Science.gov

Sample records for activation energies calculated

  1. Removing the barrier to the calculation of activation energies

    SciTech Connect

    Mesele, Oluwaseun O.; Thompson, Ward H.

    2016-10-06

    Approaches for directly calculating the activation energy for a chemical reaction from a simulation at a single temperature are explored with applications to both classical and quantum systems. The activation energy is obtained from a time correlation function that can be evaluated from the same molecular dynamics trajectories or quantum dynamics used to evaluate the rate constant itself and thus requires essentially no extra computational work.

  2. 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.

  3. The Activation Energy Of Ignition Calculation For Materials Based On Plastics

    NASA Astrophysics Data System (ADS)

    Rantuch, Peter; Wachter, Igor; Martinka, Jozef; Kuracina, Marcel

    2015-06-01

    This article deals with the activation energy of ignition calculation of plastics. Two types of polyamide 6 and one type of polypropylene and polyurethane were selected as samples. The samples were tested under isothermal conditions at several temperatures while times to ignition were observed. From the obtained data, activation energy relating to the moment of ignition was calculated for each plastics. The values for individual plastics were different. The highest activation energies (129.5 kJ.mol-1 and 106.2 kJ.mol-1) were achieved by polyamides 6, while the lowest was determined for a sample of polyurethane.

  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. Integral Equation Calculation of Solvent Activation Free Energies for Electron and Proton Transfer Reactions

    DTIC Science & Technology

    1993-11-04

    6. AUTHOR(S) P.P. Schmidt Indrani Bhattacharya- Kodali and Gregory Voth 7. PERFORMING ORGANIZATION NAME(S) AND AODRESS(ES) 8. PERIORMING ORGANIZATION...13. ABSTRACT (Maimum 200 words) The extended reference interaction site method (RISM) integral equation theory is applied to calculate the solvent...Integral Equation Calculation of Solvent Activation Free Energies for Electron and Proton Transfer Reactions Indrani Bhattacharya- Kodali and Gregory A. Voth

  6. Mechanism and activation energy of magnetic skyrmion annihilation obtained from minimum energy path calculations

    NASA Astrophysics Data System (ADS)

    Lobanov, Igor S.; Jónsson, Hannes; Uzdin, Valery M.

    2016-11-01

    The mechanism and activation energy for the annihilation of a magnetic skyrmion is studied by finding the minimum energy path for the transition in a system described by a Heisenberg-type Hamiltonian extended to include dipole-dipole, Dzyaloshinskii-Moriya, and anisotropy interactions so as to represent a Co monolayer on a Pt(111) surface. The annihilation mechanism involves isotropic shrinking of the skyrmion and slow increase of the energy until the transition state is reached after which the energy drops abruptly as the ferromagnetic final state forms. The maximum energy along the minimum energy path, which gives an estimate of the activation energy within the harmonic approximation of transition state theory, is found to be in excellent agreement with direct Langevin dynamics simulations at relatively high temperature carried out by Rohart et al. [Phys. Rev. B 93, 214412 (2016), 10.1103/PhysRevB.93.214412]. The dipole-dipole interaction, the computationally most demanding term in the Hamiltonian, is found to be important but its effect on the stability of the skyrmion and shape of the transition path can be mimicked accurately by reducing the anisotropy constant in the Hamiltonian.

  7. Density functional calculation of activation energies for lattice and grain boundary diffusion in alumina

    NASA Astrophysics Data System (ADS)

    Lei, Yinkai; Gong, Yu; Duan, Zhiyao; Wang, Guofeng

    2013-06-01

    To acquire knowledge on the lattice and grain boundary diffusion processes in alumina, we have determined the activation energies of elementary O and Al diffusive jumps in the bulk crystal, Σ3(0001) grain boundaries, and Σ3(101¯0) grain boundaries of α-Al2O3 using the first-principles density functional theory method. Specifically, we calculated the activation energies for four elementary jumps of both O and Al lattice diffusion in alumina. It was predicted that the activation energy of O lattice diffusion varied from 3.58 to 5.03 eV, while the activation energy of Al lattice diffusion ranged from 1.80 to 3.17 eV. As compared with experimental measurements, the theoretical predictions of the activation energy for lattice diffusion were lower and thus implied that there might be other high-energy diffusive jumps in the experimental alumina samples. Moreover, our results suggested that the Al lattice diffusion was faster than the O lattice diffusion in alumina, in agreement with experiment observations. Furthermore, it was found from our calculations for α-Al2O3 that the activation energies of O and Al grain boundary diffusion in the high-energy Σ3(0001) grain boundaries were significantly lower than those of the lattice diffusion. In contrast, the activation energies of O and Al grain boundary diffusion in the low-energy Σ3(101¯0) grain boundaries could be even higher than those of the lattice diffusion.

  8. CALCULATING ENERGY STORAGE DUE TO TOPOLOGICAL CHANGES IN EMERGING ACTIVE REGION NOAA AR 11112

    SciTech Connect

    Tarr, Lucas; Longcope, Dana

    2012-04-10

    The minimum current corona model provides a way to estimate stored coronal energy using the number of field lines connecting regions of positive and negative photospheric flux. This information is quantified by the net flux connecting pairs of opposing regions in a connectivity matrix. Changes in the coronal magnetic field, due to processes such as magnetic reconnection, manifest themselves as changes in the connectivity matrix. However, the connectivity matrix will also change when flux sources emerge or submerge through the photosphere, as often happens in active regions. We have developed an algorithm to estimate the changes in flux due to emergence and submergence of magnetic flux sources. These estimated changes must be accounted for in order to quantify storage and release of magnetic energy in the corona. To perform this calculation over extended periods of time, we must additionally have a consistently labeled connectivity matrix over the entire observational time span. We have therefore developed an automated tracking algorithm to generate a consistent connectivity matrix as the photospheric source regions evolve over time. We have applied this method to NOAA Active Region 11112, which underwent a GOES M2.9 class flare around 19:00 on 2010 October 16th, and calculated a lower bound on the free magnetic energy buildup of {approx}8.25 Multiplication-Sign 10{sup 30} erg over 3 days.

  9. 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.

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

    PubMed Central

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

    2016-01-01

    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

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

    PubMed

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

    2016-03-08

    We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm.

  12. Landfill Gas Energy Benefits Calculator

    EPA Pesticide Factsheets

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

  13. 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

  14. 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.

  15. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    DOE PAGES

    Zhang, Du; Yang, Weitao

    2016-10-13

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and doublemore » excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K^{4}), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.« less

  16. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    SciTech Connect

    Zhang, Du; Yang, Weitao

    2016-10-13

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and double excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K^{4}), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.

  17. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    NASA Astrophysics Data System (ADS)

    Zhang, Du; Yang, Weitao

    2016-10-01

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and double excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K4), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.

  18. 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.

  19. Activation Energy Calculations for Formamide-TiO2 and Formamide-Pt Interactions in the Presence of Water.

    PubMed

    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.

  20. 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

  1. 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)

  2. Mapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations.

    PubMed

    Nash, Anthony; Birch, Helen L; de Leeuw, Nora H

    2017-02-01

    The zinc-dependent Matrix Metalloproteinases (MMPs) found within the extracellular matrix (ECM) of vertebrates are linked to pathological processes such as arthritis, skin ulceration and cancer. Although a general backbone proteolytic mechanism is understood, crystallographic data continue to suggest an active site that is too narrow to encompass the respective substrate. We present a fully parameterised Molecular Dynamics (MD) study of the structural properties of an MMP-1-collagen crystallographic structure (Protein Data Bank - 4AUO), followed by an exploration of the free energy surface of a collagen polypeptide chain entering the active site, using a combined meta-dynamics and umbrella sampling (MDUS) approach. We conclude that the interactions between MMP-1 and the collagen substrate are in good agreement with a number of experimental studies. As such, our unrestrained MD simulations and our MDUS results, which indicate an energetic barrier for a local uncoiling and insertion event, can inform future investigations of the collagen-peptide non-bonded association steps with the active site prior to proteolytic mechanisms. The elucidation of such free energy barriers provides a better understanding of the role of the enzyme in the ECM and is important in the design of future MMP inhibitors.

  3. Combining active-space coupled-cluster methods with moment energy corrections via the CC(P;Q) methodology, with benchmark calculations for biradical transition states

    NASA Astrophysics Data System (ADS)

    Shen, Jun; Piecuch, Piotr

    2012-04-01

    We have recently suggested the CC(P;Q) methodology that can correct energies obtained in the active-space coupled-cluster (CC) or equation-of-motion (EOM) CC calculations, which recover much of the nondynamical and some dynamical electron correlation effects, for the higher-order, mostly dynamical, correlations missing in the active-space CC/EOMCC considerations. It is shown that one can greatly improve the description of biradical transition states, both in terms of the resulting energy barriers and total energies, by combining the CC approach with singles, doubles, and active-space triples, termed CCSDt, with the CC(P;Q)-style correction due to missing triple excitations defining the CC(t;3) approximation.

