. A simplified geometry representing the LHC Arc sections is then used to evaluate the different calculation methods with FLUKA. By comparing these methods and by taking into account the benchmark results, a strategy for the environmental calculations can be defined.

  4. Why does the G117H mutation considerably improve the activity of human butyrylcholinesterase against sarin? Insights from quantum mechanical/molecular mechanical free energy calculations.

    PubMed

    Yao, Yuan; Liu, Junjun; Zhan, Chang-Guo

    2012-11-01

    Human butyrylcholinesterase (BChE) is recognized as the most promising bioscavenger for organophosphorus (OP) warfare nerve agents. The G117H mutant of human BChE has been identified as a potential catalytic bioscavenger with a remarkably improved activity against OP nerve agents such as sarin, but it still does not satisfy the clinical use. For further design of the higher-activity mutants against OP nerve agents, it is essential to understand how the G117H mutation improves the activity. The reaction mechanisms and the free energy profiles for spontaneous reactivation of wild-type BChE and its G117H mutant phosphorylated by sarin have been explored, in this study, by performing first-principles quantum mechanical/molecular mechanical free energy calculations, and the remarkable role of the G117H mutation on the activity has been elucidated. For both the wild-type and G117H mutant enzymes, H438 acts as a general base to initiate the spontaneous reactivation that consists of two reaction steps: the nucleophilic attack at the phosphorus by a water molecule and decomposition of the pentacoordinated phosphorus intermediate. The calculated overall free energy barriers, i.e., 30.2 and 23.9 kcal/mol for the wild type and G117H mutant, respectively, are in good agreement with available experimental kinetic data. On the basis of the calculated results, the mutated residue (H117 in the G117H mutant) cannot initiate the spontaneous reactivation as a general base. Instead, it skews the oxyanion hole and makes the phosphorus more open to the nucleophilic water molecule, resulting in a remarkable change in the rate-determining step and significantly improved catalytic activity of human BChE. PMID:23092211

  5. Mathematical Creative Activity and the Graphic Calculator

    ERIC Educational Resources Information Center

    Duda, Janina

    2011-01-01

    Teaching mathematics using graphic calculators has been an issue of didactic discussions for years. Finding ways in which graphic calculators can enrich the development process of creative activity in mathematically gifted students between the ages of 16-17 is the focus of this article. Research was conducted using graphic calculators with…

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

    PubMed Central

    Niu, Yuzhen; Pan, Dabo; Shi, Danfeng; Bai, Qifeng; Liu, Huanxiang; Yao, Xiaojun

    2015-01-01

    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. PMID:26677850

  7. Activity-composition relations in the system CaCO 3-MgCO 3 predicted from static structure energy calculations and Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Vinograd, Victor L.; Burton, Benjamin P.; Gale, Julian D.; Allan, Neil L.; Winkler, Björn

    2007-02-01

    Thermodynamic mixing properties and subsolidus phase relations of the rhombohedral carbonate system, (1 - x) · CaCO 3 - x · MgCO 3, were modelled in the temperature range of 623-2023 K with static structure energy calculations based on well-parameterised empirical interatomic potentials. Relaxed static structure energies of a large set of randomly varied structures in a 4 × 4 × 1 supercell of R3¯c calcite ( a = 19.952 Å, c = 17.061 Å) were calculated with the General Utility Lattice Program (GULP). These energies were cluster expanded in a basis set of 12 pair-wise effective interactions. Temperature-dependent enthalpies of mixing were calculated by the Monte Carlo method. Free energies of mixing were obtained by thermodynamic integration of the Monte Carlo results. The calculated phase diagram is in good agreement with experimental phase boundaries.

  8. Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations.

    PubMed

    Hladilkova, Jana; Prokop, Zbynek; Chaloupkova, Radka; Damborsky, Jiri; Jungwirth, Pavel

    2013-11-21

    Release of halide ions is an essential step of the catalytic cycle of haloalkane dehalogenases. Here we describe experimentally and computationally the process of release of a halide anion from the buried active site of the haloalkane dehalogenase LinB. Using stopped-flow fluorescence analysis and umbrella sampling free energy calculations, we show that the anion binding is ion-specific and follows the ordering I(-) > Br(-) > Cl(-). We also address the issue of the protonation state of the catalytic His272 residue and its effect on the process of halide release. While deprotonation of His272 increases binding of anions in the access tunnel, we show that the anionic ordering does not change with the switch of the protonation state. We also demonstrate that a sodium cation could relatively easily enter the active site, provided the His272 residue is singly protonated, and replace thus the missing proton. In contrast, Na(+) is strongly repelled from the active site containing the doubly protonated His272 residue. Our study contributes toward understanding of the reaction mechanism of haloalkane dehalogenase enzyme family. Determination of the protonation state of the catalytic histidine throughout the catalytic cycle remains a challenge for future studies. PMID:24151979

  9. Good Practices in Free-energy Calculations

    NASA Technical Reports Server (NTRS)

    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.

  10. Calculating Free Energies Using Average Force

    NASA Technical Reports Server (NTRS)

    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.

  11. Activation Energy

    NASA Technical Reports Server (NTRS)

    Gadeken, Owen

    2002-01-01

    Teaming is so common in today's project management environment that most of us assume it comes naturally. We further assume that when presented with meaningful and challenging work, project teams will naturally engage in productive activity to complete their tasks. This assumption is expressed in the simple (but false) equation: Team + Work = Teamwork. Although this equation appears simple and straightforward, it is far from true for most project organizations whose reality is a complex web of institutional norms based on individual achievement and rewards. This is illustrated by the very first successful team experience from my early Air Force career. As a young lieutenant, I was sent to Squadron Officer School, which was the first in the series of Air Force professional military education courses I was required to complete during my career. We were immediately formed into teams of twelve officers. Much of the course featured competition between these teams. As the most junior member of my team, I quickly observed the tremendous pressure to show individual leadership capability. At one point early in the course, almost everyone in our group was vying to become the team leader. This conflict was so intense that it caused us to fail miserably in our first outdoor team building exercise. We spent so much time fighting over leadership that we were unable to complete any of the events on the outdoor obstacle course. This complete lack of success was so disheartening to me that I gave our team little hope for future success. What followed was a very intense period of bickering, conflict, and even shouting matches as our dysfunctional team tried to cope with our early failures and find some way to succeed. British physician and researcher Wilfred Bion (Experiences in Groups, 1961) discovered that there are powerful psychological forces inherent in all groups that divert from accomplishing their primary tasks. To overcome these restraining forces and use the potential

  12. Predicting proteinase specificities from free energy calculations.

    PubMed

    Mekonnen, Seble Merid; Olufsen, Magne; Smalås, Arne O; Brandsdal, Bjørn O

    2006-10-01

    The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96). PMID:16386933

  13. Hermes III endpoint energy calculation from photonuclear activation of 197Au and 58Ni foils

    SciTech Connect

    Parzyck, Christopher Thomas

    2014-09-01

    A new process has been developed to characterize the endpoint energy of HERMES III on a shot-to-shot basis using standard dosimetry tools from the Sandia Radiation Measurements Laboratory. Photonuclear activation readings from nickel and gold foils are used in conjunction with calcium fluoride thermoluminescent dosimeters to derive estimated electron endpoint energies for a series of HERMES shots. The results are reasonably consistent with the expected endpoint voltages on those shots.

  14. Bond-Energy and Surface-Energy Calculations in Metals

    ERIC Educational Resources Information Center

    Eberhart, James G.; Horner, Steve

    2010-01-01

    A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…

  15. Zero energy scattering calculation in Euclidean space

    NASA Astrophysics Data System (ADS)

    Carbonell, J.; Karmanov, V. A.

    2016-03-01

    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.

  16. Free-Energy Calculations. A Mathematical Perspective

    NASA Technical Reports Server (NTRS)

    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.

  17. Ultrasonic energy in liposome production: process modelling and size calculation.

    PubMed

    Barba, A A; Bochicchio, S; Lamberti, G; Dalmoro, A

    2014-04-21

    The use of liposomes in several fields of biotechnology, as well as in pharmaceutical and food sciences is continuously increasing. Liposomes can be used as carriers for drugs and other active molecules. Among other characteristics, one of the main features relevant to their target applications is the liposome size. The size of liposomes, which is determined during the production process, decreases due to the addition of energy. The energy is used to break the lipid bilayer into smaller pieces, then these pieces close themselves in spherical structures. In this work, the mechanisms of rupture of the lipid bilayer and the formation of spheres were modelled, accounting for how the energy, supplied by ultrasonic radiation, is stored within the layers, as the elastic energy due to the curvature and as the tension energy due to the edge, and to account for the kinetics of the bending phenomenon. An algorithm to solve the model equations was designed and the relative calculation code was written. A dedicated preparation protocol, which involves active periods during which the energy is supplied and passive periods during which the energy supply is set to zero, was defined and applied. The model predictions compare well with the experimental results, by using the energy supply rate and the time constant as fitting parameters. Working with liposomes of different sizes as the starting point of the experiments, the key parameter is the ratio between the energy supply rate and the initial surface area. PMID:24647821

  18. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... FEDERAL POWER ACT Charges for Headwater Benefits § 11.13 Energy gains calculations. (a) Energy gains at a... not complex or in which headwater benefits are expected to be small, calculations will be made...

  19. A Programmable Calculator Activity, x = 1/x + 1.

    ERIC Educational Resources Information Center

    Snover, Stephen L.; Spikell, Mark A.

    An activity for secondary schools is presented and discussed which may be explored with a programmable calculator. The activity is non-standard and could not be easily explored without the use of a programmable calculator. Related activities are also discussed. Flow charts and programs for different programmable calculators are presented. (MP)

  20. Energy Band Calculations for Maximally Even Superlattices

    NASA Astrophysics Data System (ADS)

    Krantz, Richard; Byrd, Jason

    2007-03-01

    Superlattices are multiple-well, semiconductor heterostructures that can be described by one-dimensional potential wells separated by potential barriers. We refer to a distribution of wells and barriers based on the theory of maximally even sets as a maximally even superlattice. The prototypical example of a maximally even set is the distribution of white and black keys on a piano keyboard. Black keys may represent wells and the white keys represent barriers. As the number of wells and barriers increase, efficient and stable methods of calculation are necessary to study these structures. We have implemented a finite-element method using the discrete variable representation (FE-DVR) to calculate E versus k for these superlattices. Use of the FE-DVR method greatly reduces the amount of calculation necessary for the eigenvalue problem.

  1. Groundwater activation calculations for E872

    SciTech Connect

    Freeman, W.S.; E872 Collaboration

    1995-08-01

    The E872 beam dump geometry has been modeled in CASIM and calculations have been done to determine the annual limits for protons n target. Results are presented using both the single resident well model (SRWM) and the newly-approved concentration model (CM). The conclusion is that the target/dump design is adequate for the maximum number of protons on target requested by the experiment, which is >1 {times} 10{sup 18} protons per year at 800 GeV.

  2. Low-energy calculations for nuclear photodisintegration

    NASA Astrophysics Data System (ADS)

    Deflorian, S.; Efros, V. D.; Leidemann, W.

    2016-03-01

    In the Standard Solar Model a central role in the nucleosynthesis is played by reactions of the kind {}{Z_1}{A_1}{X_1} + {}{Z_2}{A_2}{X_2} to {}{Z_1 + {Z_2}}{A_1 + {A_2}}Y + γ , 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.

  3. Calculation of molecular free energies in classical potentials

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2016-02-01

    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.

  4. Calculation of energy deposition distributions for simple geometries

    NASA Technical Reports Server (NTRS)

    Watts, J. W., Jr.

    1973-01-01

    When high-energy charged particles pass through a thin detector, the ionization energy loss in that detector is subject to fluctuations or straggling which must be considered in interpreting the data. Under many conditions, which depend upon the charge and energy of the incident particle and the detector geometry, the ionization energy lost by the particle is significantly different from the energy deposited in the detector. This problem divides naturally into a calculation of the energy loss that results in excitation and low-energy secondary electrons which do not travel far from their production points, and a calculation of energy loss that results in high-energy secondary electrons which can escape from the detector. The first calculation is performed using a modification of the Vavilov energy loss distribution. A cutoff energy is introduced above which all electrons are ignored and energy transferred to low energy particles is assumed to be equivalent to the energy deposited by them. For the second calculation, the trajectory of the primary particle is considered as a source of secondary high-energy electrons. The electrons from this source are transported using Monte Carlo techniques and multiple scattering theory, and the energy deposited by them in the detector is calculated. The results of the two calculations are then combined to predict the energy deposition distribution. The results of these calculations are used to predict the charge resolution of parallel-plate pulse ionization chambers that are being designed to measure the charge spectrum of heavy nuclei in the galactic cosmic-ray flux.

  5. Energy assessment: physical activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Physical activity is an important component of total energy expenditure, contributing to energy intake needs; it also provides certain health benefits. This review chapter provides state-of-the-art information to researchers and clinicians who are interested in developing research studies or interv...

  6. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer

    NASA Astrophysics Data System (ADS)

    Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.

    2015-08-01

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm-1, only slightly below the 935 cm-1 value derived from experiment.

  7. Guidelines for the analysis of free energy calculations.

    PubMed

    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. PMID:25808134

  8. Guidelines for the analysis of free energy calculations

    PubMed Central

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

    2015-01-01

    Free energy calculations based on molecular dynamics (MD) 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 at https://github.com/choderalab/pymbar–examples, 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 these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134

  9. Spectroscopically Accurate Calculations of the Rovibrational Energies of Diatomic Hydrogen

    NASA Astrophysics Data System (ADS)

    Perry, Jason

    2005-05-01

    The Born-Oppenheimer approximation has been used to calculate the rotational and vibrational states of diatomic hydrogen. Because it is an approximation, our group now wants to use a Born-Oppenheimer potential to calculate the electronic energy that has been corrected to match closely with spectroscopic results. We are using a code that has corrections for adiabatic, relativistic, radiative, and non-adiabatic effects. The rovibrational energies have now been calculated for both bound and quasi-bound states. We also want to compute quadrupole transition probabilities for diatomic hydrogen. These calculations aspire to investigate diatomic hydrogen in astrophysical environments.

  10. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  11. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  12. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  13. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  14. WAPA Daily Energy Accounting Activities

    1990-10-01

    ISA (Interchange, Scheduling, & Accounting) is the interchange scheduling system used by the DOE Western Area Power Administration to perform energy accounting functions associated with the daily activities of the Watertown Operations Office (WOO). The system's primary role is to provide accounting functions for scheduled energy which is exchanged with other power companies and power operating organizations. The system has a secondary role of providing a historical record of all scheduled interchange transactions. The followingmore » major functions are performed by ISA: scheduled energy accounting for received and delivered energy; generation scheduling accounting for both fossil and hydro-electric power plants; metered energy accounting for received and delivered totals; energy accounting for Direct Current (D.C.) Ties; regulation accounting; automatic generation control set calculations; accounting summaries for Basin, Heartland Consumers Power District, and the Missouri Basin Municipal Power Agency; calculation of estimated generation for the Laramie River Station plant; daily and monthly reports; and dual control areas.« less

  15. Science Activities in Energy: Chemical Energy.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Presented is a science activities in energy package which includes 15 activities relating to chemical energy. Activities are simple, concrete experiments for fourth, fifth and sixth grades which illustrate principles and problems relating to energy. Each activity is outlined on a single card which is introduced by a question. A teacher's…

  16. Science Activities in Energy: Electrical Energy.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Presented is a science activities in energy package which includes 16 activities relating to electrical energy. Activities are simple, concrete experiments for fourth, fifth and sixth grades which illustrate principles and problems relating to energy. Each activity is outlined in a single card which is introduced by a question. A teacher's…

  17. Science Activities in Energy: Solar Energy.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Presented is a science activities in energy package which includes 12 activities relating to solar energy. Activities are simple, concrete experiments for fourth, fifth, and sixth grades, which illustrate principles and problems relating to energy. Each activity is outlined on a single card which is introduced by a question. A teacher's supplement…

  18. New approach to calculating the potential energy of colliding nuclei

    SciTech Connect

    Kurmanov, R. S.; Kosenko, G. I.

    2014-12-15

    The differential method proposed by the present authors earlier for the reduction of volume integrals in calculating the potential energy of a compound nucleus is generalized to the case of two interacting nuclei. The Coulomb interaction energy is obtained for the cases of a sharp and a diffuse boundary of nuclei, while the nuclear interaction energy is found only for nuclei with a sharp boundary, the finiteness of the nuclear-force range being taken into account. The present method of calculations permits reducing the time it takes to compute the potential energy at least by two orders of magnitude.

  19. Calculation of Rydberg energy levels for the francium atom

    NASA Astrophysics Data System (ADS)

    Huang, Shi-Zhong; Chu, Jin-Min

    2010-06-01

    Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of the np2Po1/2 (n = 7-50) and np2Po3/2 (n = 7-50) spectrum series for the francium atom are calculated. The calculated results are in excellent agreement with the 48 measured levels, and 40 energy levels for highly excited states are predicted.

  20. Protein thermostability calculations using alchemical free energy simulations.

    PubMed

    Seeliger, Daniel; de Groot, Bert L

    2010-05-19

    Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design. PMID:20483340

  1. Changing Conceptions of Activation Energy.

    ERIC Educational Resources Information Center

    Pacey, Philip D.

    1981-01-01

    Provides background material which relates to the concept of activation energy, fundamental in the study of chemical kinetics. Compares the related concepts of the Arrhenius activation energy, the activation energy at absolute zero, the enthalpy of activation, and the threshold energy. (CS)

  2. Is ring breaking feasible in relative binding free energy calculations?

    PubMed

    Liu, Shuai; Wang, Lingle; Mobley, David L

    2015-04-27

    Our interest is relative binding free energy (RBFE) calculations based on molecular simulations. These are promising tools for lead optimization in drug discovery, computing changes in binding free energy due to modifications of a lead compound. However, in the "alchemical" framework for RBFE calculations, some types of mutations have the potential to introduce error into the computed binding free energies. Here we explore the magnitude of this error in several different model binding calculations. We find that some of the calculations involving ring breaking have significant errors, and these errors are especially large in bridged ring systems. Since the error is a function of ligand strain, which is unpredictable in advance, we believe that ring breaking should be avoided when possible. PMID:25835054

  3. Free energy calculations for molecular solids using GROMACS

    NASA Astrophysics Data System (ADS)

    Aragones, J. L.; Noya, E. G.; Valeriani, C.; Vega, C.

    2013-07-01

    In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

  4. 3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.

    PubMed

    Sergiievskyi, Volodymyr P; Fedorov, Maxim V

    2012-06-12

    In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarking of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good

  5. S-matrix calculations of energy levels of alkalilike ions

    NASA Astrophysics Data System (ADS)

    Sapirstein, Jonathan; Cheng, K. T.

    2013-05-01

    A recent S-matrix based QED calculation of energy levels of the lithium isoelectronic sequence is extended to the general case of a valence electron outside an arbitrary filled core. Formulas are presented that allow calculation of the energy levels of valence ns , np1 / 2 , np3 / 2 , nd3 / 2 , and nd5 / 2 states. Emphasis is placed on modifications of the lithiumlike formulas required because more than one core state is present, and a discussion of an unusual feature of the two-photon exchange contribution involving autoiononizing states is given. The method is illustrated with a calculation of energy levels of the sodium isoelectronic sequence, with results for 3s1 / 2 , 3p1 / 2 , and 3p3 / 2 energies tabulated for the range Z = 20 - 100 . A detailed breakdown of the calculation is given for Z = 74 . Comparison with experiment and other calculations is given, and prospects for extension of the method to ions with more complex electronic structure discussed. The work of JS was supported in part by NSF Grant No. PHY-1068065. The work of KTC was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Calculating fusion neutron energy spectra from arbitrary reactant distributions

    NASA Astrophysics Data System (ADS)

    Eriksson, J.; Conroy, S.; Andersson Sundén, E.; Hellesen, C.

    2016-02-01

    The Directional Relativistic Spectrum Simulator (DRESS) code can perform Monte-Carlo calculations of reaction product spectra from arbitrary reactant distributions, using fully relativistic kinematics. The code is set up to calculate energy spectra from neutrons and alpha particles produced in the D(d, n)3He and T(d, n)4He fusion reactions, but any two-body reaction can be simulated by including the corresponding cross section. The code has been thoroughly tested. The kinematics calculations have been benchmarked against the kinematics module of the ROOT Data Analysis Framework. Calculated neutron energy spectra have been validated against tabulated fusion reactivities and against an exact analytical expression for the thermonuclear fusion neutron spectrum, with good agreement. The DRESS code will be used as the core of a detailed synthetic diagnostic framework for neutron measurements at the JET and MAST tokamaks.

  8. Energy Adventure Center. Activity Book.

    ERIC Educational Resources Information Center

    Carlton, Linda L.

    Energy activities are provided in this student activity book. They include: (1) an energy walk; (2) forms of energy in the home; (3) energy conversion; (4) constructing a solar hot dog cooker (with instructions for drawing a parabola); (5) interviewing senior citizens to learn about energy use in the past; (6) packaging materials; (7) insulation;…

  9. Activities Handbook for Energy Education.

    ERIC Educational Resources Information Center

    DeVito, Alfred; Krockover, Gerald H.

    The purpose of this handbook is to present information about energy and to translate this information into learning activities for children. Chapter 1, "Energy: A Delicate Dilemma," presents activities intended to provide an introduction to energy and energy usage. Chapter 2, "What are the Sources of Energy?" provides background information and…

  10. Science Activities in Energy: Conservation.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Presented is a science activities in energy package which includes 14 activities relating to energy conservation. Activities are simple, concrete experiments for fourth, fifth and sixth grades, which illustrate principles and problems relating to energy. Each activity is outlined on a simple card which is introduced by a question. A teacher's…

  11. Lead Optimization Mapper: Automating free energy calculations for lead optimization

    PubMed Central

    Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P.; Summa, Christopher M.; Jaber, Vivian R.; Lim, Nathan M.; Mobley, David L.

    2013-01-01

    Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce Lead Optimization Mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license. PMID:24072356

  12. Calculated viscosity-distance dependence for some actively flowing lavas

    NASA Technical Reports Server (NTRS)

    Pieri, David

    1987-01-01

    The importance of viscosity as a gauge of the various energy and momentum dissipation regimes of lava flows has been realized for a long time. Nevertheless, despite its central role in lava dynamics and kinematics, it remains among the most difficult of flow physical properties to measure in situ during an eruption. Attempts at reconstructing the actual emplacement viscosities of lava flows from their solidified topographic form are difficult. Where data are available on the position of an advancing flow front as a function of time, it is possible to calculate the effective viscosity of the front as a function of distance from the vent, under the assumptions of a steady state regime. As an application and test of an equation given, relevant parameters from five recent flows on Mauna Loa and Kilauea were utilized to infer the dynamic structure of their aggregate flow front viscosity as they advanced, up to cessation. The observed form of the viscosity-distance relation for the five active Hawaiian flows examined appears to be exponential, with a rapid increase just before the flows stopped as one would expect.

  13. Total-energy and pressure calculations for random substitutional alloys

    SciTech Connect

    Johnson, D.D. ); Nicholson, D.M. ); Pinski, F.J. ); Gyoerffy, B.L. ); Stocks, G.M. )

    1990-05-15

    We present the details and the derivation of density-functional-based expressions for the total energy and pressure for random substitutional alloys (RSA) using the Korringa-Kohn-Rostoker Green's-function approach in combination with the coherent-potential approximation (CPA) to treat the configurational averaging. This includes algebraic cancellation of various electronic core contributions to the total energy and pressure, as in ordered-solid muffin-tin-potential calculations. Thus, within the CPA, total-energy and pressure calculations for RSA have the same foundation and have been found to have the same accuracy as those obtained in similar calculations for ordered solids. Results of our calculations for the impurity formation energy, and for the bulk moduli, the lattice parameters, and the energy of mixing as a function of concentration in fcc Cu{sub {ital c}}Zn{sub 1{minus}{ital c}} alloys show that this generalized density-functional theory will be useful in studying alloy phase stability.

  14. Magnetic field calculation and measurement of active magnetic bearings

    NASA Astrophysics Data System (ADS)

    Ding, Guoping; Zhou, Zude; Hu, Yefa

    2006-11-01

    Magnetic Bearings are typical devices in which electric energy and mechanical energy convert mutually. Magnetic Field indicates the relationship between 2 of the most important parameters in a magnetic bearing - current and force. This paper presents calculation and measurement of the magnetic field distribution of a self-designed magnetic bearing. Firstly, the static Maxwell's equations of the magnetic bearing are presented and a Finite Element Analysis (FEA) is found to solve the equations and get post-process results by means of ANSYS software. Secondly, to confirm the calculation results a Lakeshore460 3-channel Gaussmeter is used to measure the magnetic flux density of the magnetic bearing in X, Y, Z directions accurately. According to the measurement data the author constructs a 3D magnetic field distribution digital model by means of MATLAB software. Thirdly, the calculation results and the measurement data are compared and analyzed; the comparing result indicates that the calculation results are consistent with the measurement data in allowable dimension variation, which means that the FEA calculation method of the magnetic bearing has high precision. Finally, it is concluded that the magnetic field calculation and measurement can accurately reflect the real magnetic distribution in the magnetic bearing and the result can guide the design and analysis of the magnetic bearing effectively.

  15. Ion beam energy spectrum calculation via dosimetry data deconvolution.

    SciTech Connect

    Harper-Slaboszewicz, Victor Jozef; Sharp, Andrew Clinton

    2010-10-01

    The energy spectrum of a H{sup +} beam generated within the HERMES III accelerator is calculated from dosimetry data to refine future experiments. Multiple layers of radiochromic film are exposed to the beam. A graphic user interface was written in MATLAB to align the film images and calculate the beam's dose depth profile. Singular value regularization is used to stabilize the unfolding and provide the H{sup +} beam's energy spectrum. The beam was found to have major contributions from 1 MeV and 8.5 MeV protons. The HERMES III accelerator is typically used as a pulsed photon source to experimentally obtain photon impulse response of systems due to high energy photons. A series of experiments were performed to explore the use of Hermes III to generate an intense pulsed proton beam. Knowing the beam energy spectrum allows for greater precision in experiment predictions and beam model verification.

  16. Calculation of exchange energies using algebraic perturbation theory

    SciTech Connect

    Burrows, B. L.; Dalgarno, A.; Cohen, M.

    2010-04-15

    An algebraic perturbation theory is presented for efficient calculations of localized states and hence of exchange energies, which are the differences between low-lying states of the valence electron of a molecule, formed by the collision of an ion Y{sup +} with an atom X. For the case of a homonuclear molecule these are the gerade and ungerade states and the exchange energy is an exponentially decreasing function of the internuclear distance. For such homonuclear systems the theory is used in conjunction with the Herring-Holstein technique to give accurate exchange energies for a range of intermolecular separations R. Since the perturbation parameter is essentially 1/R, this method is suitable for large R. In particular, exchange energies are calculated for X{sub 2}{sup +} systems, where X is H, Li, Na, K, Rb, or Cs.

  17. Science Activities in Energy: Wind Energy.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Included in this science activities energy package are 12 activities related to wind energy for elementary students. Each activity is outlined on a single card and is introduced by a question. Topics include: (1) At what time of day is there enough wind to make electricity where you live?; (2) Where is the windiest spot on your schoolground?; and…

  18. On the calculation of classical vibrational energy exchange

    NASA Astrophysics Data System (ADS)

    Gibbons, John P.; Stettler, John D.

    1982-07-01

    A three-dimensional, Monte Carlo classical model for the calculation of vibrational energy relaxation and transfer rates for both diatomic—monatomic and diatomic—diatomic systems was developed, analyzed and implemented. Mediation by internal angular momentum changes was demonstrated to be important in these energy transfer processes. This mechanism was incorporated into the model in order to achieve statistically significant results within reasonable computer running times. This made possible the extension of the model calculations to much lower temperatures than had been previously investigated. This calculational procedure was applied to Ar—O 2, to He—O 2 and to the near resonant CO—N 2 process at several temperatures between room temperature and 4000 K with the use of exponential repulsive intermolecular potential. Three different sets of potential parameters obtained from three independent sources were used. The results were compared to experiment.

  19. The Calculation of Accurate Metal-Ligand Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)

    1997-01-01

    The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.

  20. Accurate calculation of diffraction-limited encircled and ensquared energy.

    PubMed

    Andersen, Torben B

    2015-09-01

    Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873

  1. Calculation of Mg(+)-ligand relative binding energies

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.

    1992-01-01

    The calculated relative binding energies of 16 organic molecules to Mg(+) are compared with experimental results where available. The geometries of the ligands and the Mg(+)-ligand complexes arc optimized at the self-consistent field level using a 6-31G* basis set. The Mg(+) binding energies are evaluated using second-order perturbation theory and basis sets of triple-sigma quality augmented with two sets of polarization functions. This level of theory is calibrated against higher levels of theory for selected systems. The computed binding energies are accurate to about 2 kcal/mol.

  2. TOSPAC calculations in support of the COVE 2A benchmarking activity; Yucca Mountain Site Characterization Project

    SciTech Connect

    Gauthier, J.H.; Zieman, N.B.; Miller, W.B.

    1991-10-01

    The purpose of the the Code Verification (COVE) 2A benchmarking activity is to assess the numerical accuracy of several computer programs for the Yucca Mountain Site Characterization Project of the Department of Energy. This paper presents a brief description of the computer program TOSPAC and a discussion of the calculational effort and results generated by TOSPAC for the COVE 2A problem set. The calculations were performed twice. The initial calculations provided preliminary results for comparison with the results from other COVE 2A participants. TOSPAC was modified in response to the comparison and the final calculations included a correction and several enhancements to improve efficiency. 8 refs.

  3. Three dimensional calculation of flux of low energy atmospheric neutrinos

    NASA Technical Reports Server (NTRS)

    Lee, H.; Bludman, S. A.

    1985-01-01

    Results of three-dimensional Monte Carlo calculation of low energy flux of atmospheric neutrinos are presented and compared with earlier one-dimensional calculations 1,2 valid at higher neutrino energies. These low energy neutrinos are the atmospheric background in searching for neutrinos from astrophysical sources. Primary cosmic rays produce the neutrino flux peaking at near E sub=40 MeV and neutrino intensity peaking near E sub v=100 MeV. Because such neutrinos typically deviate by 20 approximately 30 from the primary cosmic ray direction, three-dimensional effects are important for the search of atmospheric neutrinos. Nevertheless, the background of these atmospheric neutrinos is negligible for the detection of solar and supernova neutrinos.

  4. SNS Sample Activation Calculator Flux Recommendations and Validation

    SciTech Connect

    McClanahan, Tucker C.; Gallmeier, Franz X.; Iverson, Erik B.; Lu, Wei

    2015-02-01

    The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) uses the Sample Activation Calculator (SAC) to calculate the activation of a sample after the sample has been exposed to the neutron beam in one of the SNS beamlines. The SAC webpage takes user inputs (choice of beamline, the mass, composition and area of the sample, irradiation time, decay time, etc.) and calculates the activation for the sample. In recent years, the SAC has been incorporated into the user proposal and sample handling process, and instrument teams and users have noticed discrepancies in the predicted activation of their samples. The Neutronics Analysis Team validated SAC by performing measurements on select beamlines and confirmed the discrepancies seen by the instrument teams and users. The conclusions were that the discrepancies were a result of a combination of faulty neutron flux spectra for the instruments, improper inputs supplied by SAC (1.12), and a mishandling of cross section data in the Sample Activation Program for Easy Use (SAPEU) (1.1.2). This report focuses on the conclusion that the SAPEU (1.1.2) beamline neutron flux spectra have errors and are a significant contributor to the activation discrepancies. The results of the analysis of the SAPEU (1.1.2) flux spectra for all beamlines will be discussed in detail. The recommendations for the implementation of improved neutron flux spectra in SAPEU (1.1.3) are also discussed.

  5. Composite electron propagator methods for calculating ionization energies

    NASA Astrophysics Data System (ADS)

    Díaz-Tinoco, Manuel; Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V.

    2016-06-01

    Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules.

  6. Calculating Free Energy Changes in Continuum Solvation Models.

    PubMed

    Ho, Junming; Ertem, Mehmed Z

    2016-02-25

    We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. PMID:26878566

  7. Composite electron propagator methods for calculating ionization energies.

    PubMed

    Díaz-Tinoco, Manuel; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V

    2016-06-14

    Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules. PMID:27305999

  8. Binding Energy Calculations for Novel Ternary Ionic Lattices

    NASA Astrophysics Data System (ADS)

    Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo

    2002-03-01

    Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.

  9. Science Activities in Energy: Solar Energy II.

    ERIC Educational Resources Information Center

    Oak Ridge Associated Universities, TN.

    Included in this science activities energy package are 14 activities related to solar energy for secondary students. Each activity is outlined on a single card and is introduced by a question such as: (1) how much solar heat comes from the sun? or (2) how many times do you have to run water through a flat-plate collector to get a 10 degree rise in…

  10. Self-consistent calculations of alpha-decay energies

    SciTech Connect

    Tolokonnikov, S. V.; Lutostansky, Yu. S.; Saperstein, E. E.

    2013-06-15

    On the basis of the self-consistent theory of finite Fermi systems, the energies of alphadecay chains were calculated for several new superheavy nuclei discovered recently in experiments of the Dubna-Livermore Collaboration headed by Yu.Ts. Oganessian. The approach in question is implemented on the basis of the generalized method of the density functional proposed by Fayans and his coauthors. The version used here relies on the functional DF3-a proposed recently for describing a wide array of nuclear data, including data on superheavy nuclei. A detailed comparison of the results obtained on this basis with the predictions of different approaches, including the self-consistent Skyrme-Hartree-Fock method, the micro-macro method in the version developed by Sobiczewski and his coauthors, and the phenomenological method of Liran and his coauthors, is performed. The resulting alpha-decay energies are used to calculate respective lifetimes with the aid of the phenomenological Parkhomenko-Sobiczewski formula.

  11. Improved initial guess for minimum energy path calculations.

    PubMed

    Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt; Jónsson, Hannes

    2014-06-01

    A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used. PMID:24907989

  12. Improved initial guess for minimum energy path calculations

    SciTech Connect

    Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt

    2014-06-07

    A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

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

    NASA Technical Reports Server (NTRS)

    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

  14. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer

    SciTech Connect

    Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.

    2015-08-28

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be{sub 2} is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be{sub 2} from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be{sub 2}, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm{sup −1}, only slightly below the 935 cm{sup −1} value derived from experiment.

  15. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer.

    PubMed

    Deible, Michael J; Kessler, Melody; Gasperich, Kevin E; Jordan, Kenneth D

    2015-08-28

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm(-1), only slightly below the 935 cm(-1) value derived from experiment. PMID:26328827

  16. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    NASA Technical Reports Server (NTRS)

    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.

  17. Free energy calculations for a flexible water model.

    PubMed

    Habershon, Scott; Manolopoulos, David E

    2011-11-28

    In this work, we consider the problem of calculating the classical free energies of liquids and solids for molecular models with intramolecular flexibility. We show that thermodynamic integration from the fully-interacting solid of interest to a Debye crystal reference state, with anisotropic harmonic interactions derived from the Hessian of the original crystal, provides a straightforward route to calculating the Gibbs free energy of the solid. To calculate the molecular liquid free energy, it is essential to correctly account for contributions from both intermolecular and intramolecular motion; we employ thermodynamic integration to a Lennard-Jones reference fluid, coupled with direct evaluation of the molecular ro-vibrational partition function. These approaches are used to study the low-pressure classical phase diagram of the flexible q-TIP4P/F water model. We find that, while the experimental ice-I/liquid and ice-III/liquid coexistence lines are described reasonably well by this model, the ice-II phase is predicted to be metastable. In light of this finding, we go on to examine how the coupling between intramolecular flexibility and intermolecular interactions influences the computed phase diagram by comparing our results with those of the underlying rigid-body water model. PMID:21887423

  18. Free energy calculation of permeation through aquaporin-5

    NASA Astrophysics Data System (ADS)

    Bastien, David

    The work of this paper continues upon the large area of research being done on aquaporins (AQPs). AQPs are proteins that take on the role of facilitating the transfer of substances, mainly water, across cell membranes. There are many different types of AQPs, with each of these highly selective proteins conducting only certain solutes, along with unique permeability rates. The permeation characteristics of aquaporins rely mostly on the residue hydrophobicity and steric restraints of the aromatic arginine (ar/R) region of the protein channel. The purpose of this paper is to analyze the structures of aquaporin-5 (AQP5) and aquaglycerolporin (Glpf), including a radius profile of the respective protein channels, and to compare them to permeation events using steered molecular dynamics (SMD) pulling simulations. Two in silico experiments are performed in order to achieve the free Energy landscape of a single water molecule permeating through the four channels of both Aqp5 and GlpF. The equilibrium free energy curves are calculated from the non-equilibrium, irreversible work measurements using the fluctuation-dissipation theorem (FDT) of Brownian dynamicis (BD). The free energy profiles are then compared and related to the structural profiles of AQP5 and GlpF. The change in free energy across the ar/R region in AQP5 is found to be reasonably larger than that of GlpF. The free energy profiles of AQP5 and GlpF agree with the diameter profile of the channels respectively. Furthermore, free energy calculations are computed for the permeation of Na+ and Cl- ions through the central pore of Aqp5, which provide some insight into the structural mechanisms of AQP5. The free energy barrier for ion transport through the central pore is found to be very large, peaking at around 11 Kcal/mol for chloride and 20 Kcal/mol for sodium.

  19. A Simple Method to Calculate the Temperature Dependence of the Gibbs Energy and Chemical Equilibrium Constants

    ERIC Educational Resources Information Center

    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…

  20. Activities for Teaching Solar Energy.

    ERIC Educational Resources Information Center

    Mason, Jack Lee; Cantrell, Joseph S.

    1980-01-01

    Plans and activities are suggested for teaching elementary children about solar energy. Directions are included for constructing a flat plate collector and a solar oven. Activities for a solar field day are given. (SA)

  1. Variational calculations of the HT{sup +} rovibrational energies

    SciTech Connect

    Bekbaev, A. K.; Korobov, V. I.; Dineykhan, M.

    2011-04-15

    In this Brief Report, we use the exponential explicitly correlated variational basis set of the type exp(-{alpha}{sub n}R-{beta}{sub n}r{sub 1}-{gamma}{sub n}r{sub 2}) to calculate systematically the nonrelativistic bound-state energies for the hydrogen molecular ion HT{sup +}. We perform calculations for the states of the total orbital angular momentum L=0 and 1 with the complete set of vibrational quantum numbers v= 0-23, as well as for the states of L= 2-5 and v= 0-5. The E1 dipole transition moments, which are of importance for the planning of spectroscopic laser experiments, have been obtained as well.