  4. Combining active-space coupled-cluster methods with moment energy corrections via the CC(P;Q) methodology, with benchmark calculations for biradical transition states.

    PubMed

    Shen, Jun; Piecuch, Piotr

    2012-04-14

    We have recently suggested the CC(P;Q) methodology that can correct energies obtained in the active-space coupled-cluster (CC) or equation-of-motion (EOM) CC calculations, which recover much of the nondynamical and some dynamical electron correlation effects, for the higher-order, mostly dynamical, correlations missing in the active-space CC/EOMCC considerations. It is shown that one can greatly improve the description of biradical transition states, both in terms of the resulting energy barriers and total energies, by combining the CC approach with singles, doubles, and active-space triples, termed CCSDt, with the CC(P;Q)-style correction due to missing triple excitations defining the CC(t;3) approximation.

  5. 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.

  6. 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.

  7. Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies.

    PubMed

    Chaudhary, Neha; Aparoy, Polamarasetty

    2017-03-01

    COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.

  8. 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

    2012-11-06

    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.

  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. 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.

  11. Energy and mass balance calculations for incinerators

    SciTech Connect

    Lee, C.C.; Huffman, G.L.

    1998-01-01

    Calculation of energy and mass balance within an incinerator is a very important part of designing and/or evaluating the incineration process. This article describes a simple computer model used to calculate an energy and mass balance for a rotary kiln incinerator. The main purpose of the model is to assist US Environmental Protection Agency (EPA) permit writers in evaluating the adequacy of the data submitted by applicants seeking incinerator permits. The calculation is based on the assumption that a thermodynamic equilibrium condition exits within the combustion chamber. Key parameters that the model can calculate include theoretical combustion air, excess air needed for actual combustion cases, flue gas flow rate, and exit temperature.

  12. 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.

  13. 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

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

    PubMed

    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.

  15. 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

  16. 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.

  17. Monte Carlo algorithm for free energy calculation.

    PubMed

    Bi, Sheng; Tong, Ning-Hua

    2015-07-01

    We propose a Monte Carlo algorithm for the free energy calculation based on configuration space sampling. An upward or downward temperature scan can be used to produce F(T). We implement this algorithm for the Ising model on a square lattice and triangular lattice. Comparison with the exact free energy shows an excellent agreement. We analyze the properties of this algorithm and compare it with the Wang-Landau algorithm, which samples in energy space. This method is applicable to general classical statistical models. The possibility of extending it to quantum systems is discussed.

  18. 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).

  19. 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…

  20. Parallel calculations between the TC 4. 7 simplified energy calculation procedure and seven comprehensive hourly simulation energy calculation procedures

    SciTech Connect

    Kusuda, T

    1980-10-31

    The TC 4.7 simplified energy calculation method is a bin method used by the REAP procedure of the Carrier Corporation, except for the load estimating calculations. The simplified procedure was compared with hourly simulation procedures for an office building in Washington, DC. The comparison studied the extent as well as the reasons for agreement and discrepancies due to these two different types of annual energy analysis (bin method and hourly simulation methods). Results of the parallel calculations are discussed and the major reasons of discrepancies between the hourly simulation technique and the simplified TC 4.7 method are identified. Data resulting from the calculation methods are tabulated. (MCW)

  1. Perturbation energy as an alternative to the total energy calculations

    NASA Astrophysics Data System (ADS)

    Kutepov, Andrey; Antropov, Vladimir; van Schilfgaarde, Mark; Antonov, Victor

    2014-03-01

    We analyze different approaches to determine the energy from a perturbation using modern electronic structure methods. We compare the energy of perturbation from standard perturbation theory with what is obtained directly in self consistent band structure methods. The method is applied for studies such perturbations as internal magnetic field and spin orbital coupling in solids. This method is further compared with integration over the coupling constant. Numerical tests have been performed for magnetic Fe and Gd systems using the local density approximation. The main advantage of present scheme is its usefulness in methods for strongly correlated electronic systems studies where total energy calculations are not always possible. Specific calculations are performed using self consistent quasiparticle GW and LDA+U calculations for MnBi where the right value of magnetic moment and sign/value of magnetic anisotropy as a function of temperature have been obtained. This research is supported in part by the Critical Materials Institute, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy through the Ames Laboraory.

  2. 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.

  3. 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.

  4. 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…

  5. 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.

  6. 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.

  7. CHP Energy and Emissions Savings Calculator

    EPA Pesticide Factsheets

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

  8. Computational methods to calculate accurate activation and reaction energies of 1,3-dipolar cycloadditions of 24 1,3-dipoles.

    PubMed

    Lan, Yu; Zou, Lufeng; Cao, Yang; Houk, K N

    2011-12-01

    Theoretical calculations were performed on the 1,3-dipolar cycloaddition reactions of 24 1,3-dipoles with ethylene and acetylene. The 24 1,3-dipoles are of the formula X≡Y(+)-Z(-) (where X is HC or N, Y is N, and Z is CH(2), NH, or O) or X═Y(+)-Z(-) (where X and Z are CH(2), NH, or O and Y is NH, O, or S). The high-accuracy G3B3 method was employed as the reference. CBS-QB3, CCSD(T)//B3LYP, SCS-MP2//B3LYP, B3LYP, M06-2X, and B97-D methods were benchmarked to assess their accuracies and to determine an accurate method that is practical for large systems. Several basis sets were also evaluated. Compared to the G3B3 method, CBS-QB3 and CCSD(T)/maug-cc-pV(T+d)Z//B3LYP methods give similar results for both activation and reaction enthalpies (mean average deviation, MAD, < 1.5 kcal/mol). SCS-MP2//B3LYP and M06-2X give small errors for the activation enthalpies (MAD < 1.5 kcal/mol), while B3LYP has MAD = 2.3 kcal/mol. SCS-MP2//B3LYP and B3LYP give the reasonable reaction enthalpies (MAD < 5.0 kcal/mol). The B3LYP functional also gives good results for most 1,3-dipoles (MAD = 1.9 kcal/mol for 17 common 1,3-dipoles), but the activation and reaction enthalpies for ozone and sulfur dioxide are difficult to calculate by any of the density functional methods.

  9. Micro-mechanical and Structural Properties and Activation Energy Calculation of Nd2O3 Added Bi2Sr2Ca1Cu2Oy Superconducting System

    NASA Astrophysics Data System (ADS)

    Ozturk, Ozgur; Asikuzun, Elif; Coskunyurek, Murat; Kaya, Seydanur; Yilmazlar, Mustafa; Yildirim, Gurcan; Terzioglu, Cabir

    2013-03-01

    Nd added Bi-2212 superconducting samples with x =0, 0.001, 0.005, 0.01, 0.05 and 0.1 were prepared by conventional solid state reaction method and annealed at 840°C for 72 h. For the comparison, an undoped sample was produced to the same conditions. The effects of Nd addition on structural and micromechanical properties were systematically investigated. The volume fraction, lattice parameters, crystal structure and grain size of the samples were characterized using the X-ray diffractometer and Scanning Electron Microscope. In addition, this study includes determination of the activation energy of Nd in the Bi-2212 system using the magnetoresistivity measurements. And also, we were investigated the mechanical properties for all samples using the Vickers microhardness measurements. Microhardness values of the samples decrease with increasing adding and applied load. The Vickers hardness of the samples studied, exhibits the typical indentation size effect (ISE).

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

    SciTech Connect

    Hamilton, John C.

    2005-06-01

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

  11. Verification Of Energy Balance In The Ansys V5.4 Thermal Calculations

    SciTech Connect

    H. Marr; M.J. Anderson

    2001-02-08

    The objective of this calculation is to verify the energy balance of the thermal calculations analyzed by ANSYS Version (V) 5.4 solver (see Section 4). The scope of this calculation is limited to calculating the energy balance of a two-dimensional repository thermal representation using the temperatures obtained from ANSYS V5.4. The procedure, AP-3.124, Calculations (Ref. 3), and the Technical Work Plan for: Waste Package Design Description for LA (Ref. 2) are used to develop this calculation. The associated activity is the development of engineering evaluations to support the Licensing Application design activities.

  12. 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.

  13. Energy Model of Neuron Activation.

    PubMed

    Romanyshyn, Yuriy; Smerdov, Andriy; Petrytska, Svitlana

    2017-02-01

    On the basis of the neurophysiological strength-duration (amplitude-duration) curve of neuron activation (which relates the threshold amplitude of a rectangular current pulse of neuron activation to the pulse duration), as well as with the use of activation energy constraint (the threshold curve corresponds to the energy threshold of neuron activation by a rectangular current pulse), an energy model of neuron activation by a single current pulse has been constructed. The constructed model of activation, which determines its spectral properties, is a bandpass filter. Under the condition of minimum-phase feature of the neuron activation model, on the basis of Hilbert transform, the possibilities of phase-frequency response calculation from its amplitude-frequency response have been considered. Approximation to the amplitude-frequency response by the response of the Butterworth filter of the first order, as well as obtaining the pulse response corresponding to this approximation, give us the possibility of analyzing the efficiency of activating current pulses of various shapes, including analysis in accordance with the energy constraint.