  2. Prediction of Protein Solubility from Calculation of Transfer Free Energy

    PubMed Central

    Tjong, Harianto; Zhou, Huan-Xiang

    2008-01-01

    Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water. To account for the effects of pH, the protonation states of titratable side chains were sampled by running constant-pH molecular dynamics simulations. Conformations were then selected for calculations of the electrostatic solvation energy: once for the condensed phase, and once for the solution phase. The average transfer free energy from the condensed phase to the solution phase was found to predict reasonably well the variations in solubility of ribonuclease Sa and insulin with pH. This treatment of electrostatic contributions combined with a similar approach for nonelectrostatic contributions led to a quantitative rationalization of the effects of point mutations on the solubility of ribonuclease Sa. This study provides valuable insights into the physical basis of protein solubility. PMID:18515380

  3. SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

    DOE PAGESBeta

    Perfetti, Christopher M.; Rearden, Bradley T.; Martin, William R.

    2016-02-25

    Sensitivity coefficients describe the fractional change in a system response that is induced by changes to system parameters and nuclear data. The Tools for Sensitivity and UNcertainty Analysis Methodology Implementation (TSUNAMI) code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, including 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 developmentmore » of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.« less

  4. Exploiting the Properties of Aquaporin to Calculate Free Energy

    NASA Astrophysics Data System (ADS)

    Espejel, Hugo; Chen, Liao

    2010-03-01

    Aquaporins' (AQPs) main purpose is to facilitate the transfer of water molecules through a molecular membrane. We can calculate the free energy of the AQP system when water permeates through it. This is performed using the Visual Molecular Dynamics (VMD) and the Nanoscale Molecular Dynamics (NAMD) programs. In our first set of experiments, AQP is submerged in a body of water, in which case a water molecule near AQP is pulled through the protein. The data is then used to calculate the free energy using two different equations: the Jarzynski equality and the fluctuation-dissipation theorem. The values from both equations are then compared to examine their accuracy. The second set of experiments has the same set up, but now AQP is embedded in a lipid bilayer. We found that both equations give values that are much smaller than kT. This verifies that AQP is a channel for water molecules because the pulling of water gives constant values of free energy. We also found that the water molecules' negative poles were all pointing towards the center of the AQP channel. This means that the process of proton transport in AQP is overwhelmingly difficult.

  5. Understanding Iron-based catalysts with efficient Oxygen reduction activity from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Hafiz, Hasnain; Barbiellini, B.; Jia, Q.; Tylus, U.; Strickland, K.; Bansil, A.; Mukerjee, S.

    2015-03-01

    Catalysts based on Fe/N/C clusters can support the oxygen-reduction reaction (ORR) without the use of expensive metals such as platinum. These systems can also prevent some poisonous species to block the active sites from the reactant. We have performed spin-polarized calculations on various Fe/N/C fragments using the Vienna Ab initio Simulation Package (VASP) code. Some results are compared to similar calculations obtained with the Gaussian code. We investigate the partial density of states (PDOS) of the 3d orbitals near the Fermi level and calculate the binding energies of several ligands. Correlations of the binding energies with the 3d electronic PDOS's are used to propose electronic descriptors of the ORR associated with the 3d states of Fe. We also suggest a structural model for the most active site with a ferrous ion (Fe2+) in the high spin state or the so-called Doublet 3 (D3).

  6. Activation calculations for trapped protons below 200 MeV: Appendix

    NASA Technical Reports Server (NTRS)

    Laird, C. E.

    1991-01-01

    Tables are given displaying of the results of the activation calculations of metal samples and other material aboard the Long Duration Exposure Facility-1 (LDEF-1) and Spacelab-2 with the computer program, PTRAP4. The computer printouts give the reaction, the reactant product, the proton reaction cross sections as a function of the energy of the incident protons, and the activation as a function of distance into the sample from the exposed surface.

  7. Parquet decomposition calculations of the electronic self-energy

    NASA Astrophysics Data System (ADS)

    Gunnarsson, O.; Schäfer, T.; LeBlanc, J. P. F.; Merino, J.; Sangiovanni, G.; Rohringer, G.; Toschi, A.

    2016-06-01

    The parquet decomposition of the self-energy into classes of diagrams, those associated with specific scattering processes, can be exploited for different scopes. In this work, the parquet decomposition is used to unravel the underlying physics of nonperturbative numerical calculations. We show the specific example of dynamical mean field theory and its cluster extensions [dynamical cluster approximation (DCA)] applied to the Hubbard model at half-filling and with hole doping: These techniques allow for a simultaneous determination of two-particle vertex functions and self-energies and, hence, for an essentially "exact" parquet decomposition at the single-site or at the cluster level. Our calculations show that the self-energies in the underdoped regime are dominated by spin-scattering processes, consistent with the conclusions obtained by means of the fluctuation diagnostics approach [O. Gunnarsson et al., Phys. Rev. Lett. 114, 236402 (2015), 10.1103/PhysRevLett.114.236402]. However, differently from the latter approach, the parquet procedure displays important changes with increasing interaction: Even for relatively moderate couplings, well before the Mott transition, singularities appear in different terms, with the notable exception of the predominant spin channel. We explain precisely how these singularities, which partly limit the utility of the parquet decomposition and, more generally, of parquet-based algorithms, are never found in the fluctuation diagnostics procedure. Finally, by a more refined analysis, we link the occurrence of the parquet singularities in our calculations to a progressive suppression of charge fluctuations and the formation of a resonance valence bond state, which are typical hallmarks of a pseudogap state in DCA.

  8. Investigation of Multipole Electrostatics in Hydration Free Energy Calculations

    PubMed Central

    Shi, Yue; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu

    2010-01-01

    Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio (BAR) method. We have compared two approaches to derive the atomic multipoles from quantum mechanical (QM) calculations: one directly from the new distributed multipole analysis (DMA) and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-ccpVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the hydration free energy calculation. PMID:20925089

  9. Empirically corrected HEAT method for calculating atomization energies

    SciTech Connect

    Brand, Holmann V

    2008-01-01

    We describe how to increase the accuracy ofthe most recent variants ofthe HEAT method for calculating atomization energies of molecules by means ofextremely simple empirical corrections that depend on stoichiometry and the number ofunpaired electrons in the molecule. Our corrections reduce the deviation from experiment for all the HEAT variants. In particular, our corrections reduce the average absolute deviation and the root-mean-square deviation ofthe 456-QP variant to 0.18 and 0.23 kJoule/mol (i.e., 0.04 and 0.05 kcallmol), respectively.

  10. Multiple scattering calculations of relativistic electron energy loss spectra

    NASA Astrophysics Data System (ADS)

    Jorissen, K.; Rehr, J. J.; Verbeeck, J.

    2010-04-01

    A generalization of the real-space Green’s-function approach is presented for ab initio calculations of relativistic electron energy loss spectra (EELS) which are particularly important in anisotropic materials. The approach incorporates relativistic effects in terms of the transition tensor within the dipole-selection rule. In particular, the method accounts for relativistic corrections to the magic angle in orientation resolved EELS experiments. The approach is validated by a study of the graphite CK edge, for which we present an accurate magic angle measurement consistent with the predicted value.

  11. Active neutron multiplicity analysis and Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Krick, M. S.; Ensslin, N.; Langner, D. G.; Miller, M. C.; Siebelist, R.; Stewart, J. E.; Ceo, R. N.; May, P. K.; Collins, L. L., Jr.

    Active neutron multiplicity measurements of high-enrichment uranium metal and oxide samples have been made at Los Alamos and Y-12. The data from the measurements of standards at Los Alamos were analyzed to obtain values for neutron multiplication and source-sample coupling. These results are compared to equivalent results obtained from Monte Carlo calculations. An approximate relationship between coupling and multiplication is derived and used to correct doubles rates for multiplication and coupling. The utility of singles counting for uranium samples is also examined.

  12. Model for analytical calculation of nuclear photoabsorption at intermediate energies

    NASA Astrophysics Data System (ADS)

    Hütt, M.-Th.; Milstein, A. I.; Schumacher, M.

    1997-02-01

    The universal curve {σ}/{A} of nuclear photoabsorption is investigated within a Fermi gas model of nuclear matter. An energy range from pion threshold up to 400 MeV is considered. The interactions between nucleon, pion, Δ-isobar and photon are considered in the non-relativistic approximation with corrections of the order {1}/{M} taken into account with respect to proton mass. Analytical expressions are obtained, in which the influence of nuclear correlations and two-nucleon contributions is studied explicitly. The contributions of real and virtual pions are found to be sufficient to obtain agreement with experimental data in this energy range. An extension of the model calculation to nucleon knock-out reactions is discussed.

  13. Calculated photoelectron pitch angle and energy spectra. [in upper atmosphere

    NASA Technical Reports Server (NTRS)

    Mantas, G. P.; Bowhill, S. A.

    1974-01-01

    Calculations of the steady-state photoelectron energy and angular distribution in the altitude region between 120 and 1000 km are presented. The distribution is found to be isotropic at all altitudes below 250 km, while above this altitude anisotropies in both pitch angle and energy are found. The isotropy found in the angular distribution below 250 km implies that photoelectron transport below 250 km is insignificant, while the angular anisotropy found above this altitude implies a net photoelectron current in the upward direction. The energy anisotropy above 500 km arises from the selective backscattering of the low energy photoelectron population of the upward flux component by Coulomb collisions with the ambient ions. The total photoelectron flux attains its maximum value between about 40 and 70 km above the altitude at which the photoelectron production rate is maximum. The displacement of the maximum of the equilibrium flux is attributed to an increasing (with altitude) photoelectron lifetime. Photoelectrons at altitudes above that where the flux is maximum are on the average more energetic than those below that altitude.

  14. Tables for simplifying calculations of activities produced by thermal neutrons

    USGS Publications Warehouse

    Senftle, F.E.; Champion, W.R.

    1954-01-01

    The method of calculation described is useful for the types of work of which examples are given. It is also useful in making rapid comparison of the activities that might be expected from several different elements. For instance, suppose it is desired to know which of the three elements, cobalt, nickel, or vanadium is, under similar conditions, activated to the greatest extent by thermal neutrons. If reference is made to a cross-section table only, the values may be misleading unless properly interpreted by a suitable comparison of half-lives and abundances. In this table all the variables have been combined and the desired information can be obtained directly from the values of A 3??, the activity produced per gram per second of irradiation, under the stated conditions. Hence, it is easily seen that, under similar circumstances of irradiation, vanadium is most easily activated even though the cross section of one of the cobalt isotopes is nearly five times that of vanadium and the cross section of one of the nickel isotopes is three times that of vanadium. ?? 1954 Societa?? Italiana di Fisica.

  15. High energy activation data library (HEAD-2009)

    SciTech Connect

    Mashnik, Stepan G; Korovin, Yury A; Natalenko, Anatoly A; Konobeyev, Alexander Yu; Stankovskiy, A Yu

    2010-01-01

    A proton activation data library for 682 nuclides from 1 H to 210Po in the energy range from 150 MeV up to 1 GeV was developed. To calculate proton activation data, the MCNPX 2.6.0 and CASCADE/INPE codes were chosen. Different intranuclear cascade, preequilibrium, and equilibrium nuclear reaction models and their combinations were used. The optimum calculation models have been chosen on the basis of statistical correlations for calculated and experimental proton data taken from the EXFOR library of experimental nuclear data. All the data are written in ENDF-6 format. The library is called HEPAD-2008 (High-Energy Proton Activation Data). A revision of IEAF-2005 neutron activation data library has been performed. A set of nuclides for which the cross-section data can be (and were) updated using more modern and improved models is specified, and the corresponding calculations have been made in the present work. The new version of the library is called IEAF-2009. The HEPAD-2008 and IEAF-2009 are merged to the final HEAD-2009 library.

  16. High energy activation data library (HEAD-2009)

    NASA Astrophysics Data System (ADS)

    Korovin, Yu. A.; Natalenko, A. A.; Stankovskiy, A. Yu.; Mashnik, S. G.; Konobeyev, A. Yu.

    2010-12-01

    A proton activation data library for 682 nuclides from 1H to 210Po in the energy range from 150 MeV up to 1 GeV was developed. To calculate proton activation data, the MCNPX 2.6.0 and CASCADE/INPE codes were chosen. Different intranuclear cascade, preequilibrium, and equilibrium nuclear reaction models and their combinations were used. The optimum calculation models have been chosen on the basis of statistical correlations for calculated and experimental proton data taken from the EXFOR library of experimental nuclear data. All the data are written in ENDF-6 format. The library is called HEPAD-2008 (High-Energy Proton Activation Data). A revision of IEAF-2005 neutron activation data library has been performed. A set of nuclides for which the cross-section data can be (and were) updated using more modern and improved models is specified, and the corresponding calculations have been made in the present work. The new version of the library is called IEAF-2009. The HEPAD-2008 and IEAF-2009 are merged to the final HEAD-2009 library.

  17. Scattering Theory Calculations of Casimir Energies at High Curvature

    NASA Astrophysics Data System (ADS)

    Graham, Noah; Emig, Thorsten; Forrow, Aden; Jaffe, Robert; Kardar, Mehran; Maghrebi, Mohammad; Rahi, Jamal; Shpunt, Alex

    2013-03-01

    Scattering theory provides a powerful tool for capturing the response of an object to electromagnetic charge and field fluctuations. Techniques based on scattering theory have made possible a wide range of new calculations of Casimir energies. In this approach, the Casimir interaction energy for a collection of objects can be expressed in terms of the scattering T-matrices for each object individually, combined with universal translation matrices describing the objects' relative positions and orientations. These translation matrices are derived from an expansion of the free Green's function in an appropriate coordinate system, independent of the details of the objects themselves. This method proves particularly valuable for geometries involving high curvature, such as edges and tips. I will describe this approach in general terms and then give results from several problems to which it has been applied successfully. I will also discuss new developments in scattering theory that have been motivated by these problems. I would like to request that this abstract be part of a session on Casimir physics. Supported by the National Science Foundation, the US Department of Energy, the Defense Advanced Research Projects Agency, and the Deutsche Forschungsgemeinschaft

  18. Similarity criteria in calculations of the energy characteristics of a cw oxygen - iodine laser

    NASA Astrophysics Data System (ADS)

    Mezhenin, A. V.; Azyazov, V. N.

    2012-12-01

    The calculated and experimental data on the energy efficiency of a cw oxygen - iodine laser (OIL) are analysed based on two similarity criteria, namely, on the ratio of the residence time of the gas mixture in the resonator to the characteristic time of extraction of the energy stored in singlet oxygen td and on the gain-to-loss ratio Π. It is shown that the simplified two-level laser model satisfactorily predicts the output characteristics of OILs with a stable resonator at τd <= 7. Efficient energy extraction from the OIL active medium is achieved in the case of τd = 5 - 7, Π = 4 - 8.

  19. Similarity criteria in calculations of the energy characteristics of a cw oxygen - iodine laser

    SciTech Connect

    Mezhenin, A V; Azyazov, V N

    2012-12-31

    The calculated and experimental data on the energy efficiency of a cw oxygen - iodine laser (OIL) are analysed based on two similarity criteria, namely, on the ratio of the residence time of the gas mixture in the resonator to the characteristic time of extraction of the energy stored in singlet oxygen td and on the gain-to-loss ratio {Pi}. It is shown that the simplified two-level laser model satisfactorily predicts the output characteristics of OILs with a stable resonator at {tau}{sub d} {<=} 7. Efficient energy extraction from the OIL active medium is achieved in the case of {tau}{sub d} = 5 - 7, {Pi} = 4 - 8. (lasers)

  20. Soil biological activity at European scale - two calculation concepts

    NASA Astrophysics Data System (ADS)

    Krüger, Janine; Rühlmann, Jörg

    2014-05-01

    The CATCH-C project aims to identify and improve the farm-compatibility of Soil Management Practices including to promote productivity, climate change mitigation and soil quality. The focus of this work concentrates on turnover conditions for soil organic matter (SOM). SOM is fundamental for the maintenance of quality and functions of soils while SOM storage is attributed a great importance in terms of climate change mitigation. The turnover conditions depend on soil biological activity characterized by climate and soil properties. To assess the turnover conditions two model concepts are applied: (I) Biological active time (BAT) regression approach derived from CANDY model (Franko & Oelschlägel 1995) expresses the variation of air temperature, precipitation and soil texture as a timescale and an indicator of biological activity for soil organic matter (SOM) turnover. (II) Re_clim parameter within the Introductory Carbon Balance Model (Andrén & Kätterer 1997) states the soil temperature and soil water to estimate soil biological activity. The modelling includes two strategies to cover the European scale and conditions. BAT was calculated on a 20x20 km grid basis. The European data sets of precipitation and air temperature (time period 1901-2000, monthly resolution), (Mitchell et al. 2004) were used to derive long-term averages. As we focus on agricultural areas we included CORINE data (2006) to extract arable land. The resulting BATs under co-consideration of the main soil textures (clay, silt, sand and loam) were investigated per environmental zone (ENZs, Metzger et al. 2005) that represents similar conditions for precipitation, temperature and relief to identify BAT ranges and hence turnover conditions for each ENZ. Re_clim was quantified by climatic time series of more than 250 weather stations across Europe presented by Klein Tank et al. (2002). Daily temperature, precipitation and potential evapotranspiration (maximal thermal extent) were used to calculate

  1. Valence calculations of lanthanide anion binding energies: a comprehensive study

    NASA Astrophysics Data System (ADS)

    O'Malley, Steven M.; Beck, Donald R.

    2009-05-01

    We have applied a methodology of universal jls restrictions on the 4f^n subgroup of relativistic configuration-interaction calculations of progressively more complex lanthanide anionsootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 77, 012505 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 78, 012510 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A, in press.. Our completed study of the row predicts bound 6p attachments to all lanthanide ground state configurations except Yb, additional 6p attachments to excited opposite parity configurations in Tb and Lu, and 6s attachments to excited open-6s thresholds in La, Ce, Pr, and Gd. In total we predict more than 100 bound states for the lanthanide anions, and we hope this comprehensive study encourages further experimentalootnotetexte.g. V. T. Davis et al., Nucl. Instrum. Methods Phys. Res. B 241, 118 (2005).^,ootnotetexte.g. C. W. Walter et al., Phys. Rev. A 76, 052702 (2007). interest in these anions. Such measurements will be useful in ``fine tuning'' these ab initio binding energies to account for missing core-valence correlation and the approximations that were necessary in these complex calculations.

  2. Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.

    PubMed

    Morishita, Tetsuya; Itoh, Satoru G; Okumura, Hisashi; Mikami, Masuhiro

    2012-06-01

    A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule. PMID:23005238

  3. Calculation of optical second-harmonic susceptibilities and optical activity for crystals

    SciTech Connect

    Levine, Z.H.

    1994-12-31

    A new generation of nearly first-principles calculations predicts both the linear and second-harmonic susceptibilities for a variety of insulating crystals, including GaAs, GaP, AlAs, AlP, Se, {alpha}-quartz, and c-urea. The results are typically in agreement with experimental measurements. The calculations have been extended to optical activity, with somewhat less success to date. The theory, based on a simple self-energy correction to the local density approximation, and results are reviewed herein.

  4. Distributed activation energy model parameters of some Turkish coals

    SciTech Connect

    Gunes, M.; Gunes, S.K.

    2008-07-01

    A multi-reaction model based on distributed activation energy has been applied to some Turkish coals. The kinetic parameters of distributed activation energy model were calculated via computer program developed for this purpose. It was observed that the values of mean of activation energy distribution vary between 218 and 248 kJ/mol, and the values of standard deviation of activation energy distribution vary between 32 and 70 kJ/mol. The correlations between kinetic parameters of the distributed activation energy model and certain properties of coal have been investigated.

  5. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    PubMed

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-01

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197

  6. INDIVIDUALISED CALCULATION OF TISSUE IMPARTED ENERGY IN BREAST TOMOSYNTHESIS.

    PubMed

    Geeraert, N; Klausz, R; Muller, S; Bloch, I; Bosmans, H

    2016-06-01

    The imparted energy to the glandular tissue in the breast (glandular imparted energy, GIE) is proposed for an improved assessment of the individual radiation-induced risk resulting from X-ray breast imaging. GIE is computed from an estimation of the quantity and localisation of glandular tissue in the breast. After a digital breast tomosynthesis (DBT) acquisition, the volumetric glandular content (volumetric breast density, VBD) is computed from the central X-ray projection. The glandular tissue distribution is determined by labelling the DBT voxels to ensure the conservation of the VBD. Finally, the GIE is calculated by Monte Carlo computation on the resulting tissue-labelled DBT volume. For verification, the method was applied to 10 breast-shaped digital phantoms made of different glandular spheres in an adipose background, and to a digital anthropomorphic phantom. Results were compared to direct GIE computations on the phantoms considered as 'ground-truth'. The major limitations in accuracy are those of DBT, in particular the limited z-resolution. However, for most phantoms, the results can be considered as acceptable. PMID:27127209

  7. Calculating Capstone depleted uranium aerosol concentrations from beta activity measurements.

    PubMed

    Szrom, Frances; Falo, Gerald A; Parkhurst, Mary Ann; Whicker, Jeffrey J; Alberth, David P

    2009-03-01

    Beta activity measurements were used as surrogate measurements of uranium mass in aerosol samples collected during the field testing phase of the Capstone Depleted Uranium (DU) Aerosol Study. These aerosol samples generated by the perforation of armored combat vehicles were used to characterize the DU source term for the subsequent Human Health Risk Assessment (HHRA) of Capstone aerosols. Establishing a calibration curve between beta activity measurements and uranium mass measurements is straightforward if the uranium isotopes are in equilibrium with their immediate short-lived, beta-emitting progeny. For DU samples collected during the Capstone study, it was determined that the equilibrium between the uranium isotopes and their immediate short-lived, beta-emitting progeny had been disrupted when penetrators had perforated target vehicles. Adjustments were made to account for the disrupted equilibrium and for wall losses in the aerosol samplers. Values for the equilibrium fraction ranged from 0.16 to 1, and the wall loss correction factors ranged from 1 to 1.92. This paper describes the process used and adjustments necessary to calculate uranium mass from proportional counting measurements. PMID:19204483

  8. Identification of HIV Inhibitors Guided by Free Energy Perturbation Calculations

    PubMed Central

    Acevedo, Orlando; Ambrose, Zandrea; Flaherty, Patrick T.; Aamer, Hadega; Jain, Prashi; Sambasivarao, Somisetti V.

    2013-01-01

    Free energy perturbation (FEP) theory coupled to molecular dynamics (MD) or Monte Carlo (MC) statistical mechanics offers a theoretically precise method for determining the free energy differences of related biological inhibitors. Traditionally requiring extensive computational resources and expertise, it is only recently that its impact is being felt in drug discovery. A review of computer-aided anti-HIV efforts employing FEP calculations is provided here that describes early and recent successes in the design of human immunodeficiency virus type 1 (HIV-1) protease and non-nucleoside reverse transcriptase inhibitors. In addition, our ongoing work developing and optimizing leads for small molecule inhibitors of cyclophilin A (CypA) is highlighted as an update on the current capabilities of the field. CypA has been shown to aid HIV-1 replication by catalyzing the cis/trans isomerization of a conserved Gly-Pro motif in the N-terminal domain of HIV-1 capsid (CA) protein. In the absence of a functional CypA, e.g., by the addition of an inhibitor such as cyclosporine A (CsA), HIV-1 has reduced infectivity. Our simulations of acylurea-based and 1-indanylketone-based CypA inhibitors have determined that their nanomolar and micromolar binding affinities, respectively, are tied to their ability to stabilize Arg55 and Asn102. A structurally novel 1-(2,6-dichlorobenzamido) indole core was proposed to maximize these interactions. FEP-guided optimization, experimental synthesis, and biological testing of lead compounds for toxicity and inhibition of wild-type HIV-1 and CA mutants have demonstrated a dose-dependent inhibition of HIV-1 infection in two cell lines. While the inhibition is modest compared to CsA, the results are encouraging. PMID:22316150

  9. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  10. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  11. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  12. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  13. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  14. Exploring the MRCI method for calculating interaction energies: application to the HeNe potential curve

    NASA Astrophysics Data System (ADS)

    van de Bovenkamp, J.; van Mourik, T.; van Duijneveldt, F. B.

    A multi-reference configuration interaction (MRCI) method is described, which is devised for the calculation of interaction energies of van der Waals complexes and applied to calculating the HeNe potential energy curve. The MRCI calculations make use of a generalized Poplecorrection in order to account for the lack of size consistency. The orbital space is partitioned into three subspaces: the first active space (AS1), which contains the strongly occupied orbitals; the second active space (AS2), which contains the main intra-correlating orbitals; and the external space (ES). It is shown that, to keep the error below 0.2K in the excitation scheme and the active orbital space it is sufficient to include only sigma-orbitals in AS2 and to use an excitation scheme (labelled Qq-MRCI) that encompasses only up to quadruply excited configurations. The final active orbital space (AS2) turned out to be 2s(He), 2psigma(He), 3s(Ne), 3psigma(Ne) and 3dsigma(Ne). Other MRCI variants, in which most or all quadruply excited configurations were deleted from the CI expansion (Qt- and Tt-MRCI), were found to be inadequate. Using the Qq-MRCI scheme together with a 197-orbital 'interaction optimized' basis set (IO197), the MRCI interaction energy at R = 5.7 a0 was calculated to be-21.12K. The corresponding values at the MP4 and CCSD(T) levels of theory are-20.06K and-20.99K, respectively, indicating that the MP4 method is inappropriate for highly accurate calculations on this system. Fitting the calculated data using a generalized Morse function, including an additional C6/R6 term to account for a correct long-range behaviour of the potential, the MRCI well depth was calculated to be-21.16K at Req = 5.73 a0. The MRCI and CCSD(T) potentials have the same quality and are found to be in good agreement with the HartreeFock dispersion (HFD-B) potential of Keil, M., Danielson, L. J., and Dunlop, P. J., 1991, J. Chem. Phys., 94, 296. It is concluded that, for basis IO197, the CCSD(T) method is

  15. Theoretical model for calculation of helicity in solar active regions

    NASA Astrophysics Data System (ADS)

    Chatterjee, P.

    We (Choudhuri, Chatterjee and Nandy, 2005) calculate helicities of solar active regions based on the idea of Choudhuri (2003) that poloidal flux lines get wrapped around a toroidal flux tube rising through the convection zone, thereby giving rise to the helicity. Rough estimates based on this idea compare favourably with the observed magnitude of helicity. We use our solar dynamo model based on the Babcock--Leighton α-effect to study how helicity varies with latitude and time. At the time of solar maximum, our theoretical model gives negative helicity in the northern hemisphere and positive helicity in the south, in accordance with observed hemispheric trends. However, we find that, during a short interval at the beginning of a cycle, helicities tend to be opposite of the preferred hemispheric trends. Next we (Chatterjee, Choudhuri and Petrovay 2006) use the above idea along with the sunspot decay model of Petrovay and Moreno-Insertis, (1997) to estimate the distribution of helicity inside a flux tube as it keeps collecting more azimuthal flux during its rise through the convection zone and as turbulent diffusion keeps acting on it. By varying parameters over reasonable ranges in our simple 1-d model, we find that the azimuthal flux penetrates the flux tube to some extent instead of being confined to a narrow sheath outside.

  16. Path-breaking schemes for nonequilibrium free energy calculations

    NASA Astrophysics Data System (ADS)

    Chelli, Riccardo; Gellini, Cristina; Pietraperzia, Giangaetano; Giovannelli, Edoardo; Cardini, Gianni

    2013-06-01

    We propose a path-breaking route to the enhancement of unidirectional nonequilibrium simulations for the calculation of free energy differences via Jarzynski's equality [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)], 10.1103/PhysRevLett.78.2690. One of the most important limitations of unidirectional nonequilibrium simulations is the amount of realizations necessary to reach suitable convergence of the work exponential average featuring the Jarzynski's relationship. In this respect, a significant improvement of the performances could be obtained by finding a way of stopping trajectories with negligible contribution to the work exponential average, before their normal end. This is achieved using path-breaking schemes which are essentially based on periodic checks of the work dissipated during the pulling trajectories. Such schemes can be based either on breaking trajectories whose dissipated work exceeds a given threshold or on breaking trajectories with a probability increasing with the dissipated work. In both cases, the computer time needed to carry out a series of nonequilibrium trajectories is reduced up to a factor ranging from 2 to more than 10, at least for the processes under consideration in the present study. The efficiency depends on several aspects, such as the type of process, the number of check-points along the pathway and the pulling rate as well. The method is illustrated through radically different processes, i.e., the helix-coil transition of deca-alanine and the pulling of the distance between two methane molecules in water solution.

  17. Okeechobee County Energy Education Activities--Middle School Level.

    ERIC Educational Resources Information Center

    Allen, Rodney F., Ed.

    Over 60 energy education activities related to mathematics, science, social studies, and English comprise this manual for middle school teachers. Included are issues for discussion, puzzles, science investigations, story writing exercises, and energy cost calculation problems. Among the topics covered in these lessons are energy consumption…

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

    ERIC Educational Resources Information Center

    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…

  19. Evaluation of uncertainty in gravity wave potential energy calculations through GPS radio occultation measurements

    NASA Astrophysics Data System (ADS)

    Luna, D.; Alexander, P.; de la Torre, A.

    2013-09-01

    The application of the Global Positioning System (GPS) radio occultation (RO) method to the atmosphere enables the determination of height profiles of temperature, among other variables. From these measurements, gravity wave activity is usually quantified by calculating the potential energy through the integration of the ratio of perturbation and background temperatures between two given altitudes in each profile. The uncertainty in the estimation of wave activity depends on the systematic biases and random errors of the measured temperature, but also on additional factors like the selected vertical integration layer and the separation method between background and perturbation temperatures. In this study, the contributions of different parameters and variables to the uncertainty in the calculation of gravity wave potential energy in the lower stratosphere are investigated and quantified. In particular, a Monte Carlo method is used to evaluate the uncertainty that results from different GPS RO temperature error distributions. In addition, our analysis shows that RO data above 30 km height becomes dubious for gravity waves potential energy calculations.

  20. The importance of geospatial data to calculate the optimal distribution of renewable energies

    NASA Astrophysics Data System (ADS)

    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

  1. On the possibility of negative activation energies in bimolecular reactions

    NASA Technical Reports Server (NTRS)

    Jaffe, R. L.

    1978-01-01

    The temperature dependence of the rate constants for model reacting systems was studied to understand some recent experimental measurements which imply the existence of negative activation energies. A collision theory model and classical trajectory calculations are used to demonstrate that the reaction probability can vary inversely with collision energy for bimolecular reactions occurring on attractive potential energy surfaces. However, this is not a sufficient condition to ensure that the rate constant has a negative temperature dependence. On the basis of these calculations, it seems unlikely that a true bimolecular reaction between neutral molecules will have a negative activation energy.

  2. Solar Energy Project, Activities: Biology.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of biology experiments. Each unit presents an introduction; objectives; skills and knowledge needed; materials; methods; questions; recommendations for further work; and a teacher information sheet. The teacher information…

  3. Activation energy measurements of cheese

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Temperature sweeps of cheeses using small amplitude oscillatory shear tests produced values for activation energy of flow (Ea) between 30 and 44 deg C. Soft goat cheese and Queso Fresco, which are high-moisture cheeses and do not flow when heated, exhibited Ea values between 30 and 60 kJ/mol. The ...

  4. Activation Energies of Plasmonic Catalysts.

    PubMed

    Kim, Youngsoo; Dumett Torres, Daniel; Jain, Prashant K

    2016-05-11

    The activation energy of a catalytic reaction serves not only as a metric of the efficacy of a catalyst but also as a potential indicator of mechanistic differences between the catalytic and noncatalytic reaction. However, activation energies are quite underutilized in the field of photocatalysis. We characterize in detail the effect of visible light excitation on the activation enthalpy of an electron transfer reaction photocatalyzed by plasmonic Au nanoparticles. We find that in the presence of visible light photoexcitation, the activation enthalpy of the Au nanoparticle-catalyzed electron transfer reaction is significantly reduced. The reduction in the activation enthalpy depends on the excitation wavelength, the incident laser power, and the strength of a hole scavenger. On the basis of these results, we argue that the activation enthalpy reduction is directly related to the photoelectrochemical potential built-up on the Au nanoparticle under steady-state light excitation, analogous to electrochemical activation. Under optimum light excitation conditions, a potential as high as 240 mV is measured. The findings constitute more precise insights into the mechanistic role and energetic contribution of plasmonic excitation to chemical reactions catalyzed by transition metal nanoparticles. PMID:27064549

  5. Enhanced photoelectrochemical activity for Cu and Ti doped hematite: The first principles calculations

    SciTech Connect

    Meng, X. Y.; Qin, G. W.; Li, S.; Ren, Y. P.; Pei, W. L.; Zuo, L.; Wen, X. H.

    2011-03-14

    To improve photoelectrochemical (PEC) activity of hematite, the modification of energy band by doping 3d transition metal ions Cu and Ti into {alpha}-Fe{sub 2}O{sub 3} were studied via the first-principles calculations with density function theory (DFT)+U method. The results show that the band gap of hematite is {approx}2.1 eV and n-type dopant Ti improves the electric conductivity, confirmed by recent experiments. The p-type dopant Cu enhances the utilization ratio of solar energy, shifts both valance, and conduction band edges to a higher energy level, satisfying hydrogen production in the visible light driven PEC water splitting without voltage bias.

  6. Trypsin-Ligand Binding Free Energy Calculation with AMOEBA

    PubMed Central

    Shi, Yue; Jiao, Dian; Schnieders, Michael J.; Ren, Pengyu

    2010-01-01

    The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was found to be the driving force for the binding. Structural analysis shows that the ligands form hydrogen bonds with residues and water molecules nearby in a competitive fashion. The dependence of binding free energy on molecular dipole moment and polarizability was also studied. While the binding free energy is independent on the dipole moment, it shows a negative correlation with the polarizability. PMID:19965178

  7. Extending the energy range of materials activation modelling

    NASA Astrophysics Data System (ADS)

    Forrest, R. A.

    2004-08-01

    Activation calculations are an essential contribution to understanding the interactions of fusion materials with neutrons. The existing state-of-the-art tools such as EASY-2003 enable calculations to be carried out with neutrons up to 20 MeV. Plans to expose fusion components to high neutron fluxes include the IFMIF materials testing facility. This accelerator-based device will produce neutrons with a high-energy tail up to about 55 MeV. In order to carry out activation calculations on materials exposed to such neutrons it is necessary to extend the energy range of the data libraries. An extension of the European Activation System (EASY) to a new version, EASY-2004, for testing has been completed. The existing reactions have been extended up to 60 MeV and new classes of reactions added using calculated cross sections. Results of preliminary calculations in an IFMIF relevant neutron field are given.

  8. Analytical calculation of proton linear energy transfer in voxelized geometries including secondary protons

    NASA Astrophysics Data System (ADS)

    Sanchez-Parcerisa, D.; Cortés-Giraldo, M. A.; Dolney, D.; Kondrla, M.; Fager, M.; Carabe, A.

    2016-02-01

    In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm-1) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process.

  9. Synthesis, structure, theoretical calculations and biological activity of sulfonate active ester new derivatives

    NASA Astrophysics Data System (ADS)

    Ghazzali, Mohamed; Khattab, Sherine A. N.; Elnakady, Yasser A.; Al-Mekhlafi, Fahd A.; Al-Farhan, Khalid; El-Faham, Ayman

    2013-08-01

    A series of naphthyl and tolyl sulfonate ester were synthesized and characterized by H NMR. X-ray single crystal diffraction experiments established the molecular structure of three new sulfonate esters derivatives, and spectral data agree with these in solution. The observed hydrogen bonding is discussed on the basis of crystal structural analyses and DFT/MP2 geometry optimization quantum calculations. Antimicrobial activities were screened for selected compounds against three human cancer cell lines and Mosquito Culex pipiens larvae.

  10. A simplified confinement method for calculating absolute free energies and free energy and entropy differences.

    PubMed

    Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin

    2013-01-24

    A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. PMID:23268557

  11. Subtleties in Energy Calculations in the Image Method

    ERIC Educational Resources Information Center

    Taddei, M. M.; Mendes, T. N. C.; Farina, C.

    2009-01-01

    In this pedagogical work, we point out a subtle mistake that can be made by undergraduate or graduate students in the computation of the electrostatic energy of a system containing charges and perfect conductors if they naively use the image method. Specifically, we show that naive expressions for the electrostatic energy for these systems…

  12. A calculation of the diffusion energies for adatoms on surfaces of F.C.C. metals

    NASA Technical Reports Server (NTRS)

    Halicioglu, T.; Pound, G. M.

    1979-01-01

    The activation energies for diffusion were determined for gold, platinum and iridium adatoms on plane and plane PT surfaces and were found to be in good agreement with the measurements reported by Bassett and Webber. The Lennard-Jones pair potentials were used to model the interatomic forces, and relaxation of the substrate atoms in near proximity to the adatom was considered in detail. The present calculations clarify the mechanism of the observed two-dimensional diffusion of platinum and iridium atoms on a plane PT surface. The results are compared with those obtained using Morse potential functions and different relaxation techniques.

  13. Oxyfluoroborate host glass for upconversion application: phonon energy calculation

    NASA Astrophysics Data System (ADS)

    Abdel-Baki, Manal; El-Diasty, Fouad

    2016-04-01

    Reducing the glass phonon energy is an essential procedure to achieve high efficient radiative upconversion process. The degree of covalence of chemical bonds is responsible for the high oscillator strength of intracenter transitions in rare-earth ions. So, conversion covalent to ionic glass character is proposed as a structure-sensitive criterion that controls the phonon energy of the glasses. A series of oxyfluoro aluminum-borate host glasses used for upconversion application is prepared by the conventional melt-quenching technique. Through lithium oxide substitution by lithium fluoride, the ionic-covalent property of Li+ ion successes to regulate the band gap energies of the studied glasses. Furthermore, a new method to determine the glass phonon energy is offered.

  14. Accurate potential energy curve of the LiH+ molecule calculated with explicitly correlated Gaussian functions.

    PubMed

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations. PMID:24697449

  15. Accurate potential energy curve of the LiH+ molecule calculated with explicitly correlated Gaussian functions

    NASA Astrophysics Data System (ADS)

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-01

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

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

    PubMed

    Horn, Paul R; Head-Gordon, Martin

    2016-02-28

    In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint. PMID:26931692

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

    NASA Astrophysics Data System (ADS)

    Horn, Paul R.; Head-Gordon, Martin

    2016-02-01

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

  18. Atomization energies from coupled-cluster calculations augmented with explicitly-correlated perturbation theory.

    SciTech Connect

    Klopper, W.; Ruscic, B.; Tew, D. P.; Bischoff, F. A.; Wolfsegger, S.; Chemical Sciences and Engineering Division; Univ. Karlsruhe

    2008-11-17

    The atomization energies of the 105 molecules in the test set of Bakowies [D. Bakowies, J. Chem. Phys. 127 (2007) 084105] have been computed with an estimated standard deviation (from the values compiled in the Active Thermochemical Tables) of {+-}0.1 kJ/mol per valence electron in the molecule. Equilibrium geometries and harmonic vibrational frequencies were calculated at the all-electron CCSD(T)/cc-pCVTZ level, that is, at the level of coupled-cluster theory with singles, doubles and non-iterative triples in a correlation-consistent polarized core-valence triple-zeta basis. Single-point energy calculations were performed at the all-electron CCSD(T) level in a correlation-consistent polarized core-valence quadruple-zeta basis (cc-pCVQZ), and several corrections were added: (i) a correction for the basis-set truncation error, obtained from second-order perturbation theory using Slater-type geminals (MP2-F12 theory), (ii) a correction for the effect of anharmonicity on the zero-point vibrational energy, (iii) a relativistic correction, (iv) a correction for the difference between the full CCSDT model (coupled-cluster theory with singles, doubles and triples) and the CCSD(T) approximation, and (v) a correction for connected quadruple excitations obtained from CCSDT(Q) calculations. The correction for the basis-set truncation error was obtained from MP2-F12 calculations by scaling the MP2 basis-set truncation error by an empirically optimized 'interference factor' of f{sub int} = 0.78. The reference values from the Active Thermochemical Tables for 73 molecules in the test set, the equilibrium geometries, the harmonic vibrational frequencies, and all of the energy corrections represent valuable data for performance assessments of additivity schemes that will be developed in the future, in which the basis-set truncation error will be calculated at the level of coupled-cluster theory using Slater-type geminals (CC-F12 theory). Such a scheme will be free of empirical

  19. Energy levels of isoelectronic impurities by large scale LDA calculations

    SciTech Connect

    Li, Jingbo; Wang, Lin-Wang

    2002-11-22

    Isoelectronic impurity states are localized states induced by stoichiometric single atom substitution in bulk semiconductor. Photoluminescence spectra indicate deep impurity levels of 0.5 to 0.9eV above the top of valence band for systems like: GaN:As, GaN:P, CdS:Te, ZnS:Te. Previous calculations based on small supercells seemingly confirmed these experimental results. However, the current ab initio calculations based on thousand atom supercells indicate that the impurity levels of the above systems are actually much shallower(0.04 to 0.23 eV), and these impurity levels should be compared with photoluminescence excitation spectra, not photoluminescence spectra.

  20. Protein unfolding from free-energy calculations: Integration of the Gaussian network model with bond binding energies

    NASA Astrophysics Data System (ADS)

    Srivastava, Amit; Granek, Rony

    2015-02-01

    Motivated by single molecule experiments, we study thermal unfolding pathways of four proteins, chymotrypsin inhibitor, barnase, ubiquitin, and adenylate kinase, using bond network models that combine bond energies and elasticity. The protein elasticity is described by the Gaussian network model (GNM), to which we add prescribed bond binding energies that are assigned to all (nonbackbone) connecting bonds in the GNM of native state and assumed identical for simplicity. Using exact calculation of the Helmholtz free energy for this model, we consider bond rupture single events. The bond designated for rupture is chosen by minimizing the free-energy difference for the process, over all (nonbackbone) bonds in the network. Plotting the free-energy profile along this pathway at different temperatures, we observe a few major partial unfolding, metastable or stable, states, that are separated by free-energy barriers and change role as the temperature is raised. In particular, for adenylate kinase we find three major partial unfolding states, which is consistent with single molecule FRET experiments [Pirchi et al., Nat. Commun. 2, 493 (2011), 10.1038/ncomms1504] for which hidden Markov analysis reveals between three and five such states. Such states can play a major role in enzymatic activity.

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

    NASA Astrophysics Data System (ADS)

    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

    NASA Astrophysics Data System (ADS)

    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. Advancing QCD-based calculations of energy loss

    NASA Astrophysics Data System (ADS)

    Tywoniuk, Konrad

    2013-08-01

    We give a brief overview of the basics and current developments of QCD-based calculations of radiative processes in medium. We put an emphasis on the underlying physics concepts and discuss the theoretical uncertainties inherently associated with the fundamental parameters to be extracted from data. An important area of development is the study of the single-gluon emission in medium. Moreover, establishing the correct physical picture of multi-gluon emissions is imperative for comparison with data. We will report on progress made in both directions and discuss perspectives for the future.

  4. Turbulent energy exchange: Calculation and relevance for profile prediction

    SciTech Connect

    Candy, J.

    2013-08-15

    The anomalous heat production due to turbulence is neither routinely calculated in nonlinear gyrokinetic simulations nor routinely retained in profile prediction studies. In this work, we develop a symmetrized method to compute the exchange which dramatically reduces the intermittency in the time-dependent moment, thereby improving the accuracy of the time-average. We also examine the practical impact on transport-timescale simulations, and show that the exchange has only a minor impact on profile evolution for a well-studied DIII-D discharge.

  5. Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors.

    PubMed

    Tripathi, Sunil Kumar; Muttineni, Ravikumar; Singh, Sanjeev Kumar

    2013-10-01

    Molecular docking, free energy calculation and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 3,5-diaminoindazoles, imidazo(1,2-b)pyridazines and triazolo(1,5-a) pyridazines series of Cyclin-dependent kinase (CDK2) inhibitors. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviations (RMSDs). We found different binding sites namely catalytic, inhibitory phosphorylation, cyclin binding and CKS-binding site of the CDK2 contributing towards the binding of these compounds. Moreover, correlation between free energy of binding and biological activity yielded a statistically significant correlation coefficient. Finally, three representative protein-ligand complexes were subjected to molecular dynamics simulation to determine the stability of the predicted conformations. The low value of the RMSDs between the initial complex structure and the energy minimized final average complex structure suggests that the derived docked complexes are close to equilibrium. We suggest that the phenylacetyl type of substituents and cyclohexyl moiety make the favorable interactions with a number of residues in the active site, and show better inhibitory activity to improve the pharmacokinetic profile of compounds against CDK2. The structure-based drug design strategy described in this study will be highly useful for the development of new inhibitors with high potency and selectivity. PMID:23727278

  6. Energy Activities for the Primary Classroom. Revised.

    ERIC Educational Resources Information Center

    Tierney, Blue, Comp.

    An energy education program at the primary level should help students to understand the nature and importance of energy, consider different energy sources, learn about energy conservation, prepare for energy related careers, and become energy conscious in other career fields. The activities charts, readings, and experiments provided in this…

  7. Improved thrust calculations of active magnetic bearings considering fringing flux

    NASA Astrophysics Data System (ADS)

    Jang, Seok-Myeong; Kim, Kwan-Ho; Ko, Kyoung-Jin; Choi, Ji-Hwan; Sung, So-Young; Lee, Yong-Bok

    2012-04-01

    A methodology for deriving fringing permeance in axisymmetric devices such as active thrust magnetic bearings (ATMBs) is presented. The methodology is used to develop an improved equivalent magnetic circuit (EMC) for ATMBs, which considers the fringing effect. This EMC was used to characterize the force between the housing and mover and the dependence of thrust and inductance on the air gap and input current, respectively. These characteristics were validated by comparison with those obtained by the finite element method and in experiments.

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

    SciTech Connect

    Larsen, Edward

    2013-06-17

    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. An artificial energy method for calculating flows with shocks

    NASA Technical Reports Server (NTRS)

    Rose, M. E.

    1980-01-01

    The artificial-viscosity method, first proposed by von Neumann and Richtmyer, introduces an artificial viscous pressure term in regions of compression such that an increase in entropy occurs in shock transition zones. The paper describes how dissipative flows can be induced by reducing the total energy available for adiabatic processes in shock zones. A class of inviscid fluid flows, called semiflows, is described in which the flows exhibit thermodynamic differences. Induced dissipative flows modify the pressure in regions of compression in a manner analogous to the artificial-viscosity method and for a gas, the effect is equivalent to suitably modifying the gas constant in the equation of state. By employing MacCormack's method and the usual non-adiabatic equations, numerical solutions of a Riemann problem are compared with the modified artificial energy method, showing that the dissipation effect predicted by the analytical formulation is reflected in the numerical method as well.

  10. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  11. Calculating Capstone Depleted Uranium Aerosol Concentrations from Beta Activity Measurements

    SciTech Connect

    Szrom, Fran; Falo, Gerald A.; Parkhurst, MaryAnn; Whicker, Jeffrey J.; Alberth, David P.

    2009-03-01

    Beta activity measurements were used as surrogate measurements of uranium mass in aerosol samples collected during the field testing phase of the Capstone Depleted Uranium (DU) Aerosol Study. These aerosol samples generated by the perforation of armored combat vehicles were used to characterize the depleted uranium (DU) source term for the subsequent human health risk assessment (HHRA) of Capstone aerosols. Establishing a calibration curve between beta activity measurements and uranium mass measurements is straightforward if the uranium isotopes are in equilibrium with their immediate short-lived, beta-emitting progeny. For DU samples collected during the Capstone study, it was determined that the equilibrium between the uranium isotopes and their immediate short lived, beta-emitting progeny had been disrupted when penetrators had perforated target vehicles. Adjustments were made to account for the disrupted equilibrium and for wall losses in the aerosol samplers. Correction factors for the disrupted equilibrium ranged from 0.16 to 1, and the wall loss correction factors ranged from 1 to 1.92.

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

    SciTech Connect

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

    2006-03-15

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2008-05-21

    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. PMID:18500853

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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. PMID:26616778

  17. Energy Storage. Teachers Guide. Science Activities in Energy.

    ERIC Educational Resources Information Center

    Jacobs, Mary Lynn, Ed.

    Included in this science activities energy package for students in grades 4-10 are 12 activities related to energy storage. Each activity is outlined on the front and back of a single sheet and is introduced by a key question. Most of the activities can be completed in the classroom with materials readily available in any community. Among the…

  18. Analytical calculation of proton linear energy transfer in voxelized geometries including secondary protons.

    PubMed

    Sanchez-Parcerisa, D; Cortés-Giraldo, M A; Dolney, D; Kondrla, M; Fager, M; Carabe, A

    2016-02-21

    In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm(-1)) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process. PMID:26840945

  19. Inconsistencies and ambiguities in calculating enzyme activity: The case of laccase.

    PubMed

    Baltierra-Trejo, Eduardo; Márquez-Benavides, Liliana; Sánchez-Yáñez, Juan Manuel

    2015-12-01

    Laccase is a key enzyme in the degradation of lignin by fungi. Reports indicate that the activity of this enzyme ranges from 3.5 to 484,000 U L(-1). Our aim was to analyze how laccase activity is calculated in the literature, and to determine statistically whether variations in activity are due to biological properties or to inconsistencies in calculation. We found a general lack of consensus on the definition of enzyme activity, and enzymes are sometimes characterized in terms of reaction rate and specific activity. Moreover, enzyme activity is calculated using at least seven different equations. Therefore, it is critical to standardize the calculation of laccase activity in order to compare results directly. PMID:26459230

  20. Heart rate calculation from ensemble brain wave using wavelet and Teager-Kaiser energy operator.

    PubMed

    Srinivasan, Jayaraman; Adithya, V

    2015-01-01

    Electroencephalogram (EEG) signal artifacts are caused by various factors, such as, Electro-oculogram (EOG), Electromyogram (EMG), Electrocardiogram (ECG), movement artifact and line interference. The relatively high electrical energy cardiac activity causes EEG artifacts. In EEG signal processing the general approach is to remove the ECG signal. In this paper, we introduce an automated method to extract the ECG signal from EEG using wavelet and Teager-Kaiser energy operator for R-peak enhancement and detection. From the detected R-peaks the heart rate (HR) is calculated for clinical diagnosis. To check the efficiency of our method, we compare the HR calculated from ECG signal recorded in synchronous with EEG. The proposed method yields a mean error of 1.4% for the heart rate and 1.7% for mean R-R interval. The result illustrates that, proposed method can be used for ECG extraction from single channel EEG and used in clinical diagnosis like estimation for stress analysis, fatigue, and sleep stages classification studies as a multi-model system. In addition, this method eliminates the dependence of additional synchronous ECG in extraction of ECG from EEG signal process. PMID:26737640

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

    SciTech Connect

    Perfetti, Christopher M; Rearden, Bradley T

    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.

  2. THE MAGNETIC ENERGY-HELICITY DIAGRAM OF SOLAR ACTIVE REGIONS

    SciTech Connect

    Tziotziou, Kostas; Georgoulis, Manolis K.; Raouafi, Nour-Eddine

    2012-11-01

    Using a recently proposed nonlinear force-free method designed for single-vector magnetograms of solar active regions, we calculate the instantaneous free magnetic energy and relative magnetic helicity budgets in 162 vector magnetograms corresponding to 42 different active regions. We find a statistically robust, monotonic correlation between the free magnetic energy and the relative magnetic helicity in the studied regions. This correlation implies that magnetic helicity, in addition to free magnetic energy, may be an essential ingredient for major solar eruptions. Eruptive active regions appear well segregated from non-eruptive ones in both free energy and relative helicity with major (at least M-class) flares occurring in active regions with free energy and relative helicity exceeding 4 Multiplication-Sign 10{sup 31} erg and 2 Multiplication-Sign 10{sup 42} Mx{sup 2}, respectively. The helicity threshold agrees well with estimates of the helicity contents of typical coronal mass ejections.

  3. Calculating kinetics parameters and reactivity changes with continuous-energy Monte Carlo

    SciTech Connect

    Kiedrowski, Brian C; Brown, Forrest B; Wilson, Paul

    2009-01-01

    The iterated fission probability interpretation of the adjoint flux forms the basis for a method to perform adjoint weighting of tally scores in continuous-energy Monte Carlo k-eigenvalue calculations. Applying this approach, adjoint-weighted tallies are developed for two applications: calculating point reactor kinetics parameters and estimating changes in reactivity from perturbations. Calculations are performed in the widely-used production code, MCNP, and the results of both applications are compared with discrete ordinates calculations, experimental measurements, and other Monte Carlo calculations.

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

    PubMed

    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. PMID:26487189

  5. Free energy calculations on snake venom metalloproteinase BaP1.

    PubMed

    Lingott, Torsten; Merfort, Irmgard; Steinbrecher, Thomas

    2012-06-01

    BaP1 is a snake venom metalloproteinase from the venom of Bothrops asper, showing high structural homology with the catalytic domain of human adamalysins and matrix metalloproteinases. It induces the release of cytokines, like interleukin-1 and tumor necrosis factor alpha. Recently, the high-resolution crystal structure of BaP1 with a bound inhibitor became available, representing an interesting model concerning inhibitor design for medicinally important metalloproteinases such as tumor necrosis factor alpha-converting enzyme and MMP13. We here use computational modeling to gain a better understanding about the binding properties of various ligands to BaP1, with a focus on computing ligand binding free energies. The obtained results should be of general significance for future research on medicinally important metalloproteinases. We have investigated the binding of the original inhibitor in detail and calculated its binding strength using MMP/GBSA free energy calculations. Additionally, the binding strengths of alternative ligands have been computed, and two of them are predicted and experimentally verified to strongly inhibit the enzyme. A suggestion for chemical modifications of BaP1 inhibitors could be made to guide future synthesis efforts. Furthermore, a contribution to the proteolytic reaction mechanism of metzincins is given. The pK value of the catalytically active glutamic acid residue 143 has been found to be significantly raised when compared with a free glutamate side chain. Calculations on other matrix metalloproteinases confirmed that this is not confined to BaP1, but seems to be a common feature of metzincins. PMID:22385614

  6. Energy Activities for Junior High Science.

    ERIC Educational Resources Information Center

    Beaver, David; And Others

    This document is a collection of six energy education activities for junior high school science. Its purpose is to help promote knowledge about energy, provide laboratory experiences, provoke inquiry, and relate energy to society through the science curriculum. The six activities are designed to take one to three class periods. Two of the…

  7. Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.

    2016-06-01

    The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.

  8. LCS/CINDER`90 accelerator tunnel activation calculations for the APT 1700-MeV accelerator tunnel

    SciTech Connect

    Court, J.D.; Snow, E.C.; Wilson, W.B.; Pitcher, E.R.

    1998-09-01

    Calculations have been done to determine the amount of activation in the linac components and tunnel air for the Accelerator Production of Tritium 1700-MeV superconducting linac. Proton transport is accomplished through the use of the LAHET Code System. Particle production and depletion from proton and high-energy neutron reactions, calculated in LAHET, as well as low-energy neutron fluxes calculated by MCNP, are passed to the radionuclide production code CINDER`90 to determine the source terms at various times after irradiation. The upper limit on total air activation based on conservative assumptions, for the entire tunnel air volume, was found to be 4.77 Ci after a nine-month irradiation. This is reduced to 0.09 Ci after a 10-hour cooling off period. The total activation for the full 1-km of beamline components was found to be less than 4 kCi, with the half-lives of the highest contributors ranging from 12 years to 2 minutes. This beamline component activation calculation was done for an irradiation time of 40 years, which is the anticipated lifetime of the superconducting linac.

  9. Ab initio calculations of accurate dissociation energy and analytic potential energy function for the second excited state B1Π of 7LiH

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong

    2006-12-01

    The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.

  10. A Simple Approach for the Calculation of Energy Levels of Light Atoms

    ERIC Educational Resources Information Center

    Woodyard, Jack R., Sr.

    1972-01-01

    Describes a method for direct calculation of energy levels by using elementary techniques. Describes the limitations of the approach but also claims that with a minimum amount of labor a student can get greater understanding of atomic physics problems. (PS)

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

    PubMed

    Ghosh, Soumya; Hammes-Schiffer, Sharon

    2015-01-01

    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. PMID:26263083

  12. Determining characteristics of melting cheese by activation energy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Activation energy of flow (Ea) between 30 and 44 deg C was measured from temperature sweeps of various cheeses to determine its usefulness in predicting rheological behavior upon heating. Seven cheese varieties were heated in a rheometer from 22 to 70 deg C, and Ea was calculated from the resulting ...

  13. Activation energy measurements in rheological analysis of cheese

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Activation energy of flow (Ea) was calculated from temperature sweeps of cheeses with contrasting characteristics to determine its usefulness in predicting rheological behavior upon heating. Cheddar, Colby, whole milk Mozzarella, low moisture part skim Mozzarella, Parmesan, soft goat, and Queso Fre...

  14. Energy Conservation Activity Packet, Grade 5.

    ERIC Educational Resources Information Center

    Bakke, Ruth

    This activity packet for grade 5 is one of a series developed in response to concern for energy conservation. It contains activities that stress an energy conservation ethic and includes many values clarification activities for grade five. The packet is divided into two parts and provides the teacher with background information, concepts and…

  15. Global calculations of microscopic energies and nuclear deformations: Isospin dependence of the spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Wu, Zhe-Ying; Qi, Chong; Wyss, Ramon; Liu, Hong-Liang

    2015-08-01

    Background: The deviation between different model calculations that may occur when one goes toward regions where the masses are unknown is getting increased attention. This is related to the uncertainties of the different models which may have not been fully understood. Purpose: To explore in detail the effect of the isospin dependence of the spin-orbital force in the Woods-Saxon potential on global binding energy and deformation calculations. Method: The microscopic energies and nuclear deformations of about 1850 even-even nuclei are calculated systematically within the macroscopic-microscopic framework using three Woods-Saxon parametrizations, with different isospin dependencies, which were constructed mainly for nuclear spectroscopy calculations. Calculations are performed in the deformation space (β2,γ ,β4) . Both the monopole and doubly stretched quadrupole interactions are considered for the pairing channel. Results: The ground-state deformations obtained by the three calculations are quite similar to each other. Large differences are seen mainly in neutron-rich nuclei and in superheavy nuclei. Systematic calculations on the shape-coexisting second minima are also presented. As for the microscopic energies of the ground states, the results are also very close to each other. Only in a few cases the difference is larger than 2 MeV. The total binding energy is estimated by adding the macroscopic energy provided by the usual liquid drop model with its parameters fitted through the least square root and minimax criteria. Calculations are also compared with the results of other macroscopic-microscopic mass models. Conclusions: All the three calculations give similar values for the deformations, microscopic energies, and binding energies of most nuclei. One may expect to have a better understanding of the isospin dependence of the spin-orbital force with more data on proton- and neutron-rich nuclei.

  16. Wind Energy Finance (WEF): An Online Calculator for Economic Analysis of Wind Projects

    SciTech Connect

    Not Available

    2004-02-01

    This brochure provides an overview of Wind Energy Finance (WEF), a free online cost of energy calculator developed by the National Renewable Energy Laboratory that provides quick, detailed economic evaluation of potential utility-scale wind energy projects. The brochure lists the features of the tool, the inputs and outputs that a user can expect, visuals of the screens and a Cash Flow Results table, and contact information.

  17. A New Approach for Surface Energy Calculations Applicable to High-throughput Design of New Interfaces

    NASA Astrophysics Data System (ADS)

    Ratsch, Christian; Kaminski, Jakub

    In this talk we will present a new approach for the calculation of surface energies of periodic crystal. For non-polar materials slabs (which are terminated by two identical surfaces) the task of calculating the surface energy is trivial. But it is more problematic for polar systems where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed new approach addresses this problem. It relies on carefully chosen capping atoms and the assumptions that their bond energy contributions can be used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surfaces energies with errors as low as 2%. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations. Our approach is suitable for high-throughput screening of new material interfaces, as accurate calculations of surface energies can be performed in an unsupervised algorithm. A New Approach for Surface Energy Calculations Applicable to High-throughput Design of New Interfaces.

  18. Variational calculation of highly excited rovibrational energy levels of H2O2.

    PubMed

    Polyansky, Oleg L; Kozin, Igor N; Ovsyannikov, Roman I; Małyszek, Paweł; Koput, Jacek; Tennyson, Jonathan; Yurchenko, Sergei N

    2013-08-15

    Results are presented for highly accurate ab initio variational calculation of the rotation-vibration energy levels of H2O2 in its electronic ground state. These results use a recently computed potential energy surface and the variational nuclear-motion programs WARV4, which uses an exact kinetic energy operator, and TROVE, which uses a numerical expansion for the kinetic energy. The TROVE calculations are performed for levels with high values of rotational excitation, J up to 35. The purely ab initio calculations of the rovibrational energy levels reproduce the observed levels with a standard deviation of about 1 cm(-1), similar to that of the J = 0 calculation, because the discrepancy between theory and experiment for rotational energies within a given vibrational state is substantially determined by the error in the vibrational band origin. Minor adjustments are made to the ab initio equilibrium geometry and to the height of the torsional barrier. Using these and correcting the band origins using the error in J = 0 states lowers the standard deviation of the observed-calculated energies to only 0.002 cm(-1) for levels up to J = 10 and 0.02 cm(-1) for all experimentally known energy levels, which extend up to J = 35. PMID:23611762

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

    SciTech Connect

    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.

  20. Energy and power limits for microbial activity

    NASA Astrophysics Data System (ADS)

    LaRowe, D.; Amend, J.

    2014-12-01

    The goal of this presentation is to describe a quantitative framework for determining how energy limits microbial activity, biomass and, ultimately, biogeochemical processes. Although this model can be applied to any environment, its utility is demonstrated in marine sediments, which are an attractive test habitat because they encompass a broad spectrum of energy levels, varying amounts of biomass and are ubiquitous. The potential number of active microbial cells in Arkonas Basin (Baltic Sea) sediments are estimated as a function of depth by quantifying the amount of energy that is available to them and the rate at which it is supplied: power. The amount of power supplied per cubic centimeter of sediment is determined by calculating the Gibbs energy of fermentation and sulfate reduction in combination with the rate of particulate organic carbon, POC, degradation. The Reactive Continuum Model (Boudreau and Ruddick, 1991), RCM, is used to determine the rate at which POC is made available for microbial consumption. The RCM represents POC as containing a range of different types of organic compounds whose ability to be consumed by microorganisms varies as a function of the age of the sediment and on the distribution of compound types that were initially deposited. The sediment age model and RCM parameters determined by (Mogollon et al., 2012) are used. The power available for fermentation and sulfate reduction coupled to H2 and acetate oxidation varies from 10-8 W cm-3 at the sediment water interface to between 10-11 - 10-12 W cm-3 at 3.5 meters below the seafloor, mbsf. Using values of maintenance powers for each of these catabolic activities taken from the literature, the total number of active cells in these sediments similarly decreases from just less than 108 cell cm-3 at the SWI to 4.6 x 104 cells cm-3 at 3.5 mbsf. The number of moles of POC decreases from 2.6 x 10-5 to 9.5 x 10-6, also becoming more recalcitrant with depth. Boudreau, B. P. and Ruddick, B. R

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

    NASA Astrophysics Data System (ADS)

    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.

  2. Primer: The DOE Wind Energy Program's Approach to Calculating Cost of Energy: July 9, 2005 - July 8, 2006

    SciTech Connect

    George, K.; Schweizer, T.

    2008-01-01

    This report details the methodology used by DOE to calculate levelized cost of wind energy and demonstrates the variation in COE estimates due to different financing assumptions independent of wind generation technology.

  3. The Effect of Calculator-Based Ranger Activities on Students' Graphing Ability.

    ERIC Educational Resources Information Center

    Kwon, Oh Nam

    2002-01-01

    Addresses three issues of Calculator-based Ranger (CBR) activities on graphing abilities: (a) the effect of CBR activities on graphing abilities; (b) the extent to which prior knowledge about graphing skills affects graphing ability; and (c) the influence of instructional styles on students' graphing abilities. Indicates that CBR activities are…

  4. Nuclear data processing for energy release and deposition calculations in the MC21 Monte Carlo code

    SciTech Connect

    Trumbull, T. H.

    2013-07-01

    With the recent emphasis in performing multiphysics calculations using Monte Carlo transport codes such as MC21, the need for accurate estimates of the energy deposition-and the subsequent heating - has increased. However, the availability and quality of data necessary to enable accurate neutron and photon energy deposition calculations can be an issue. A comprehensive method for handling the nuclear data required for energy deposition calculations in MC21 has been developed using the NDEX nuclear data processing system and leveraging the capabilities of NJOY. The method provides a collection of data to the MC21 Monte Carlo code supporting the computation of a wide variety of energy release and deposition tallies while also allowing calculations with different levels of fidelity to be performed. Detailed discussions on the usage of the various components of the energy release data are provided to demonstrate novel methods in borrowing photon production data, correcting for negative energy release quantities, and adjusting Q values when necessary to preserve energy balance. Since energy deposition within a reactor is a result of both neutron and photon interactions with materials, a discussion on the photon energy deposition data processing is also provided. (authors)

  5. Phenomenological calculation of nuclear binding energy and density with Yukawa-potentials

    NASA Astrophysics Data System (ADS)

    Scheid, W.

    2016-01-01

    In this paper, we study a phenomenological collective model for the calculation of the nuclear density and ground state binding energy of nuclei. The proton density is assumed proportional to the nuclear density. The total binding energy of the nuclear matter consists of the binding energy of infinite nuclear matter, of two Yukawa-potentials, of the Coulomb-energy and of the symmetry-energy. The parameters of the Yukawa-potential are fitted with the Bethe-Weizsäcker (BW) mass formula. The resulting binding energies and nuclear densities agree quite satisfying with known nuclear values.

  6. Surface energy of talc and chlorite: Comparison between electronegativity calculation and immersion results.

    PubMed

    Douillard, Jean-Marc; Salles, Fabrice; Henry, Marc; Malandrini, Harold; Clauss, Frédéric

    2007-01-15

    The surface energies of talc and chlorite is computed using a simple model, which uses the calculation of the electrostatic energy of the crystal. It is necessary to calculate the atomic charges. We have chosen to follow Henry's model of determination of partial charges using scales of electronegativity and hardness. The results are in correct agreement with a determination of the surface energy obtained from an analysis of the heat of immersion data. Both results indicate that the surface energy of talc is lower than the surface energy of chlorite, in agreement with observed behavior of wettability. The influence of Al and Fe on this phenomenon is discussed. Surface energy of this type of solids seems to depend more strongly on the geometry of the crystal than on the type of atoms pointing out of the surface; i.e., the surface energy depends more on the physics of the system than on its chemistry. PMID:17081554

  7. PERTURB: A program for calculating vibrational energies by generalized algebraic quantization

    NASA Astrophysics Data System (ADS)

    Fried, Laurence E.; Ezra, Gregory S.

    1988-09-01

    We describe PERTURB, a special purpose algebraic manipulation program which calculates vibrational eigenvalues in coupled oscillator systems. PERTURB implements the method of generalized algebraic quantization (AQ), in which Van Vleck perturbation theory is formulated in a mock phase space. The phase space formulation enables quantum and classical perturbation theory to be treated on the same footing, and allows the systematic calculation of corrections to classical perturbation results in powers of h̷. Generalized AQ is a powerful and efficient technique for calculating semiclassical vibrational energy levels. In many cases, including just the first correction to classical perturbation theory yields highly accurate energies.

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

    SciTech Connect

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

    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)

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

    SciTech Connect

    Perfetti, Christopher M; Rearden, Bradley 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 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.

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

    NASA Astrophysics Data System (ADS)

    Perfetti, Christopher M.; Rearden, Bradley T.

    2014-06-01

    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.

  11. A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases

    PubMed Central

    Rucker, Robert; Oelschlaeger, Peter; Warshel, Arieh

    2010-01-01

    DNA polymerase β (pol β) is a small eukaryotic enzyme with the ability to repair short single-stranded DNA gaps that has found use as a model system for larger replicative DNA polymerases. For all DNA polymerases, the factors determining their catalytic power and fidelity are the interactions between the bases of the base pair, amino acids near the active site, and the two magnesium ions. In this report, we study effects of all three aspects on human pol β transition state (TS) binding free energies by reproducing a consistent set of experimentally determined data for different structures. Our calculations comprise the combination of four different base pairs (incoming pyrimidine nucleotides incorporated opposite both matched and mismatched purines) with four different pol β structures (wild type and three separate mutations of ionized residues to alanine). We decompose the incoming deoxynucleoside 5′-triphosphate-TS, and run separate calculations for the neutral base part and the highly charged triphosphate part, using different dielectric constants in order to account for the specific electrostatic environments. This new approach improves our ability to predict the effect of matched and mismatched base pairing and of mutations in DNA polymerases on fidelity and may be a useful tool in studying the potential of DNA polymerase mutations in the development of cancer. It also supports our point of view with regards to the origin of the structural control of fidelity, allowing for a quantified description of the fidelity of DNA polymerases. PMID:19842163

  12. Intrinsic free energy in active nematics

    NASA Astrophysics Data System (ADS)

    Thampi, Sumesh P.; Doostmohammadi, Amin; Golestanian, Ramin; Yeomans, Julia M.

    2015-10-01

    Basing our arguments on the theory of active liquid crystals, we demonstrate, both analytically and numerically, that the activity can induce an effective free energy which enhances ordering in extensile systems of active rods and in contractile suspensions of active discs. We argue that this occurs because any ordering fluctuation is enhanced by the flow field it produces. A phase diagram in the temperature-activity plane compares ordering due to a thermodynamic free energy to that resulting from the activity. We also demonstrate that activity can drive variations in concentration, but for a different physical reason that relies on the separation of hydrodynamic and diffusive time scales.

  13. Simple energy-calculation method for solar industrial-process-heat steam systems

    NASA Astrophysics Data System (ADS)

    Gee, R. C.

    1983-01-01

    Designing a solar industrial process heat (IPH) system, sizing its components and predicting its annual energy delivery requires a method for calculating solar system performance. A calculation method that is accurate, easy to use, accounts for the impact of all important system parameters, and does not require use of a computer is described. Only simple graphs and a hand calculator are required to predict annual collector field performance and annual system losses. The energy calculation method is applicable to a variety of solar system configurations. The calculation method applied only to parabolic trough steam generation systems that do not employ thermal storage is described. Both flash tank and unfired boiler steam systems are covered.

  14. Simple energy-calculation method for solar industrial-process-heat steam systems

    SciTech Connect

    Gee, R.

    1983-01-01

    Designing a solar industrial-process heat (IPH) system, sizing its components and predicting its annual energy delivery requires a method for calculating solar system performance. A calculation method that is accurate, easy to use, accounts for the impact of all important system parameters, and does not require use of a computer is described. Only simple graphs and a hand calculator are required to predict annual collector field performance and annual system losses. The energy-calculation method is applicable to a variety of solar-system configurations. The calculation method applied only to parabolic-trough steam-generation systems that do not employ thermal storage is described. Both flash tank and unfired-boiler steam systems are covered.

  15. Quantum mechanical resonance calculations using an energy selected basis in hyperspherical coordinates

    NASA Astrophysics Data System (ADS)

    Montgomery, Jason

    2007-12-01

    Scattering resonances play a key role in many chemical processes, including unimolecular and bimolecular reactions and photodissociation. A significant theoretical emphasis over the past several decades has been placed on accurate resonance calculations for polyatomic systems. In spite of such efforts, a quantum treatment of molecular systems which exhibit a high density of states and strong coordinate coupling near dissociation remains a formidable task. The research described herein employs improved quantum mechanical methods to calculate a representation of nuclear motion, both bound and unbound, which is used subsequently to calculate accurate resonance energies and lifetimes for two triatomic systems: the neon trimer and ozone. Specifically, theory and results are given regarding the construction of an optimal, L2 eigenbasis using techniques such as the discrete variable representation, the energy selected basis (ESB) method, and iterative diagonalization methods. A new energy selection method is also developed and implemented for the neon trimer. Subsequent resonance calculations are described which make use of the artificial boundary inhomogeneity (ABI) method, adapted to work with the above mentioned ESB and hyperspherical coordinates. The ABI method is used to calculate a set of linearly independent wavefunctions (LIWs) at a given energy for the representation of the scattering wavefunction. Resonance parameters are obtained by imposing scattering boundary conditions on a linear combination of LIWs and solving for the S-matrix, S, its energy derivative, dS/dE, and the Smith lifetime matrix, Q. When available, comparisons are made with previously reported calculations.

  16. Meson self-energies calculated by the relativistic particle-hole-antiparticle representation

    SciTech Connect

    Nakano, M.; Noda, N.; Mitsumori, T.; Koide, K.; Kouno, H.; Hasegawa, A.; Liu, L.

    1997-12-01

    A new formulation of meson self-energies is introduced for {sigma},{omega},{pi},{rho},{delta}, and {eta} mesons on the basis of the particle-hole-antiparticle representation. We have studied the difference between the meson self-energy (MSE) of this representation and the MSE of the traditional density-Feynman (DF) representation. It is shown that the new formulation describes exactly the physical processes such as particle-hole excitations or particle-antiparticle excitations, and that, on the other hand, the meson self-energy based on the DF representation includes unphysical components. By numerical calculations, the meson self-energies describing the particle-hole excitations are shown to be close to each other for most of the meson self-energy in low momentum (R{lt}500 MeV) and low energy (R{sub 0}{lt}200 MeV). This fact implies that former calculations using the low momentum and low-energy part do not change greatly. The density part of the density-Feynman representation has been shown to have a resonant structure around the energy of particle-antiparticle excitation, which causes a large difference between the two representations in the meson spectrum calculations. Our investigation concludes that the former calculations based on the density-Feynman representation are not invalidated in many cases, but the particle-hole-antiparticle representation is more appropriate to treat exactly the physical processes. {copyright} {ital 1997} {ital The American Physical Society}

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

    ERIC Educational Resources Information Center

    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…

  18. CALCULATION OF ELECTRON AFFINITIES OF POLYCYCLIC AROMATIC HYDROCARBONS AND SOVATION ENERGIES OF THEIR ANIONS

    EPA Science Inventory

    Electron affinities (EAs) and free energies for electron attachment have been calculated for 42 polynuclear aromatic hydrocarbons and related molecules by a variety of theoretical models, including Koopmans' theorem methods and the L1E method from differences in energy between th...

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

    SciTech Connect

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

    2012-07-01

    More and more MOX fuels are used in all over the world in the past several decades. Compared with UO{sub 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 {sup 240}Pu and {sup 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)

  20. CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals.

    PubMed

    Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav

    2016-02-14

    A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol(-1) on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems. PMID:26874495

  1. CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals

    NASA Astrophysics Data System (ADS)

    Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav

    2016-02-01

    A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol-1 on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.

  2. Peruvian upwelling plankton respiration: calculations of carbon flux, nutrient retention efficiency, and heterotrophic energy production

    NASA Astrophysics Data System (ADS)

    Packard, T. T.; Osma, N.; Fernández-Urruzola, I.; Codispoti, L. A.; Christensen, J. P.; Gómez, M.

    2015-05-01

    Oceanic depth profiles of plankton respiration are described by a power function, RCO2 = (RCO2)0 (z/z0)b, similar to the vertical carbon flux profile. Furthermore, because both ocean processes are closely related, conceptually and mathematically, each can be calculated from the other. The exponent b, always negative, defines the maximum curvature of the respiration-depth profile and controls the carbon flux. When |b| is large, the carbon flux (FC) from the epipelagic ocean is low and the nutrient retention efficiency (NRE) is high, allowing these waters to maintain high productivity. The opposite occurs when |b| is small. This means that the attenuation of respiration in ocean water columns is critical in understanding and predicting both vertical FC as well as the capacity of epipelagic ecosystems to retain their nutrients. The ratio of seawater RCO2 to incoming FC is the NRE, a new metric that represents nutrient regeneration in a seawater layer in reference to the nutrients introduced into that layer via FC. A depth profile of FC is the integral of water column respiration. This relationship facilitates calculating ocean sections of FC from water column respiration. In an FC section and in a NRE section across the Peruvian upwelling system we found an FC maximum and a NRE minimum extending down to 400 m, 50 km off the Peruvian coast over the upper part of the continental slope. Finally, considering the coupling between respiratory electron transport system activity and heterotrophic oxidative phosphorylation promoted the calculation of an ocean section of heterotrophic energy production (HEP). It ranged from 250 to 500 J d-1 m-3 in the euphotic zone to less than 5 J d-1 m-3 below 200 m on this ocean section.

  3. Peru upwelling plankton respiration: calculations of carbon flux, nutrient retention efficiency and heterotrophic energy production

    NASA Astrophysics Data System (ADS)

    Packard, T. T.; Osma, N.; Fernández-Urruzola, I.; Codispoti, L. A.; Christensen, J. P.; Gómez, M.

    2014-11-01

    Oceanic depth profiles of plankton respiration are described by a power function, RCO2 = (RCO2)0(z/z0)b similar to the vertical carbon flux profile. Furthermore, because both ocean processes are closely related, conceptually and mathematically, each can be calculated from the other. The exponent (b), always negative, defines the maximum curvature of the respiration depth-profile and controls the carbon flux. When b is large, the C flux (FC) from the epipelagic ocean is low and the nutrient retention efficiency (NRE) is high allowing these waters to maintain high productivity. The opposite occurs when b is small. This means that the attenuation of respiration in ocean water columns is critical in understanding and predicting both vertical FC as well as the capacity of epipelagic ecosystems to retain their nutrients. The NRE is a new metric defined as the ratio of nutrient regeneration in a seawater layer to the nutrients introduced into that layer via FC. A depth-profile of FC is the integral of water column respiration. This relationship facilitates calculating ocean sections of FC from water column respiration. In a FC section across the Peru upwelling system we found a FC maximum extending down to 400 m, 50 km off the Peru coast. Finally, coupling respiratory electron transport system activity to heterotrophic oxidative phosphorylation promoted the calculation of an ocean section of heterotrophic energy production (HEP). It ranged from 250 to 500 J d-1 m-3 in the euphotic zone, to less than 5 J d-1 m-3 below 200 m on this ocean section.

  4. Complete calculation of electroweak corrections for polarized Møller scattering at high energies

    NASA Astrophysics Data System (ADS)

    Zykunov, V. A.