  14. 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…

  15. 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…

  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. Tests of MULTIMODE calculations of rovibrational energies of CH 4

    NASA Astrophysics Data System (ADS)

    Wu, Jiayan; Huang, Xinchuan; Carter, Stuart; Bowman, Joel M.

    2006-08-01

    We report variational calculations of rovibrational energies of CH 4 using the code MULTIMODE and an ab initio force field of Schwenke and Partridge. The systematic convergence of the energies with respect to the level of mode coupling is presented. Converged vibrational energies calculated using the five-mode representation of the potential for zero total angular momentum are compared with previous, benchmark calculations based on Radau coordinates using this force field for zero total angular momentum and for J = 1. Very good agreement with the previous benchmark calculations is found.

  18. Density functional theory for comprehensive orbital energy calculations.

    PubMed

    Nakata, Ayako; Tsuneda, Takao

    2013-08-14

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

  19. Calculation of the energy levels of lithium-like ions

    NASA Astrophysics Data System (ADS)

    Nadykto, B. A.

    An attempt is made to develop a straightforward and sufficiently accurate method for calculating the energies of complex ion states. The method is based on Bohr's computational model and Sommerfeld's model in relativistic form (for circular orbits only). The method proposed here makes it possible to calculate excited ion states having different atomic and quantum numbers. A similar method can be used for calculating the energies of ion states with the number of electrons exceeding three.

  20. Energy deposition calculated by PHITS code in Pb spallation target

    NASA Astrophysics Data System (ADS)

    Yu, Quanzhi

    2016-01-01

    Energy deposition in a Pb spallation target irradiated by high energetic protons was calculated by PHITS2.52 code. The validation of the energy deposition and neutron production calculated by PHITS code was performed. Results show good agreements between the simulation results and the experimental data. Detailed comparison shows that for the total energy deposition, PHITS simulation result was about 15% overestimation than that of the experimental data. For the energy deposition along the length of the Pb target, the discrepancy mainly presented at the front part of the Pb target. Calculation indicates that most of the energy deposition comes from the ionizations of the primary protons and the produced secondary particles. With the event generator mode of PHITS, the deposit energy distribution for the particles and the light nulclei is presented for the first time. It indicates that the primary protons with energy more than 100 MeV are the most contributors to the total energy deposition. The energy depositions peaking at 10 MeV and 0.1 MeV, are mainly caused by the electrons, pions, d, t, 3He and also α particles during the cascade process and the evaporation process, respectively. The energy deposition density caused by different proton beam profiles are also calculated and compared. Such calculation and analyses are much helpful for better understanding the physical mechanism of energy deposition in the spallation target, and greatly useful for the thermal hydraulic design of the spallation target.

  1. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. Guidelines for the analysis of free energy calculations

    NASA Astrophysics Data System (ADS)

    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, http://arxiv.org/abs/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.

  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.

  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. Calculation of astrophysical S factor at low energy levels

    NASA Astrophysics Data System (ADS)

    Andic, Halil Ibrahim; Ozer, Okan

    2017-02-01

    Nuclear reactions are very important for the structure, evolution, nucleosynthesis and various observational manifestations of main-sequence stars, white dwarfs and neutron stars. For astrophysical applications, one needs to know value of S-factor for many reactions at low energies. The experimental measurements of cross-sections at such low energies are essentially not easily available since the Coulomb barrier. Theoretical calculations are model dependent, so that nuclear physics uncertainties of calculated S-factor can be substantial. Using the supersymmetric quantum mechanics one can obtain the supersymmetric partner potential that can vary by several orders of magnitude in the energy range of a given reaction in the calculation of S factor. Since the determination of reaction rates requires accurate values of cross sections at very low energies, then in order to eliminate the main part of the energy dependence of these cross sections one makes use of the astrophysical S-factor in Taylor Expansion series about zero-energy.

  10. 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.

  11. Protein Thermostability Calculations Using Alchemical Free Energy Simulations

    PubMed Central

    Seeliger, Daniel; de Groot, Bert L.

    2010-01-01

    Abstract 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

  12. 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)

  13. 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…

  14. Large scale self energy calculations for ion-surface interactions

    NASA Astrophysics Data System (ADS)

    Kürpick, P.; Thumm, U.

    1996-03-01

    We present large scale non-perturbative self energy calculations for the interaction of an ion with a metal surface. Using both the simple jellium potential and more sophisticated ab initio potentials(P. J. Jennings, R. O. Jones and M. Weinert, Phys. Rev. B, 37), 6113 (1988)., we study the complex self energy matrix for various n-manifolds allowing for the calculation of diabatic and adiabatic non-perturbative level shifts and widths, and hybrid orbitals(P. Kürpick and U.Thumm, to be published.). Besides this self energy calculations a new adiabatic close--coupling calculation is being developed that will be applied to the interaction of ions in various charge states with metal surfaces.

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

    NASA Astrophysics Data System (ADS)

    Kaya, Cemal; Kaya, Savaş; Banerjee, Priyabrata

    2017-01-01

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

  16. 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…

  17. 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;…

  18. Towards a standardized setup for surface energy calculations

    NASA Astrophysics Data System (ADS)

    Kaminski, Jakub W.; Kratzer, Peter; Ratsch, Christian

    2017-02-01

    High-throughput design of new materials with desired electronic properties, based on screening of large collections of crystal structures organized in the from of libraries or databases require fast, widely applicable, consistent and unsupervised methods to calculate the property of interest. In this work we present an approach for the calculation of surface energies of two-dimensional periodic crystal lattices which meets all these requirements. For materials slabs which are terminated with two identical surfaces, the task of calculating the surface energy is trivial. More problematic are the cases 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 approach addresses this problem. It relies on appropriately chosen capping atoms, whose bonding energy contributions are 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 surface energies with errors that are below 10%, and that are as low as 2% in many cases. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations.

  19. 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.

  20. 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…

  1. 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.

  2. 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.

  3. 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…

  4. Perspective: Alchemical free energy calculations for drug discovery

    NASA Astrophysics Data System (ADS)

    Mobley, David L.; Klimovich, Pavel V.

    2012-12-01

    Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery.

  5. The calculation of band gap energy in zinc oxide films

    NASA Astrophysics Data System (ADS)

    Arif, Ali; Belahssen, Okba; Gareh, Salim; Benramache, Said

    2015-01-01

    We investigated the optical properties of undoped zinc oxide thin films as the n-type semiconductor; the thin films were deposited at different precursor molarities by ultrasonic spray and spray pyrolysis techniques. The thin films were deposited at different substrate temperatures ranging between 200 and 500 °C. In this paper, we present a new approach to control the optical gap energy of ZnO thin films by concentration of the ZnO solution and substrate temperatures from experimental data, which were published in international journals. The model proposed to calculate the band gap energy with the Urbach energy was investigated. The relation between the experimental data and theoretical calculation suggests that the band gap energies are predominantly estimated by the Urbach energies, film transparency, and concentration of the ZnO solution and substrate temperatures. The measurements by these proposal models are in qualitative agreements with the experimental data; the correlation coefficient values were varied in the range 0.96-0.99999, indicating high quality representation of data based on Equation (2), so that the relative errors of all calculation are smaller than 4%. Thus, one can suppose that the undoped ZnO thin films are chemically purer and have many fewer defects and less disorder owing to an almost complete chemical decomposition and contained higher optical band gap energy.

  6. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

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

    2017-02-16

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

  7. Atomistic calculations of dislocation core energy in aluminium

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  8. 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.

  9. The theoretical shape of sucrose crystals from energy calculations

    NASA Astrophysics Data System (ADS)

    Saska, Michael; Myerson, Allan S.

    1983-05-01

    The surface energies of individual crystallographic faces of crystalline sucrose were calculated using two forms of the 6-exp (Buckingham) potential. Hydrogen bond energies were calculated as a sum of O-H, O…H and O…O interactions where the Lippincott-Schroeder short-range potential was used for O-H and O…H pairs and the 6-exp potential for the non-bonded O…O interactions. Assuming that the surface energy equals half of the cohesive energy of the crystal, the attachment and surface energies of most of the faces found on as sucrose crystal were calculated. A computer program was written to draw the theoretical shape of crystals given the positions (central distances) of its faces. The resulting sucrose shapes are elongated along the c-axis. It is argued that the c-axis elongated habit is an intrinsic shape for vapor grown sucrose crystals (if realizable) and it is suggested that the usual shapes of solution grown sucrose crystals can be explained in terms of solvent (water) adsorption.

  10. Effects of internal gain assumptions in building energy calculations

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Perkins, R.

    The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations. Heating and cooling loads from simulations using the Department of Energy 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.

  11. 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)

  12. 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.

  13. Calculated stacking-fault energies of elemental metals

    NASA Astrophysics Data System (ADS)

    Rosengaard, N. M.; Skriver, H. L.