    2009-09-01

    A complete calculation of electroweak radiative corrections to observables of polarized Møller scattering at high energies was performed. This calculation took explicitly into account contributions caused by hard bremsstrahlung. A FORTRAN code that permitted including radiative corrections to high-energy Møller scattering under arbitrary electron-detection conditions was written. It was shown that the electroweak corrections caused by hard bremsstrahlung were rather strongly dependent on the choice of experimental cuts and changed substantially the polarization asymmetry in the region of high energies and over a broad interval of scattering angles.

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

    ERIC Educational Resources Information Center

    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)

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

    SciTech Connect

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

    2015-05-21

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

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

    PubMed

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

    2015-05-21

    The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared. PMID:26001454

  8. Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

  9. Calculation of bond dissociation energies of diatomic molecules using bond function basis sets with counterpoise corrections

    SciTech Connect

    Li, Z.; Pan, Y.K.; Tao, F.M.

    1996-01-15

    Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.

  10. Solar Energy Education. Renewable energy activities for biology

    SciTech Connect

    Not Available

    1982-01-01

    An instructional aid for teachers is presented that will allow biology students the opportunity to learn about renewable energy sources. Some of the school activities include using leaves as collectors of solar energy, solar energy stored in wood, and a fuel value test for green and dry woods. A study of organic wastes as a source of fuel is included. (BCS)

  11. Solar energy education. Renewable energy activities for general science

    SciTech Connect

    Not Available

    1985-01-01

    Renewable energy topics are integrated with the study of general science. The literature is provided in the form of a teaching manual and includes such topics as passive solar homes, siting a home for solar energy, and wind power for the home. Other energy topics are explored through library research activities. (BCS)

  12. Analytic calculation of the energy-momentum tensor in heavy ion collisions from color glass condensate

    NASA Astrophysics Data System (ADS)

    Li, Ming; Kapusta, Joseph I.

    2016-08-01

    We generalize calculations of the energy-momentum tensor for classical gluon fields in the boost-invariant McLerran-Venugopalan model using the small-τ power series expansion method. Results to all orders for the energy density and pressures are given in the leading Q2 approximation and with the inclusion of estimated running coupling effects. The energy density and transverse pressure decrease monotonically with time while the longitudinal pressure starts from a negative value and increases towards zero.

  13. Validation of a new formula for calculating the energy requirements of burn patients.

    PubMed

    Allard, J P; Pichard, C; Hoshino, E; Stechison, S; Fareholm, L; Peters, W J; Jeejeebhoy, K N

    1990-01-01

    In a previous study, we analyzed the roles of the estimated basal energy expenditure (EBEE) calculated by the Harris-Benedict equation, caloric intake (CI), total burn surface area (TBSA), body temperature (Temp) and number of post-burn days (PBD) in order to estimate the resting energy expenditure (EE) of burn patients. By multiple regression analysis we found that the measured EE (MEE) is best approximated by the following formula: -4343 + (10.5 x %TBSA) + (0.23 x CI) + (0.84 x EBEE) + (114 x Temp (degree C)) - (4.5 x PBD), r = 0.82, p less than 0.001, (Toronto formula (TF)). To validate this, 10 patients with a mean TBSA of 49.1 +/- 5.5% had their resting MEE done by indirect calorimetry when fed either by the TF or by 2 x EBEE. The caloric intake when on 2 x EBEE was 3260 +/- 45 kcal/day which significantly exceeded the MEE (2765 +/- 101 kcal/day, p less than 0.001). The caloric intake when on the TF was 2542 +/- 52 kcal/day and matches the MEE which was 2537 +/- 86 kcal/day (NS). These results show that the TF matches the MEE very closely. With the addition of a factor of activity for the 24-hr EE, it can be used to accurately feed individual burn patients. PMID:2112617

  14. Energy-efficiency testing activities of the Mobile Energy Laboratory

    SciTech Connect

    Parker, G.B.

    1991-01-01

    This report summarizes energy-efficiency testing activities during the first and second quarters of fiscal year 1990 applying the Mobile Energy Laboratory (MEL) testing capabilities. Four MELs, developed by the US Department of Energy (DOE) Federal Energy Management Program (FEMP), are administered by Pacific Northwest Laboratory (PNL) for energy testing and program support functions at federal facilities. The using agencies principally fund MEL applications, while DOE/FEMP funds program administration and capability enhancement activities. This report fulfills the requirements established in the MEL Use Plan (PNL-6861) for semiannual reporting on energy-efficiency testing activities using the MEL capabilities. The MEL Use Committee, formally established in 1989, developed the MEL Use Plan and meets semiannually to establish priorities for energy-efficient testing applications using the MEL capabilities.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

    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) are useful because the double layer effects are reduced. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in solute geometry and solvent configuration. In this Letter, an approach for calculating the electrochemical solvent 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 complex in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.

  17. Calculation of the characteristics of clinical high-energy photon beams with EGS5-MPI

    NASA Astrophysics Data System (ADS)

    Shimizu, M.; Morishita, Y.; Kato, M.; Kurosawa, T.; Tanaka, T.; Takata, N.; Saito, N.

    2014-03-01

    A graphite calorimeter has been developed as a Japanese primary standard of absorbed dose to water in the high-energy photon beams from a clinical linac. To obtain conversion factors for the graphite calorimeter, the beam characteristics of the high-energy photon beams from the clinical linac at National Metrology Institute of Japan were calculated with the EGS5 Monte Carlo simulation code. To run the EGS5 code on High Performance Computing machines that have more than 1000 CPU cores, we developed the EGS5 parallelisation package "EGS5-MPI" by implementing a message-passing interface. We calculated the photon energy spectra, which are in good agreement with those previously calculated by D. Sheikh-Bagheri and D. W. O. Rogers (Med. Phys. 29 3). We also estimated the percentage-depth-dose distributions of photon beams from the linac using the calculated photon energy spectra. These calculated percentage-depth-dose distributions were compared with our measured distributions and were found they are in good agreement as well. We will calculate conversion factors for the graphite calorimeter using our results.

  18. Comparison between calculation and measurement of energy deposited by 800 MeV protons

    SciTech Connect

    Loewe, W.E.

    1980-04-03

    The High Energy Transport Code, HETC, was obtained from the Radiation Shielding Information Center (RSIC) at Oak Ridge National Laboratory and altered as necessary to run on a CDC 7600 using the LTSS software in use at LLNL. HETC was then used to obtain calculated estimates of energy deposited, for comparison with a series of benchmark experiments done by LLNL. These experiments used proton beams of various energies incident on well-defined composite targets in good geometry. In this report, two aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam are discussed. Both aspects involve the fact that workers at SAI had previously used their version of HETC to calculate this experiment and reported their comparison with the measured data. The first aspect addressed is that their calculated data and LLNL calculations do not agree, suggesting an error in the conversion process from the RSIC code. The second aspect is not independent of the first, but is of sufficient importance to merit separate emphasis. It is that the SAI calculations agree well with experiments at the detector plate located some distance from the shower plate, whereas the LLNL calculations show a clearcut discrepancy there in comparison with the experiment. A contract was let in January 1980 by LLNL with SAI in order to obtain full details on the two cited aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam. The ensuing discussion is based on the final report of that contracted work.

  19. Solar Energy Project, Activities: General Solar Topics.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of activities which introduce students to concepts and issues relating to solar energy. Lessons frequently presented in the context of solar energy as it relates to contemporary energy problems. Each unit presents an introduction; objectives; necessary skills and knowledge; materials; method;…

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

    PubMed

    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. PMID:27214306

  1. The fast neutron fluence and the activation detector activity calculations using the effective source method and the adjoint function

    SciTech Connect

    Hep, J.; Konecna, A.; Krysl, V.; Smutny, V.

    2011-07-01

    This paper describes the application of effective source in forward calculations and the adjoint method to the solution of fast neutron fluence and activation detector activities in the reactor pressure vessel (RPV) and RPV cavity of a VVER-440 reactor. Its objective is the demonstration of both methods on a practical task. The effective source method applies the Boltzmann transport operator to time integrated source data in order to obtain neutron fluence and detector activities. By weighting the source data by time dependent decay of the detector activity, the result of the calculation is the detector activity. Alternatively, if the weighting is uniform with respect to time, the result is the fluence. The approach works because of the inherent linearity of radiation transport in non-multiplying time-invariant media. Integrated in this way, the source data are referred to as the effective source. The effective source in the forward calculations method thereby enables the analyst to replace numerous intensive transport calculations with a single transport calculation in which the time dependence and magnitude of the source are correctly represented. In this work, the effective source method has been expanded slightly in the following way: neutron source data were performed with few group method calculation using the active core calculation code MOBY-DICK. The follow-up neutron transport calculation was performed using the neutron transport code TORT to perform multigroup calculations. For comparison, an alternative method of calculation has been used based upon adjoint functions of the Boltzmann transport equation. Calculation of the three-dimensional (3-D) adjoint function for each required computational outcome has been obtained using the deterministic code TORT and the cross section library BGL440. Adjoint functions appropriate to the required fast neutron flux density and neutron reaction rates have been calculated for several significant points within the RPV

  2. Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations

    NASA Astrophysics Data System (ADS)

    Dieterich, Johannes M.; Werner, Hans-Joachim; Mata, Ricardo A.; Metz, Sebastian; Thiel, Walter

    2010-01-01

    Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol-1. The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

  3. Scaling equations to model variations in operating conditions for activation calculations

    SciTech Connect

    Ho, S.K.

    1994-11-01

    A simple approximate scheme of calculating the variations of fusion activation-induced radioactive inventories with reactor operating conditions (power and time) by scaling equations is formulated. Application of the scheme to evaluate radiological dose-contributing activation products for HT-9 ferritic steel first wall shows decent agreements with numerical results.

  4. Assessing the performance of popular QM methods for calculation of conformational energies of trialanine

    NASA Astrophysics Data System (ADS)

    Li, Yongxiu; Zhang, Saiqun; Zhang, John Z. H.; He, Xiao

    2016-05-01

    Accurate description of the conformational energies of the amino acids is essential for molecular dynamics simulation of protein structures. In this study, we compute the relative energies at 51 conformations for a trialanine tetrapeptide at different levels of theory. The computed energies at various theoretical levels, including the semiempirical DFTB method, HF, DFT, MP2 and CCSD(T), are compared with each other. The calculated energies from density-fitting local CCSD(T)/CBS (complete basis set) calculations are taken as the benchmark. The accuracy of the theoretical methods is highly dependent on the electronic correlation and dispersion corrections as well as the size of the basis sets. The involvement of the empirical dispersion energies in HF and DFT methods consistently improves their performance. Considering both the accuracy and computational efficiency, the Minnesota density functional M06-L-D and M06-2X-D are efficient and accurate for modeling of trialanine structures.

  5. Radioactivity of Potassium Solutions: A Comparison of Calculated Activity to Measured Activity from Gross Beta Counting and Gamma Spectroscopy

    SciTech Connect

    Gaylord, R F

    2005-07-26

    In order to determine if the measured beta activity for a solution containing potassium was exactly as predicted, particularly since the CES gas counter is not calibrated specifically with K-40, an experiment was conducted to compare measured activities from two radioanalytical methods (gamma spectroscopy and gas proportional counting) to calculated activities across a range of potassium concentrations. Potassium, being ubiquitous and naturally radioactive, is a well-known and common interference in gross beta counting methods. By measuring the observed beta activity due to K-40 in potassium-containing solutions across a wide range of concentrations, it was found that the observed beta activity agrees well with the beta activity calculated from the potassium concentration measured by standard inorganic analytical techniques, such as ICP-OES, and that using the measured potassium concentration to calculate the expected beta activity, and comparing this to the observed beta activity to determine if potassium can account for all the observed activity in a sample, is a valid technique. It was also observed that gamma spectroscopy is not an effective means of measuring K-40 activity below approximately 700 pCi/L, which corresponds to a solution with approximately 833 mg/L total potassium. Gas proportional counting for gross beta activity has a much lower detection limit, typically 20-50 picoCi/L for a liquid low in total dissolved solids, which corresponds to a potassium concentration of approximately 30-70 ppm K.

  6. Ab initio calculation of accurate dissociation energy, potential energy curve and dipole moment function for the A1Σ+ state 7LiH molecule

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Yang, Xiang-Dong; Zhu, Zun-Lue

    2006-05-01

    The reasonable dissociation limit of the A1Σ+ state 7LiH molecule is obtained. The accurate dissociation energy and the equilibrium geometry of this state are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space for the first time. The whole potential energy curve and the dipole moment function for the A1Σ+ state are calculated over a wide internuclear separation range from about 0.1 to 1.4 nm. The calculated equilibrium geometry and dissociation energy of this potential energy curve are of Re=0.2487 nm and De=1.064 eV, respectively. The unusual negative values of the anharmonicity constant and the vibration-rotational coupling constant are of ωeχe=-4.7158cm-1 and αe=-0.08649cm-1, respectively. The vertical excitation energy from the ground to the A1Σ+ state is calculated and the value is of 3.613 eV at 0.15875 nm (the equilibrium position of the ground state). The highly anomalous shape of this potential energy curve, which is exceptionally flat over a wide radial range around the equilibrium position, is discussed in detail. The harmonic frequency value of 502.47cm-1 about this state is approximately estimated. Careful comparison of the theoretical determinations with those obtained by previous theories about the A1Σ+ state dissociation energy clearly shows that the present calculations are much closer to the experiments than previous theories, thus represents an improvement.

  7. Hybrid energy harvesting using active thermal backplane

    NASA Astrophysics Data System (ADS)

    Kim, Hyun-Wook; Lee, Dong-Gun

    2016-04-01

    In this study, we demonstrate the concept of a new hybrid energy harvesting system by combing solar cells with magneto-thermoelectric generator (MTG, i.e., thermal energy harvesting). The silicon solar cell can easily reach high temperature under normal operating conditions. Thus the heated solar cell becomes rapidly less efficient as the temperature of solar cell rises. To increase the efficiency of the solar cell, air or water-based cooling system is used. To surpass conventional cooling devices requiring additional power as well as large working space for air/water collectors, we develop a new technology of pairing an active thermal backplane (ATB) to solar cell. The ATB design is based on MTG technology utilizing the physics of the 2nd order phase transition of active ferromagnetic materials. The MTG is cost-effective conversion of thermal energy to electrical energy and is fundamentally different from Seebeck TEG devices. The ATB (MTG) is in addition to being an energy conversion system, a very good conveyor of heat through both conduction and convection. Therefore, the ATB can provide dual-mode for the proposed hybrid energy harvesting. One is active convective and conductive cooling for heated solar cell. Another is active thermal energy harvesting from heat of solar cell. These novel hybrid energy harvesting device have potentially simultaneous energy conversion capability of solar and thermal energy into electricity. The results presented can be used for better understanding of hybrid energy harvesting system that can be integrated into commercial applications.

  8. Energy and Energy Conservation Activities for High School Students.

    ERIC Educational Resources Information Center

    Bottinelli, Charles A., Ed.; Dow, John O., Ed.

    This manual contains fifteen energy activities suitable for high school physical and environmental science and mathematics classrooms. The activities are independent, each having its own objectives, introduction, and background information. A special section of each activity is written for the instructor and contains limits, sample data, and…

  9. Monte Carlo calculations of characteristic quantities of low-energy electron irradiation to spacecraft dielectrics

    NASA Astrophysics Data System (ADS)

    Tan, Zhenyu; Dong, Lei; Tang, Fule

    2012-08-01

    The calculations of the characteristic quantities of low-energy electron (⩽20 keV) irradiation to the five typical spacecraft dielectrics, i.e. epoxy, kapton, mylar, polyethylene, and teflon, have been performed by means of Monte Carlo method. These characteristic quantities include the electron backscattering coefficient, the depth distributions of both energy deposition and deposited electrons, and the maximum penetration depth of deposited electrons in the dielectrics. A Monte Carlo model has been specifically constructed for simulating the transport of low-energy electrons in spacecraft dielectrics (organic materials). In this model, the description of the inelastic scattering of energetic electron is based on the dielectric approach developed previously and the Born-Ochkur's exchange correction is included. Especially, the optical energy loss functions of organic materials can be obtained using an empirical evaluation. In addition, the mean cross section based on the Mott model is proposed for calculating the elastic scattering of energetic electrons in organic materials for high simulation efficiency. The constructed Monte Carlo model has been examined by a series of calculations and comparisons with the reported experiments and other theoretical results. For the dielectrics under consideration and in the energy range of E0 ⩽ 20 keV, the calculated electron backscattering coefficients and the extrapolated range of deposited electrons are listed at selected energies in numerical form for convenient use, and an empirical expression of estimating the extrapolated range in the energy range of 1-20 keV is given. The distribution characteristics of both energy deposition and deposited electrons are presented, and it is found that kapton and mylar present the close characteristic quantities for each other, which is of significance for the choice of the dielectrics in design of spacecraft. The characteristic quantity calculations presented in this work are a

  10. Calculation of intensity of high energy muon groups observed deep underground

    NASA Technical Reports Server (NTRS)

    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.

  11. Development of Continuous-Energy Eigenvalue Sensitivity Coefficient Calculation Methods in the Shift Monte Carlo Code

    SciTech Connect

    Perfetti, Christopher M; Martin, William R; Rearden, Bradley T; Williams, Mark L

    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 neutron and gamma ray energy spectra for fusion reactor shield design: comparison with experiment

    SciTech Connect

    Santoro, R.T.; Alsmiller, R.G. Jr.; Barnes, J.M.; Chapman, G.T.

    1980-08-01

    Integral experiments that measure the transport of approx. 14 MeV D-T neutrons through laminated slabs of proposed fusion reactor shield materials have been carried out. Measured and calculated neutron and gamma ray energy spectra are compared as a function of the thickness and composition of stainless steel type 304, borated polyethylene, and Hevimet (a tungsten alloy), and as a function of detector position behind these materials. The measured data were obtained using a NE-213 liquid scintillator using pulse-shape discrimination methods to resolve neutron and gamma ray pulse height data and spectral unfolding methods to convert these data to energy spectra. The calculated data were obtained using two-dimensional discrete ordinates radiation transport methods in a complex calculational network that takes into account the energy-angle dependence of the D-T neutrons and the nonphysical anomalies of the S/sub n/ method.

  13. Maximizing the solar energy storage of the four substituted norbornadiene-quadricyclane system: DFT calculations

    NASA Astrophysics Data System (ADS)

    Vessally, Esmail; Aryana, Soma

    2016-01-01

    The purpose of this research is to study the solar energy storage in norbornadiene ( 1)/quadricyclane ( 2) system by four direct attachments of substituents at two carbon atoms on both sides of the double bonds C2=C3 and C5=C6 in 1 X and 2 X; calculating the relative energies at B3LYP/6-311++G** level of theory. The solar energy storage of four electron donating substituents, (push-push effect), X (X =-NH2,-OH) and four electron withdrawing substituents, (pull-pull effect) X (X =-CO2H,-CONH2,-NO2 and CN) were examined. The solar absorption bands were calculated for 1 X. The DFT calculations reveal that the bands were shifted to the visible spectrum region when the electron withdrawing substituents were used rather than the electron donating substituents.

  14. Monte Carlo calculations of high energy nucleon meson cascades and applications to galactic cosmic ray transport

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Alsmiller, R. G., Jr.; Chandler, K. C.

    1972-01-01

    Results obtained using a recently developed calculational method for determining the nucleon-meson cascade induced in thick materials by high-energy nucleons and charged pions are presented. The calculational method uses the intranuclear-cascade-evaporation model to treat nonelastic collisions by particles with energies approximately or smaller than GeV and an extrapolation model at higher energies. The following configurations are considered: (1) 19.2-GeV/c protons incident on iron; (2) 30.3-GeV/c protons incident on iron; (3) solar and galactic protons incident on the moon, and (4) galactic protons incident on tissue. For the first three configurations, experimental results are available and comparisons between the experimental and calculated results are given.

  15. Infrared Spectra and Calculated Binding Energies of γ-BUTYROLACTONE Dimers and Trimers

    NASA Astrophysics Data System (ADS)

    Willis, Eric; Baumann, Chris

    2014-06-01

    Infrared spectra for matrix-isolated γ-butyrolactone and γ-butyrolactone-d_6 were obtained. The carbonyl stretching mode occurs at 1803 cm-1 for the monomer species, 1786 cm-1 for the dimer species, and 1774 cm-1 for the trimer species (1797, 1789 and 1770 cm-1 for the deuterated isotopomer.) Vibrational frequencies calculated using density functional theory are in agreement with the experimental values. Density functional theory was used to calculate the structures and binding energies of γ-butyrolactone dimers and trimers. Binding energies of 55-58 kJ mol-1 are predicted for the dimer structures. Optimized geometries for stacked and ring trimer structures have been calculated, with predicted binding energies of up to 68 kJ mol-1.

  16. Ab initio calculations on collisions of low energy electrons with polyatomic molecules

    SciTech Connect

    Rescigno, T.N.

    1991-08-01

    The Kohn variational method is one of simplest, and oldest, techniques for performing scattering calculations. Nevertheless, a number of formal problems, as well as practical difficulties associated with the computation of certain required matrix elements, delayed its application to electron--molecule scattering problems for many years. This paper will describe the recent theoretical and computational developments that have made the complex'' Kohn variational method a practical tool for carrying out calculations of low energy electron--molecule scattering. Recent calculations on a number of target molecules will also be summarized. 41 refs., 7 figs.

  17. Efficient calculation of potential energy surfaces for the generation of vibrational wave functions

    NASA Astrophysics Data System (ADS)

    Rauhut, Guntram

    2004-11-01

    An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations—within the computation of the potential—on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan).

  18. Efficient calculation of potential energy surfaces for the generation of vibrational wave functions.

    PubMed

    Rauhut, Guntram

    2004-11-15

    An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations--within the computation of the potential--on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan). PMID:15538851

  19. Model potential calculation of the thermal donor energy spectrum in silicon

    NASA Astrophysics Data System (ADS)

    Chen, C. S.; Schroder, D. K.

    1988-06-01

    The two-parameter model potential originally proposed by Ning and Sah [Phys. Rev. B 4, 3468 (1971)] for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schröter, and Bourret [J. Appl. Phys. 56, 1670 (1984)].

  20. Model potential calculation of the thermal donor energy spectrum in silicon

    SciTech Connect

    Chen, C.S.; Schroder, D.K.

    1988-06-15

    The two-parameter model potential originally proposed by Ning and Sah (Phys. Rev. B 4, 3468 (1971)) for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schroeter, and Bourret (J. Appl. Phys. 56, 1670 (1984)).

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

    NASA Astrophysics Data System (ADS)

    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.

  2. Calculation of energy barriers for magnetic vortices in sub-100 nm dots

    NASA Astrophysics Data System (ADS)

    Lapa, Pavel; King, Andrew; Roshchin, Igor V.

    2012-10-01

    In a magnetic vortex, the magnetization is curling in plane everywhere except the ``core,'' where it is out of plane. Interest in switching of magnetic vortices in nanodots is stimulated by their potential application for magnetic memories and nano-oscillators. By combining analytical and micromagnetic techniques, we calculated energy barriers for vortex switching in 20 nm-thick iron dots as a function of applied in-plane field and dot diameter. Using analytical formula for magnetization distribution in the vortex,footnotetextN. A. Usov and S. E. Peschany, J. Magn. Magn. Mater. 118, 290 (1992). we performed micromagnetic calculations of the dot energy for different vortex core positions. In contrast to the ``rigid body approximation,'' the core size and core shape in our calculations were varied to achieve the energy minimum for every core displacement. The energy barriers required for vortex nucleation and annihilation were calculated as a function of magnetic field. By comparing these barriers to the thermal energy kBT we obtained the temperature dependences of the vortex nucleation and annihilation fields in good agreement with the experiment.footnotetextR. K. Dumas et al., Appl. Phys. Lett. 91, 202501 (2007).

  3. Symmetry adapted cluster-configuration interaction calculation of the photoelectron spectra of famous biological active steroids

    NASA Astrophysics Data System (ADS)

    Abyar, Fatemeh; Farrokhpour, Hossein

    2014-11-01

    The photoelectron spectra of some famous steroids, important in biology, were calculated in the gas phase. The selected steroids were 5α-androstane-3,11,17-trione, 4-androstane-3,11,17-trione, cortisol, cortisone, corticosterone, dexamethasone, estradiol and cholesterol. The calculations were performed employing symmetry-adapted cluster/configuration interaction (SAC-CI) method using the 6-311++G(2df,pd) basis set. The population ratios of conformers of each steroid were calculated and used for simulating the photoelectron spectrum of steroid. It was found that more than one conformer contribute to the photoelectron spectra of some steroids. To confirm the calculated photoelectron spectra, they compared with their corresponding experimental spectra. There were no experimental gas phase Hesbnd I photoelectron spectra for some of the steroids of this work in the literature and their calculated spectra can show a part of intrinsic characteristics of this molecules in the gas phase. The canonical molecular orbitals involved in the ionization of each steroid were calculated at the HF/6-311++g(d,p) level of theory. The spectral bands of each steroid were assigned by natural bonding orbital (NBO) calculations. Knowing the electronic structures of steroids helps us to understand their biological activities and find which sites of steroid become active when a modification is performing under a biological pathway.

  4. Validation and Benchmarking of a Practical Free Magnetic Energy and Relative Magnetic Helicity Budget Calculation in Solar Magnetic Structures

    NASA Astrophysics Data System (ADS)

    Moraitis, K.; Tziotziou, K.; Georgoulis, M. K.; Archontis, V.

    2014-12-01

    In earlier works we introduced and tested a nonlinear force-free (NLFF) method designed to self-consistently calculate the coronal free magnetic energy and the relative magnetic helicity budgets of observed solar magnetic structures. In principle, the method requires only a single, photospheric or low-chromospheric, vector magnetogram of a quiet-Sun patch or an active region and performs calculations without three-dimensional magnetic and velocity-field information. In this work we strictly validate this method using three-dimensional coronal magnetic fields. Benchmarking employs both synthetic, three-dimensional magnetohydrodynamic simulations and nonlinear force-free field extrapolations of the active-region solar corona. Our time-efficient NLFF method provides budgets that differ from those of more demanding semi-analytical methods by a factor of approximately three, at most. This difference is expected to come from the physical concept and the construction of the method. Temporal correlations show more discrepancies that are, however, soundly improved for more complex, massive active regions, reaching correlation coefficients on the order of, or exceeding, 0.9. In conclusion, we argue that our NLFF method can be reliably used for a routine and fast calculation of the free magnetic energy and relative magnetic helicity budgets in targeted parts of the solar magnetized corona. As explained in this article and in previous works, this is an asset that can lead to valuable insight into the physics and triggering of solar eruptions.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

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

    PubMed

    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. PMID:25807150

  7. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

    The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining

  8. Phenomenological Rashba model for calculating the electron energy spectrum on a cylinder

    NASA Astrophysics Data System (ADS)

    Savinskiĭ, S. S.; Belosludtsev, A. V.

    2007-05-01

    The energy spectrum of an electron on the surface of a cylinder is calculated using the Pauli equation with an additional term that takes into account the spin-orbit interaction. This term is taken in the approximation of a phenomenological Rashba model, which provides exact expressions for the wave functions and the electron energy spectrum on the cylinder surface in a static magnetic field.

  9. Variational calculation of energy levels for metastable states of antiprotonic helium

    NASA Astrophysics Data System (ADS)

    Hu, Mu-Hong; Yao, Si-Meng; Wang, Yi; Li, Wang; Gu, Ying-Ying; Zhong, Zhen-Xiang

    2016-06-01

    We apply the variational method in Hylleraas coordinates to solve the energy eigenvalue problem for antiprotonic helium molecular systems including p bar 3 He+ and p bar 4 He+. The numerical accuracy on the nonrelativistic energies is shown to reach 10-17, thus the precision of our results is only limited by the width of the metastable states. Expectation values of the Dirac delta operators for these states are also calculated.

  10. Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Donev, Aleksandar; Stillinger, Frank H.; Torquato, Salvatore

    2007-07-01

    We present a new event-driven molecular dynamics (MD) algorithm for measuring the free energy of nearly jammed packings of spherical and non-spherical hard particles. This Bounding Cell Molecular Dynamics (BCMD) algorithm exactly calculates the free-energy of a single-occupancy cell (SOC) model in which each particle is restricted to a neighborhood of its initial position using a hard-wall bounding cell. Our MD algorithm generalizes previous ones in the literature by enabling us to study non-spherical particles as well as to measure the free-energy change during continuous irreversible transformations. Moreover, we make connections to the well-studied problem of computing the volume of convex bodies in high dimensions using random walks. We test and verify the numerical accuracy of the method by comparing against rigorous asymptotic results for the free energy of jammed and isostatic disordered packings of both hard spheres and ellipsoids, for which the free energy can be calculated directly as the volume of a high-dimensional simplex. We also compare our results to previously published Monte Carlo results for hard-sphere crystals near melting and jamming and find excellent agreement. We have successfully used the BCMD algorithm to determine the configurational and free-volume contributions to the free energy of glassy states of binary hard disks [A. Donev, F.H. Stillinger, S. Torquato, Do binary hard disks exhibit an ideal glass transition? Phys. Rev. Lett. 96 (22) (2006) 225502]. The algorithm can also be used to determine phases with locally- or globally-minimal free energy, to calculate the free-energy cost of point and extended crystal defects, or to calculate the elastic moduli of glassy or crystalline solids, among other potential applications.

  11. Effects of activation energy and activation volume on the temperature-dependent viscosity of water.

    PubMed

    Kwang-Hua, Chu Rainer

    2016-08-01

    Water transport in a leaf is vulnerable to viscosity-induced changes. Recent research has suggested that these changes may be partially due to variation at the molecular scale, e.g., regulations via aquaporins, that induce reductions in leaf hydraulic conductance. What are the quantitative as well as qualitative changes in temperature-dependent viscosity due to the role of aquaporins in tuning activation energy and activation volume? Using the transition-state approach as well as the boundary perturbation method, we investigate temperature-dependent viscosity tuned by activation energy and activation volume. To validate our approach, we compare our numerical results with previous temperature-dependent viscosity measurements. The rather good fit between our calculations and measurements confirms our present approach. We have obtained critical parameters for the temperature-dependent (shear) viscosity of water that might be relevant to the increasing and reducing of leaf hydraulic conductance. These parameters are sensitive to temperature, activation energy, and activation volume. Once the activation energy increases, the (shear) viscosity of water increases. Our results also show that as the activation volume increases (say, 10^{-23}m^{3}), the (shear) viscosity of water decreases significantly and the latter induces the enhancing of leaf hydraulic conductance. Within the room-temperature regime, a small increase in the activation energy will increase the water viscosity or reduce the leaf hydraulic conductance. Our approach and results can be applied to diverse plant or leaf attributes. PMID:27627349

  12. EnergyPlus Analysis Capabilities for Use in California Building Energy Efficiency Standards Development and Compliance Calculations

    SciTech Connect

    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

  13. Comparison of Measured Dark Current Distributions with Calculated Damage Energy Distributions in HgCdTe

    NASA Technical Reports Server (NTRS)

    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.

  14. MCHF calculations of isotope shifts; I program implementation and test runs II large-scale active space calculations

    SciTech Connect

    Joensson, P.; Fischer, C.F.

    1994-03-30

    A new isotope shift program, part of the MCHF atomic structure package, has been written and tested. The program calculates the isotope shift of an atomic level from MCHF or CI wave functions. The program is specially designed to be used with very large CI expansions, for which angular data cannot be stored on disk. To explore the capacity of the program, large-scale isotope shift calculations have been performed for a number of low lying levels in B I and B II. From the isotope shifts of these levels the transition isotope shift have been calculated for the resonance transitions in B I and B II. The calculated transition isotope shifts in B I are in very good agreement with experimental shifts, and compare favourably with shifts obtained from a many-body perturbation calculation.

  15. Continuous energy, multi-dimensional discrete ordinates transport calculations for problem dependent resonance treatment

    NASA Astrophysics Data System (ADS)

    Zhong, Zhaopeng

    In the past twenty 20 years considerable progress has been made in developing new methods for solving the multi-dimensional transport problem. However the effort devoted to the resonance self-shielding calculation has lagged, and much less progress has been made in enhancing resonance-shielding techniques for generating problem-dependent multi-group cross sections (XS) for the multi-dimensional transport calculations. In several applications, the error introduced by self-shielding methods exceeds that due to uncertainties in the basic nuclear data, and often they can be the limiting factor on the accuracy of the final results. This work is to improve the accuracy of the resonance self-shielding calculation by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. A new method has been developed, it can calculate the continuous-energy neutron fluxes for the whole two-dimensional domain, which can be utilized as weighting function to process the self-shielded multi-group cross sections for reactor analysis and criticality calculations, and during this process, the two-dimensional heterogeneous effect in the resonance self-shielding calculation can be fully included. A new code, GEMINEWTRN (Group and Energy-Pointwise Methodology Implemented in NEWT for Resonance Neutronics) has been developed in the developing version of SCALE [1], it combines the energy pointwise (PW) capability of the CENTRM [2] with the two-dimensional discrete ordinates transport capability of lattice physics code NEWT [14]. Considering the large number of energy points in the resonance region (typically more than 30,000), the computational burden and memory requirement for GEMINEWTRN is tremendously large, some efforts have been performed to improve the computational efficiency, parallel computation has been implemented into GEMINEWTRN, which can save the computation and memory requirement a lot; some energy points reducing

  16. A Method for Calculating Fermi Energy and Carrier Concentrations in Semiconducts

    ERIC Educational Resources Information Center

    Gaylord, T. K.; Linxwiler, J. N., Jr.

    1976-01-01

    An efficient numerical method for calculating the Fermi energy, the free electron and free hole concentrations, and the ionized impurity conductors in a semiconductor material is described. The method allows freedom with respect to type of material, temperature, and amount and type of donor and acceptor impurities. (Author/CP)

  17. Microscopic calculations of nuclear and neutron matter, symmetry energy and neutron stars

    DOE PAGESBeta

    Gandolfi, S.

    2015-02-01

    We present Quantum Monte Carlo calculations of the equation of state of neutron matter. The equation of state is directly related to the symmetry energy and determines the mass and radius of neutron stars, providing then a connection between terrestrial experiments and astronomical observations. As a result, we also show preliminary results of the equation of state of nuclear matter.

  18. Calculation of the vacuum condensates of the trace of the energy-momentum tensor

    SciTech Connect

    Ksenzov, V. G.

    2008-04-15

    It is shown that a modification of the effective potential proposed by A.A. Migdal and Shifman makes it possible to calculate the vacuum condensates of the trace of the energy-momentum tensor in massless theories in various spacetime dimensions.

  19. Calculations of the heights, periods, profile parameters, and energy spectra of wind waves

    NASA Technical Reports Server (NTRS)

    Korneva, L. A.

    1975-01-01

    Sea wave behavior calculations require the precalculation of wave elements as well as consideration of the spectral functions of ocean wave formation. The spectrum of the random wave process is largely determined by the distribution of energy in the actual wind waves observed on the surface of the sea as expressed in statistical and spectral characteristics of the sea swell.

  20. Kinetic energies to analyze the experimental auger electron spectra by density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Endo, Kazunaka

    2016-02-01

    In the Auger electron spectra (AES) simulations, we define theoretical modified kinetic energies of AES in the density functional theory (DFT) calculations. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. This method is applied to simulate Auger electron spectra (AES) of 2nd periodic atom (Li, Be, B, C, N, O, F)-involving substances (LiF, beryllium, boron, graphite, GaN, SiO2, PTFE) by deMon DFT calculations using the model molecules of the unit cell. Experimental KVV (valence band electrons can fill K-shell core holes or be emitted during KVV-type transitions) AES of the (Li, O) atoms in the substances agree considerably well with simulation of AES obtained with the maximum kinetic energies of the atoms, while, for AES of LiF, and PTFE substance, the experimental F KVV AES is almost in accordance with the spectra from the transitionstate kinetic energy calculations.

  1. Hyperspherical hidden crossing calculation of Ps formation in low-energy e+-Na collisions

    NASA Astrophysics Data System (ADS)

    Ward, S. J.; Shertzer, J.

    2011-05-01

    The hyperspherical hidden crossing method (HHCM) can provide important insight into scattering processes. Previously, we have used the HHCM to calculate the Ps(1s)-formation cross section in low-energy e+-H and e+-Li collisions. Here we apply the HHCM to low-energy e+-Na collisions. We use the Peach model potential and treat e+e-Na+ as an effective three-body system. We calculate the Ps(1s)-formation cross sections for 0 <= L <= 3 and compare our results with a hyperspherical close-coupling calculation. The HHCM provides an explanation for the small S-wave Ps(1s)-formation cross section. The S-wave Stückelberg phase is close to π for the three collision systems due to destructive interference between the two amplitudes that correspond to different paths leading to Ps(1s) formation.

  2. Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo

    2015-05-01

    We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.

  3. Automated calculation of surface energy fluxes with high-frequency lake buoy data

    USGS Publications Warehouse

    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.

  4. On calculating the energy characteristics of a metal film with a dielectric coating

    NASA Astrophysics Data System (ADS)

    Babich, A. V.

    2014-02-01

    A method for calculating the characteristics of a metal film in a dielectric surroundings is suggested. The most interesting case of asymmetric metal-dielectric sandwiches, in which the dielectrics on both sides of the film are different, is considered in the context of the Kohn-Sham modified method. The spectrum, the electron work function, and the surface energy of polycrystalline and single-crystal films placed into passive insulators are calculated for the first time. In general, the dielectric surroundings leads to a negative change in the electron work function and the surface energy. In addition to size-effect-related changes, the shift of the work function is determined by the arithmetic mean of the dielectric constants of the surrounding media. Calculations have been performed for Na, Al, and Pb.

  5. Calculation of converged rovibrational energies and partition function for methane using vibrational-rotational configuration interaction.

    PubMed

    Chakraborty, Arindam; Truhlar, Donald G; Bowman, Joel M; Carter, Stuart

    2004-08-01

    The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. PMID:15260761

  6. Calculation of energy levels and transition amplitudes for barium and radium.

    SciTech Connect

    Dzuba, V. A.; Flambaum, V. V.; Physics; Univ. of New South Wales

    2007-01-01

    The radium atom is a promising system for studying parity and time invariance violating weak interactions. However, available experimental spectroscopic data for radium are insufficient for designing an optimal experimental setup. We calculate the energy levels and transition amplitudes for radium states of significant interest. Forty states corresponding to all possible configurations consisting of the 7s, 7p and 6d single-electron states as well as the states of the 7s8s, 7s8p and 7s7d configurations have been calculated. The energies of ten of these states corresponding to the 6d{sup 2}, 7s8s, 7p{sup 2} and 6d7p configurations are not known from experiment. Calculations for barium are used to control the accuracy.

  7. An efficient method for energy levels calculation using full symmetry and exact kinetic energy operator: Tetrahedral molecules

    SciTech Connect

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2015-03-07

    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 AB{sub 4} 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){sup −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 CH{sub 4} molecule is demonstrated.

  8. An efficient method for energy levels calculation using full symmetry and exact kinetic energy operator: Tetrahedral molecules

    NASA Astrophysics Data System (ADS)

    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.

  9. Calculated Energy Levels, Oscillator Strengths and Lifetimes in Al-like Argon

    NASA Astrophysics Data System (ADS)

    Gupta, G. P.; Msezane, A. Z.

    Excitation energies, oscillator strengths and transition probabilities for electric-dipole-allowed and inter-combination transitions among the 25 LS levels belonging to the (1s22s22p6)3s23p, 3s3p2, 3s23d, 3p3, 3s3p3d, 3s24s, 3s24p, 3s24d, 3s24f and 3s3p4s configurations of Ar VI are calculated using extensive configuration-interaction (CI) wave functions. From our transition probabilities we have also calculated the radiative lifetimes of doublet and quartet states of Ar VI. Our results are compared with other available theoretical calculations and the experimental data. To assess the importance of relativistic effects on our calculated values, we have also carried out calculations in the intermediate-coupling scheme. These effects are incorporated through the Breit-Pauli approximation via spin-orbit, spin-other-orbit, spin-spin, Darwin and mass correction terms. Small adjustments to the diagonal elements of the Hamiltonian matrices have been made so that the energy splittings are as close as possible to the experimental values. The energy splitting of 54 fine-structure levels, the oscillator strengths and transition probabilities for some strong dipole-allowed and intercombination transitions and the lifetimes of some fine-structure levels are presented and compared with available experimental and other theoretical values. Our lifetime for the 3s3p(1Po)3d(2Po) level calculated in intermediate-coupling scheme, while differing significantly from our LS value, shows excellent agreement with the experimental result of Pinnington et al. In this calculation we also predict new data for several levels where no other theoretical and experimental results are available.

  10. Summary report for ITER Task -- D4: Activation calculations for the stainless steel ITER design

    SciTech Connect

    Attaya, H.

    1995-02-01

    Detailed activation analysis for ITER has been performed as a part of ITER Task D4. The calculations have been performed for the shielding blanket (SS/water) and for the breeding blanket (LiN) options. The activation code RACC-P, which has been modified under IFER Task-D-10 for pulsed operation, has been used in this analysis. The spatial distributions of the radioactive inventory, decay heat, biological hazard potential, and the contact dose were calculated for the two designs for different operation modes and targeted fluences. A one-dimensional toroidal geometrical model has been utilized to determine the neutron fluxes in the two designs. The results are normalized for an inboard and outboard neutron wall loadings of 0.91 and 1.2 MW/M{sup 2}, respectively. The point-wise distributions of the decay gamma sources have been calculated everywhere in the reactor at several times after the shutdown of the two designs and are then used in the transport code ONEDANT to calculate the biological dose everywhere in the reactor. The point-wise distributions of all the responses have also been calculated. These calculations have been performed for neutron fluences of 3.0 MWa/M{sup 2}, which corresponds to the target fluence of ITER, and 0.1 MWa/M{sup 2}, which is anticipated to correspond to the beginning of an extended maintenance period.

  11. A method for calculating strain energy release rate based on beam theory

    NASA Technical Reports Server (NTRS)

    Sun, C. T.; Pandey, R. K.

    1993-01-01

    The Timoshenko beam theory was used to model cracked beams and to calculate the total strain energy release rate. The root rotation of the beam segments at the crack tip were estimated based on an approximate 2D elasticity solution. By including the strain energy released due to the root rotations of the beams during crack extension, the strain energy release rate obtained using beam theory agrees very well with the 2D finite element solution. Numerical examples were given for various beam geometries and loading conditions. Comparisons with existing beam models were also given.

  12. Calculating splittings between energy levels of different symmetry using path-integral methods.

    PubMed

    Mátyus, Edit; Althorpe, Stuart C

    2016-03-21

    It is well known that path-integral methods can be used to calculate the energy splitting between the ground and the first excited state. Here we show that this approach can be generalized to give the splitting patterns between all the lowest energy levels from different symmetry blocks that lie below the first-excited totally symmetric state. We demonstrate this property numerically for some two-dimensional models. The approach is likely to be useful for computing rovibrational energy levels and tunnelling splittings in floppy molecules and gas-phase clusters. PMID:27004864

  13. Calculations of hydrogen atom multiphoton energy level shifts, transition amplitudes and ionization probabilities

    NASA Astrophysics Data System (ADS)

    Whitney, K. G.; Chang, C. S.

    2008-07-01

    Analyses of the resonant multiphoton ionization of atoms require knowledge of ac Stark energy shifts and of multiphoton, bound-to-bound state, transition amplitudes. In this paper, we consider the three-photon photoionization of hydrogen atoms at frequencies that are at and surrounding the two-photon 1s to 2s resonance. AC energy shift sums of both the 1s and 2s states are calculated as a function of the laser frequency along with two-photon 1s → 2s resonant transition amplitude sums. These quantities are calculated using an extended version of a method, which has often been employed in a variety of ways, of calculating these sums by expressing them in terms of solutions to a variety of differential equations that are derived from the different sums being evaluated. We demonstrate how exact solutions are obtained to these differential equations, which lead to exact evaluations of the corresponding sums. A variety of different cases are analysed, some involving analytic continuation, some involving real number analysis and some involving complex number analysis. A dc Stark sum calculation of the 2s state is carried out to illustrate the case where analytic continuation, pole isolation and pole subtraction are required and where the calculation can be carried out analytically; the 2s state, ac Stark shift sum calculations involve a case where no analytic continuation is required, but where the solution to the differential equation produces complex numbers owing to the finite photoionization lifetime of the 2s state. Results from these calculations are then used to calculate three-photon ionization probabilities of relevance to an analysis of the multiphoton ionization data published by Kyrala and Nichols (1991 Phys. Rev. A 44, R1450).

  14. Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

    NASA Astrophysics Data System (ADS)

    Rod, Thomas H.; Rydberg, Patrik; Ryde, Ulf

    2006-05-01

    We compare free energy calculations for the methyl transfer reaction catalyzed by catechol O-methyltransferase using the quantum mechanical/molecular mechanical free energy method with implicit and explicit solvents. An analogous methylation reaction in a solution is also studied. For the explicit solvent model, we use the three-point transferable intermolecular potential model, and for the implicit model, we use the generalized Born molecular volume model as implemented in CHARMM. We find that activation and reaction free energies calculated with the two models are very similar, despite some structural differences that exist. A significant change in the polarization of the environment occurs as the reaction proceeds. This is more pronounced for the reaction in a solution than for the enzymatic reaction. For the enzymatic reaction, most of the changes take place in the protein rather than in the solvent, and, hence, the benefit of having an instantaneous relaxation of the solvent degrees of freedom is less pronounced for the enzymatic reaction than for the reaction in a solution. This is a likely reason why energies of the enzyme reaction are less sensitive to the choice of atomic radii than are energies of the reaction in a solution.

  15. A highly efficient hybrid method for calculating the hydration free energy of a protein.

    PubMed

    Oshima, Hiraku; Kinoshita, Masahiro

    2016-03-30

    We develop a new method for calculating the hydration free energy (HFE) of a protein with any net charge. The polar part of the energetic component in the HFE is expressed as a linear combination of four geometric measures (GMs) of the protein structure and the generalized Born (GB) energy plus a constant. The other constituents in the HFE are expressed as linear combinations of the four GMs. The coefficients (including the constant) in the linear combinations are determined using the three-dimensional reference interaction site model (3D-RISM) theory applied to sufficiently many protein structures. Once the coefficients are determined, the HFE and its constituents of any other protein structure are obtained simply by calculating the four GMs and GB energy. Our method and the 3D-RISM theory give perfectly correlated results. Nevertheless, the computation time required in our method is over four orders of magnitude shorter. PMID:26576506

  16. Efficient ab initio free energy calculations by classically assisted trajectory sampling

    NASA Astrophysics Data System (ADS)

    Wilson, Hugh F.

    2015-12-01

    A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.

  17. Learning Approach on the Ground State Energy Calculation of Helium Atom

    SciTech Connect

    Shah, Syed Naseem Hussain

    2010-07-28

    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. Learning Approach on the Ground State Energy Calculation of Helium Atom

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

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

    2014-05-14

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

  20. Long-lived activation products in TRIGA Mark II research reactor concrete shield: calculation and experiment

    NASA Astrophysics Data System (ADS)

    Žagar, Tomaž; Božič, Matjaž; Ravnik, Matjaž

    2004-12-01

    In this paper, a process of long-lived activity determination in research reactor concrete shielding is presented. The described process is a combination of experiment and calculations. Samples of original heavy reactor concrete containing mineral barite were irradiated inside the reactor shielding to measure its long-lived induced radioactivity. The most active long-lived (γ emitting) radioactive nuclides in the concrete were found to be 133Ba, 60Co and 152Eu. Neutron flux, activation rates and concrete activity were calculated for actual shield geometry for different irradiation and cooling times using TORT and ORIGEN codes. Experimental results of flux and activity measurements showed good agreement with the results of calculations. Volume of activated concrete waste after reactor decommissioning was estimated for particular case of Jožef Stefan Institute TRIGA reactor. It was observed that the clearance levels of some important long-lived isotopes typical for barite concrete (e.g. 133Ba, 41Ca) are not included in the IAEA and EU basic safety standards.

  1. Neutron Unfolding Code System for Calculating Neutron Flux Spectra from Activation Data of Dosimeter Foils.

    1982-04-30

    Version 00 As a part of the measurement and analysis plan for the Dosimetry Experiment at the "JOYO" experimental fast reactor, neutron flux spectral analysis is performed using the NEUPAC (Neutron Unfolding Code Package) code system. NEUPAC calculates the neutron flux spectra and other integral quantities from the activation data of the dosimeter foils.

  2. Office Occupations--Clerical--Calculators. Kit No. 75. Instructor's Manual [and] Student Learning Activity Guide.

    ERIC Educational Resources Information Center

    Stewart, Ada

    An instructor's manual and student activity guide on the clerical use of calculators are provided in this set of prevocational education materials which focuses on the vocational area of office occupations. (This set of materials is one of ninety-two prevocational education sets arranged around a cluster of seven vocational offerings: agriculture,…

  3. Operational Control Procedures for the Activated Sludge Process, Part III-A: Calculation Procedures.

    ERIC Educational Resources Information Center

    West, Alfred W.

    This is the second in a series of documents developed by the National Training and Operational Technology Center describing operational control procedures for the activated sludge process used in wastewater treatment. This document deals exclusively with the calculation procedures, including simplified mixing formulas, aeration tank…

  4. Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density using proximal Radial Distribution Functions

    PubMed Central

    Lin, Bin; Wong, Ka-Yiu; Hu, Char; Kokubo, Hironori; Pettitt, B. Montgomery

    2011-01-01

    Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy. PMID:21765968

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

    SciTech Connect

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

    2011-07-07

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

  6. Comparison of Measured Leakage Current Distributions with Calculated Damage Energy Distributions in HgCdTe

    NASA Technical Reports Server (NTRS)

    Marshall, C. J.; Ladbury, R.; Marshall, P. W.; Reed, R. A.; Howe, C.; Weller, B.; Mendenhall, M.; Waczynski, A.; Jordan, T. M.; Fodness, B.

    2006-01-01

    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 distribution were extracted from Monte Carlo simulations and combined to form a damage distribution using the analytic techniques first described in [I]. The calculations show that the high energy recoils from the nuclear inelastic reactions (calculated using the Monte Car10 code MCNPX [2]) produce a pronounced skewing of the damage energy distribution. The nuclear elastic component (also calculated using the MCNPX) has a negligible effect on the shape of the damage distribution. The Coulombic contribution was calculated using MRED [3,4], a Geant4 [4,5] 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.

  7. Calculations of planar defect energies in substitutional alloys using the special-quasirandom-structure approach

    NASA Astrophysics Data System (ADS)

    de Jong, Maarten; Qi, Liang; Olmsted, David L.; van de Walle, Axel; Asta, Mark

    2016-03-01

    A method is described for calculating the energetics of planar defects in alloys based on the special-quasirandom-structure (SQS) approach. We examine the accuracy of the approach employing atomistic calculations based on a classical embedded-atom-method (EAM) interatomic potential for hexagonal close packed (hcp) alloys, for which benchmark results can be obtained by direct configurational averaging. The results of these calculations demonstrate that the SQS-based approach can be employed to derive the concentration dependence of the energies of twin boundaries, unstable stacking faults, and surfaces to within an accuracy of approximately 10%. The SQS considered in this study contain up to 72 atoms and hence are small enough to be considered in first-principles density-functional-theory (DFT) based calculations. The application of the SQS-based approach in direct DFT-based calculations is demonstrated in a study of the concentration dependence of interfacial energies for {11 2 ¯1 } twins in hcp Ti-Al alloys.

  8. Energy Loss Calculations for Target Thickness Determinations using SRIM and Excel

    NASA Astrophysics Data System (ADS)

    Pawlak, A. S.; Greene, J. P.

    2011-10-01

    The thickness of a thin target foil can be determined by measuring the energy loss of alpha particles that travel through it. In the Target Laboratory of the Physics Division at Argonne National Laboratory (ANL), this is accomplished by measuring the energy loss of the 5812 keV alpha particles emitted by a 2 49 Cf source using a silicon detector set-up. The energy loss is translated into the target foil thickness using the stopping power for 4He in the target material obtained from the stopping/range tables provided by SRIM. This calculation has until recently been carried out using a program developed for this purpose, ``ENELOSS.'' This program uses the stopping/range tables from the original work published by Ziegler. Additionally, due to its design, ENELOSS is unable to easily accommodate targets made from compounds. In order to perform theses measurements using the most recent SRIM data, and to better calculate the thickness of compound targets, we have developed a ``Thickness Calculation'' spreadsheet using Microsoft Excel. This spreadsheet approach is not limited to elemental targets and employs stopping/range tables from the most recent edition of SRIM available on the web. The calculations obtained allow for more accurate target thicknesses and automates the process conveniently for repetitive measurements. This work was supported by the U.S. DoE, Nuclear Physics Division, under Contract No. W-31-109-Eng-38.

  9. Energy and angular dependence of active-type personal dosemeter for high-energy neutron.

    PubMed

    Rito, Hirotaka; Yamauchi, Tomoya; Oda, Keiji

    2011-07-01

    In order to develop an active-type personal dosemeter having suitable sensitivity to high-energy neutrons, the characteristic response of silicon surface barrier detector has been investigated experimentally and theoretically. An agreement of the shape of pulse-height distribution, its change with radiator thickness and the relative sensitivity was confirmed between the calculated and experimental results for 14.8-MeV neutrons. The angular dependence was estimated for other neutron energies, and found that the angular dependence decreased with the incident energy. The reason was also discussed with regard to the radiator thickness relative to maximum range of recoil protons. PMID:21613268

  10. High-energy neutrinos from active galactic nuclei

    NASA Technical Reports Server (NTRS)

    Stecker, F. W.; Done, C.; Salamon, M. H.; Sommers, P.

    1991-01-01

    The spectrum and high-energy neutrino background flux from photomeson production in active galactic nuclei (AGN) is calculated using the recent UV and X-ray observations to define the photon fields and an accretion-disk shock-acceleration model for producing high-energy particles. Collectively, AGN produce the dominant isotropic neutrino background between 10,000 and 10 to the 10th GeV, detectable with current instruments. AGN neutrinos should produce a sphere of stellar disruption which may explain the 'broad-line region' seen in AGN.

  11. Structure-activity correlations for organophosphorus ester anticholinesterases. Part 2: CNDO/2 calculations applied to ester hydrolysis rates

    NASA Technical Reports Server (NTRS)

    Johnson, H.; Kenley, R. A.; Rynard, C.; Golub, M. A.

    1984-01-01

    Quantitative structure-activity relationships are presented for the hydrolysis of organophosphorus esters, RR'P(O)X, where R and R' are alkyl and/or alkoxy groups and X is fluorine, chlorine or a phenoxy group. CNDO/2 calculations provide values for molecular parameters that correlate with alkaline hydrolysis rates. For each subset of esters with the same leaving group, X, the CNDO-derived net atomic charge at the central phosphorus atom correlates well with the alkaline hydrolysis rate constants. For the whole set of esters with different leaving groups, equations are derived that relate charge, orbital energy and bond order to the hydrolysis rate constants.

  12. Hybrid variational-perturbation method for calculating ro-vibrational energy levels of polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Pavlyuchko, A. I.; Yurchenko, S. N.; Tennyson, Jonathan

    2015-07-01

    A procedure for calculation of rotational-vibrational states of medium-sized molecules is presented. It combines the advantages of variational calculations and perturbation theory. The vibrational problem is solved by diagonalising a Hamiltonian matrix, which is partitioned into two sub-blocks. The first, smaller sub-block includes matrix elements with the largest contribution to the energy levels targeted in the calculations. The second, larger sub-block comprises those basis states which have little effect on these energy levels. Numerical perturbation theory, implemented as a Jacobi rotation, is used to compute the contributions from the matrix elements of the second sub-block. Only the first sub-block needs to be stored in memory and diagonalised. Calculations of the vibrational-rotational energy levels also employ a partitioning of the Hamiltonian matrix into sub-blocks, each of which corresponds either to a single vibrational state or a set of resonating vibrational states, with all associated rotational levels. Physically, this partitioning is efficient when the Coriolis coupling between different vibrational states is small. Numerical perturbation theory is used to include the cross-contributions from different vibrational states. Separate individual sub-blocks are then diagonalised, replacing the diagonalisation of a large Hamiltonian matrix with a number of small matrix diagonalisations. Numerical examples show that the proposed hybrid variational-perturbation method greatly speeds up the variational procedure without significant loss of precision for both vibrational-rotational energy levels and transition intensities. The hybrid scheme can be used for accurate nuclear motion calculations on molecules with up to 15 atoms on currently available computers.

  13. Toward understanding as photosynthetic biosignatures: light harvesting and energy transfer calculation

    NASA Astrophysics Data System (ADS)

    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

  14. Development of continuous-energy eigenvalue sensitivity coefficient calculation methods in the shift Monte Carlo Code

    SciTech Connect

    Perfetti, C.; Martin, W.; Rearden, B.; Williams, M.

    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)

  15. An Exact Calculation of Electron-Ion Energy Splitting in a Hot Plasma

    SciTech Connect

    Singleton, Robert L

    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}.

  16. X-alpha calculation of transition energies in multiply ionized atoms

    NASA Technical Reports Server (NTRS)

    Ringers, D. A.; Chen, M. H.

    1974-01-01

    It is shown that the accuracy of calculations can be improved if appropriate (different) values of alpha are used for each configuration. Alternatively, the Slater Transition state can be used, wherein a total energy difference is related to a difference in single electron eigenvalues. By a series expansion, the value of alpha for an excited configuration can be related to its value for the ground state configuration. The terms Delta alpha (delta Epsilon/delta alpha) exhibit a similar dependence on atomic number as the ground state values of alpha. Results of sample calculations are reported and compared with experiment.

  17. Calculation of quasiparticle energy spectrum of silicon using the correlated Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Ishihara, Takamitsu; Yamagami, Hiroshi; Matsuzawa, Kazuya; Yasuhara, Hiroshi

    1999-06-01

    We present quasiparticle energy spectrum calculations of silicon using the correlated Hartree-Fock method proposed by Yasuhara and Takada [Phys. Rev. B 43, 7200 (1991)], in which the information on the effective mass of an electron liquid is included in the form of a nonlocal spin-parallel potential in addition to a local potential. The calculated band gaps of silicon are much improved, compared with the local density approximation values. The minimum indirect band gap is evaluated to be 1.37 eV.

  18. A refined quartic potential energy surface and large scale vibrational calculations for S0 thiophosgene.

    PubMed

    Rashev, Svetoslav; Moule, David C

    2015-04-01

    In this work we present a full 6D quartic potential energy surface (PES) for S0 thiophosgene in curvilinear symmetrized bond-angle coordinates. The PES was refined starting from an ab initio field derived from acc-pVTZ basis set with CCSD(T) corrections for electron correlation. In the present calculations we used our variational method that was recently tested on formaldehyde and some of its isotopomers, along with additional improvements. The lower experimentally known vibrational levels for 35Cl2CS were reproduced quite well in the calculations, which can be regarded as a test for the feasibility of the obtained quartic PES. PMID:25615683

  19. Feasibility of a wavelet expansion method to treat energy in cell calculations

    SciTech Connect

    Van Rooijen, W. F. G.

    2012-07-01

    This paper discusses the application of the Discrete Wavelet Transform (DWT) for the functional expansion of the energy variable in a cell calculation. The motivation of the work is the desire to obtain a self-shielding methodology in which the treatment of the energy variable in a given material region can be automatically adapted to the complexity of the cross section in that region. Unfortunately, the work presented in this paper shows that it is generally not possible to obtain the desired adaptivity. The most fundamental reason is that in a multi-region system, the energy dependence of the flux in a given material region is a function of the energy dependent cross sections and sources in all material regions through which the neutrons have crossed before entering into the present material. The complexity of the energy dependence of the cross section in a material region is thus not necessarily linked to the energy dependence of the flux in that region. If one sacrifices the objective of adaptivity, then an accurate method can be obtained using the DWT as a functional expansion. However, the resulting system of equations is more complicated than the direct solution of a hyper-fine group calculation. The conclusion is thus that the DWT approach is not very practical. (authors)

  20. Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

    NASA Astrophysics Data System (ADS)

    Hošek, Petr; Spiwok, Vojtěch

    2016-01-01

    Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

  1. Potential energy surface and second virial coefficient of methane-water from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Akin-Ojo, Omololu; Szalewicz, Krzysztof

    2005-10-01

    Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03kcal /mol at a geometry where H2O is the proton donor, HO -H⋯CH4, with the O-H-C angle of 165°, while the secondary minimum, with an energy of -0.72kcal/mol, has CH4 in the role of the proton donor (H3C -H⋯OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.

  2. First-principles calculation of defect formation energies and electronic properties in stannate pyrochlores

    SciTech Connect

    Chen, Z, J; Xiao, H. Y.; Zu, Xiaotao T.; Gao, Fei

    2008-11-01

    The electronic structures and defect formation energies for a series of stannate pyrochlores Ln2Sn2O7 *Ln=La, Pr, Nd, Sm, Gd, Tb, Ho, Er, Lu, and Y* have been investigated using the first-principles total energy calculations. The calculated results show that Ln-site cation ionic radius, x-O48f, lattice constant and the covalency of the *Sn–O48f* bond have a significant affect on the defect formation energies. The cation-antisite defect has the lowest formation energy, as compared with that of other defects, indicating that cation disorder causes local oxygen disordering. The present studies suggest that Lu2Sn2O7 is the most resistant to ion beam-induced amorphization. The electronic structure calculations reveal that Ln2Sn2O7 compounds have direct band gaps of 2.64– 2.95 eV at the * point in the Brillouin zone. © 2008 American Institute of Physics.

  3. Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane

    SciTech Connect

    Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas

    2014-04-28

    Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.

  4. Nanoscale Properties and Stability Simulations of Alkali Activated Cement Phases from First Principle Calculations

    NASA Astrophysics Data System (ADS)

    Ozcelik, Ongun; White, Claire

    Using first principle density functional calculations, we present the nanoscale properties of interactions, local bonds, charge distributions, mechanical properties and strength of alkali activated cement phases which are the most promising alternative to the ordinary Portland cement with a much lower cost to the environment. We present results on the stability and long term durability of various alkali activated cement structures, effects of external alkali agents on their properties and ways of utilizing them for further applications. We compare the calculated properties of alkali activated cement with those of ordinary Portland cement and contribute to the formation of long term durability data of these phases. Comparison with X-ray and neutron scattering experiment results are also provided via pair distribution functions extracted from simulation results.

  5. Comparison of Fixed versus Calculated Activity of Radioiodine for the Treatment of Graves Disease in Adults

    PubMed Central

    Dominguez, Paulette N.; Jimeno, Cecilia A.; Obaldo, Jerry M.; Ogbac, Ruben V.

    2016-01-01

    Background Radioactive iodine as a treatment modality has been shown in several studies to be a safe and effective therapy for Graves disease. However, there is still no uniformity regarding optimal dosing method. The aim of this study is to compare the efficacy of calculated and fixed dosing of radioiodine for the treatment of Graves disease. Methods A hundred twenty-two patients diagnosed with Graves disease were randomized to receive either fixed or calculated dose of radioiodine. Those randomized to fixed activity received either low fixed activity at 9.9 mCi for thyroid gland size <40 g or high fixed activity at 14.9 mCi for thyroid gland size 40 to 80 g, and those grouped to calculated activity received 160 µCi/g of thyroid tissue adjusted for 24 hours radioiodine uptake. Thyroid function tests (free thyroxine [T4] and thyroid stimulating hormone [TSH]) were monitored at 10, 16, and 24 weeks after radioactive iodine therapy. The primary outcome, treatment failure was defined as persistently elevated free T4 and low TSH. Results Of the 122 patients randomized, 56 in the fixed dose group and 56 in the calculated dose group completed the follow-up. At the end of 6 months, the percentage of treatment failure was 37.50% in the calculated dose group versus 19.64% in the fixed dose group with a relative risk of 0.53 (95% confidence interval, 0.28 to 0.98) favoring the fixed dose group. Conclusion Fixed dose radioiodine has a significantly lower incidence of persistent hyperthyroidism at 6 months post-radioactive therapy. PMID:26996425

  6. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    NASA Astrophysics Data System (ADS)

    Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Yang, Weitao

    2009-04-01

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  7. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    SciTech Connect

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-04-28

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  8. Solar Energy Education. Renewable energy activities for earth science

    SciTech Connect

    Not Available

    1980-01-01

    A teaching manual is provided to aid teachers in introducing renewable energy topics to earth science students. The main emphasis is placed on solar energy. Activities for the student include a study of the greenhouse effect, solar gain for home heating, measuring solar radiation, and the construction of a model solar still to obtain fresh water. Instructions for the construction of apparatus to demonstrate a solar still, the greenhouse effect and measurement of the altitude and azimuth of the sun are included. (BCS)

  9. A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

    A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}

  10. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    SciTech Connect

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  11. Prediction of (1)P Rydberg energy levels of beryllium based on calculations with explicitly correlated Gaussians.

    PubMed

    Bubin, Sergiy; Adamowicz, Ludwik

    2014-01-14

    Benchmark variational calculations are performed for the seven lowest 1s(2)2s np ((1)P), n = 2...8, states of the beryllium atom. The calculations explicitly include the effect of finite mass of (9)Be nucleus and account perturbatively for the mass-velocity, Darwin, and spin-spin relativistic corrections. The wave functions of the states are expanded in terms of all-electron explicitly correlated Gaussian functions. Basis sets of up to 12,500 optimized Gaussians are used. The maximum discrepancy between the calculated nonrelativistic and experimental energies of 1s(2)2s np ((1)P) →1s(2)2s(2) ((1)S) transition is about 12 cm(-1). The inclusion of the relativistic corrections reduces the discrepancy to bellow 0.8 cm(-1). PMID:24437871

  12. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    NASA Astrophysics Data System (ADS)

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-01

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  13. GPU-based acceleration of free energy calculations in solid state physics

    NASA Astrophysics Data System (ADS)

    Januszewski, Michał; Ptok, Andrzej; Crivelli, Dawid; Gardas, Bartłomiej

    2015-07-01

    Obtaining a thermodynamically accurate phase diagram through numerical calculations is a computationally expensive problem that is crucially important to understanding the complex phenomena of solid state physics, such as superconductivity. In this work we show how this type of analysis can be significantly accelerated through the use of modern GPUs. We illustrate this with a concrete example of free energy calculation in multi-band iron-based superconductors, known to exhibit a superconducting state with oscillating order parameter (OP). Our approach can also be used for classical BCS-type superconductors. With a customized algorithm and compiler tuning we are able to achieve a 19×speedup compared to the CPU (119×compared to a single CPU core), reducing calculation time from minutes to mere seconds, enabling the analysis of larger systems and the elimination of finite size effects.

  14. Improved Coefficient Calculator for the California Energy Commission 6 Parameter Photovoltaic Module Model

    SciTech Connect

    Dobos, A. P.

    2012-05-01

    This paper describes an improved algorithm for calculating the six parameters required by the California Energy Commission (CEC) photovoltaic (PV) Calculator module model. Rebate applications in California require results from the CEC PV model, and thus depend on an up-to-date database of module characteristics. Currently, adding new modules to the database requires calculating operational coefficients using a general purpose equation solver - a cumbersome process for the 300+ modules added on average every month. The combination of empirical regressions and heuristic methods presented herein achieve automated convergence for 99.87% of the 5487 modules in the CEC database and greatly enhance the accuracy and efficiency by which new modules can be characterized and approved for use. The added robustness also permits general purpose use of the CEC/6 parameter module model by modelers and system analysts when standard module specifications are known, even if the module does not exist in a preprocessed database.

  15. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach

    PubMed Central

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-01-01

    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. PMID:26418190

  16. Efficient first-principles calculation of the quantum kinetic energy and momentum distribution of nuclei.

    PubMed

    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. PMID:23005275

  17. Efficient calculation of the polarizability: a simplified effective-energy technique

    NASA Astrophysics Data System (ADS)

    Berger, J. A.; Reining, L.; Sottile, F.

    2012-09-01

    In a recent publication [J.A. Berger, L. Reining, F. Sottile, Phys. Rev. B 82, 041103(R) (2010)] we introduced the effective-energy technique to calculate in an accurate and numerically efficient manner the GW self-energy as well as the polarizability, which is required to evaluate the screened Coulomb interaction W. In this work we show that the effective-energy technique can be used to further simplify the expression for the polarizability without a significant loss of accuracy. In contrast to standard sum-over-state methods where huge summations over empty states are required, our approach only requires summations over occupied states. The three simplest approximations we obtain for the polarizability are explicit functionals of an independent- or quasi-particle one-body reduced density matrix. We provide evidence of the numerical accuracy of this simplified effective-energy technique as well as an analysis of our method.

  18. Calculation of positron binding energies using the generalized any particle propagator theory

    SciTech Connect

    Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés

    2014-09-21

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.

  19. Conservation Activities Related to Energy: Energy Activities for Urban Elementary Students, K-6.

    ERIC Educational Resources Information Center

    Schmidt, Joan S.; And Others

    Presented are simple activities, experiments, and demonstrations relating to energy conservation in the home. Activities are divided into four areas: (1) kitchen, (2) house, (3) transportation, and (4) heating and cooling. The material has been designed to require a minimum of preparation. Activity and game masters are provided. Activities may be…

  20. Calculated dipole moment and energy in collision of a hydrogen molecule and a hydrogen atom

    NASA Technical Reports Server (NTRS)

    Patch, R. W.

    1973-01-01

    Calculations were carried out using three Slater-type 1s orbitals in the orthogonalized valencebond theory of McWeeny. Each orbital exponent was optimized, the H2 internuclear distance was varied from 7.416 x 10 to the -11th power to 7.673 x 10 to the -11th power m (1.401 to 1.450 bohrs). The intermolecular distance was varied from 1 to 4 bohrs (0.5292 to 2.117 x 10 to the 10th power). Linear, scalene, and isosceles configurations were used. A weighted average of the interaction energies was taken for each intermolecular distance. Although energies are tabulated, the principal purpose was to calculate the electric dipole moment and its derivative with respect to H2 internuclear distance.

  1. Calculating alpha Eigenvalues in a Continuous-Energy Infinite Medium with Monte Carlo

    SciTech Connect

    Betzler, Benjamin R.; Kiedrowski, Brian C.; Brown, Forrest B.; Martin, William R.

    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.

  2. The ground-state potential energy curve of the radium dimer from relativistic coupled cluster calculations

    NASA Astrophysics Data System (ADS)

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas

    2015-08-01

    The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm-1, and a harmonic vibrational frequency of 20.5 cm-1. The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 103, C8 = 6.978 × 105, and C10 = 8.786 × 107 atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment.

  3. S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence

    SciTech Connect

    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.

  4. Microscopic calculation of interacting boson model parameters by potential-energy surface mapping

    SciTech Connect

    Bentley, I.; Frauendorf, S.

    2011-06-15

    A coherent state technique is used to generate an interacting boson model (IBM) Hamiltonian energy surface which is adjusted to match a mean-field energy surface. This technique allows the calculation of IBM Hamiltonian parameters, prediction of properties of low-lying collective states, as well as the generation of probability distributions of various shapes in the ground state of transitional nuclei, the last two of which are of astrophysical interest. The results for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium, and erbium nuclei are compared with experiment.

  5. Calculation of free energies in fluid membranes subject to heterogeneous curvature fields

    NASA Astrophysics Data System (ADS)

    Agrawal, Neeraj J.; Radhakrishnan, Ravi

    2009-07-01

    We present a computational methodology for incorporating thermal effects and calculating relative free energies for elastic fluid membranes subject to spatially dependent intrinsic curvature fields using the method of thermodynamic integration. Based on a simple model for the intrinsic curvature imposed only in a localized region of the membrane, we employ thermodynamic integration to calculate the free-energy change as a function of increasing strength of the intrinsic curvature field and a thermodynamic cycle to compute free-energy changes for different sizes of the localized region. By explicitly computing the free-energy changes and by quantifying the loss of entropy accompanied with increasing membrane deformation, we show that the membrane stiffness increases with increasing intrinsic field, thereby, renormalizing the membrane bending rigidity. The second main conclusion of this work is that the entropy of the membrane decreases with increasing size of the localized region subject to the curvature field. Our results help to quantify the free-energy change when a planar membrane deforms under the influence of curvature-inducing proteins at a finite temperature.

  6. Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation

    PubMed Central

    Pan, Keyao; Deem, Michael W.

    2011-01-01

    Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody binding free energy (ΔΔG) induced by amino acid substitution at each position in epitope B of the H3N2 influenza hemagglutinin, the key target for antibody. A substitution with positive ΔΔG value decreases the antibody binding constant. On average an uncharged to charged amino acid substitution generates the highest ΔΔG values. Also on average, substitutions between small amino acids generate ΔΔG values near to zero. The 21 sites in epitope B have varying expected free energy differences for a random substitution. Historical amino acid substitutions in epitope B for the A/Aichi/2/1968 strain of influenza A show that most fixed and temporarily circulating substitutions generate positive ΔΔG values. We propose that the observed pattern of H3N2 virus evolution is affected by the free energy landscape, the mapping from the free energy landscape to virus fitness landscape, and random genetic drift of the virus. Monte Carlo simulations of virus evolution are presented to support this view. PMID:21691431

  7. Calculations of binding energies and masses of heavy quarkonia using renormalon cancellation

    NASA Astrophysics Data System (ADS)

    Contreras, Carlos; Cvetič, Gorazd; Gaete, Patricio

    2004-08-01

    We use various methods of Borel integration to calculate the binding ground energies and masses of bb¯ and tt¯ quarkonia. The methods take into account the leading infrared renormalon structure of the (hard+)soft part of the binding energies E(s), and of the corresponding quark pole masses mq, where the contributions of these singularities in M(s)=2mq+E(s) cancel. Beforehand, we carry out the separation of the binding energy into its (hard+)soft and ultrasoft parts. The resummation formalisms are applied to expansions of mq and E(s) in terms of quantities which do not involve renormalon ambiguity, such as MS¯ mass mq and αs(μ). The renormalization scales μ are different in calculations of mq, E(s) and E(us). The mass mb is extracted, and the binding energies Ett¯ and the peak (resonance) energies Eres. for tt¯ production are obtained.

  8. Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

    PubMed

    Cecchini, M; Krivov, S V; Spichty, M; Karplus, M

    2009-07-23

    Conformational free-energy differences are key quantities for understanding important phenomena in molecular biology that involve large structural changes of macromolecules. In this paper, an improved version of the confinement approach, which is based on earlier developments, is used to determine the free energy of individual molecular states by progressively restraining the corresponding molecular structures to pure harmonic basins, whose absolute free energy can be computed by normal-mode analysis. The method is used to calculate the free-energy difference between two conformational states of the alanine dipeptide in vacuo, and of the beta-hairpin from protein G with an implicit solvation model. In all cases, the confinement results are in excellent agreement with the ones obtained from converged equilibrium molecular dynamics simulations, which have a much larger computational cost. The systematic and statistical errors of the results are evaluated and the origin of the errors is identified. The sensitivity of the calculated free-energy differences to structure-based definitions of the molecular states is discussed. A variant of the method, which closes the thermodynamic cycle by a quasi-harmonic rather than harmonic analysis, is introduced. The latter is proposed for possible use with explicit solvent simulations. PMID:19552392

  9. ACDOS1: a computer code to calculate dose rates from neutron activation of neutral beamlines and other fusion-reactor components

    SciTech Connect

    Keney, G.S.

    1981-08-01

    A computer code has been written to calculate neutron induced activation of neutral-beam injector components and the corresponding dose rates as a function of geometry, component composition, and time after shutdown. The code, ACDOS1, was written in FORTRAN IV to calculate both activity and dose rates for up to 30 target nuclides and 50 neutron groups. Sufficient versatility has also been incorporated into the code to make it applicable to a variety of general activation problems due to neutrons of energy less than 20 MeV.

  10. USING TIME VARIANT VOLTAGE TO CALCULATE ENERGY CONSUMPTION AND POWER USE OF BUILDING SYSTEMS

    SciTech Connect

    Makhmalbaf, Atefe; Augenbroe , Godfried

    2015-12-09

    Buildings are the main consumers of electricity across the world. However, in the research and studies related to building performance assessment, the focus has been on evaluating the energy efficiency of buildings whereas the instantaneous power efficiency has been overlooked as an important aspect of total energy consumption. As a result, we never developed adequate models that capture both thermal and electrical characteristics (e.g., voltage) of building systems to assess the impact of variations in the power system and emerging technologies of the smart grid on buildings energy and power performance and vice versa. This paper argues that the power performance of buildings as a function of electrical parameters should be evaluated in addition to systems’ mechanical and thermal behavior. The main advantage of capturing electrical behavior of building load is to better understand instantaneous power consumption and more importantly to control it. Voltage is one of the electrical parameters that can be used to describe load. Hence, voltage dependent power models are constructed in this work and they are coupled with existing thermal energy models. Lack of models that describe electrical behavior of systems also adds to the uncertainty of energy consumption calculations carried out in building energy simulation tools such as EnergyPlus, a common building energy modeling and simulation tool. To integrate voltage-dependent power models with thermal models, the thermal cycle (operation mode) of each system was fed into the voltage-based electrical model. Energy consumption of systems used in this study were simulated using EnergyPlus. Simulated results were then compared with estimated and measured power data. The mean square error (MSE) between simulated, estimated, and measured values were calculated. Results indicate that estimated power has lower MSE when compared with measured data than simulated results. Results discussed in this paper will illustrate the

  11. Bimodality emerges from transport model calculations of heavy ion collisions at intermediate energy

    NASA Astrophysics Data System (ADS)

    Mallik, S.; Das Gupta, S.; Chaudhuri, G.