    1993-05-01

    We have performed ab initio calculations of twin, intrinsic, and extrinsic face-centered-cubic stacking faults for all the 3d, 4d, and 5d transition metals by means of a Green's-function technique, based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The results are in excellent agreement with recent layer Korringa-Kohn-Rostoker Green's-function calculations where stacking-fault energies for Ni, Cu, Rh, Pd, Ag, Ir, and Au were found by means of the so-called force theorem. We find that the self-consistent fault energies for all the metals in the three transition series vary with atomic number essentially as the calculated structural energy differences between the face-centered-cubic and the hexagonal-close-packed phases. In addition we find that the simple relations between the different types of fault energies predicted by models based on the local atomic coordination are obeyed to a high degree of accuracy.

  14. Surface energy balance calculations for small northern lakes

    NASA Astrophysics Data System (ADS)

    Binyamin, J.; Rouse, W. R.; Davies, J. A.; Oswald, C. J.; Schertzer, W. M.

    2006-12-01

    An energy balance model is used to determine diurnal surface energy balance components for three different sized high-latitude Canadian lakes in the Mackenzie River Basin (MRB) during the open water seasons of 2000, 2001, and 2002. Surface net radiation is derived from the component fluxes of the radiation balance. Turbulent heat fluxes are calculated using the aerodynamic method with input from local meteorological stations and experimentally derived drag coefficients. Lake heat storage, determined as a residual of the surface energy balance, is used together with measured water temperature profiles to calculate the daily mixing layer depth. The model uses readily available meteorological inputs for radiation calculations.Verification results for surface energy balance components show mean bias error (MBE) generally less than 5% of the mean measured daily fluxes and root mean square error (RMSE) less than 38%, which decreases to less than 16% for 10-day averaging periods. The model tends to overestimate net radiation by 7% and latent and sensible heat fluxes by about 4% and 1%, respectively, on average. Inferred slab layer depths indicate that the shallowest lake was isothermal while the deeper lakes showed temporal variations as expected.

  15. Efficient free energy calculations of quantum systems through computer simulations

    NASA Astrophysics Data System (ADS)

    Antonelli, Alex; Ramirez, Rafael; Herrero, Carlos; Hernandez, Eduardo

    2009-03-01

    In general, the classical limit is assumed in computer simulation calculations of free energy. This approximation, however, is not justifiable for a class of systems in which quantum contributions for the free energy cannot be neglected. The inclusion of quantum effects is important for the determination of reliable phase diagrams of these systems. In this work, we present a new methodology to compute the free energy of many-body quantum systems [1]. This methodology results from the combination of the path integral formulation of statistical mechanics and efficient non-equilibrium methods to estimate free energy, namely, the adiabatic switching and reversible scaling methods. A quantum Einstein crystal is used as a model to show the accuracy and reliability the methodology. This new method is applied to the calculation of solid-liquid coexistence properties of neon. Our findings indicate that quantum contributions to properties such as, melting point, latent heat of fusion, entropy of fusion, and slope of melting line can be up to 10% of the calculated values using the classical approximation. [1] R. M. Ramirez, C. P. Herrero, A. Antonelli, and E. R. Hernández, Journal of Chemical Physics 129, 064110 (2008)

  16. CAS SCF/CI calculations of potential energy surfaces of He 3+ and He 2+

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Liao, M. Z.; Lin, S. H.

    1987-12-01

    Complete active space MC SCF (CAS SCF) calculations followed by second-order configuration interaction (SOCI) calculations are carried out on the potential energy surfaces (bending surface, linear surfaces) of the 2Σ g+ ground state of He 3+. The potential minimum for the 2Σ g+ state occurs at a linear geometry with HeHe bond length of 1.248 Å. The binding energy of He 3+ with respect to He + He + + He was calculated to be 2.47 eV at the SOCI level. The energy required to dissociate He 3+ ( 2Σ g+) into He 2+ ( 2Σ u+) and He( 1S) is calculated to be 0.14 eV. The same level of SOCI calculations of He 2+ yield a De value of 2.36 eV.

  17. A comparison of internal energy calculation methods for diatomic molecules

    NASA Technical Reports Server (NTRS)

    Liu, Yen; Shakib, Farzin; Vinokur, Marcel

    1990-01-01

    Various methods of calculating the internal energy of diatomic molecules are studied. An accurate and efficient method for computing the eigenvalues of the vibrational Schroedinger equation for an arbitrary potential is developed. The method is based on a finite-element discretization using the cubic Lobatto element. A combination of spectrum slicing and the Laguerre algorithm is used to solve for the eigenvalues. A simple method to compute the quasi-bound states is presented. For N2 molecules, all vibrational-rotational states of eleven available electronic potentials are computed, and summed to obtain the exact internal energy function with temperature. The total computation required 314 seconds of CPU-time on NASA's Cray 2 computer. Various approximate models are discussed and compared with the exact numerical simulation. It is shown that the splitting of the macroscopic internal energy into separate electronic, rotational, and vibrational energies is not justified at high temperatures.

  18. Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

    PubMed Central

    Jorgensen, William L.; Thomas, Laura L.

    2009-01-01

    An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 – 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes. PMID:19936324

  19. 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

  20. 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.

  1. Ab Initio Calculations for the Surface Energy of Silver Nanoclusters

    NASA Astrophysics Data System (ADS)

    Medasani, Bharat; Vasiliev, Igor; Park, Young Ho

    2007-03-01

    We apply first principles computational methods to study the surface energy and the surface stress of silver nanoparticles. The structures, energies and lattice contractions of spherical Ag nanoclusters are calculated in the framework of density functional theory combined with the generalized gradient approximation. Our calculations predict the surface energies of Ag nanoclusters to be in the range of 1-2 J/m^2. These values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m^2 derived from the Kelvin equation for free Ag nanoparticles. From the lattice contraction and the nearest neighbor interatomic distance, we estimate the surface stress of the silver nanoclusters to be in the the range of 1-1.45 N/m. This result suggests that a liquid droplet model can be employed to evaluate the surface energy and the surface stress of Ag nanoparticles. K. K. Nanda et al., Phys. Rev. Lett. 91, 106102 (2003).

  2. Expected Energy Method for Electro-Optical SNR Calculations.

    DTIC Science & Technology

    1984-02-02

    r’AD-Ri39 984 EXPECTED ENERGY METHOD FOR ELECTPO-OPTICRL SNR i/i CALCULRTIONS(U) MASSRCHUSETTS INST OF TECH LEXINGTON LINCOLN LAB G J MAYER 82 FEB 84...ENERGY METHOD FOR ELECTRO-OPTICAL SNR CALCULATIONS * Ci. MA YER Group 9 TECHNICAL REPORT 634 2 FEBRUARY 1984 Approved for public release; distribution...analysis of image and sensor element configuration. This method allows the optimal pixel size to be selected to maximize the expected SNR for any point

  3. Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.

    PubMed

    Evenhuis, Christian R; Manthe, Uwe

    2008-07-14

    A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.

  4. Effects of internal gain assumptions in building energy calculations

    SciTech Connect

    Christensen, C.; Perkins, R.

    1981-01-01

    The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results of this study indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.

  5. Effects of internal gain assumptions in building energy calculations

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Perkins, R.

    1981-01-01

    The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multifamily-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.

  6. Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

    PubMed Central

    2016-01-01

    Binding selectivity is a requirement for the development of a safe drug, and it is a critical property for chemical probes used in preclinical target validation. Engineering selectivity adds considerable complexity to the rational design of new drugs, as it involves the optimization of multiple binding affinities. Computationally, the prediction of binding selectivity is a challenge, and generally applicable methodologies are still not available to the computational and medicinal chemistry communities. Absolute binding free energy calculations based on alchemical pathways provide a rigorous framework for affinity predictions and could thus offer a general approach to the problem. We evaluated the performance of free energy calculations based on molecular dynamics for the prediction of selectivity by estimating the affinity profile of three bromodomain inhibitors across multiple bromodomain families, and by comparing the results to isothermal titration calorimetry data. Two case studies were considered. In the first one, the affinities of two similar ligands for seven bromodomains were calculated and returned excellent agreement with experiment (mean unsigned error of 0.81 kcal/mol and Pearson correlation of 0.75). In this test case, we also show how the preferred binding orientation of a ligand for different proteins can be estimated via free energy calculations. In the second case, the affinities of a broad-spectrum inhibitor for 22 bromodomains were calculated and returned a more modest accuracy (mean unsigned error of 1.76 kcal/mol and Pearson correlation of 0.48); however, the reparametrization of a sulfonamide moiety improved the agreement with experiment. PMID:28009512

  7. Calculating Free Energy Changes in Continuum Solvation Models

    SciTech Connect

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

    We recently showed for a large dataset 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 the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. 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 bimolecular 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 kJ mol-1 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. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.

  8. Calculating Free Energy Changes in Continuum Solvation Models

    DOE PAGES

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

    We recently showed for a large dataset 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 the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations,more » as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular 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 kJ mol-1 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. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less

  9. Quantum Monte Carlo calculations of the dimerization energy of borane.

    PubMed

    Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele

    2011-09-07

    Accurate thermodynamic data are required to improve the performance of chemical hydrides that are potential hydrogen storage materials. Boron compounds are among the most interesting candidates. However, different experimental measurements of the borane dimerization energy resulted in a rather wide range (-34.3 to -39.1) ± 2 kcal/mol. Diffusion Monte Carlo (DMC) simulations usually recover more than 95% of the correlation energy, so energy differences rely less on error cancellation than other methods. DMC energies of BH(3), B(2)H(6), BH(3)CO, CO, and BH(2)(+) allowed us to predict the borane dimerization energy, both via the direct process and indirect processes such as the dissociation of BH(3)CO. Our D(e) = -43.12(8) kcal/mol, corrected for the zero point energy evaluated by considering the anharmonic contributions, results in a borane dimerization energy of -36.59(8) kcal/mol. The process via the dissociation of BH(3)CO gives -34.5(2) kcal/mol. Overall, our values suggest a slightly less D(e) than the most recent W4 estimate D(e) = -44.47 kcal/mol [A. Karton and J. M. L. Martin, J. Phys. Chem. A 111, 5936 (2007)]. Our results show that reliable thermochemical data for boranes can be predicted by fixed node (FN)-DMC calculations.

  10. 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.

  11. Free energy perturbation calculations on glucosidase-inhibitor complexes.

    PubMed

    Ruiza, F M; Grigera, J Raúl

    2005-09-01

    Free energy perturbation studies have been performed on Glucoamylase II (471) from Aspergillus awamori var. X100 complexed with three different inhibitors: (+)lentiginosine, (+)(1S,2S,7R,8aS) 1,2,7-trihydroxyindolizidine, (+)(1S,2S,7S,8aS) 1,2,7-trihydroxyindolizidine and the inactive compound (+)(1S,7R,8aS)-1,7-dihydroxyindolizidine. Molecular dynamic simulations were carried out using a recently developed procedure for fast Free Energy Perturbation calculations. In this procedure only a sphere of 1.8 nm around the central atom of the inhibitor is considered in the calculations. Crystallographic restraints are applied over this reduced system using a generated electron density map. The obtained values for the free energy differences agree with experimental data showing the importance of fast calculations in drug design even when the crystallographic structure of the complex is not available. As the method uses only the crystallographic structure of the receptor, it is possible to test the possible efficiency of even still not synthesised ligands, making the pre-selection of compounds much easy and faster.

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

    PubMed

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

    2013-08-15

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

  13. Free energy calculations: an efficient adaptive biasing potential method.

    PubMed

    Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul

    2010-05-06

    We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.

  14. Dirac Calculations for Proton Inelastic Scattering at Intermediate Energies

    NASA Astrophysics Data System (ADS)

    El-Nohy, N. A.; El-Hammamy, M. N.; Aly, N. E.; Abdel-Moneim, A. M.; Hamza, A. F.

    2016-12-01

    Relativistic proton inelastic scattering from different targets (16O, 24Mg, 28Si, 40Ca, 54Fe, 58Ni, 90Zr, 154Sm, 176Yb, and 208Pb) at intermediate energies is analyzed in the framework of phenomenological optical potentials based on the Dirac formalism. Parameters of the Dirac phenomenological potential with Woods Saxon (WS) shape are obtained. The first order vibrational collective model with one phonon is used to calculate the transition optical potentials to the first low-lying excited state (2+) of the investigated target nuclei. Also, the variation of deformation length ( δ) with energy and mass number is studied. It is noticed that the deformation length increases slightly with energy at intermediate range.

  15. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    PubMed

    Fouda, Adam; Ryde, Ulf

    2016-11-08

    We have examined how the self-interaction error in density-functional theory (DFT) calculations affects energies calculated on large systems (600-1000 atoms) involving several charged groups. We employ 18 different quantum mechanical (QM) methods, including Hartree-Fock, as well as pure, hybrid, and range-separated DFT methods. They are used to calculate reaction and activation energies for three different protein models in vacuum, in a point-charge surrounding, or with a continuum-solvent model. We show that pure DFT functionals give rise to a significant delocalization of the charges in charged groups in the protein, typically by ∼0.1 e, as evidenced from the Mulliken charges. This has a clear effect on how the surroundings affect calculated reaction and activation energies, indicating that these methods should be avoided for DFT calculations on large systems. Fortunately, methods such as CAM-B3LYP, BHLYP, and M06-2X give results that agree within a few kilojoules per mole, especially when the calculations are performed in a point-charge surrounding. Therefore, we recommend these methods to estimate the effect of the surroundings with large QM systems (but other QM methods may be used to study the intrinsic reaction and activation energies).

  16. 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.

  17. Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

    PubMed

    Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G

    2013-11-07

    A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into

  18. SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

    DOE PAGES

    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

  19. SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

    SciTech Connect

    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 development 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.

  20. 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.

  1. 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.

  2. 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.

  3. Energy dependence of hadronic activity

    NASA Astrophysics Data System (ADS)

    Gabriel, T. A.; Groom, D. E.; Job, P. K.; Mokhov, N. V.; Stevenson, G. R.

    1994-01-01

    Two features of high-energy hadronic cascades have long been known to shielding specialists: a) in a high-energy hadronic cascade in a given material (incident E ≳ 10 GeV), the relative abundance and spectrum of each hadronic species responsible for most of the energy deposition is independent of the energy or species of the incident hadron, and b) because π0 production bleeds off more and more energy into the electromagnetic sector as the energy of the incident hadron increases, the absolute level of this low-energy hadronic activity ( E ≲ 1 GeV) rises less rapidly than the incident energy, and in fact rises very nearly as a power of the incident energy. Both features are of great importance in hadron calorimetry, where it is the "universal spectrum" which makes possible the definition of an intrinsic {e}/{h}, and the increasing fraction of the energy going into π0's which leads to the energy dependence of {e}/{π}. We present evidence for the "universal spectrum," and use an induction argument and simulation results to demonstrate that the low-energy activity ss Em, with 0.80 ≲ m ≲ 0.85. The hadronic activity produced by incident pions is 15-20% less than that initiated by protons.

  4. 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…

  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

    2016-02-09

    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.

  6. Free-energy calculation of structure-H hydrates

    NASA Astrophysics Data System (ADS)

    Okano, Yamato; Yasuoka, Kenji

    2006-01-01

    A molecular-dynamics (MD) simulation of structure-H hydrates was performed under constant pressure and temperature with 6120 TIP4P water molecules, 900 OPLS-UA methane molecules, and 180 large molecular guest substance (LMGS) molecules. The LMGS molecules were represented in the form of a one-site Lennard-Jones (LJ) model using the LJ parameters σ and ɛ. In order to clarify the thermodynamic stability of structure-H hydrates, we calculated the free-energy difference, changing on the σ and ɛ only of the LMGS molecules. In this simulation, stable crystals of structure-H hydrates and a minimum value of ΔG were obtained at σ ˜6.2Å and large values of ɛ. All simulations were performed using the special-purpose computer hardware MDGRAPE-2.

  7. Parallel Calculation of CCSDT and Mk-MRCCSDT Energies.

    PubMed

    Prochnow, Eric; Harding, Michael E; Gauss, Jürgen

    2010-08-10

    A scheme for the parallel calculation of energies at the coupled-cluster singles, doubles, and triples (CCSDT) level of theory, several approximate iterative CCSDT schemes (CCSDT-1a, CCSDT-1b, CCSDT-2, CCSDT-3, and CC3), and for the state-specific multireference coupled-cluster ansatz suggested by Mukherjee with a full treatment of triple excitations (Mk-MRCCSDT) is presented. The proposed scheme is based on the adaptation of a highly efficient serial coupled-cluster code leading to a communication-minimized implementation by parallelizing the time-determining steps. The parallel algorithm is tailored for affordable cluster architectures connected by standard communication networks such as Gigabit Ethernet. In this way, CCSDT and Mk-MRCCSDT computations become feasible even for larger molecular systems and basis sets. An analysis of the time-determining steps for CCSDT and Mk-MRCCSDT, namely the computation of the triple-excitation amplitudes and their individual contributions, is carried out. Benchmark calculations are presented for the N2O, ozone, and benzene molecules, proving that the parallelization of these steps is sufficient to obtain an efficient parallel scheme. A first application to the case of 2,6-pyridyne using a triple-ζ quality basis (222 basis functions) is presented demonstrating the efficiency of the current implementation.

  8. Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid.

    PubMed

    Saouane, Sofiane; Buth, Gernot; Fabbiani, Francesca P A

    2013-11-01

    The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by the PIXEL method brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure, PIXEL lattice energy calculations confirm the predominance of the Coulombic term (-379.1 kJ mol(-1)) ahead of the polarization (-141.4 kJ mol(-1)), dispersion (-133.7 kJ mol(-1)) and repulsion (266.3 kJ mol(-1)) contributions.