    2016-04-01

    This work is a continuation of our effort [S. Mallik, S. Das Gupta, and G. Chaudhuri, Phys. Rev. C 91, 034616 (2015)], 10.1103/PhysRevC.91.034616 to examine if signatures of a phase transition can be extracted from transport model calculations of heavy ion collisions at intermediate energy. A signature of first-order phase transition is the appearance of a bimodal distribution in Pm(k ) in finite systems. Here Pm(k ) is the probability that the maximum of the multiplicity distribution occurs at mass number k . Using a well-known model for event generation [Botzmann-Uehling-Uhlenbeck (BUU) plus fluctuation], we study two cases of central collision: mass 40 on mass 40 and mass 120 on mass 120. Bimodality is seen in both the cases. The results are quite similar to those obtained in statistical model calculations. An intriguing feature is seen. We observe that at the energy where bimodality occurs, other phase-transition-like signatures appear. There are breaks in certain first-order derivatives. We then examine if such breaks appear in standard BUU calculations without fluctuations. They do. The implication is interesting. If first-order phase transition occurs, it may be possible to recognize that from ordinary BUU calculations. Probably the reason this has not been seen already is because this aspect was not investigated before.

  12. Calculation of electron transfer reorganization energies using the finite difference Poisson-Boltzmann model.

    PubMed Central

    Sharp, K A

    1998-01-01

    A description is given of a method to calculate the electron transfer reorganization energy (lambda) in proteins using the linear or nonlinear Poisson-Boltzmann (PB) equation. Finite difference solutions to the linear PB equation are then used to calculate lambda for intramolecular electron transfer reactions in the photosynthetic reaction center from Rhodopseudomonas viridis and the ruthenated heme proteins cytochrome c, myoglobin, and cytochrome b and for intermolecular electron transfer between two cytochrome c molecules. The overall agreement with experiment is good considering both the experimental and computational difficulties in estimating lambda. The calculations show that acceptor/donor separation and position of the cofactors with respect to the protein/solvent boundary are equally important and, along with the overall polarizability of the protein, are the major determinants of lambda. In agreement with previous studies, the calculations show that the protein provides a low reorganization environment for electron transfer. Agreement with experiment is best if the protein polarizability is modeled with a low (<8) average effective dielectric constant. The effect of buried waters on the reorganization energy of the photosynthetic reaction center was examined and found to make a contribution ranging from 0.05 eV to 0.27 eV, depending on the donor/acceptor pair. PMID:9512022

  13. Considerations on the acoustic energy radiated by toothed gears. [model for calculating noise intensity

    NASA Technical Reports Server (NTRS)

    Popinceanu, N. G.; Kremmer, I.

    1974-01-01

    A mechano-acoustic model is reported for calculating acoustic energy radiated by a working gear. According to this model, a gear is an acoustic coublet formed of the two wheels. The wheel teeth generate cylindrical acoustic waves while the front surfaces of the teeth behave like vibrating pistons. Theoretical results are checked experimentally and good agreement is obtained with open gears. The experiments show that the air noise effect is negligible as compared with the structural noise transmitted to the gear box.

  14. New algorithms for the Vavilov distribution calculation and the corresponding energy loss sampling

    SciTech Connect

    Chibani, O. |

    1998-10-01

    Two new algorithms for the fast calculation of the Vavilov distribution within the interval 0.01 {le} {kappa} {le} 10, where neither the Gaussian approximation nor the Landau distribution may be used, are presented. These algorithms are particularly convenient for the sampling of the corresponding random energy loss. A comparison with the exact Vavilov distribution for the case of protons traversing Al slabs is given.

  15. Accurate potential energy curve of the LiH{sup +} molecule calculated with explicitly correlated Gaussian functions

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  16. Dual-energy CT-based material extraction for tissue segmentation in Monte Carlo dose calculations

    NASA Astrophysics Data System (ADS)

    Bazalova, Magdalena; Carrier, Jean-François; Beaulieu, Luc; Verhaegen, Frank

    2008-05-01

    Monte Carlo (MC) dose calculations are performed on patient geometries derived from computed tomography (CT) images. For most available MC codes, the Hounsfield units (HU) in each voxel of a CT image have to be converted into mass density (ρ) and material type. This is typically done with a (HU; ρ) calibration curve which may lead to mis-assignment of media. In this work, an improved material segmentation using dual-energy CT-based material extraction is presented. For this purpose, the differences in extracted effective atomic numbers Z and the relative electron densities ρe of each voxel are used. Dual-energy CT material extraction based on parametrization of the linear attenuation coefficient for 17 tissue-equivalent inserts inside a solid water phantom was done. Scans of the phantom were acquired at 100 kVp and 140 kVp from which Z and ρe values of each insert were derived. The mean errors on Z and ρe extraction were 2.8% and 1.8%, respectively. Phantom dose calculations were performed for 250 kVp and 18 MV photon beams and an 18 MeV electron beam in the EGSnrc/DOSXYZnrc code. Two material assignments were used: the conventional (HU; ρ) and the novel (HU; ρ, Z) dual-energy CT tissue segmentation. The dose calculation errors using the conventional tissue segmentation were as high as 17% in a mis-assigned soft bone tissue-equivalent material for the 250 kVp photon beam. Similarly, the errors for the 18 MeV electron beam and the 18 MV photon beam were up to 6% and 3% in some mis-assigned media. The assignment of all tissue-equivalent inserts was accurate using the novel dual-energy CT material assignment. As a result, the dose calculation errors were below 1% in all beam arrangements. Comparable improvement in dose calculation accuracy is expected for human tissues. The dual-energy tissue segmentation offers a significantly higher accuracy compared to the conventional single-energy segmentation.

  17. Weather data for simplified energy calculation methods. Volume IV. United States: WYEC data

    SciTech Connect

    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.

  18. Use of SCALE Continuous-Energy Monte Carlo Tools for Eigenvalue Sensitivity Coefficient Calculations

    SciTech Connect

    Perfetti, Christopher M; Rearden, Bradley T

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  20. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.

    PubMed

    Lundborg, Magnus; Lindahl, Erik

    2015-01-22

    Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized. PMID:25343332

  1. Calculations of ADS with deep subcritical uranium active cores - comparison with experiments and predictions

    NASA Astrophysics Data System (ADS)

    Zhivkov, P.; Furman, W.; Stoyanov, Ch

    2014-09-01

    The main characteristics of the neutron field formed within the massive (512 kg) natural uranium target assembly (TA) QUINTA irradiated by deuteron beam of JINR Nuclotron with energies 1,2,4, and 8 GeV as well as the spatial distributions and the integral numbers of (n,f), (n,γ) and (n,xn)- reactions were calculated and compared with experimental data [1] . The MCNPX 27e code with ISABEL/ABLA/FLUKA and INCL4/ABLA models of intra-nuclear cascade (INC) and experimental cross-sections of the corresponding reactions were used. Special attention was paid to the elucidation of the role of charged particles (protons and pions) in the fission of natural uranium of TA QUINTA. Extensive calculations have been done for quasi-infinite (with very small neutron leakage) depleted uranium TA BURAN having mass about 20 t which are intended to be used in experiments at Nuclotron in 2014-2016. As in the case of TA QUINTA which really models the central zone of TA BURAN the total numbers of fissions, produced 239Pu nuclei and total neutron multiplicities are predicted to be proportional to proton or deuteron energy up to 12 GeV. But obtained values of beam power gain are practically constant in studied incident energy range and are approximately four. These values are in contradiction with the experimental result [2] obtained for the depleted uranium core weighting three tons at incident proton energy 0.66 GeV.

  2. Theoretical ROVibrational Energies (TROVE): A robust numerical approach to the calculation of rovibrational energies for polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Thiel, Walter; Jensen, Per

    2007-10-01

    We present a new computational method with associated computer program TROVE (Theoretical ROVibrational Energies) to perform variational calculations of rovibrational energies for general polyatomic molecules of arbitrary structure in isolated electronic states. The (approximate) nuclear kinetic energy operator is represented as an expansion in terms of internal coordinates. The main feature of the computational scheme is a numerical construction of the kinetic energy operator, which is an integral part of the computation process. Thus the scheme is self-contained, i.e., it requires no analytical pre-derivation of the kinetic energy operator. It is also general, since it can be used in connection with any internal coordinates. The method represents an extension of our model for pyramidal XY 3 molecules reported previously [S.N. Yurchenko, M. Carvajal, P. Jensen, H. Lin, J.J. Zheng, W. Thiel, Mol. Phys. 103 (2005) 359]. Non-rigid molecules are treated in the Hougen-Bunker-Johns approach [J.T. Hougen, P.R. Bunker, J.W.C. Johns, J. Mol. Spectrosc. 34 (1970) 136]. In this case, the variational calculations employ a numerical finite basis representation for the large-amplitude motion using basis functions that are generated by Numerov-Cooley integration of the appropriate one-dimensional Schrödinger equation.

  3. Calculation of absorbed dose around a facility for disposing of low activity natural radioactive waste (C3-dump).

    PubMed

    Jansen, J T M; Zoetelief, J

    2005-01-01

    A C3-dump is a facility for disposing of low activity natural radioactive waste containing the uranium series 238U, the thorium series 232Th and 40K. Only the external radiation owing to gamma rays, X-rays and annihilation photons is considered in this study. For two situations--the semi-infinite slab and the tourist geometry--the conversion coefficients from specific activity to air kerma rate at 1 m above the relevant level are calculated. In the first situation the waste material is in contact with the air but in the tourist geometry it is covered with a 1.35 m thick layer. For the calculations, the Monte Carlo radiation transport code MCNP is used. The yield and photon energy for each radionuclide are according to the database of Oak Ridge National Laboratory. For the tourist situation, the depth-dose distribution through the covering layer is calculated and extrapolated to determine the exit dose. PMID:16604673

  4. Research on the Calculated Methods of Active Control Value for Antenna Panel Deformations under Gravity

    NASA Astrophysics Data System (ADS)

    Fu, L.; Zhong, W. Y.; Qiao, H. H.; Liu, G. X.; Qian, H. L.

    2015-07-01

    The methods of ideal reflector surface, two-parameter, five-parameter, and six-parameter best-fit paraboloid are presented in this paper. Based on these methods, the adjustment values of gravity deformations are calculated for the main reflector of large-scale Cassegrain antenna. Accordingly, the positions of subreflector are corrected, and the effects of offset-focus on electric performance are also analyzed. Taking Shanghai 65 m antenna as a research object, the adjustment values of actuator and hexapod, the accuracy of the main reflector surface, and the pointing error after offsetting the focus are contrasted. As a result, the method of six-parameter best-fit paraboloid is ideal to calculate active control value for antenna panels after the effects of feed defocus have been adjusted and modified. The results offer data for the active control of antenna.

  5. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.

    PubMed

    Kaus, Joseph W; McCammon, J Andrew

    2015-05-21

    Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein-ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

  6. Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations

    PubMed Central

    2016-01-01

    Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

  7. The measurement and calculation of nanodosimetric energy distributions for electrons and photons

    NASA Astrophysics Data System (ADS)

    Evans, Thomas Michael

    1997-09-01

    Low dose and low dose rate fields constitute the majority of radiation exposure scenarios in radiation protection. Conversely, very little epidemiological or physical data are available at these levels. This situation exists because the parameters characterizing low dose and low dose rate environments are difficult to assess at cellular levels where the fundamental biological effects from radiation insults occur. The quantities required for a complete biological assessment are the distribution of energy deposition in biological targets and the cellular response to such insults. A new detector to measure physical energy depositions on nanometer scales was developed in this thesis. A computational tool was also developed to calculate clustered distributions of energy deposition from electrons and photons. A dosimeter has been developed which characterizes energy depositions from charged particles in nanometer dimensions. The dosimeter is a threshold-type detector based on the temperature response of the superheated liquid droplet detector (SLDD). SLDDs based on Freon-115 have been designed and tested. A data acquisition system that measures the acoustic signals from bubble nucleation events has been developed. An original electron track code, ESLOW3.1, has been developed. The code simulates electron tracks on an event-by-event basis down to an absolute minimum of 20 eV. The transport medium is water vapor. The cross sections have been compared with published data and theoretical models where available. Trial calculations of pertinent quantities are in good agreement with published results. A new operational quantity, the cluster spectrum, given the symbol c(/varepsilon), has been defined. This quantity is measured by the SLDD operated in nanodosimetry mode. The performance of the SLDD has been tested with a 60Co point source. The effective measurement range of the nanodosimeter is between 60 and 500 eV of energy deposition. Measured values of c(/varepsilon) are

  8. Star sub-pixel centroid calculation based on multi-step minimum energy difference method

    NASA Astrophysics Data System (ADS)

    Wang, Duo; Han, YanLi; Sun, Tengfei

    2013-09-01

    The star's centroid plays a vital role in celestial navigation, star images which be gotten during daytime, due to the strong sky background, have a low SNR, and the star objectives are nearly submerged in the background, takes a great trouble to the centroid localization. Traditional methods, such as a moment method, weighted centroid calculation method is simple but has a big error, especially in the condition of a low SNR. Gaussian method has a high positioning accuracy, but the computational complexity. Analysis of the energy distribution in star image, a location method for star target centroids based on multi-step minimum energy difference is proposed. This method uses the linear superposition to narrow the centroid area, in the certain narrow area uses a certain number of interpolation to pixels for the pixels' segmentation, and then using the symmetry of the stellar energy distribution, tentatively to get the centroid position: assume that the current pixel is the star centroid position, and then calculates and gets the difference of the sum of the energy which in the symmetric direction(in this paper we take the two directions of transverse and longitudinal) and the equal step length(which can be decided through different conditions, the paper takes 9 as the step length) of the current pixel, and obtain the centroid position in this direction when the minimum difference appears, and so do the other directions, then the validation comparison of simulated star images, and compare with several traditional methods, experiments shows that the positioning accuracy of the method up to 0.001 pixel, has good effect to calculate the centroid of low SNR conditions; at the same time, uses this method on a star map which got at the fixed observation site during daytime in near-infrared band, compare the results of the paper's method with the position messages which were known of the star, it shows that :the multi-step minimum energy difference method achieves a better

  9. Calculating impacts of energy standards on energy demand in U.S. buildings with uncertainty in an integrated assessment model

    SciTech Connect

    Scott, Michael J.; Daly, Don S.; Hathaway, John E.; Lansing, Carina S.; Liu, Ying; McJeon, Haewon C.; Moss, Richard H.; Patel, Pralit L.; Peterson, Marty J.; Rice, Jennie S.; Zhou, Yuyu

    2015-10-01

    In this paper, an integrated assessment model (IAM) uses a newly-developed Monte Carlo analysis capability to analyze the impacts of more aggressive U.S. residential and commercial building-energy codes and equipment standards on energy consumption and energy service costs at the state level, explicitly recognizing uncertainty in technology effectiveness and cost, socioeconomics, presence or absence of carbon prices, and climate impacts on energy demand. The paper finds that aggressive building-energy codes and equipment standards are an effective, cost-saving way to reduce energy consumption in buildings and greenhouse gas emissions in U.S. states. This conclusion is robust to significant uncertainties in population, economic activity, climate, carbon prices, and technology performance and costs.

  10. A Digital Program for Calculating the Interaction Between Flexible Structures, Unsteady Aerodynamics and Active Controls

    NASA Technical Reports Server (NTRS)

    Peele, E. L.; Adams, W. M., Jr.

    1979-01-01

    A computer program, ISAC, is described which calculates the stability and response of a flexible airplane equipped with active controls. The equations of motion relative to a fixed inertial coordinate system are formulated in terms of the airplane's rigid body motion and its unrestrained normal vibration modes. Unsteady aerodynamic forces are derived from a doublet lattice lifting surface theory. The theoretical basis for the program is briefly explained together with a description of input data and output results.

  11. Monte Carlo dose calculation improvements for low energy electron beams using eMC.

    PubMed

    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

  12. A new formula to calculate activity of superoxide dismutase in indirect assays.

    PubMed

    Zhang, Chen; Bruins, Marieke E; Yang, Zhi-Qiang; Liu, Shu-Tao; Rao, Ping-Fan

    2016-06-15

    To calculate superoxide dismutase (SOD) activity rapidly and accurately by indirect SOD assays, a formula based on the ratio of the catalytic speed of SOD to the reaction speed of the indicator with superoxide anion was deduced. The accuracy of this formula was compared with the conventional formula based on inhibition in five indirect SOD assays. The new formula was validated in nearly the entire SOD activity range, whereas the conventional formula was validated only during inhibition of 40-60%. This formula might also be used for the assays of other enzymes. PMID:27033009

  13. Design, synthesis, characterization, quantum-chemical calculations and anti-inflammatory activity of novel series of thiophene derivatives

    NASA Astrophysics Data System (ADS)

    Helal, M. H.; Salem, M. A.; Gouda, M. A.; Ahmed, N. S.; El-Sherif, A. A.

    2015-08-01

    Interaction of 1-(4-morpholinophenyl)ethanone 1 with either malononitrile or ethyl cyanoacetate 2 afforded Knoevenagel-Cope product 3. In subsequent treatment of 3 with sulfur, the 2-aminothiophene derivatives (4a, 4b) are formed under basic conditions. The solvent-free reaction of thiophene derivative 4a with ethyl cyanoacetate afforded thieno[2,3-d][1,3]oxazine derivative 6. The base catalyzed condensation of 2-aminothiophene derivative (4a) with ethyl cyanoacetate afforded N-(thieno-2-yl) cyanoacetamide derivative 7. The latter was used to synthesize different heterocyclic derivatives comprising, pyridine and coumarin rings. Also, several substituted thieno[2,3-d]pyrimidines have been prepared from reaction of 2-aminothiophene-3-carbonitrile 4b with some electrophilic reagents. The structure of the newly compounds were confirmed on the basis of elemental analysis and spectral data. The molecular modeling of the synthesized compounds has been drawn and their molecular parameters were calculated. Also, valuable information is obtained from calculation of the molecular parameters including electronegativity, net dipole moment of the compounds, total energy, electronic energy, binding energy, HOMO and LUMO energy. Evaluation of anti-inflammatory activity of the tested compounds was performed in albino rats by producing carrageenan induced paw oedema and measuring the zone of inflammation at different time intervals i.e. 1, 2, 3 and 4 h after carrageenan injection. Results indicated that most of the tested compounds showed moderate to good activity comparable to indomethacin. Also, compound 16 with additional morpholine ring beside the thiophene ring inhibits carrageenan induced paw oedema more than the standard indomethacin drug at all the time scales studied. Thus, compound 16 is considered as a promising compound for further modification to obtain clinically useful anti-inflammatory agent.

  14. Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.

    PubMed

    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

  15. Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.

    PubMed

    Giovan, Stefan M; Scharein, Robert G; Hanke, Andreas; Levene, Stephen D

    2014-11-01

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases. PMID:25381542

  16. Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations.

    PubMed

    Zeller, Fabian; Zacharias, Martin

    2014-06-27

    Generalized Born (GB) implicit solvent models are widely used in molecular dynamics simulations to evaluate the interactions of biomolecular complexes. The continuum treatment of the solvent results in significant computational savings in comparison to an explicit solvent representation. It is, however, not clear how accurately the GB approach reproduces the absolute free energies of biomolecular binding. On the basis of induced dissociation by means of umbrella sampling simulations, the absolute binding free energies of small proline-rich peptide ligands and a protein receptor were calculated. Comparative simulations according to the same protocol were performed by employing an explicit solvent model and various GB-type implicit solvent models in combination with a nonpolar surface tension term. The peptide ligands differed in a key residue at the peptide-protein interface, including either a nonpolar, a neutral polar, a positively charged, or a negatively charged group. For the peptides with a neutral polar or nonpolar interface residue, very good agreement between the explicit solvent and GB implicit solvent results was found. Deviations in the main separation free energy contributions are smaller than 1 kcal/mol. In contrast, for peptides with a charged interface residue, significant deviations of 2-4 kcal/mol were observed. The results indicate that recent GB models can compete with explicit solvent representations in total binding free energy calculations as long as no charged residues are present at the binding interface. PMID:24941018

  17. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    NASA Astrophysics Data System (ADS)

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-11-01

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  18. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    SciTech Connect

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-11-07

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  19. HETC96/MORSE calculations of activations in KEK beam stop and room by 500-MeV protons and comparisons with experiments

    SciTech Connect

    Fu, C.Y.; Gabriel, T.A.

    1997-05-01

    The 1996 version of HETC has a pre-equilibrium reaction model to bridge the gap between the existing intranuclear-cascade and evaporation models. This code was used to calculate proton-induced activations, to calculate neutron fluxes for neutron energies above 19.6 MeV, and to write the neutron source for lower energies to be transported further by MORSE. For MORSE, the HILO cross section library was used for neutron transport for all detectors. Additionally for the {sup 197}Au(n, {gamma}) detector, the BUGLE96 library was used to study the effects of the low-lying {sup 57}Fe inelastic levels and the resonance self-shielding in iron. Neutron fluxes were obtained from the track-length estimator for detectors inside the beam stop and from the boundary-crossing estimator for detectors attached to the surfaces of the concrete walls. Activation cross sections given in JAERI-Data/Code are combined with the calculated neutron fluxes to get the saturated activities induced by neutrons. C/E values are too low (0.5) for Fe(N, {chi}){sup 54}Mn, close to unity for Cu(n, {chi}){sup 58}Co, and too high (6.0) for {sup 197}Au (n, {gamma}){sup 198}Au. It is difficult to interpret the disagreements because most of the activation cross sections are also calculated and their uncertainties are not known. However, the calculated results are in good agreement with those calculated by others using different codes. Calculated results for four of the ten activations reported here have not been done previously, and among the four, {sup 197}Au(n, {gamma}) is the most bothersome because its cross section is the most well known while the calculated activations for most detector locations are in largest disagreement with experiments.

  20. Recent advances in QM/MM free energy calculations using reference potentials☆

    PubMed Central

    Duarte, Fernanda; Amrein, Beat A.; Blaha-Nelson, David; Kamerlin, Shina C.L.

    2015-01-01

    Background Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. PMID:25038480

  1. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational–rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane

    SciTech Connect

    Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu

    2015-01-28

    We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  2. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational-rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane

    NASA Astrophysics Data System (ADS)

    Mielke, Steven L.; Truhlar, Donald G.

    2015-01-01

    We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P-6) to O(P-12), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ˜1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  3. A program to calculate non-bonded interaction energy in biomolecular aggregates.

    PubMed

    Sundaram, K; Prasad, C V

    1982-02-01

    This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416

  4. S-model calculations for high-energy-electron-impact double ionization of helium

    NASA Astrophysics Data System (ADS)

    Gasaneo, G.; Mitnik, D. M.; Randazzo, J. M.; Ancarani, L. U.; Colavecchia, F. D.

    2013-04-01

    In this paper the double ionization of helium by high-energy electron impact is studied. The corresponding four-body Schrödinger equation is transformed into a set of driven equations containing successive orders in the projectile-target interaction. The transition amplitude obtained from the asymptotic limit of the first-order solution is shown to be equivalent to the familiar first Born approximation. The first-order driven equation is solved within a generalized Sturmian approach for an S-wave (e,3e) model process with high incident energy and small momentum transfer corresponding to published measurements. Two independent numerical implementations, one using spherical and the other hyperspherical coordinates, yield mutual agreement. From our ab initio solution, the transition amplitude is extracted, and single differential cross sections are calculated and could be taken as benchmark values to test other numerical methods in a previously unexplored energy domain.

  5. Measurements and calculations of neutron scattering angular distributions over a wide mass and energy range

    SciTech Connect

    Hansen, L.F.

    1985-05-01

    Neutron elastic and inelastic differential cross sections for targets between /sup 9/Be and /sup 239/Pu at energies, E > 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed. 17 refs.

  6. [Improvement of anti-stokes energy transfer between rare earth ions--2. Numerical calculation and analysis].

    PubMed

    Chen, Xiao-bo; Wang, Ce; Kang, Dong-guo; Sawanobori, Naruhito; Wang, Shui-feng; Li, Yong-liang; Wang, Ping

    2010-08-01

    The dynamics of all levels were calculated numerically in the present article for Er(0.5)Yb(3):FOV oxyfluoride nanophase vitroceramics. The population dynamical processes were analyzed carefully. It was found for the first time that traditional phonon-assisted energy transfer theory of rare earth ion energy transfer can not well explain the observed experimental calibrated results, as it does not take into account the difference between Stokes and anti-Stokes process. A coefficient, the improved factor of the intensity ratio of Stokes to anti-Stokes process in quantum Raman theory compared to classical Raman theory, was introduced for the first time to successfully describe the anti-Stokes energy transfer. The theoretical improvement results are coincident with experiments very well. This improvement is very significant and indispensable when the photonics of nanomaterials is probed. PMID:20939297

  7. Variational calculations with explicit energy functionals for fermion systems at zero temperature

    NASA Astrophysics Data System (ADS)

    Takano, M.; Suzuki, T.; Sakumichi, N.

    2016-03-01

    The variational method with explicit energy functionals (EEFs) is applied to infinite neutron matter. Starting from the Argonne v8’ two-body potential and the repulsive part of the Urbana IX three-body potential, the energy per neutron is expressed explicitly with the spin-dependent central, tensor, and spin-orbit distribution functions. This EEF is constructed as an extension of the previously proposed one for the Argonne v6’ potential, including central and tensor forces. The Euler-Lagrange equations derived from this EEF are solved numerically. The obtained fully minimized energy with this EEF is in good agreement with that obtained from the auxiliary field diffusion Monte Carlo calculation.

  8. Measurements and Calculations of Neutron Scattering Angular Distributions over a Wide Mass and Energy Range

    NASA Astrophysics Data System (ADS)

    Hansen, L. F.

    Neutron elastic and inelastic differential cross sections for targets between (9)Be and (239)Pu at energies, E 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed.

  9. First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

    DOE PAGESBeta

    Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

    2014-10-21

    A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and themore » dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less

  10. First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

    SciTech Connect

    Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

    2014-10-21

    A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1benergy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.

  11. Free energy calculations using dual-level Born-Oppenheimer molecular dynamics

    NASA Astrophysics Data System (ADS)

    Retegan, Marius; Martins-Costa, Marilia; Ruiz-López, Manuel F.

    2010-08-01

    We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

  12. Free Energies of Redox Half-Reactions from First-Principles Calculations.

    PubMed

    Tazhigulov, Ruslan N; Bravaya, Ksenia B

    2016-07-01

    Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values. PMID:27295124

  13. Solar Energy Project, Activities: Chemistry & Physics.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of chemistry and physics experiments. Each unit presents an introduction to the unit; objectives; required skills and knowledge; materials; method; questions; recommendations for further work; and a teacher information sheet.…

  14. Solar Energy Project, Activities: Junior High Science.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of the junior high science curriculum. Each unit presents an introduction; objectives; skills and knowledge needed; materials; methods; questions; recommendations for further work; and a teacher information sheet. The teacher…

  15. Solar Energy Project, Activities: Earth Science.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of earth science experiments. Each unit presents an introduction; objectives; skills and knowledge needed; materials; method; questions; recommendations for further study; and a teacher information sheet. The teacher…

  16. Energy Activities for Junior High Social Studies.

    ERIC Educational Resources Information Center

    Minnesota State Energy Agency, St. Paul.

    The document contains seven learning activities for junior high students on the energy situation. Objectives are to help students gain understanding and knowledge about the relationships between humans and their social and physical environments; solve problems and clarify issues; examine personal beliefs and values; and recognize the relationships…

  17. Hardee County Energy Activities - Middle School Level.

    ERIC Educational Resources Information Center

    Allen, Rodney F., Ed.

    Described are over 70 activities designed to help students develop writing skills by examining energy issues. Intended for middle school students, the lessons were developed by Hardee County, Florida teachers. Learning strategies employed include class discussions, analogies, word puzzles, letter writing, sentence completions, vocabulary building…

  18. Activation energy of water structural transitions

    NASA Astrophysics Data System (ADS)

    Kholmanskiy, Alexander

    2015-06-01

    In this work, the nature of molecular motions that dominate in the thermodynamics of anomalies of liquid water properties in the range of 0-100 °C has been studied. Temperature dependencies of water properties have been approximated by exponential functions and the activation energies for water structure transitions have been evaluated. The activation energy values were compared with the energy spectra of characteristic vibrations and with those of cooperative molecular motion in the lattice-type structure of hydrogen bonds. It has been found that it is the reaction of hydrogen bond breaking that mainly limits the abnormal dynamics of water viscosity, self-diffusion, dielectric relaxation time and electric conductivity. It has been assumed that the thermodynamics of cooperative motion and resonance phenomena in water clusters form a basis for the differentiation mechanism of extrema points in temperature dependencies of water density, isobaric heat capacity, sound velocity, surface tension coefficient and compressibility.

  19. Revisiting the finite temperature string method for the calculation of reaction tubes and free energies.

    PubMed

    Vanden-Eijnden, Eric; Venturoli, Maddalena

    2009-05-21

    An improved and simplified version of the finite temperature string (FTS) method [W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005)] is proposed. Like the original approach, the new method is a scheme to calculate the principal curves associated with the Boltzmann-Gibbs probability distribution of the system, i.e., the curves which are such that their intersection with the hyperplanes perpendicular to themselves coincides with the expected position of the system in these planes (where perpendicular is understood with respect to the appropriate metric). Unlike more standard paths such as the minimum energy path or the minimum free energy path, the location of the principal curve depends on global features of the energy or the free energy landscapes and thereby may remain appropriate in situations where the landscape is rough on the thermal energy scale and/or entropic effects related to the width of the reaction channels matter. Instead of using constrained sampling in hyperplanes as in the original FTS, the new method calculates the principal curve via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve. As shown here, this modification results in greater algorithmic simplicity. As a by-product, it also gives the free energy associated with the Voronoi tessellation. The new method can be applied both in the original Cartesian space of the system or in a set of collective variables. We illustrate FTS on test-case examples and apply it to the study of conformational transitions of the nitrogen regulatory protein C receiver domain using an elastic network model and to the isomerization of solvated alanine dipeptide. PMID:19466817

  20. Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

    PubMed

    Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

    2008-02-13

    Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency. PMID:21693886

  1. Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only)

    NASA Astrophysics Data System (ADS)

    Domain, C.; Olsson, P.; Becquart, C. S.; Legris, A.; Guillemoles, J. F.

    2008-02-01

    Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

  2. Calculation of energy levels, {ital E}1 transition amplitudes, and parity violation in francium

    SciTech Connect

    Dzuba, V.A.; Flambaum, V.V.; Sushkov, O.P.

    1995-05-01

    Many-body perturbation theory in the screened Coulomb interaction was used to calculate energy levels, {ital E}1 trransition amplitudes, and the parity-nonconserving (PNC) {ital E}1 amplitude of the 7{ital s}-8{ital s} transition in francium. The method takes into account the core-polarization effect, the second-order correlations, and the three dominating sequences of higher-order correlation diagrams: screening of the electron-electron interaction, particle-hole interaction, and the iterations of the self-energy operator. The result for the PNC amplitude for {sup 223}Fr is {ital E}1(7{ital s}-8{ital s})=(1.59{plus_minus}{similar_to}1%){times}10{sup {minus}10}{ital iea}{sub {ital B}}({minus}{ital Q}{sub {ital W}}/{ital N}), where {ital Q}{sub {ital W}} is the weak charge of the nucleus, {ital N}=136 is the number of neutrons, {ital e}={vert_bar}{ital e}{vert_bar} is the elementary charge, and {ital a}{sub {ital B}} is the Bohr radius. Our prediction for the position of the 8{ital s} energy level of Fr, which has not been measured yet, is 13 110 cm{sup {minus}1} below the limit of the continuous spectrum. The accuracy of the calculations was controlled by comparison with available experimental data and analogous calculations for cesium. It is estimated to be {similar_to}0.1% for the energy levels and {similar_to}1% for the transition amplitudes.

  3. Calculation of electron trajectory and energy deposition in no screening region

    NASA Astrophysics Data System (ADS)

    Kia, Mohammad Reza; Noshad, Houshyar

    2016-01-01

    The probability density function (PDF) of energy for inelastic collision is obtained by solving the integro-differential form of the quantity equation with the Bhabha differential cross section for particles with spin 1/2. Hence, the total PDF in no screening region is determined by folding theory with the following two assumptions: (1) the electron loses energy by collision and radiation and (2) the electron velocity does not change with a thin absorber. Therefore, a set of coupled stochastic differential equations based on the deviation and energy loss PDFs for electron is presented to obtain the electron trajectory inside the target. The energy PDFs for an electron beam with incident energy of 15.7 MeV inside aluminum and copper are calculated. Besides, the dose distributions for an electron beam with incident energies of 20, 10.2, 6, and 0.5 MeV in water are obtained. The results are in excellent agreement with the experimental data reported in the literature.

  4. Gamma-ray energy buildup factor calculations and shielding effects of some Jordanian building structures

    NASA Astrophysics Data System (ADS)

    Sharaf, J. M.; Saleh, H.

    2015-05-01

    The shielding properties of three different construction styles, and building materials, commonly used in Jordan, were evaluated using parameters such as attenuation coefficients, equivalent atomic number, penetration depth and energy buildup factor. Geometric progression (GP) method was used to calculate gamma-ray energy buildup factors of limestone, concrete, bricks, cement plaster and air for the energy range 0.05-3 MeV, and penetration depths up to 40 mfp. It has been observed that among the examined building materials, limestone offers highest value for equivalent atomic number and linear attenuation coefficient and the lowest values for penetration depth and energy buildup factor. The obtained buildup factors were used as basic data to establish the total equivalent energy buildup factors for three different multilayer construction styles using an iterative method. The three styles were then compared in terms of fractional transmission of photons at different incident photon energies. It is concluded that, in case of any nuclear accident, large multistory buildings with five layers exterior walls, style A, could effectively attenuate radiation more than small dwellings of any construction style.

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

    PubMed

    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 (<|error|> = 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. PMID:26180998

  6. Importance of light scattering properties of cloud particles on calculating the earth energy cycle

    NASA Astrophysics Data System (ADS)

    Letu, H.; Nakajima, T. Y.; Nagao, T. M.; Ishimoto, H.

    2013-12-01

    The Earth is an open system, and the energy cycle of the Earth is not always a certain amount. In other words, the energy cycle in the nature is imbalance. A better understanding of the earth energy cycle is very important to study global climate change. the IPCC-AR4 reported that the cloud in the atmosphere are still characterized by large uncertainties in the estimation of their effects on energy sysle of the Earth's atmosphere. There are two types of cloud in the atmosphere, which are Cirrus and warm water cloud. In order to strongly reflect visible wavelength from sun light, thick water cloud has the effect of cooling the earth surface. When Cirrus is compared to water cloud, temperature is almost lower. Thus, there is a feature that Cirrus is easy to absorb long-wave radiation than warm water cloud. However, in order to quantitatively evaluate the reflection and absorption characteristics of cloud on remote senssing application and energy cycle of the imbalance of nature, it is necessary to obtain the scattering properties of cloud particles. Since the shapes of the water cloud particle are close to spherical, scattering properties of the particles can be calculated accurately by the Mie theory. However, Cirrus particles have a complex shape, including hexagonal, plate, and other non- spherical shapes. Different from warm water cloud partical, it is required to use several different light scattering methods when calculating the light scattering properties of the non-spherical Cirrus cloud particals. Ishimoto et al. [2010, 2012] and Masuda et al. [2012] developed the Finite-Difference Time Domain method (FDTD) and Improved Geometrical-Optics Method (IGOM) for the solution of light scattering by non-spherical particles. Nakajima et al [1997,2009] developed the LIght Scattering solver for Arbitral Shape particle (Lisas)-Geometrical-Optics Method (GOM) and Surface Integral Equations Method of Müller-type (SIEMM) to calculate the light scattering properties for

  7. Alternative Approaches to Calculate Benefits of an Energy Imbalance Market With Wind and Solar Energy: Preprint

    SciTech Connect

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

    PubMed

    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. PMID:26080356

  9. On the importance of full-dimensionality in low-energy molecular scattering calculations

    PubMed Central

    Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof

    2016-01-01

    Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm−1 in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870

  10. On the importance of full-dimensionality in low-energy molecular scattering calculations.

    PubMed

    Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof

    2016-01-01

    Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm(-1) in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870

  11. Calculation of excitation energies from the CC2 linear response theory using Cholesky decomposition

    SciTech Connect

    Baudin, Pablo; Marín, José Sánchez; Cuesta, Inmaculada García; Sánchez de Merás, Alfredo M. J.

    2014-03-14

    A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitioning form of the CC2 equations which reduces the dimension of the problem and avoids the storage of doubles amplitudes. We present calculation of excitation energies of benzene using a hierarchy of basis sets and compare the results with conventional CC2 calculations. The reduction of the scaling is evaluated as well as the effect of the Cholesky decomposition parameter on the quality of the results. The new algorithm is used to perform an extrapolation to complete basis set investigation on the spectroscopically interesting benzylallene conformers. A set of calculations on medium-sized molecules is carried out to check the dependence of the accuracy of the results on the decomposition thresholds. Moreover, CC2 singlet excitation energies of the free base porphin are also presented.

  12. Electron range-energy relationships for calculating backscattering coefficients in elemental and compound semiconductors

    NASA Astrophysics Data System (ADS)

    Rouabah, Z.; Bouzid, A.; Champion, C.; Bouarissa, N.

    2011-06-01

    Backscattering coefficients for electrons normally impinging on Si, Ge, GaN, GaAs and InSb targets have been calculated by using the Vicanek and Urbassek theory [M. Vicanek, H.M. Urbassek, Phys. Rev. B 44 (1991) 7234] for incident energies ≤5 keV. Electron range has been calculated from various semi-empirical analytical expressions. The cross-sections used to describe the electron transport are determined via the appropriate analytical expression given by Jablonski [A. Jablonski, Phys. Rev. B 58 (1998) 16470] whose new improved version has been recently reported by Rouabah et al. [Z. Rouabah, N. Bouarissa, C. Champion, N. Bouaouadja, Appl. Surf. Sci. 255 (2009) 6217]. The results may be seen as the first predictions for low-energy electron backscattering coefficients impinging on GaN, GaAs and InSb semiconductors. The models used in the calculation of the electron range affect both the accuracy and behaviour of the electron backscattering coefficients.

  13. The Magnetic Free Energy in Active Regions

    NASA Technical Reports Server (NTRS)

    Metcalf, Thomas R.; Mickey, Donald L.; LaBonte, Barry J.

    2001-01-01

    The magnetic field permeating the solar atmosphere governs much of the structure, morphology, brightness, and dynamics observed on the Sun. The magnetic field, especially in active regions, is thought to provide the power for energetic events in the solar corona, such as solar flares and Coronal Mass Ejections (CME) and is believed to energize the hot coronal plasma seen in extreme ultraviolet or X-rays. The question remains what specific aspect of the magnetic flux governs the observed variability. To directly understand the role of the magnetic field in energizing the solar corona, it is necessary to measure the free magnetic energy available in active regions. The grant now expiring has demonstrated a new and valuable technique for observing the magnetic free energy in active regions as a function of time.