  9. Effects of energy spectrum on dose distribution calculations for high energy electron beams.

    PubMed

    Toutaoui, Abdelkader; Khelassi-Toutaoui, Nadia; Brahimi, Zakia; Chami, Ahmed Chafik

    2009-01-01

    In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities.

  10. Effects of energy spectrum on dose distribution calculations for high energy electron beams

    PubMed Central

    Toutaoui, Abdelkader; Khelassi-Toutaoui, Nadia; Brahimi, Zakia; Chami, Ahmed Chafik

    2009-01-01

    In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities. PMID:20126560

  11. Activation energetics of actinide diffusion in UO2 from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Becker, Udo

    2013-02-01

    Diffusion of actinides in uranium dioxide plays an important role in determining thermodynamic and mechanic properties of the material. Activation energies of Th, U, Np, and Pu diffusion in uranium dioxide were systematically studied using first-principles calculations. The generalized gradient approximation and projector-augmented wave methods with on-site Coulomb repulsive interaction were applied within Density Functional Theory and Plane Wave framework. Two diffusion paths, one along the lattice <1 1 0> direction and the other along the lattice <1 0 0> direction, were examined in the face-centered cubic UO2 structure. The results show that the <1 1 0> path has lower migration energy than the <1 0 0> path. Under the assumption of a vacancy-assisted jump diffusion mechanism, the major contribution to the activation energy is the migration energy, followed by the vacancy formation energy and vacancy binding energy, where the last has the lowest contribution. However, differences in the activation energies among different actinides stem from both the migration and vacancy binding energies, both of which decrease with atomic number. While discrepancies between the absolute values of the calculated and experimentally observed activation energies remain, this study shows a correlation between activation energy and atomic number and an asymptotic relation between activation energy and ionic radius of the actinides. The present study suggests that the migration of the actinides through the uranium dioxide lattice is closely correlated to the number of 5f electrons and the size of the diffusing atoms.

  12. Ab initio calculations of generalized-stacking-fault energy surfaces and surface energies for FCC metals

    NASA Astrophysics Data System (ADS)

    Wu, Xiao-Zhi; Wang, Rui; Wang, Shao-Feng; Wei, Qun-Yi

    2010-08-01

    The ab initio calculations have been used to study the generalized-stacking-fault energy (GSFE) surfaces and surface energies for the closed-packed (1 1 1) plane in FCC metals Cu, Ag, Au, Ni, Al, Rh, Ir, Pd, Pt, and Pb. The GSFE curves along <112> (1 1 1) direction and <110> (1 1 1) direction, and surface energies have been calculated from first principles. Based on the translational symmetry of the GSFE surfaces, the fitted expressions have been obtained from the Fourier series. Our results of the GSFEs and surface energies agree better with experimental results. The metals Al, Pd, and Pt have low γ/γI value, so full dislocation will be observed easily; while Cu, Ag, Au, and Ni have large γ/γI value, so it is preferred to create partial dislocation. From the calculations of surface energies, it is confirmed that the VIII column elements Ni, Rh, Ir, Pd, and Pt have higher surface energies than other metals.

  13. Chemical activation through super energy transfer collisions.

    PubMed

    Smith, Jonathan M; Nikow, Matthew; Ma, Jianqiang; Wilhelm, Michael J; Han, Yong-Chang; Sharma, Amit R; Bowman, Joel M; Dai, Hai-Lung

    2014-02-05

    Can a molecule be efficiently activated with a large amount of energy in a single collision with a fast atom? If so, this type of collision will greatly affect molecular reactivity and equilibrium in systems where abundant hot atoms exist. Conventional expectation of molecular energy transfer (ET) is that the probability decreases exponentially with the amount of energy transferred, hence the probability of what we label "super energy transfer" is negligible. We show, however, that in collisions between an atom and a molecule for which chemical reactions may occur, such as those between a translationally hot H atom and an ambient acetylene (HCCH) or sulfur dioxide, ET of chemically significant amounts of energy commences with surprisingly high efficiency through chemical complex formation. Time-resolved infrared emission observations are supported by quasi-classical trajectory calculations on a global ab initio potential energy surface. Results show that ∼10% of collisions between H atoms moving with ∼60 kcal/mol energy and HCCH result in transfer of up to 70% of this energy to activate internal degrees of freedom.

  14. 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…

  15. 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.

  16. On the calculation of absolute macromolecular binding free energies

    PubMed Central

    Luo, Hengbin; Sharp, Kim

    2002-01-01

    The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B → AB with an association constant KAB is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of KAB is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior. PMID:12149474

  17. 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…

  18. 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 ...

  19. First-principles calculations of the OH- adsorption energy on perovskite oxide

    NASA Astrophysics Data System (ADS)

    Ohzuku, Hideo; Ikeno, Hidekazu; Yamada, Ikuya; Yagi, Shunsuke

    2016-08-01

    The oxygen evolution reaction (OER) that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal-air batteries and direct solar water splitting. ABO3 perovskite oxides have been extensively studied because of their high catalytic OER activity. In the present study, the OH- adsorption process on the perovskite surface about different B site cations was investigated by the first-principles calculations. We concluded that the adsorption energy of SrFeO3 surface is larger than that of SrTiO3.

  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. Activation Calculation for a Fusion Experimental Breeder, Feb-E

    NASA Astrophysics Data System (ADS)

    Feng, K. M.

    2003-06-01

    Using an activation calculation code FDKR and its associated data library AF-DCDLIB to calculate the radioactivity, decay heat, waste disposal rating and biological hazard potential from activation products, actinides and fission products in the FEB-E. The codes and libraries used in calculation are introduced briefly, and calculation results and decay curves of related hazards after the shutdown of one-year operation of the FEB-E are given. Results obtained show that the total radioactivity inventory, decay heat and BHP at shutdown are 5.74 × 1013MBq, 8.34MW and 4.08 × 108km3 of air for 316SS structure material, respectively.

  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. 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.

  4. 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.

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

    PubMed

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

    2016-02-15

    Dietary fiber (DF) contributes to the energy value of foods and including it in the calculation of total food energy has been recommended for food composition databases. The present study aimed to investigate the impact of including energy provided by the DF fermentation in the calculation of food energy. Total energy values of 1753 foods from the Brazilian Food Composition Database were calculated with or without the inclusion of DF energy. The energy values were compared, through the use of percentage difference (D%), in individual foods and in daily menus. Appreciable energy D% (⩾10) was observed in 321 foods, mainly in the group of vegetables, legumes and fruits. However, in the Brazilian typical menus containing foods from all groups, only D%<3 was observed. In mixed diets, the DF energy may cause slight variations in total energy; on the other hand, there is appreciable energy D% for certain foods, when individually considered.

  6. 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…

  7. 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.

  8. Spatiotemporal characteristics of electrocortical brain activity during mental calculation.

    PubMed

    Vansteensel, Mariska J; Bleichner, Martin G; Freudenburg, Zac V; Hermes, Dora; Aarnoutse, Erik J; Leijten, Frans S S; Ferrier, Cyrille H; Jansma, Johan Martijn; Ramsey, Nick F

    2014-12-01

    Mental calculation is a complex mental procedure involving a frontoparietal network of brain regions. Functional MRI (fMRI) studies have revealed interesting characteristics of these regions, but the precise function of some areas remains elusive. In the present study, we used electrocorticographic (ECoG) recordings to chronometrically assess the neuronal processes during mental arithmetic. A calculation task was performed during presurgical 3T fMRI scanning and subsequent ECoG monitoring. Mental calculation induced an increase in fMRI blood oxygen level dependent signal in prefrontal, parietal and lower temporo-occipital regions. The group-fMRI result was subsequently used to cluster the implanted electrodes into anatomically defined regions of interest (ROIs). We observed remarkable differences in high frequency power profiles between ROIs, some of which were closely associated with stimulus presentation and others with the response. Upon stimulus presentation, occipital areas were the first to respond, followed by parietal and frontal areas, and finally by motor areas. Notably, we demonstrate that the fMRI activation in the middle frontal gyrus/precentral gyrus is associated with two subfunctions during mental calculation. This finding reveals the significance of the temporal dynamics of neural ensembles within regions with an apparent uniform function. In conclusion, our results shed more light on the spatiotemporal aspects of brain activation during a mental calculation task, and demonstrate that the use of fMRI data to cluster ECoG electrodes is a useful approach for ECoG group analysis.

  9. 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.

  10. Mathematical method to calculate full-energy peak efficiency of detectors based on transfer technique

    NASA Astrophysics Data System (ADS)

    Gouda, M. M.; Hamzawy, A.; Badawi, M. S.; El-Khatib, A. M.; Thabet, A. A.; Abbas, M. I.

    2016-02-01

    The full-energy peak efficiency of high-purity germanium well-type detector is extremely important to calculate the absolute activities of natural and artificial radionuclides for samples with low radioactivity. In this work, the efficiency transfer method in an integral form is proposed to calculate the full-energy peak efficiency and to correct the coincidence summing effect for a high-purity germanium well-type detector. This technique is based on the calculation of the ratio of the effective solid angles subtended by the well-type detector with cylindrical sources measured inside detector cavity and an axial point source measured out the detector cavity including the attenuation of the photon by the absorber system. This technique can be easily applied in establishing the efficiency calibration curves of well-type detectors. The calculated values of the efficiency are in good agreement with the experimental calibration data obtained with a mixed γ-ray standard source containing 60Co and 88Y.

  11. Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

    2012-03-01

    Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

  12. Free energy calculation from umbrella sampling using Bayesian inference

    NASA Astrophysics Data System (ADS)

    Bernstein, Noam; Stecher, Thomas; Csányi, Gábor

    2013-03-01

    Using simulations to obtain information about the free energy of a system far from its free energy minima requires biased sampling, for example using a series of harmonic umbrella confining potentials to scan over a range of collective variable values. One fundamental distinction between existing methods that use this approach is in what quantities are measured and how they are used: histograms of the system's probability distribution in WHAM, or gradients of the potential of mean force for umbrella integration (UI) and the single-sweep radial basis function (RBF) approach. Here we present a method that reconstructs the free energy from umbrella sampling data using Bayesian inference that effectively uses all available information from multiple umbrella windows. We show that for a single collective variable, our method can use histograms, gradients, or both, to match or outperform WHAM and UI in the accuracy of free energy for a given amount of total simulation time. In higher dimensions, our method can effectively use gradient information to reconstruct the multidimensional free energy surface. We test our method for the alanine polypeptide model system, and show that it is more accurate than a RBF reconstruction for sparse data, and more stable for abundant data.

  13. Implications for High Energy Blazar Spectra from Intergalactic Absorption Calculations

    NASA Technical Reports Server (NTRS)

    Stecker, F

    2008-01-01

    Given a knowledge of the density spectra intergalactic low energy photons as a function of redshift, one can derive the intrinsic gamma-ray spectra and luminosities of blazars over a range of redshifts and look for possible trends in blazar evolution. Stecker, Baring & Summerlin have found some evidence hinting that TeV blazars with harder spectra have higher intrinsic TeV gamma-ray luminosities and indicating that there may be a correlation of spectral hardness and luminosity with redshift. Further work along these lines, treating recent observations of the blazers lES02291+200 and 3C279 in the TeV and sub-TeV energy ranges, has recently been explored by Stecker & Scully. GLAST will observe and investigate many blazars in the GeV energy range and will be sensitive to blazers at higher redshifts. I examine the implications high redshift gamma-ray absorption for both theoretical and observational blazer studies.

  14. Accelerating atomistic calculations of quantum energy eigenstates on graphic cards

    NASA Astrophysics Data System (ADS)

    Rodrigues, Walter; Pecchia, A.; Lopez, M.; Auf der Maur, M.; Di Carlo, A.

    2014-10-01

    Electronic properties of nanoscale materials require the calculation of eigenvalues and eigenvectors of large matrices. This bottleneck can be overcome by parallel computing techniques or the introduction of faster algorithms. In this paper we report a custom implementation of the Lanczos algorithm with simple restart, optimized for graphical processing units (GPUs). The whole algorithm has been developed using CUDA and runs entirely on the GPU, with a specialized implementation that spares memory and reduces at most machine-to-device data transfers. Furthermore parallel distribution over several GPUs has been attained using the standard message passing interface (MPI). Benchmark calculations performed on a GaN/AlGaN wurtzite quantum dot with up to 600,000 atoms are presented. The empirical tight-binding (ETB) model with an sp3d5s∗+spin-orbit parametrization has been used to build the system Hamiltonian (H).

  15. 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.

  16. 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.

  17. 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.

  18. 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…

  19. 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…

  20. 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.

  1. Potential Energy Calculations for Collinear Cluster Tripartition Fission Events

    NASA Astrophysics Data System (ADS)

    Unzhakova, A. V.; Pashkevich, V. V.; Pyatkov, Y. V.

    2014-09-01

    Strutinsky shell correction calculations were performed to describe the recent experimental results on collinear ternary fission. Collinear Cluster Tripartion fission events were studied experimentally in neutron induced fission of 235U, where the missing mass in the detected binary decay was suggested to characterize fission event as a collinear tripartition; and in spontaneous fission of 252Cf, where the direct detection of the three fission fragments has been used to confirm the existence of the Collinear Cluster Tripartition channel with a probability of 4.7×10-3 relative to the binary fission events.

  2. 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.

  3. Relativistic Calculations and Measurements of Energies, Auger Rates, and Lifetimes.

    DTIC Science & Technology

    1982-12-01

    Research and Industry, Denton, Texas, 8-10 November 1982. 7. B. Crasemann: "Efectos Relativ’sticos y de QED Sobre las Transiciones Rayos - X y Auger Entre...INNER-SHELL IONIZATION BY PROTONS X -RAY EMISSION BREIT INTERACTION AUGER TRANSITIONS DIRAC-HARTREE-SLATER COMPUTATIONS SYNCHROTRON RADIATION RESONANT...computations, including relativistic and quantum- electrodynamic effects, of atomic energy levels and of x -ray and Auger transitions in atoms with one or

  4. Computational efficiences for calculating rare earth f^n energies

    NASA Astrophysics Data System (ADS)

    Beck, Donald R.

    2009-05-01

    RecentlyootnotetextD. R. Beck and E. J. Domeier, Can. J. Phys. Walter Johnson issue, Jan. 2009., we have used new computational strategies to obtain wavefunctions and energies for Gd IV 4f^7 and 4f^65d levels. Here we extend one of these techniques to allow efficent inclusion of 4f^2 pair correlation effects using radial pair energies obtained from much simpler calculationsootnotetexte.g. K. Jankowski et al., Int. J. Quant. Chem. XXVII, 665 (1985). and angular factors which can be simply computedootnotetextD. R. Beck and C. A. Nicolaides, Excited States in Quantum Chemistry, C. A. Nicolaides and D. R. Beck (editors), D. Reidel (1978), p. 105ff.. This is a re-vitalization of an older ideaootnotetextI. Oksuz and O. Sinanoglu, Phys. Rev. 181, 54 (1969).. We display relationships between angular factors involving the exchange of holes and electrons (e.g. f^6 vs f^8, f^13d vs fd^9). We apply the results to Tb IV and Gd IV, whose spectra is largely unknown, but which may play a role in MRI medicine as endohedral metallofullerenes (e.g. Gd3N-C80ootnotetextM. C. Qian and S. N. Khanna, J. Appl. Phys. 101, 09E105 (2007).). Pr III results are in good agreement (910 cm-1) with experiment. Pu I 5f^2 radial pair energies are also presented.

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

    PubMed

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

    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(+), Cl(-), and Ag(+) 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 (DeltaG(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(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(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(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.

  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. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    PubMed

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  8. Enzymatic minimum free energy path calculations using swarms of trajectories.

    PubMed

    Sanchez-Martinez, Melchor; Field, Martin; Crehuet, Ramon

    2015-01-22

    The development of approaches for simulating rare events in complex molecular systems is a central concern in chemical physics. In recent work, Roux and co-workers proposed a novel, swarms of trajectories (SoT) method for determining the transition paths of such events. It consists of the dynamical refinement on the system's free energy surface of a putative transition path that is parametrized in terms of a set of collective variables (CVs) that are identified as being important for the transition. In this work, we have implemented the SoT method and used it to investigate the catalytic mechanisms of two enzymatic reactions using hybrid QM/MM potentials. Our aim has been to test the performance of SoT for enzyme systems and to devise robust simulation protocols that can be employed in future studies of this type. We identify the conditions under which converged results can be obtained using inertial and Brownian dynamical evolutions of the CVs, show that the inclusion of several CVs can give significant additional insight into the mechanisms of the reactions, and show that the use of minimum energy paths as starting guesses can greatly accelerate path refinement.

  9. A surface hopping algorithm for nonadiabatic minimum energy path calculations.

    PubMed

    Schapiro, Igor; Roca-Sanjuán, Daniel; Lindh, Roland; Olivucci, Massimo

    2015-02-15

    The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.

  10. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

    NASA Astrophysics Data System (ADS)

    Zhang, Dawei

    2017-03-01

    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.

  11. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

    PubMed Central

    Zhang, Dawei

    2017-01-01

    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems. PMID:28300179

  12. Advanced Quantum Mechanical Calculation of Superheavy Ions: Energy Levels, Radiation and Finite Nuclear Size Effects

    SciTech Connect

    Glushkov, Alexander V.; Gurnitskaya, E.P.; Loboda, A.V.

    2005-10-26

    Advanced quantum approach to calculation of spectra for superheavy ions with an account of relativistic, correlation, nuclear, radiative effects is developed and based on the gauge invariant quantum electrodynamics (QED) perturbation theory (PT). The Lamb shift polarization part is calculated in the Ueling approximation, self-energy part is defined within a new non-PT procedure of Ivanov-Ivanova. Calculation results for energy levels, hyperfine structure parameters of some heavy elements ions are presented.