  14. Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

    PubMed

    Rosta, Edina; Haranczyk, Maciej; Chu, Zhen T; Warshel, Arieh

    2008-05-01

    Reliable studies of enzymatic reactions by combined quantum mechanical/molecular mechanics (QM(ai)/MM) approaches with an ab initio description of the quantum region presents a major challenge to computational chemists. The main problem is the need for very large computer time to evaluate the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. One of the most obvious options for accelerating QM/MM simulations is the use of an average solvent potential. In fact, the idea of using an average solvent potential is rather obvious and has implicitly been used in Langevin dipole/QM calculations. However, in the case of explicit solvent models the practical implementations are more challenging, and the accuracy of the averaging approach has not been validated. The present study introduces the average effect of the fluctuating solvent charges by using equivalent charge distributions, which are updated every m steps. Several models are evaluated in terms of the resulting accuracy and efficiency. The most effective model divides the system into an inner region with N explicit solvent atoms and an external region with two effective charges. Different models are considered in terms of the division of the solvent system and the update frequency. Another key element of our approach is the use of the free energy perturbation (FEP) and/or linear response approximation treatments that guarantees the evaluation of the rigorous solvation free energy. Special attention is paid to the convergence of the calculated solvation free energies and the corresponding solute polarization. The performance of the method is examined by evaluating the solvation of a water molecule and a formate ion in water and also the dipole moment of water in water solution. Remarkably, it is found that different averaging procedures eventually converge to the same value but some protocols provide optimal ways of obtaining the final QM(ai)/MM converged results. The

  15. Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution

    PubMed Central

    Rosta, Edina; Haranczyk, Maciej; Chu, Zhen T.; Warshel, Arieh

    2009-01-01

    Reliable studies of enzymatic reactions by combined quantum mechanical /molecular mechanics (QM(ai)/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for very large computer time to evaluate the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. One of the most obvious options for accelerating QM/MM simulations is the use of an average solvent potential. In fact the idea of using an average solvent potential is rather obvious and has implicitly been used in Langevin dipole / QM calculations. However, in the case of explicit solvent models the practical implementations are more challenging and the accuracy of the averaging approach has not been validated. The present study introduces the average effect of the fluctuating solvent charges by using equivalent charge distributions, which are updated every m steps. Several models are evaluated in terms of the resulting accuracy and efficiency. The most effective model divides the system into an inner region with N explicit solvent atoms and an external region with two effective charges. Different models are considered in terms of the division of the solvent system and the update frequency. Another key element of our approach is the use of the free energy perturbation (FEP) and/or linear response approximation (LRA) treatments that guarantees the evaluation of the rigorous solvation free energy. Special attention is paid to the convergence of the calculated solvation free energies and the corresponding solute polarization. The performance of the method is examined by evaluating the solvation of a water molecule and a formate ion in water and also the dipole moment of water in water solution. Remarkably, it is found that different averaging procedures eventually converge to the same value but some protocols provide optimal ways of obtaining the final QM(ai)/MM converged

  16. Calculation of energy-barrier lowering by incoherent switching in spin-transfer torque magnetoresistive random-access memory

    SciTech Connect

    Munira, Kamaram; Visscher, P. B.

    2015-05-07

    To make a useful spin-transfer torque magnetoresistive random-access memory (STT-MRAM) device, it is necessary to be able to calculate switching rates, which determine the error rates of the device. In a single-macrospin model, one can use a Fokker-Planck equation to obtain a low-current thermally activated rate ∝exp(−E{sub eff}/k{sub B}T). Here, the effective energy barrier E{sub eff} scales with the single-macrospin energy barrier KV, where K is the effective anisotropy energy density and V the volume. A long-standing paradox in this field is that the actual energy barrier appears to be much smaller than this. It has been suggested that incoherent motions may lower the barrier, but this has proved difficult to quantify. In the present paper, we show that the coherent precession has a magnetostatic instability, which allows quantitative estimation of the energy barrier and may resolve the paradox.

  17. Intercomparison measurements with energy deposition spectrometer Liulin and TEPC Hawk at HIMAC, and related calculations with PHITS

    NASA Astrophysics Data System (ADS)

    Ploc, Ondrej; Uchihori, Yukio; Kitamura, H.; Kodaira, S.; Dachev, Tsvetan; Spurny, Frantisek; Jadrnickova, Iva; Mrazova, Zlata; Kubancak, Jan

    Liulin type detectors are recently used in a wide range of cosmic radiation measurements, e.g. at alpine observatories, onboard aircrafts and spacecrafts. They provide energy deposition spectra up to 21 MeV, higher energy deposition events are stored in the last (overflow) channel. Their main advantages are portability (about the same size as a pack of cigarettes) and ability to record spectra as a function of time, so they can be used as personal dosimeters. Their well-known limitations are: (i) the fact that they are not tissue equivalent, (ii) they can be used as LET spectrometer only under specific conditions (e.g. broad parallel beam), and (iii) that the energy deposition event from particles of LETH20¿35 keV/µm is stored in the overflow bin only so the spectral information is missing. Tissue equivalent proportional counter (TEPC) Hawk has no of these limitations but on the other hand, it cannot be used as personal dosimeter because of its big size (cylinder of 16 cm diameter and 34 cm long). An important fraction of dose equivalent onboard spacecrafts is caused by heavy ions. This contribution presents results from intercomparison measurements with Liulin and Hawk at Heavy Ion Medical Accelerator in Chiba (HIMAC) and cyclotron beams, and related calculations with PHITS (Particle and Heavy-ion Transport code System). Following particles/ions and energies were used: protons 70 MeV, He 150 MeV, Ne 400 MeV, C 135 MeV, C 290 MeV, and Fe 500 MeV. Calculations of LET spectra by PHITS were performed for both, Liulin and Hawk. In case of Liulin, the dose equivalent was calculated using simulations in which several tissue equivalent materials were used as active volume instead of the silicon diode. Dose equivalents calculated in such way was compared with that measured with Hawk. LET spectra measured with Liulin and Hawk were compared for each ion at several points behind binary filters along the Brag curve. Good agreement was observed for some configurations; for

  18. DENSITY FUNCTIONAL CALCULATION OF ENERGIES AND VIBRATIONAL FREQUENCIES OF GLUCOSE AND GLUCOSE-WATER COMPLEXES: WATER PLACEMENT AND GLUCOSE CONFORMATIONAL EFFECTS ON THE CALCULATED INFRARED SPECTRUM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The structures and energies of glucose and glucose monohydrates have been calculated at the B3LYP/6-311++G** level of theory. Both the alpha and beta anomers were studied, with all possible combinations of hydroxymethyl rotamer (gg, gt, or tg) and hydroxyl orientation (clockwise or counter-clockwis...

  19. [Energy and memory efficient calculation of the accommodation demand in the artificial accommodation system].

    PubMed

    Nagel, J A; Beck, C; Harms, H; Stiller, P; Guth, H; Stachs, O; Bretthauer, G

    2010-12-01

    Presbyopia and cataract are gaining more and more importance in the ageing society. Both age-related complaints are accompanied with a loss of the eye's ability to accommodate. A new approach to restore accommodation is the Artificial Accommodation System, an autonomous micro system, which will be implanted into the capsular bag instead of a rigid intraocular lens. The Artificial Accommodation System will, depending on the actual demand for accommodation, autonomously adapt the refractive power of its integrated optical element. One possibility to measure the demand for accommodation non-intrusively is to analyse eye movements. We present an efficient algorithm, based on the CORDIC technique, to calculate the demand for accommodation from magnetic field sensor data. It can be shown that specialised algorithms significantly shorten calculation time without violating precision requirements. Additionally, a communication strategy for the wireless exchange of sensor data between the implants of the left and right eye is introduced. The strategy allows for a one-sided calculation of the demand for accommodation, resulting in an overall reduction of calculation time by 50 %. The presented methods enable autonomous microsystems, such as the Artificial Accommodation System, to save significant amounts of energy, leading to extended autonomous run-times. PMID:21157661

  20. TASK 2.5.4 DEVELOPMENT OF AN ENERGY SAVINGS CALCULATOR

    SciTech Connect

    Miller, William A; New, Joshua Ryan; Desjarlais, Andre Omer; Huang, Joe; Erdem, Ender; Ronnen, Levinson

    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

  1. Absolute Binding Free Energy Calculations: On the Accuracy of Computational Scoring of Protein-ligand Interactions

    PubMed Central

    Singh, Nidhi; Warshel, Arieh

    2010-01-01

    Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic Linear Response Approximation (LRA/β version) and its variants including the Linear Interaction Energy (LIE) to the more approximated and considerably faster scaled Protein Dipoles Langevin Dipoles (PDLD/S-LRA version), as well as the less rigorous Molecular Mechanics Poisson–Boltzmann/Surface Area (MM/PBSA) and Generalized Born/Surface Area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/β, the LIE, the PDLD/S-LRA/β and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the non-electrostatic term. On the average, the PDLD/S-LRA/β performs effectively. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies due to its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/β appears to offer an appealing option for the final stages of massive screening approaches. PMID:20186976

  2. Application of the Activity-Based Costing Method for Unit-Cost Calculation in a Hospital

    PubMed Central

    Javid, Mahdi; Hadian, Mohammad; Ghaderi, Hossein; Ghaffari, Shahram; Salehi, Masoud

    2016-01-01

    Background: Choosing an appropriate accounting system for hospital has always been a challenge for hospital managers. Traditional cost system (TCS) causes cost distortions in hospital. Activity-based costing (ABC) method is a new and more effective cost system. Objective: This study aimed to compare ABC with TCS method in calculating the unit cost of medical services and to assess its applicability in Kashani Hospital, Shahrekord City, Iran. Methods: This cross-sectional study was performed on accounting data of Kashani Hospital in 2013. Data on accounting reports of 2012 and other relevant sources at the end of 2012 were included. To apply ABC method, the hospital was divided into several cost centers and five cost categories were defined: wage, equipment, space, material, and overhead costs. Then activity centers were defined. ABC method was performed into two phases. First, the total costs of cost centers were assigned to activities by using related cost factors. Then the costs of activities were divided to cost objects by using cost drivers. After determining the cost of objects, the cost price of medical services was calculated and compared with those obtained from TCS. Results: The Kashani Hospital had 81 physicians, 306 nurses, and 328 beds with the mean occupancy rate of 67.4% during 2012. Unit cost of medical services, cost price of occupancy bed per day, and cost per outpatient service were calculated. The total unit costs by ABC and TCS were respectively 187.95 and 137.70 USD, showing 50.34 USD more unit cost by ABC method. ABC method represented more accurate information on the major cost components. Conclusion: By utilizing ABC, hospital managers have a valuable accounting system that provides a true insight into the organizational costs of their department. PMID:26234974

  3. Reynolds stress calculations of homogeneous turbulent shear flow with bounded energy states

    NASA Technical Reports Server (NTRS)

    Speziale, Charles G.; Abid, R.

    1992-01-01

    Reynolds stress calculations of homogeneous turbulent shear flow are conducted with a second-order closure model modified to account for non-equilibrium vortex stretching in the dissipation rate transport equation, as recently proposed by Bernard and Speziale. As with the earlier reported k-epsilon model calculations incorporating this vortex stretching effect, a production-equals-dissipation equilibrium is obtained with bounded turbulent kinetic energy and dissipation. However, this equilibrium is not achieved until the dimensionless time greater than 60, an elapsed time that is at least twice as large as any of those considered in previous numerical and physical experiments on homogeneous shear flow. Direct quantitative comparisons between the model predictions and the results of experiments are quite favorable. In particular, it is shown that the inclusion of this non-equilibrium vortex stretching effect has the capability of explaining the significant range of production to dissipation ratios observed in experiments.

  4. Reynolds stress calculations of homogeneous turbulent shear flow with bounded energy states

    NASA Technical Reports Server (NTRS)

    Speziale, Charles G.; Abid, R.

    1993-01-01

    Reynolds stress calculations of homogeneous turbulent shear flow are conducted with a second-order closure model modified to account for nonequilibrium vortex stretching in the dissipation rate transport equation as recently proposed by Bernard and Speziale (1992). As with the earlier reported K-epsilon model calculations incorporating this vortex stretching effect, a production-equals-dissipation equilibrium is obtained with bounded turbulent kinetic energy and dissipation. However, this equilibrium is now not achieved until the dimensionless time St greater than 60 - an elapsed time that is at least twice as large as any of those considered in previous numerical and physical experiments on homogeneous shear flow. Direct quantitative comparisons between the model predictions and the results of experiments are quite favorable. In particular, it is shown that the inclusion of this nonequilibrium vortex stretching effect has the capability of explaining the significant range of production to dissipation ratios observed in experiments.

  5. Density functional theory calculations of magnetocrystalline anisotropy energies for (Fe1-xCox)2B

    DOE PAGESBeta

    Daene, Markus; Kim, Soo Kyung; Surh, Michael P.; Aberg, Daniel; Benedict, Lorin X.

    2015-06-15

    We present and discuss density functional theory calculations of magnetic properties of the family of ferromagnetic compounds, (Fe1-xCox)2B, focusing specifically on the magnetocrystalline anisotropy energy (MAE). Using periodic supercells of various sizes (up to 96 atoms), it is shown that the general qualitative features of the composition dependence of the MAE is in agreement with experimental findings, while our predicted magnitudes are larger than those of experiment. We find that the use of small supercells (6 and 12-atom) favors larger MAE values relative to a statistical sample of configurations constructed with 96-atom supercells. As a result, the effect of latticemore » relaxations is shown to be small. Calculations of the Curie temperature for this alloy are also presented.« less

  6. Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

    2016-02-01

    We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

  7. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design.

    PubMed

    Chen, Wei; Chang, Chia-En; Gilson, Michael K

    2004-11-01

    The second generation Mining Minima method yields binding affinities accurate to within 0.8 kcal/mol for the associations of alpha-, beta-, and gamma-cyclodextrin with benzene, resorcinol, flurbiprofen, naproxen, and nabumetone. These calculations require hours to a day on a commodity computer. The calculations also indicate that the changes in configurational entropy upon binding oppose association by as much as 24 kcal/mol and result primarily from a narrowing of energy wells in the bound versus the free state, rather than from a drop in the number of distinct low-energy conformations on binding. Also, the configurational entropy is found to vary substantially among the bound conformations of a given cyclodextrin-guest complex. This result suggests that the configurational entropy must be accounted for to reliably rank docked conformations in both host-guest and ligand-protein complexes. In close analogy with the common experimental observation of entropy-enthalpy compensation, the computed entropy changes show a near-linear relationship with the changes in mean potential plus solvation energy. PMID:15339804

  8. Configurational space discretization and free energy calculation in complex molecular systems.

    PubMed

    Wang, Kai; Long, Shiyang; Tian, Pu

    2016-01-01

    We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy. PMID:26974524

  9. An energy transfer method for 4D Monte Carlo dose calculation

    PubMed Central

    Siebers, Jeffrey V.; Zhong, Hualiang

    2008-01-01

    This article presents a new method for four-dimensional Monte Carlo dose calculations which properly addresses dose mapping for deforming anatomy. The method, called the energy transfer method (ETM), separates the particle transport and particle scoring geometries: Particle transport takes place in the typical rectilinear coordinate system of the source image, while energy deposition scoring takes place in a desired reference image via use of deformable image registration. Dose is the energy deposited per unit mass in the reference image. ETM has been implemented into DOSXYZnrc and compared with a conventional dose interpolation method (DIM) on deformable phantoms. For voxels whose contents merge in the deforming phantom, the doses calculated by ETM are exactly the same as an analytical solution, contrasting to the DIM which has an average 1.1% dose discrepancy in the beam direction with a maximum error of 24.9% found in the penumbra of a 6 MV beam. The DIM error observed persists even if voxel subdivision is used. The ETM is computationally efficient and will be useful for 4D dose addition and benchmarking alternative 4D dose addition algorithms. PMID:18841862

  10. Path integral calculation of free energies: quantum effects on the melting temperature of neon.

    PubMed

    Ramírez, R; Herrero, C P; Antonelli, A; Hernández, E R

    2008-08-14

    The path integral formulation has been combined with several methods to determine free energies of quantum many-body systems, such as adiabatic switching and reversible scaling. These techniques are alternatives to the standard thermodynamic integration method. A quantum Einstein crystal is used as a model to demonstrate the accuracy and reliability of these free energy methods in quantum simulations. Our main interest focuses on the calculation of the melting temperature of Ne at ambient pressure, taking into account quantum effects in the atomic dynamics. The free energy of the solid was calculated by considering a quantum Einstein crystal as reference state, while for the liquid, the reference state was defined by the classical limit of the fluid. Our findings indicate that, while quantum effects in the melting temperature of this system are small, they still amount to about 6% of the melting temperature, and are therefore not negligible. The particle density as well as the melting enthalpy and entropy of the solid and liquid phases at coexistence is compared to results obtained in the classical limit and also to available experimental data. PMID:18715054

  11. Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies.

    PubMed

    Setny, Piotr; Zacharias, Martin

    2010-07-01

    A simple, semiheuristic solvation model based on a discrete, BCC grid of solvent cells has been presented. The model utilizes a mean field approach for the calculation of solute-solvent and solvent-solvent interaction energies and a cellular automata based algorithm for the prediction of solvent distribution in the presence of solute. The construction of the effective Hamiltonian for a solvent cell provides an explicit coupling between orientation-dependent water-solute electrostatic interactions and water-water hydrogen bonding. The water-solute dispersion interaction is also explicitly taken into account. The model does not depend on any arbitrary definition of the solute-solvent interface nor does it use a microscopic surface tension for the calculation of nonpolar contributions to the hydration free energies. It is demonstrated that the model provides satisfactory predictions of hydration free energies for drug-like molecules and is able to reproduce the distribution of buried water molecules within protein structures. The model is computationally efficient and is applicable to arbitrary molecules described by atomistic force field. PMID:20552986

  12. Configurational space discretization and free energy calculation in complex molecular systems

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Long, Shiyang; Tian, Pu

    2016-03-01

    We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy.

  13. An energy transfer method for 4D Monte Carlo dose calculation.

    PubMed

    Siebers, Jeffrey V; Zhong, Hualiang

    2008-09-01

    This article presents a new method for four-dimensional Monte Carlo dose calculations which properly addresses dose mapping for deforming anatomy. The method, called the energy transfer method (ETM), separates the particle transport and particle scoring geometries: Particle transport takes place in the typical rectilinear coordinate system of the source image, while energy deposition scoring takes place in a desired reference image via use of deformable image registration. Dose is the energy deposited per unit mass in the reference image. ETM has been implemented into DOSXYZnrc and compared with a conventional dose interpolation method (DIM) on deformable phantoms. For voxels whose contents merge in the deforming phantom, the doses calculated by ETM are exactly the same as an analytical solution, contrasting to the DIM which has an average 1.1% dose discrepancy in the beam direction with a maximum error of 24.9% found in the penumbra of a 6 MV beam. The DIM error observed persists even if voxel subdivision is used. The ETM is computationally efficient and will be useful for 4D dose addition and benchmarking alternative 4D dose addition algorithms. PMID:18841862

  14. Accurate calculation of the dissociation energy of the highly anharmonic system ClHCl(-).

    PubMed

    Stein, Christopher; Oswald, Rainer; Botschwina, Peter; Peterson, Kirk A

    2015-05-28

    Accurate bond dissociation energies (D0) are reported for different isotopologues of the highly anharmonic system ClHCl(-). The mass-independent equilibrium dissociation energy De was obtained by a composite method with frozen-core (fc) CCSD(T) as the basic contribution. Basis sets as large as aug-cc-pV8(+d)Z were employed, and extrapolation to the complete basis set (CBS) limit was carried out. Explicitly correlated calculations with the CCSD(T)-F12b method were also performed to support the conventionally calculated values. Core-core and core-valence correlation, scalar relativity, and higher-order correlation were considered as well. Two mass-dependent contributions, namely, the diagonal Born-Oppenheimer correction and the difference in zero-point energies between the complex and the HCl fragment, were then added in order to arrive at precise D0 values. Results for (35)ClH(35)Cl(-) and (35)ClD(35)Cl(-) are 23.81 and 23.63 kcal/mol, respectively, with estimated uncertainties of 0.05 kcal/mol. In contrast to FHF(-) ( Stein , C. ; Oswald , R. ; Sebald , P. ; Botschwina , P. ; Stoll , H. , Peterson , K. A. Mol. Phys. 2013 , 111 , 2647 - 2652 ), the D0 values of the bichloride species are larger than their De counterparts, which is an unusual situation in hydrogen-bonded systems. PMID:25405989

  15. Configurational space discretization and free energy calculation in complex molecular systems

    PubMed Central

    Wang, Kai; Long, Shiyang; Tian, Pu

    2016-01-01

    We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy. PMID:26974524

  16. Calculation of Zeeman splitting and Zeeman transition energies of spherical quantum dot in uniform magnetic field

    NASA Astrophysics Data System (ADS)

    Çakır, Bekir; Atav, Ülfet; Yakar, Yusuf; Özmen, Ayhan

    2016-08-01

    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.

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

    PubMed Central

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    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. PMID:26863418

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

    PubMed

    Verma, Sharad; Grover, Sonam; Tyagi, Chetna; Goyal, Sukriti; Jamal, Salma; Singh, Aditi; Grover, Abhinav

    2016-01-01

    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. PMID:26863418

  19. Accurate Monte Carlo modeling of cyclotrons for optimization of shielding and activation calculations in the biomedical field

    NASA Astrophysics Data System (ADS)

    Infantino, Angelo; Marengo, Mario; Baschetti, Serafina; Cicoria, Gianfranco; Longo Vaschetto, Vittorio; Lucconi, Giulia; Massucci, Piera; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano

    2015-11-01

    Biomedical cyclotrons for production of Positron Emission Tomography (PET) radionuclides and radiotherapy with hadrons or ions are widely diffused and established in hospitals as well as in industrial facilities and research sites. Guidelines for site planning and installation, as well as for radiation protection assessment, are given in a number of international documents; however, these well-established guides typically offer analytic methods of calculation of both shielding and materials activation, in approximate or idealized geometry set up. The availability of Monte Carlo codes with accurate and up-to-date libraries for transport and interactions of neutrons and charged particles at energies below 250 MeV, together with the continuously increasing power of nowadays computers, makes systematic use of simulations with realistic geometries possible, yielding equipment and site specific evaluation of the source terms, shielding requirements and all quantities relevant to radiation protection. In this work, the well-known Monte Carlo code FLUKA was used to simulate two representative models of cyclotron for PET radionuclides production, including their targetry; and one type of proton therapy cyclotron including the energy selection system. Simulations yield estimates of various quantities of radiological interest, including the effective dose distribution around the equipment, the effective number of neutron produced per incident proton and the activation of target materials, the structure of the cyclotron, the energy degrader, the vault walls and the soil. The model was validated against experimental measurements and comparison with well-established reference data. Neutron ambient dose equivalent H*(10) was measured around a GE PETtrace cyclotron: an average ratio between experimental measurement and simulations of 0.99±0.07 was found. Saturation yield of 18F, produced by the well-known 18O(p,n)18F reaction, was calculated and compared with the IAEA recommended

  20. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

    PubMed

    Rosta, Edina; Woodcock, H Lee; Brooks, Bernard R; Hummer, Gerhard

    2009-08-01

    We describe a method for the systematic improvement of reaction coordinates in quantum mechanical/molecular mechanical (QM/MM) calculations of reaction free-energy profiles. In umbrella-sampling free-energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (approximately 10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations. PMID:19462398

  1. Artificial reaction coordinate “tunneling” in free energy calculations: the catalytic reaction of RNase H

    PubMed Central

    Rosta, Edina; Woodcock, H. Lee; Brooks, Bernard R.; Hummer, Gerhard

    2011-01-01

    We describe a method for the systematic improvement of reaction coordinates in quantum mechanical / molecular mechanical (QM/MM) calculations of reaction free energy profiles. In umbrella-sampling free energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (~10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free energy calculations. PMID:19462398

  2. Fast vibrational calculation of anharmonic OH-stretch frequencies for two low-energy noradrenaline conformers

    NASA Astrophysics Data System (ADS)

    Benoit, David M.

    2008-12-01

    We introduce a new reduced-coupling technique to accelerate direct calculations of a selected number of vibrational frequencies in large molecular systems. Our method combines the advantages of the single-to-all correlation-corrected vibrational self-consistent field (STA-CC-VSCF) approach [D. M. Benoit, J. Chem. Phys. 125, 244110 (2006)] with those of the fast-CC-VSCF technique [D. M. Benoit, J. Chem. Phys. 120, 562 (2004)] and allows the ab initio calculation of only the relevant parts of the required potential energy surface (PES). We demonstrate, using a set of five aliphatic alcohol molecules, that the new fast-STA-CC-VSCF method is accurate and leads to very substantial time gains for the computations of the PES. We then use the fast-STA-CC-VSCF method to accelerate the computation of the OH-stretch and NH-stretch frequencies of the two lowest-energy conformers of noradrenaline, namely, AG1a and GG1a. Our new approach enables us to run the calculation 89 times faster than the standard CC-VSCF technique and makes it possible to use a high-level MP2/TZP description of the PES. We demonstrate that the influence of the strong mode-mode couplings is crucial for a realistic description of the particular OH-stretch vibrational signature of each conformer. Finally, of the two possible low-energy conformers, we identify AG1a as the one most likely to have been observed in the experiments of Snoek et al. [Mol. Phys. 101, 1239 (2003)].

  3. Energy Expenditure During Extravehicular Activity Through Apollo

    NASA Technical Reports Server (NTRS)

    Paul, Heather L.

    2011-01-01

    Monitoring crew health during manned space missions has always been an important factor to ensure that the astronauts can complete the missions successfully and within safe physiological limits. The necessity of real-time metabolic rate monitoring during extravehicular activities (EVAs) came into question during the Gemini missions, when the energy expenditure required to complete EVA tasks exceeded the life support capabilities for cooling and humidity control and crewmembers (CMs) ended the EVAs fatigued and overworked. This paper discusses the importance of real-time monitoring of metabolic rate during EVA, and provides a historical look at energy expenditure during EVA through the Apollo program.

  4. Energy Expenditure During Extravehicular Activity Through Apollo

    NASA Technical Reports Server (NTRS)

    Paul, Heather L.

    2012-01-01

    Monitoring crew health during manned space missions has always been an important factor to ensure that the astronauts can complete the missions successfully and within safe physiological limits. The necessity of real-time metabolic rate monitoring during extravehicular activities (EVAs) came into question during the Gemini missions, when the energy expenditure required to complete EVA tasks exceeded the life support capabilities for cooling and humidity control and, as a result, crew members ended the EVAs fatigued and overworked. This paper discusses the importance of real-time monitoring of metabolic rate during EVAs, and provides a historical look at energy expenditure during EVAs through the Apollo Program.

  5. Basis set effects on the intermolecular interaction energies of methane dimers obtained by the Moeller-Plesset perturbation theory calculation

    SciTech Connect

    Tsuzuki, Seiji; Tanabe, Kazutoshi )

    1991-03-21

    Intermolecular interaction energies of methane dimer were calculated by using several basis sets up to 6-311G(3d,4p) with electron correlation energy correction by the Moeller-Plesset perturbation method and basis set superposition error (BSSE) correction by the counterpoise method to evaluate the basis set effect. The calculated interaction energies depended on the basis set considerably. Whereas the interaction energies of repulsive component calculated at HF level were not affected by the change of basis set, the dispersion energy component dependent greatly on the basis set used. The dispersion energies calculated with the Moeller-Plesset second- and third-order perturbation by using 6-311G(2d,2p) basis set were 0-10% and 4-6% smaller than those obtained with the fourth-order (MP4(SDTQ)) perturbation, respectively. The BSSE's calculated by the counterpoise method were still about 30% of the calculated intermolecular interaction energies for the conformers of energy minima event at the MP4(SDTQ)/6-311G(2d,2p) level. The calculated interaction potentials of dimers at the MP4(SDTQ)/6-311G(2d,2p) level were considerably shallower than those obtained by MM2 force fields but were close to the potentials given by the Williams potential and by the recently reported MM3 force field.

  6. Calculation tool for transported geothermal energy using two-step absorption process

    DOE Data Explorer

    Kyle Gluesenkamp

    2016-02-01

    This spreadsheet allows the user to calculate parameters relevant to techno-economic performance of a two-step absorption process to transport low temperature geothermal heat some distance (1-20 miles) for use in building air conditioning. The parameters included are (1) energy density of aqueous LiBr and LiCl solutions, (2) transportation cost of trucking solution, and (3) equipment cost for the required chillers and cooling towers in the two-step absorption approach. More information is available in the included public report: "A Technical and Economic Analysis of an Innovative Two-Step Absorption System for Utilizing Low-Temperature Geothermal Resources to Condition Commercial Buildings"

  7. Angular-overlap calculation of the Jahn-Teller stabilization energie for f-orbital degeneracies

    SciTech Connect

    Warren, K.D.

    1980-03-01

    The angular-overlap model is applied to the calculation of the linear Jahn-Teller coupling constants for f-orbital degeneracies. The MX/sub 6/, O/sub h/, chromophore is treated as representative of the highest symmetry commonly occurring in the lanthanide and actinide series, and it is shown that, even when spin-orbit effects are taken into account, 5f orbital degeneracies may lead to significant Jahn-Teller stabilization energies. The operation of this effect for F/sup 1/ GAMMA/sub 8/ states is considered. 2 tables.

  8. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP\\H-REMD) for absolute ligand binding free energy calculations.

    SciTech Connect

    Jiang, W.; Roux, B.

    2010-09-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters '{lambda}' can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor {lambda} in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the interconversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter {lambda} and the boosting potential, in an extended dual array of coupled {lambda}- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of the T4 lysozyme was calculated. The tests demonstrate that the dual {lambda}-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  9. One pot synthesis of biologically active pregnane derivatives, their single crystal structures, spectroscopic characterization and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Sethi, Arun; Bhatia, Akriti; Bhatia, Gitika; Shrivastava, Atul; Prakash, Rohit

    2013-11-01

    One pot allylic oxidation of 3β-acetoxypregna-5,16-diene-20-one (2) and nucleophilic addition at C-16 position of 3β-hydroxypregna-5,16-diene-20-one (3) yielded 3β-acetoxypregna-5,16-diene-7,20-dione (4) and 3β-hydroxy-16α-(5'-hydroxypentyloxy)-pregn-5-ene-20-one (5) respectively in high yield. A detailed theoretical study supported by X-ray analysis of compounds 4 and 5 has been carried out. Conformational analysis of compounds 4 and 5 was done with the help of crystal structure, which crystallize out in orthorhombic form having P212121 space group. Structural characterization of compounds 4 and 5 was done with the aid of 1H, 13C NMR, IR, UV, ESI-MS and ESI-HRMS. The molecular geometries and vibrational frequencies for compounds 4 and 5 in the ground state were calculated using the Density functional theory (DFT) with 6-31G(d,p) basis set and compared with experimental data. 1H and 13C nuclear magnetic resonance magnetic shifts of 4 and 5 were calculated using GIAO method and compared with the experimental data. UV-Vis spectra of both the compounds were recorded and electronic properties such as HOMO-LUMO energies were calculated by time dependent TD-DFT approach. The compounds were screened for their anti-hyperlipidemic and anti-oxidant activity.

  10. A Method for the Calculation of Lattice Energies of Complex Crystals with Application to the Oxides of Molybdenum

    NASA Technical Reports Server (NTRS)

    Chaney, William S.

    1961-01-01

    A theoretical study has been made of molybdenum dioxide and molybdenum trioxide in order to extend the knowledge of factors Involved in the oxidation of molybdenum. New methods were developed for calculating the lattice energies based on electrostatic valence theory, and the coulombic, polarization, Van der Waals, and repulsion energie's were calculated. The crystal structure was examined and structure details were correlated with lattice energy.

  11. Ferrocenyl-substituted dinuclear Cu(II) complex: Synthesis, spectroscopy, electrochemistry, DFT calculations and catecholase activity

    NASA Astrophysics Data System (ADS)

    Emirik, Mustafa; Karaoğlu, Kaan; Serbest, Kerim; Menteşe, Emre; Yilmaz, Ismail

    2016-02-01

    A new ferrocenyl-substituted heterocyclic hydrazide ligand and its Cu(II) complex were prepared. The DFT calculations were performed to determine the electronic and molecular structures of the title compounds. The electronic spectra were calculated by using time-dependent DFT method, and the transitions were correlated with the molecular orbitals of the compounds. The bands assignments of IR spectra were achieved in the light of the theoretical vibrational spectral data and total energy distribution values calculated at DFT/B3LYP/6-311++G(d,p) level. The redox behaviors of the ferrocene derivatives were investigated by cyclic voltammetry. The compounds show reversible redox couple assignable to Fc+/Fc couple. The copper(II) complex behaves as an effective catalyst towards oxidation of 3,5-di-tert-butylcatechol to its corresponding quinone derivative in DMF saturated with O2. The reaction follows Michaelis-Menten enzymatic reaction kinetics with turnover numbers 2.32 × 103.

  12. Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.

    PubMed

    Lee, Tai-Sung; Radak, Brian K; Huang, Ming; Wong, Kin-Yiu; York, Darrin M

    2014-01-14

    The variational free energy profile (vFEP) method is extended to two dimensions and tested with molecular simulation applications. The proposed 2D-vFEP approach effectively addresses the two major obstacles to constructing free energy profiles from simulation data using traditional methods: the need for overlap in the re-weighting procedure and the problem of data representation. This is especially evident as these problems are shown to be more severe in two dimensions. The vFEP method is demonstrated to be highly robust and able to provide stable, analytic free energy profiles with only a paucity of sampled data. The analytic profiles can be analyzed with conventional search methods to easily identify stationary points (e.g. minima and first-order saddle points) as well as the pathways that connect these points. These "roadmaps" through the free energy surface are useful not only as a post-processing tool to characterize mechanisms, but can also serve as a basis from which to direct more focused "on-the-fly" sampling or adaptive force biasing. Test cases demonstrate that 2D-vFEP outperforms other methods in terms of the amount and sparsity of the data needed to construct stable, converged analytic free energy profiles. In a classic test case, the two dimensional free energy profile of the backbone torsion angles of alanine dipeptide, 2D-vFEP needs less than 1% of the original data set to reach a sampling accuracy of 0.5 kcal/mol in free energy shifts between windows. A new software tool for performing one and two dimensional vFEP calculations is herein described and made publicly available. PMID:24505217

  13. Thermodynamic Derivation of the Activation Energy for Ice Nucleation

    NASA Technical Reports Server (NTRS)

    Barahona, D.

    2015-01-01

    Cirrus clouds play a key role in the radiative and hydrological balance of the upper troposphere. Their correct representation in atmospheric models requires an understanding of the microscopic processes leading to ice nucleation. A key parameter in the theoretical description of ice nucleation is the activation energy, which controls the flux of water molecules from the bulk of the liquid to the solid during the early stages of ice formation. In most studies it is estimated by direct association with the bulk properties of water, typically viscosity and self-diffusivity. As the environment in the ice-liquid interface may differ from that of the bulk, this approach may introduce bias in calculated nucleation rates. In this work a theoretical model is proposed to describe the transfer of water molecules across the ice-liquid interface. Within this framework the activation energy naturally emerges from the combination of the energy required to break hydrogen bonds in the liquid, i.e., the bulk diffusion process, and the work dissipated from the molecular rearrangement of water molecules within the ice-liquid interface. The new expression is introduced into a generalized form of classical nucleation theory. Even though no nucleation rate measurements are used to fit any of the parameters of the theory the predicted nucleation rate is in good agreement with experimental results, even at temperature as low as 190 K, where it tends to be underestimated by most models. It is shown that the activation energy has a strong dependency on temperature and a weak dependency on water activity. Such dependencies are masked by thermodynamic effects at temperatures typical of homogeneous freezing of cloud droplets; however, they may affect the formation of ice in haze aerosol particles. The new model provides an independent estimation of the activation energy and the homogeneous ice nucleation rate, and it may help to improve the interpretation of experimental results and the

  14. Parameter-free calculation of charge-changing cross sections at high energy

    NASA Astrophysics Data System (ADS)

    Suzuki, Y.; Horiuchi, W.; Terashima, S.; Kanungo, R.; Ameil, F.; Atkinson, J.; Ayyad, Y.; Cortina-Gil, D.; Dillmann, I.; Estradé, A.; Evdokimov, A.; Farinon, F.; Geissel, H.; Guastalla, G.; Janik, R.; Knoebel, R.; Kurcewicz, J.; Litvinov, Yu. A.; Marta, M.; Mostazo, M.; Mukha, I.; Nociforo, C.; Ong, H. J.; Pietri, S.; Prochazka, A.; Scheidenberger, C.; Sitar, B.; Strmen, P.; Takechi, M.; Tanaka, J.; Tanihata, I.; Vargas, J.; Weick, H.; Winfield, J. S.

    2016-07-01

    Charge-changing cross sections at high energies are expected to provide useful information on nuclear charge radii. No reliable theory to calculate the cross section has yet been available. We develop a formula using Glauber and eikonal approximations and test its validity with recent new data on carbon isotopes measured at around 900 A MeV. We first confirm that our theory reproduces the cross sections of 12,13,14C+12C consistently with the known charge radii. Next we show that the cross sections of C-1912 on a proton target are all well reproduced provided the role of neutrons is accounted for. We also discuss the energy dependence of the charge-changing cross sections.

  15. Initial energy partitioning and some excavation stage phenomenology in laboratory-scale cratering calculations in clay

    NASA Technical Reports Server (NTRS)

    Austin, M. G.; Thomsen, J. M.; Ruhl, S. F.

    1982-01-01

    One impact and two explosive cratering calculations have been analyzed with emphasis on the early excavation stage. The early excavation stage is here defined as that part of the excavation stage that occurs after energy partitioning is 90% complete, but before the cratering flow field can be well described by Z-type flow fields with values of Z uniformly greater than two. Impact generated flow fields seem to have a much longer early excavation stage than explosion generated flow fields, due possibly to the slower momentum transfer versus energy transfer rate between projectile and target. During this time when the projectile retains a significant portion of its original momentum, Z values less than two are observed in the impact generated flow field. Z values less than two are not observed at any time in the explosion generated flow fields.

  16. Calculation of the energy loss in giant magnetic impedance elements using the complex magnetic permeability spectra

    NASA Astrophysics Data System (ADS)

    Rustemaj, Driton; Mukherjee, Debashis

    2013-01-01

    The giant magnetic impedance (GMI) effect in ferromagnetic materials has been investigated for sensing applications. The GMI properties were evaluated via numerical solution of the complex magnetic permeability of the material. MATLAB simulation was carried out to study the frequency dependence of magnetic permeability via obtaining solutions of the Landau-Lifshitz-Gilbert (LLG) and the Maxwell's equations. The results indicate that the complex magnetic permeability peaks at a frequency of 6 GHz, corresponding to the ferromagnetic resonant (FMR) frequency, where the energy loss is maximum. A variation of the Gilbert damping parameter (α) associated with the LLG equation inversely affects this peak value. The area under the curve of complex magnetic permeability, calculated through counting the number of pixels within the image, provides an estimate of the average energy loss density within the material and appears to be consistent with the variation of the peak intensity.

  17. Calculation of energy relaxation rates of fast particles by phonons in crystals

    SciTech Connect

    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.

  18. Free energy dependence of pure phase iron doped bismuth titanate from first principles calculations.

    PubMed

    Mayfield, Cedric L; Subramanian, Vaidyanathan Ravi; Huda, Muhammad N

    2015-08-12

    A density functional theory study of Fe substitutions in Bi2Ti2O7 photocatalyst (Fe-BTO) is presented. It models an experiment where H2 production of Fe-BTO peaked for samples loaded with 1% Fe concentration then decreased for samples with heavier loadings. The total energy calculations were used to determine defect formation energies and the chemical potential landscape that suggests the observed formation of Fe2O3 (in samples at 2% Fe concentration) was detrimental to H2 production. Doping configurations as a function of oxygen chemical potential are discussed, and the chemical potential ranges that avoid formation of the Fe2O3 phase in Fe-BTO are predicted. PMID:26199200

  19. Free energy dependence of pure phase iron doped bismuth titanate from first principles calculations

    NASA Astrophysics Data System (ADS)

    Mayfield, Cedric L.; (Ravi Subramanian, Vaidyanathan; Huda, Muhammad N.

    2015-08-01

    A density functional theory study of Fe substitutions in Bi2Ti2O7 photocatalyst (Fe-BTO) is presented. It models an experiment where H2 production of Fe-BTO peaked for samples loaded with 1% Fe concentration then decreased for samples with heavier loadings. The total energy calculations were used to determine defect formation energies and the chemical potential landscape that suggests the observed formation of Fe2O3 (in samples at 2% Fe concentration) was detrimental to H2 production. Doping configurations as a function of oxygen chemical potential are discussed, and the chemical potential ranges that avoid formation of the Fe2O3 phase in Fe-BTO are predicted.

  20. Electron binding energies of anionic alkali metal triatomics from partial fourth order electron propagator theory calculations

    NASA Astrophysics Data System (ADS)

    Ortiz, J. V.

    1988-11-01

    Vertical ionization energies of Li-3, Na-3, LiNa-2, and Li2Na- are calculated with ab initio electron propagator theory. D∞h and C∞v isomers for the heteronuclear triatomics are considered. Two doublet final states with Σ symmetry are considered for each case. Koopmans's theorem, second order, third order, and partial fourth order results form a steadily converging series. Outer valence approximation results are not similar and are probably inferior to the partial fourth order results. Convergence of results with respect to the order of electron interaction in the propagator self-energy and with respect to basis set saturation is achieved to within 0.1 eV.

  1. Development of the activation analysis calculational methodology for the Spallation Neutron Source (SNS)

    SciTech Connect

    Odano, N.; Johnson, J.O.; Charton, L.A.; Barnes, J.M.

    1998-03-01

    For the design of the proposed Spallation Neutron Source (SNS), activation analyses are required to determine the radioactive waste streams, on-line material processing requirements remote handling/maintenance requirements, potential site contamination and background radiation levels. For the conceptual design of the SNS, the activation analyses were carried out using the high-energy transport code HETC96 coupled with MCNP to generate the required nuclide production rates for the ORIHET95 isotope generation code. ORIHET95 utilizes a matrix-exponential method to study the buildup and decay of activities for any system for which the nuclide production rates are known. In this paper, details of the developed methodology adopted for the activation analyses in the conceptual design of the SNS are presented along with some typical results of the analyses.

  2. GEDAE-LaB: A Free Software to Calculate the Energy System Contributions during Exercise

    PubMed Central

    Bertuzzi, Rômulo; Melegati, Jorge; Bueno, Salomão; Ghiarone, Thaysa; Pasqua, Leonardo A.; Gáspari, Arthur Fernandes; Lima-Silva, Adriano E.; Goldman, Alfredo

    2016-01-01

    Purpose 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. Methods Eleven participants performed the following tests: 1) a maximal cycling incremental test to measure the ventilatory threshold and maximal oxygen uptake (V˙O2max); 2) a cycling workload constant test at moderate domain (90% ventilatory threshold); 3) a cycling workload constant test at severe domain (110% V˙O2max). 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. Results 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). Conclusion 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

  3. Active Control by Conservation of Energy Concept

    NASA Technical Reports Server (NTRS)

    Maestrello, Lucio

    2000-01-01

    Three unrelated experiments are discussed; each was extremely sensitive to initial conditions. The initial conditions are the beginnings of the origins of the information that nonlinearity displays. Initial conditions make the phenomenon unstable and unpredictable. With the knowledge of the initial conditions, active control requires far less power than that present in the system response. The first experiment is on the control of shocks from an axisymmetric supersonic jet; the second, control of a nonlinear panel response forced by turbulent boundary layer and sound; the third, control of subharmonic and harmonics of a panel forced by sound. In all three experiments, control is achieved by redistribution of periodic energy response such that the energy is nearly preserved from a previous uncontrolled state. This type of active control improves the performance of the system being controlled.

  4. Get Current: Switch on Clean Energy Activity Book

    SciTech Connect

    2014-06-01

    Switching on clean energy technologies means strengthening the economy while protecting the environment. This activity book for all ages promotes energy awareness, with facts on different types of energy and a variety of puzzles in an energy theme.

  5. Accurate variational calculations and analysis of the HOCl vibrational energy spectrum

    SciTech Connect

    Skokov, S.; Qi, J.; Bowman, J.M.; Yang, C.; Gray, S.K.; Peterson, K.A. |; Mandelshtam, V.A.

    1998-12-01

    Large scale variational calculations for the vibrational states of HOCl are performed using a recently developed, accurate {ital ab initio} potential energy surface. Three different approaches for obtaining vibrational states are employed and contrasted; a truncation/recoupling scheme with direct diagonalization, the Lanczos method, and Chebyshev iteration with filter diagonalization. The complete spectrum of bound states for nonrotating HOCl is computed and analyzed within a random matrix theory framework. This analysis indicates almost entirely regular dynamics with only a small degree of chaos. The nearly regular spectral structure allows us to make assignments for the most significant part of the spectrum, based on analysis of coordinate expectation values and eigenfunctions. Ground state dipole moments and dipole transition probabilities are also calculated using accurate {ital ab initio} data. Computed values are in good agreement with available experimental data. Some exact rovibrational calculations for J=1, including Coriolis coupling, are performed. The exact results are nearly identical with those obtained from the adiabatic rotation approximation and very close to those from the centrifugal sudden approximation, thus indicating a very small degree of asymmetry and Coriolis coupling for the HOCl molecule. {copyright} {ital 1998 American Institute of Physics.}

  6. A Gaussian quadrature method for total energy analysis in electronic state calculations

    NASA Astrophysics Data System (ADS)

    Fukushima, Kimichika

    This article reports studies by Fukushima and coworkers since 1980 concerning their highly accurate numerical integral method using Gaussian quadratures to evaluate the total energy in electronic state calculations. Gauss-Legendre and Gauss-Laguerre quadratures were used for integrals in the finite and infinite regions, respectively. Our previous article showed that, for diatomic molecules such as CO and FeO, elliptic coordinates efficiently achieved high numerical integral accuracy even with a numerical basis set including transition metal atomic orbitals. This article will generalize straightforward details for multiatomic systems with direct integrals in each decomposed elliptic coordinate determined from the nuclear positions of picked-up atom pairs. Sample calculations were performed for the molecules O3 and H2O. This article will also try to present, in another coordinate, a numerical integral by partially using the Becke's decomposition published in 1988, but without the Becke's fuzzy cell generated by the polynomials of internuclear distance between the pair atoms. Instead, simple nuclear weights comprising exponential functions around nuclei are used. The one-center integral is performed with a Gaussian quadrature pack in a spherical coordinate, included in the author's original program in around 1980. As for this decomposition into one-center integrals, sample calculations are carried out for Li2.

  7. Potential energy curves via double electron-attachment calculations: Dissociation of alkali metal dimers

    NASA Astrophysics Data System (ADS)

    Musiał, Monika; Kowalska-Szojda, Katarzyna; Lyakh, Dmitry I.; Bartlett, Rodney J.

    2013-05-01

    The recently developed method [M. Musiał, J. Chem. Phys. 136, 134111 (2012), 10.1063/1.3700438] to study double electron attached states has been applied to the description of the ground and excited state potential energy curves of the alkali metal dimers. The method is based on the multireference coupled cluster scheme formulated within the Fock space formalism for the (2,0) sector. Due to the use of the efficient intermediate Hamiltonian formulation, the approach is free from the intruder states problem. The description of the neutral alkali metal dimers is accomplished via attaching two electrons to the corresponding doubly ionized system. This way is particularly advantageous when a closed shell molecule dissociates into open shell subunits while its doubly positive cation generates the closed shell fragments. In the current work, we generate the potential energy curves for the ground and multiple excited states of the Li2 and Na2 molecules. In all cases the potential energy curves are smooth for the entire range of interatomic distances (from the equilibrium point to the dissociation limit). Based on the calculated potential energy curves, we are able to compute spectroscopic parameters of the systems studied.

  8. Full dimension Rb2He ground triplet potential energy surface and quantum scattering calculations.

    PubMed

    Guillon, Grégoire; Viel, Alexandra; Launay, Jean-Michel

    2012-05-01

    We have developed a three-dimensional potential energy surface for the lowest triplet state of the Rb(2)He complex. A global analytic fit is provided as in the supplementary material [see supplementary material at http://dx.doi.org/10.1063/1.4709433 for the corresponding Fortran code]. This surface is used to perform quantum scattering calculations of (4)He and (3)He colliding with (87)Rb(2) in the partial wave J = 0 at low and ultralow energies. For the heavier helium isotope, the computed vibrational relaxation probabilities show a broad and strong shape resonance for a collisional energy of 0.15 K and a narrow Feshbach resonance at about 17 K for all initial Rb(2) vibrational states studied. The broad resonance corresponds to an efficient relaxation mechanism that does not occur when (3)He is the colliding partner. The Feshbach resonance observed at higher collisional energy is robust with respect to the isotopic substitution. However, its effect on the vibrational relaxation mechanism is faint for both isotopes. PMID:22583230

  9. Full dimension Rb2He ground triplet potential energy surface and quantum scattering calculations

    NASA Astrophysics Data System (ADS)

    Guillon, Grégoire; Viel, Alexandra; Launay, Jean-Michel

    2012-05-01

    We have developed a three-dimensional potential energy surface for the lowest triplet state of the Rb2He complex. A global analytic fit is provided as in the supplementary material [see supplementary material at http://dx.doi.org/10.1063/1.4709433E-JCPSA6-136-034218 for the corresponding Fortran code]. This surface is used to perform quantum scattering calculations of 4He and 3He colliding with 87Rb2 in the partial wave J = 0 at low and ultralow energies. For the heavier helium isotope, the computed vibrational relaxation probabilities show a broad and strong shape resonance for a collisional energy of 0.15 K and a narrow Feshbach resonance at about 17 K for all initial Rb2 vibrational states studied. The broad resonance corresponds to an efficient relaxation mechanism that does not occur when 3He is the colliding partner. The Feshbach resonance observed at higher collisional energy is robust with respect to the isotopic substitution. However, its effect on the vibrational relaxation mechanism is faint for both isotopes.

  10. Calculation Of A Micro Discharge Energy Balance With PIC-MCC Method

    SciTech Connect

    Benstaali, W.; Belasri, A.; Hagelaar, G. J. M.; Boeuf, J. P.

    2008-09-23

    In this paper, we present a 1D Particle in Cell with Monte Carlo Collisions model, developed in order to calculate the energy balance in a micro-discharge, under conditions similar to those of a Plasma Display Panel (PDP) cell. The discharge takes place in a xenon-neon (10%-;90%) mixture at 560 torr and for a gap length of 100 {mu}m. The model is used to analyze in details the energy deposition during the discharge pulse. The results show the amount of energy dissipated by ions (collisions in the gas and on the cathode), by electrons (excitation of the different electronic states, ionization), and their variations with the applied voltage. This model will be used in the future to test the approximations of the fluid models which are generally used to optimize PDP operating conditions, and to check whether or not fluid models can correctly predict the trends in the variations of the energy balance with parameters such as voltage, pressure, gas mixture.

  11. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

    PubMed

    Ohno, Kazuki; Mitsui, Takashi; Tanida, Yoshiaki; Matsuura, Azuma; Fujitani, Hideaki; Niimi, Tatsuya; Orita, Masaya

    2011-02-01

    Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein/ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1)/inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects. PMID:20480380

  12. Weather data for simplified energy calculation methods. Volume III. Western United States: TRY data

    SciTech Connect

    Olsen, A.R.; Moreno, S.; Deringer, J.; Watson, C.R.

    1984-08-01

    The objective 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 24 cities in the continental United States using Test Reference Year (TRY) source weather 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. Weather data for simplified energy calculation methods. Volume II. Middle United States: TRY data

    SciTech Connect

    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 22 cities in the continental United States using Test Reference Year (TRY) source weather 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.

  14. Correlation matrix renormalization approximation for total-energy calculations of correlated electron systems

    SciTech Connect

    Yao, Y. X.; Liu, Jun; Wang, Cai-Zhuang; Ho, Kai-Ming

    2014-01-23

    We generalized the commonly used Gutzwiller approximation for calculating the electronic structure and total energy of strongly correlated electron systems. In our method, the evaluation of one-body and two-body density matrix elements of the Hamiltonian is simplified using a renormalization approximation to achieve better scaling of the computational effort as a function of system size. To achieve a clear presentation of the concept and methodology, we describe the detailed formalism for a finite hydrogen system with minimal basis set. We applied the correlation matrix renormalization approximation approach to a H2 dimer and H8 cubic fragment with minimal basis sets, as well as a H2 molecule with a large basis set. The results compare favorably with sophisticated quantum chemical calculations. We believe our approach can serve as an alternative way to build up the exchange-correlation energy functional for an improved density functional theory description of systems with strong electron correlations.

  15. Weather data for simplified energy calculation methods. Volume I. Eastern United States: TRY data

    SciTech Connect

    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 in the continental United States using Test Reference Year (TRY) source weather 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.

  16. The ground-state potential energy curve of the radium dimer from relativistic coupled cluster calculations.

    PubMed

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas

    2015-08-28

    The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm(-1), and a harmonic vibrational frequency of 20.5 cm(-1). The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 10(3), C8 = 6.978 × 10(5), and C10 = 8.786 × 10(7) atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment. PMID:26328843

  17. Calculation of energy levels, lifetimes and radiative data for La XXIX to Sm XXXIV

    NASA Astrophysics Data System (ADS)

    Goyal, Arun; Khatri, Indu; Aggarwal, Sunny; Singh, A. K.; Mohan, Man

    2016-01-01

    We present the most comprehensive atomic data for La XXIX to Sm XXXIV with single electron excitation from M-shell to N-shell and N-shell to higher shells. We have presented energy levels, lifetimes and radiative data using Multi-configuration Dirac-Fock (MCDF) method for the lowest 27 states belonging to the configuration 3d104l (l = 0 , 1 , 2 , 3), 3d105l (l = 0 , 1 , 2 , 3 , 4), 3d106l (l = 0 , 1 , 2 , 3 , 4) and 3d94s2. We have also considered relativistic effects by incorporating quantum electrodynamics (QED) and Breit corrections. We have made comparisons of our presented results with available theoretical as well as experimental results and a good agreement is achieved. Further, we have also reported energy levels by performing distorted wave calculations with fully relativistic flexible atomic code (FAC). The calculations match well with MCDF results. Additionally, we have investigated the effect of nuclear charge on transition wavelength and radiative rates for strong Extreme Ultraviolet (EUV) transitions from n = 4 → 4. We believe that our reported data in this work may be useful in various applications of lanthanide ions related to broad area of research such as applied physics, laser physics and astrophysics etc.

  18. Rovibrational bound states of neon trimer: quantum dynamical calculation of all eigenstate energy levels and wavefunctions.

    PubMed

    Yang, Benhui; Chen, Wenwu; Poirier, Bill

    2011-09-01

    Exact quantum dynamics calculations of the eigenstate energy levels and wavefunctions for all bound rovibrational states of the Ne(3) trimer (J = 0-18) have been performed using the ScalIT suite of parallel codes. These codes employ a combination of highly efficient methods, including phase-space optimized discrete variable representation, optimal separable basis, and preconditioned inexact spectral transform methods, together with an effective massive parallelization scheme. The Ne(3) energy levels and wavefunctions were computed using a pair-wise Lennard-Jones potential. Jacobi coordinates were used for the calculations, but to identify just those states belonging to the totally symmetric irreducible representation of the G(12) complete nuclear permutation-inversion group, wavefunctions were plotted in hyperspherical coordinates. "Horseshoe" states were observed above the isomerization barrier, but the horseshoe localization effect is weaker than in Ar(3). The rigid rotor model is found to be applicable for only the ground and first excited vibrational states at low J; fitted rotational constant values are presented. PMID:21913762

  19. The model of calculation the adhesion force and energy for coatings deposited by magnetron sputtering

    NASA Astrophysics Data System (ADS)

    Tkachenko, E. A.; Postnikov, D. V.; Blesman, A. I.; Polonyankin, D. A.

    2016-02-01

    The paper justifies the usefulness of preliminary ion implantation before forming the protective coating by magnetron sputtering in order to improve its adhesion and hence the coating durability. The important characteristics of coatings include the adhesion force and energy. To select the optimal modes of coatings formation, materials and equipment it is proposed the theoretical method of the adhesion force calculation in binary metallic systems. The adhesion force and energy depend on the elemental distribution in the depth of the coating and on the single bond force as in the substrate and in the coating. In addition the adhesion force is also determined by the coefficient taking into account the reduction of the possible bond number and depending on the surface purity and the structural defects presence. The developed model includes all of the above factors. The elements distribution over the depth of the coating was estimated using a kinetic model of mass transfer by vacancy mechanism. The paper presents the results of the adhesion force calculation for the chromium coating on the surface of A21382 steel.

  20. Improving iterative surface energy balance convergence for remote sensing based flux calculation

    NASA Astrophysics Data System (ADS)

    Dhungel, Ramesh; Allen, Richard G.; Trezza, Ricardo

    2016-04-01

    A modification of the iterative procedure of the surface energy balance was purposed to expedite the convergence of Monin-Obukhov stability correction utilized by the remote sensing based flux calculation. This was demonstrated using ground-based weather stations as well as the gridded weather data (North American Regional Reanalysis) and remote sensing based (Landsat 5, 7) images. The study was conducted for different land-use classes in southern Idaho and northern California for multiple satellite overpasses. The convergence behavior of a selected Landsat pixel as well as all of the Landsat pixels within the area of interest was analyzed. Modified version needed multiple times less iteration compared to the current iterative technique. At the time of low wind speed (˜1.3 m/s), the current iterative technique was not able to find a solution of surface energy balance for all of the Landsat pixels, while the modified version was able to achieve it in a few iterations. The study will facilitate many operational evapotranspiration models to avoid the nonconvergence in low wind speeds, which helps to increase the accuracy of flux calculations.

  1. Calculation of free energies and chemical potentials for gas hydrates using Monte Carlo simulations.

    PubMed

    Wierzchowski, S J; Monson, P A

    2007-06-28

    We describe a method for calculating free energies and chemical potentials for molecular models of gas hydrate systems using Monte Carlo simulations. The method has two components: (i) thermodynamic integration to obtain the water and guest molecule chemical potentials as functions of the hydrate occupancy; (ii) calculation of the free energy of the zero-occupancy hydrate system using thermodynamic integration from an Einstein crystal reference state. The approach is applicable to any classical molecular model of a hydrate. We illustrate the methodology with an application to the structure-I methane hydrate using two molecular models. Results from the method are also used to assess approximations in the van der Waals-Platteeuw theory and some of its extensions. It is shown that the success of the van der Waals-Platteeuw theory is in part due to a cancellation of the error arising from the assumption of a fixed configuration of water molecules in the hydrate framework with that arising from the neglect of methane-methane interactions. PMID:17530795

  2. Neutron spectra and dose equivalents calculated in tissue for high-energy radiation therapy

    SciTech Connect

    Kry, Stephen F.; Howell, Rebecca M.; Salehpour, Mohammad; Followill, David S.

    2009-04-15

    Neutrons are by-products of high-energy radiation therapy and a source of dose to normal tissues. Thus, the presence of neutrons increases a patient's risk of radiation-induced secondary cancer. Although neutrons have been thoroughly studied in air, little research has been focused on neutrons at depths in the patient where radiosensitive structures may exist, resulting in wide variations in neutron dose equivalents between studies. In this study, we characterized properties of neutrons produced during high-energy radiation therapy as a function of their depth in tissue and for different field sizes and different source-to-surface distances (SSD). We used a previously developed Monte Carlo model of an accelerator operated at 18 MV to calculate the neutron fluences, energy spectra, quality factors, and dose equivalents in air and in tissue at depths ranging from 0.1 to 25 cm. In conjunction with the sharply decreasing dose equivalent with increased depth in tissue, the authors found that the neutron energy spectrum changed drastically as a function of depth in tissue. The neutron fluence decreased gradually as the depth increased, while the average neutron energy decreased sharply with increasing depth until a depth of approximately 7.5 cm in tissue, after which it remained nearly constant. There was minimal variation in the quality factor as a function of depth. At a given depth in tissue, the neutron dose equivalent increased slightly with increasing field size and decreasing SSD; however, the percentage depth-dose equivalent curve remained constant outside the primary photon field. Because the neutron dose equivalent, fluence, and energy spectrum changed substantially with depth in tissue, we concluded that when the neutron dose equivalent is being determined at a depth within a patient, the spectrum and quality factor used should be appropriate for depth rather than for in-air conditions. Alternately, an appropriate percent depth-dose equivalent curve should be

  3. Free energy calculation of water addition coupled to reduction of aqueous RuO4-

    NASA Astrophysics Data System (ADS)

    Tateyama, Yoshitaka; Blumberger, Jochen; Ohno, Takahisa; Sprik, Michiel

    2007-05-01

    Free energy calculations were carried out for water addition coupled reduction of aqueous ruthenate, RuO4-+H2O +e-→[RuO3(OH)2]2-, using Car-Parrinello molecular dynamics simulations. The full reaction is divided into the reduction of the tetrahedral monoanion, RuO4-+e-→RuO42-, followed by water addition, RuO42-+H2O →[RuO3(OH)2]2-. The free energy of reduction is computed from the fluctuations of the vertical energy gap using the MnO4-+e -→MnO42- 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 -0.62eV relative to the normal hydrogen electrode. This is in good agreement with the experimental value of -0.59eV, 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 [RuO3(OH)]- and subsequent transport of the created hydroxide ion to the fifth coordination site of Ru.

  4. Track structure simulations at relativistic energies: an update on cross section calculations

    NASA Astrophysics Data System (ADS)

    Dingfelder, Michael

    Charged particle track structure simulations follow the primary, as well as all (produced) sec-ondary particles in an event-by-event matter, from starting or ejection energies down to total stopping. They provide detailed information on the spacial distributions of energy depositions, interaction types, and radical species produced. These quantities provide a starting point to describe the interaction of the radiation with matter of biological interest and to explore and estimate the effects of radiation quality on various biological responses of these systems. Of special interest is liquid water which serves as surrogate for soft tissue. Ionization and excitation cross sections for bare charged particles can be calculated within the framework of the (relativistic) plane-wave Born approximation or the (relativistic) Bethe approximation. Both theories rely on a realistic model of the dielectric response function of the material under consideration and need to address relativistic medium polarization effects like the Fermi-density effect in a consistent way. In this talk we will review and present new and updated aspects of charged particle cross section calculations for relativistic heavy ions with liquid water and other materials of biological interest. This includes an updated model for the dielectric response function of liquid water to better reflect new data from inelastic X-ray scattering (IXS) experiments using synchrotron radiation and a model for the dielectric response function of calcium, which serves as a bone surrogate. We will also discuss the implementation of relativistic effect, especially of the Fermi-density effect into the cross section calculations. This work is supported by the National Aeronautics and Space Administration (NASA), grant no. NNJ04HF39G.

  5. Electron ionization cross-section calculations for liquid water at high impact energies

    NASA Astrophysics Data System (ADS)

    Bousis, C.; Emfietzoglou, D.; Hadjidoukas, P.; Nikjoo, H.; Pathak, A.

    2008-04-01

    Cross-sections for the ionization of liquid water is perhaps the most essential set of data needed for modeling electron transport in biological matter. The complexity of ab initio calculations for any multi-electron target has led to largely heuristic semi-empirical models which take advantage elements of the Bethe, dielectric and binary collision theories. In this work we present various theoretical models for calculating total ionization cross-sections (TICSs) for liquid water over the 10 keV-1 MeV electron energy range. In particular, we extend our recent dielectric model calculations for liquid water to relativistic energies using both the appropriate kinematic corrections and the transverse part. Comparisons are made with widely used atomic and molecular TICS models such as those of Khare and co-workers, Kim-Rudd, Deutsch-Märk, Vriens and Gryzinski. The required dipole oscillator strength was provided by our recent optical-data model which is based on the latest experimental data for liquid water. The TICSs computed by the above models differ by up to 40% from the dielectric results. The best agreement (to within ∼10%) was obtained by Khare's original model and an approximate form of Gryzinski's model. In contrast, the binary-encounter-dipole (BED) models of both Kim-Rudd and Khare and co-workers resulted in ∼10-20% higher TICS values, while discrepancies increased to ∼30-40% when their simpler binary-encounter-Bethe (BEB) versions were used. Finally, we discuss to what extent the accuracy of the TICS is indicative of the reliability of the underlying differential cross-sections.

  6. Sensitivity of low energy brachytherapy Monte Carlo dose calculations to uncertainties in human tissue composition

    SciTech Connect

    Landry, Guillaume; Reniers, Brigitte; Murrer, Lars; Lutgens, Ludy; Bloemen-Van Gurp, Esther; Pignol, Jean-Philippe; Keller, Brian; Beaulieu, Luc; Verhaegen, Frank

    2010-10-15

    Purpose: The objective of this work is to assess the sensitivity of Monte Carlo (MC) dose calculations to uncertainties in human tissue composition for a range of low photon energy brachytherapy sources: {sup 125}I, {sup 103}Pd, {sup 131}Cs, and an electronic brachytherapy source (EBS). The low energy photons emitted by these sources make the dosimetry sensitive to variations in tissue atomic number due to the dominance of the photoelectric effect. This work reports dose to a small mass of water in medium D{sub w,m} as opposed to dose to a small mass of medium in medium D{sub m,m}. Methods: Mean adipose, mammary gland, and breast tissues (as uniform mixture of the aforementioned tissues) are investigated as well as compositions corresponding to one standard deviation from the mean. Prostate mean compositions from three different literature sources are also investigated. Three sets of MC simulations are performed with the GEANT4 code: (1) Dose calculations for idealized TG-43-like spherical geometries using point sources. Radial dose profiles obtained in different media are compared to assess the influence of compositional uncertainties. (2) Dose calculations for four clinical prostate LDR brachytherapy permanent seed implants using {sup 125}I seeds (Model 2301, Best Medical, Springfield, VA). The effect of varying the prostate composition in the planning target volume (PTV) is investigated by comparing PTV D{sub 90} values. (3) Dose calculations for four clinical breast LDR brachytherapy permanent seed implants using {sup 103}Pd seeds (Model 2335, Best Medical). The effects of varying the adipose/gland ratio in the PTV and of varying the elemental composition of adipose and gland within one standard deviation of the assumed mean composition are investigated by comparing PTV D{sub 90} values. For (2) and (3), the influence of using the mass density from CT scans instead of unit mass density is also assessed. Results: Results from simulation (1) show that variations

  7. X-ray Single Crystal Structure, DFT Calculations and Biological Activity of 2-(3-Methyl-5-(pyridin-2'-yl)-1H-pyrazol-1-yl) Ethanol.

    PubMed

    Radi, Smaail; Attayibat, Ahmed; El-Massaoudi, Mohamed; Salhi, Amin; Eddike, Driss; Tillard, Monique; Mabkhot, Yahia N

    2016-01-01

    A pyridylpyrazole bearing a hydroxyethyl substituent group has been synthesized by condensation of (Z)-4-hydroxy-4-(pyridin-2-yl)but-3-en-2-one with 2-hydroxyethylhydrazine. The compound was well characterized and its structure confirmed by single crystal X-ray diffraction. Density functional calculations have been performed using DFT method with 6-31G* basis set. The HOMO-LUMO energy gap, binding energies and electron deformation densities are calculated at the DFT (BLYP, PW91, PWC) level. The electrophilic f(-) and nucleophilic f(+) Fukui functions and also the electrophilic and nucleophilic Parr functions are well adapted to find the electrophile and nucleophile centers in the molecule. The title compound has been tested for its DPPH radical scavenging activity which is involved in aging processes, anti-inflammatory, anticancer and wound healing activity. Compound is also found with a significant antioxidant activity, probably due to the ability to donate a hydrogen atom to the DPPH radical. PMID:27527141

  8. Energy Savings Calculations for Heat Island Reduction Strategies in Baton Rouge, Sacramento and Salt Lake City

    SciTech Connect

    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 rate-payers from

  9. Analytic variational calculation of the ground-state binding energy of hydrogen in intermediate and intense magnetic fields

    NASA Technical Reports Server (NTRS)

    Wilson, L. W.

    1974-01-01

    The present work investigates analytically the effect of an intermediate or intense magnetic field, such as probably exist in white dwarfs and near pulsars, on the binding energy of the hydrogen ground state. A wave-function 'prescription' is given for an analytic variational calculation of the binding energy. The calculation still gives a smooth transition between intermediate and intense fields. An explicit calculation of the ground-state binding energy as B goes to infinity is provided for the Yafet et al. (1956) trial function.

  10. Calculation of a mirror asymmetric effect in electron scattering from chiral targets. [in optically active medium

    NASA Technical Reports Server (NTRS)

    Rich, A.; Van House, J.; Hegstrom, R. A.

    1982-01-01

    A dynamical calculation is presented of the helicity induced in an initially unpolarized electron beam after elastic scattering from an optically active medium, a process analogous to the circular polarization induced in unpolarized light following Rayleigh scattering from chiral targets. The calculation is based on the bound helical electron model of a chiral molecule, according to which the major contribution to the helicity is provided by the perturbation of the electron bound state by the spin-orbit interaction of the bound electrons moving in the electric field of the molecular core. The net helicity acquired is found to depend directly on a molecular asymmetry factor and the square of the atomic number of the heaviest atom in an asymmetric environment. For the case of carbon, the induced helicity is on the order of 0.00001, which would account for its lack of observation in a recent experiment. Results may have implications for the origin of optical activity in biological molecules by the differential ionization of D and L isomers by beta-decay electrons.

  11. Assessment of Uncertainty in the Determination of Activation Energy for Polymeric Materials

    NASA Technical Reports Server (NTRS)

    Darby, Stephania P.; Landrum, D. Brian; Coleman, Hugh W.

    1998-01-01

    An assessment of the experimental uncertainty in obtaining the kinetic activation energy from thermogravimetric analysis (TGA) data is presented. A neat phenolic resin, Borden SC1O08, was heated at three heating rates to obtain weight loss vs temperature data. Activation energy was calculated by two methods: the traditional Flynn and Wall method based on the slope of log(q) versus 1/T, and a modification of this method where the ordinate and abscissa are reversed in the linear regression. The modified method produced a more accurate curve fit of the data, was more sensitive to data nonlinearity, and gave a value of activation energy 75 percent greater than the original method. An uncertainty analysis using the modified method yielded a 60 percent uncertainty in the average activation energy. Based on this result, the activation energy for a carbon-phenolic material was doubled and used to calculate the ablation rate In a typical solid rocket environment. Doubling the activation energy increased surface recession by 3 percent. Current TGA data reduction techniques that use the traditional Flynn and Wall approach to calculate activation energy should be changed to the modified method.

  12. Simple thermodynamic model of unassisted proton shuttle uncoupling and prediction of activity from calculated speciation, lipophilicity, and molecular geometry.

    PubMed

    Martineau, Louis C

    2012-06-21

    A mechanistic model of uncoupling of oxidative phosphorylation by lipophilic weak acids (i.e. proton shuttles) was developed for the purposes of predicting the relative activity of xenobiotics of widely varying structure and of guiding the design of optimized derivatives. The model is based on thermodynamic premises not formulated elsewhere that allow for the calculation of steady-state conditions and of rate of energy dissipation on the basis of acid-dissociation and permeability behavior, the later estimated from partitioning behavior and geometric considerations. Moreover, permeability of either the neutral or of the ionized species is proposed to be effectively enhanced under conditions of asymmetrical molecular distribution. Finally, special considerations were developed to accommodate multi-protic compounds. The comparison of predicted to measured activity for a diverse testset of 48 compounds of natural origin spanning a wide range of activity yielded a Spearman's rho of 0.90. The model was used to tentatively identify several novel proton shuttles, as well as to elucidate core structures particularly conducive to proton shuttle activity from which optimized derivatives can be designed. Principles of design were formulated and examples of derivatives projected to be active at concentrations on the order of 10(-7)M are proposed. Among these are di-protic compounds predicted to shuttle two protons per cycle iteration and proposed to maximally exploit the proton shuttle mechanism. This work promotes the design of highly active, yet easily-metabolized uncouplers for therapeutic applications, namely the indirect activation of AMP-kinase, as well as for various industrial applications where low persistence is desirable. PMID:22425608

  13. Energy and Man's Environment: Activity Guide. An Interdisciplinary Teacher's Guide to Energy and Environmental Activities.

    ERIC Educational Resources Information Center

    Jones, John, Ed.

    This publication provides the goals, concepts, objectives, and rationale for the six activity guides in this series of energy education materials. The organization of this series, as presented in this publication, centers around six goals which correspond to the activity guides. Under each goal are several concepts, which in turn, have several…

  14. Calculation of stellar structure. IV. Results using a detailed energy generation subroutine.

    NASA Astrophysics Data System (ADS)

    Rouse, C. A.

    1995-12-01

    The results from two solar model calculations using the "energy.for" energy generation and neutrino flux code (Bahcall & Pinsonneault 1992) are presented. The models of the present Sun were generated using the program described in the first three papers of this series and using only the helium abundance profile from the Bahcall & Ulrich (1988) (BU) standard model in the present model structure calculations. One model is a simulation of the BU model and yields a ^37^Cl solar neutrino counting rate of 7.0SNU (compared to 7.9SNU for the BU model) and a ^71^Ga neutrino experiment counting rate between 112 and 137SNU (compared to 132SNU for the BU model). The second model has a postulated small high-Z core (Rouse 1983) and yields a ^37^Cl neutrino experiment counting rate of 2.45SNU that is within one sigma of the Homestake Collaboration observed rate of (2.55+/-0.25)SNU (see Parke 1995). It yields a ^71^Ga neutrino experiment counting rate between 89 and 103SNU that is within one sigma of the GALLEX Collaboration neutrino experiment observed rate of (79+/-12)SNU (see Parke 1995). The theoretical ^8^B solar neutrino flux and the observed Kamiokande ^8^B flux (Hirata et al. 1989) are discussed regarding the puzzle of explaining both the chlorine experiment results and the Kamiokande results. The modification of the energy.for code for use in the current Rouse program is described. Consistency of a high-Z core solar model with theories of star formation from pre-stellar nuclei (Krat 1952; Urey 1956; Huang 1957) is suggested.

  15. A big data approach to the ultra-fast prediction of DFT-calculated bond energies

    PubMed Central

    2013-01-01

    Background The rapid access to intrinsic physicochemical properties of molecules is highly desired for large scale chemical data mining explorations such as mass spectrum prediction in metabolomics, toxicity risk assessment and drug discovery. Large volumes of data are being produced by quantum chemistry calculations, which provide increasing accurate estimations of several properties, e.g. by Density Functional Theory (DFT), but are still too computationally expensive for those large scale uses. This work explores the possibility of using large amounts of data generated by DFT methods for thousands of molecular structures, extracting relevant molecular properties and applying machine learning (ML) algorithms to learn from the data. Once trained, these ML models can be applied to new structures to produce ultra-fast predictions. An approach is presented for homolytic bond dissociation energy (BDE). Results Machine learning models were trained with a data set of >12,000 BDEs calculated by B3LYP/6-311++G(d,p)//DFTB. Descriptors were designed to encode atom types and connectivity in the 2D topological environment of the bonds. The best model, an Associative Neural Network (ASNN) based on 85 bond descriptors, was able to predict the BDE of 887 bonds in an independent test set (covering a range of 17.67–202.30 kcal/mol) with RMSD of 5.29 kcal/mol, mean absolute deviation of 3.35 kcal/mol, and R2 = 0.953. The predictions were compared with semi-empirical PM6 calculations, and were found to be superior for all types of bonds in the data set, except for O-H, N-H, and N-N bonds. The B3LYP/6-311++G(d,p)//DFTB calculations can approach the higher-level calculations B3LYP/6-311++G(3df,2p)//B3LYP/6-31G(d,p) with an RMSD of 3.04 kcal/mol, which is less than the RMSD of ASNN (against both DFT methods). An experimental web service for on-line prediction of BDEs is available at http://joao.airesdesousa.com/bde. Conclusion Knowledge could be automatically extracted by

  16. Benchmark calculations with correlated molecular wave functions. VII. Binding energy and structure of the HF dimer

    SciTech Connect

    Peterson, K.A. ); Dunning, T.H. Jr. )

    1995-02-01

    The hydrogen bond energy and geometry of the HF dimer have been investigated using the series of correlation consistent basis sets from aug-cc-pVDZ to aug-cc-pVQZ and several theoretical methods including Moller--Plesset perturbation and coupled cluster theories. Estimates of the complete basis set (CBS) limit have been derived for the binding energy of (HF)[sub 2] at each level of theory by utilizing the regular convergence characteristics of the correlation consistent basis sets. CBS limit hydrogen bond energies of 3.72, 4.53, 4.55, and 4.60 kcal/mol are estimated at the SCF, MP2, MP4, and CCSD(T) levels of theory, respectively. CBS limits for the intermolecular F--F distance are estimated to be 2.82, 2.74, 2.73, and 2.73 A, respectively, for the same correlation methods. The effects of basis set superposition error (BSSE) on both the binding energies and structures have also been investigated for each basis set using the standard function counterpoise (CP) method. While BSSE has a negligible effect on the intramolecular geometries, the CP-corrected F--F distance and binding energy differ significantly from the uncorrected values for the aug-cc-pVDZ basis set; these differences decrease regularly with increasing basis set size, yielding the same limits in the CBS limit. Best estimates for the equilibrium properties of the HF dimer from CCSD(T) calculations are [ital D][sub [ital e

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  18. Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole.

    PubMed

    Muthu, S; Uma Maheswari, J; Srinivasan, S; Isac paulraj, E

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N(6)-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials. PMID:23831980

  19. Energy and Man's Environment Activity Guide: An Interdisciplinary Teacher's Guide to Energy and Environmental Activities, Section Four - Impacts of Energy.

    ERIC Educational Resources Information Center

    Jones, John, Ed.

    This publication presents the activities pertaining to the fourth goal of this activity guide series. The activities in this publication focus on the socioeconomic effects of energy uses and crises and the understandings needed to assess those effects. These materials are appropriate for middle school and junior high school students. These…

  20. Energy and Man's Environment Activity Guide: An Interdisciplinary Teacher's Guide to Energy and Environmental Activities, Section One - Sources of Energy.

    ERIC Educational Resources Information Center

    Jones, John, Ed.

    This publication presents the activities pertaining to the first goal of this activity guide series. The activities in this publication focus primarily on the availability of resources, forms of energy, natural laws, and socioeconomic considerations. These materials are appropriate for middle school and junior high school students. These…