  13. Radiation damage/activity calculation for CSNS target station

    NASA Astrophysics Data System (ADS)

    Yin, W.; Liang, T. J.; Yu, Q. Z.; Jia, X. J.

    2010-03-01

    The radiation damages have been performed for Chinese spallation neutron source (CSNS) target center components that relies on Monte Carlo simulation code MCNPX. During the calculation, Bertini intranuclear cascade model, three level-density formulation GCCI, and multistage pre-equilibrium model MPM on which are provided within MCNPX are employed. We calculate the displacement per atom (DPA) and afterheat of the tungsten target, the stainless steel target vessel window and the aluminum alloy moderator vessel. As a hundred kW-level source, these spallation center components have the lifetime more than 5 year. We also give the activity for the T0 chopper of the beam line HIPD to get the primary data for making out a maintenance scenario.

  14. 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.

  15. 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.

  16. Effect of blood activity on dosimetric calculations for radiopharmaceuticals

    NASA Astrophysics Data System (ADS)

    Zvereva, Alexandra; Petoussi-Henss, Nina; Li, Wei Bo; Schlattl, Helmut; Oeh, Uwe; Zankl, Maria; Graner, Frank Philipp; Hoeschen, Christoph; Nekolla, Stephan G.; Parodi, Katia; Schwaiger, Markus

    2016-11-01

    The objective of this work was to investigate the influence of the definition of blood as a distinct source on organ doses, associated with the administration of a novel radiopharmaceutical for positron emission tomography-computed tomography (PET/CT) imaging—(S)-4-(3-18F-fluoropropyl)-L-glutamic acid (18F-FSPG). Personalised pharmacokinetic models were constructed based on clinical PET/CT images from five healthy volunteers and blood samples from four of them. Following an identifiability analysis of the developed compartmental models, person-specific model parameters were estimated using the commercial program SAAM II. Organ doses were calculated in accordance to the formalism promulgated by the Committee on Medical Internal Radiation Dose (MIRD) and the International Commission on Radiological Protection (ICRP) using specific absorbed fractions for photons and electrons previously derived for the ICRP reference adult computational voxel phantoms. Organ doses for two concepts were compared: source organ activities in organs parenchyma with blood as a separate source (concept-1); aggregate activities in perfused source organs without blood as a distinct source (concept-2). Aggregate activities comprise the activities of organs parenchyma and the activity in the regional blood volumes (RBV). Concept-1 resulted in notably higher absorbed doses for most organs, especially non-source organs with substantial blood contents, e.g. lungs (92% maximum difference). Consequently, effective doses increased in concept-1 compared to concept-2 by 3-10%. Not considering the blood as a distinct source region leads to an underestimation of the organ absorbed doses and effective doses. The pronounced influence of the blood even for a radiopharmaceutical with a rapid clearance from the blood, such as 18F-FSPG, suggests that blood should be introduced as a separate compartment in most compartmental pharmacokinetic models and blood should be considered as a distinct source in

  17. Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method.

    PubMed

    Jin, Xinsheng; Zhang, John Z H; He, Xiao

    2017-03-30

    In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

  18. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.

    PubMed

    Gapsys, Vytautas; Seeliger, Daniel; de Groot, Bert L

    2012-07-10

    The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations.

  19. Expeditious Stochastic Calculation of Random-Phase Approximation Energies for Thousands of Electrons in Three Dimensions.

    PubMed

    Neuhauser, Daniel; Rabani, Eran; Baer, Roi

    2013-04-04

    A fast method is developed for calculating the random phase approximation (RPA) correlation energy for density functional theory. The correlation energy is given by a trace over a projected RPA response matrix, and the trace is taken by a stochastic approach using random perturbation vectors. For a fixed statistical error in the total energy per electron, the method scales, at most, quadratically with the system size; however, in practice, due to self-averaging, it requires less statistical sampling as the system grows, and the performance is close to linear scaling. We demonstrate the method by calculating the RPA correlation energy for cadmium selenide and silicon nanocrystals with over 1500 electrons. We find that the RPA correlation energies per electron are largely independent of the nanocrystal size. In addition, we show that a correlated sampling technique enables calculation of the energy difference between two slightly distorted configurations with scaling and a statistical error similar to that of the total energy per electron.

  20. Aerosol activation: parameterised versus explicit calculation for global models

    NASA Astrophysics Data System (ADS)

    Tost, H.; Pringle, K.; Metzger, S.; Lelieveld, J.

    2009-04-01

    A key process in studies of the aerosol indirect effects on clouds is the activation of particles into droplets at 100% relative humidity. To model this process in cloud, meteorological and climate models is a difficult undertaking because of the wide range of scales involved. The chemical composition of the atmospheric aerosol, originating from both air pollution and natural sources, substantially impacts the aerosol water uptake and growth due to its hygroscopicity. In this study a comparison of aerosol activation, using state-of-the-art aerosol activation parameterisations, and explicit activation due to hygroscopic growth is performed.For that purpose we apply the GMXe aerosol model - treating both dynamic and thermodynamic aerosol properties - within the EMAC (ECHAM5/MESSy Atmospheric chemistry, an atmospheric chemistry general circulation) model. This new aerosol model can explicitely calculate the water uptake of aerosols due to hygroscopicity, allowing the growth of aerosol particles into the regimes of cloud droplets in case of sufficient water vapour availability. Global model simulations using both activation schemes will be presented and compared, elucidating the advantages of each approach.

  1. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.

    PubMed

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil

    2013-01-28

    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.charmm-gui.org/input/gbinding ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.

  2. Optimal algorithm to improve the calculation accuracy of energy deposition for betavoltaic MEMS batteries design

    NASA Astrophysics Data System (ADS)

    Li, Sui-xian; Chen, Haiyang; Sun, Min; Cheng, Zaijun

    2009-11-01

    Aimed at improving the calculation accuracy when calculating the energy deposition of electrons traveling in solids, a method we call optimal subdivision number searching algorithm is proposed. When treating the energy deposition of electrons traveling in solids, large calculation errors are found, we are conscious of that it is the result of dividing and summing when calculating the integral. Based on the results of former research, we propose a further subdividing and summing method. For β particles with the energy in the entire spectrum span, the energy data is set only to be the integral multiple of keV, and the subdivision number is set to be from 1 to 30, then the energy deposition calculation error collections are obtained. Searching for the minimum error in the collections, we can obtain the corresponding energy and subdivision number pairs, as well as the optimal subdivision number. The method is carried out in four kinds of solid materials, Al, Si, Ni and Au to calculate energy deposition. The result shows that the calculation error is reduced by one order with the improved algorithm.

  3. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

    PubMed Central

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil

    2013-01-01

    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly web interface, CHARMM-GUI Ligand Binder (http://www.charmm-gui.org/input/gbinding), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently setup the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three non-polar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). CHARMM-GUI Ligand Binder provides a convenient and reliable way to setup the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems. PMID:23205773

  4. 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.

  5. 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)

  6. 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)

  7. 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.

  8. 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.

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

    SciTech Connect

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

    2003-03-01

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

  10. Alternative analytically calculation procedure of two-center kinetic energy integral in molecular coordinate system

    NASA Astrophysics Data System (ADS)

    Mamedov, Bahtiyar Akber; Copuroglu, Ebru

    2017-02-01

    By using the Löwdin-α function method, we have analytically calculated the two-center kinetic energy integrals over Slater type orbitals (STOs). The two-center kinetic energy integrals are presented in terms of the two-center overlap integrals. A new approach is applicable to accurate calculations of two-center kinetic energy integral over STOs for arbitrary values of scaling parameters and interatomic distances. Obtained results show that the proposed method is easy to apply to the real systems, and has better calculation CPU time with compared to the existing approximations.

  11. Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method.

    PubMed

    Simoncini, David; Nakata, Hiroya; Ogata, Koji; Nakamura, Shinichiro; Zhang, Kam Yj

    2015-02-01

    Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

  12. 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.

  13. 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…

  14. CASSCF/CI calculations of low-lying states and potential energy surfaces of Au3

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Liao, M. Z.

    1987-05-01

    Complete active space MCSCF (CASSCF) and second-order configuration interaction (SOCI) calculations of low-lying electronic states [2B2,2A1] of Au3 as well as the 1Σ+g state of Au2 are carried out. The bending potential energy surfaces of 2A1 and 2B2 states are also presented. A barrier is found in the potential energy surface of the 2A1 state in moving from the linear to bent structure. Two nearly-degenerate structures are found for the ground state. The 2Σ+u state arising from the linear structure with an Au-Au bond length of 2.66 Å is only 3.2 kcal/mol below the 2A1 bent state. The equilibrium geometry of the 2A1 state is an isosceles triangle with an apex angle of 54°. The Au3 cluster is found to be more stable than the gold dimer. The effect of d correlation is studied on Au2 by carrying out MRSDCI (multireference singles and doubles CI) calculations on the 1Σ+g state of Au2 which include excitations from the d orbitals.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. [Calculation of energy losses in the participants of the skiing expedition to the North Pole].

    PubMed

    Efremov, V V; Ushakov, A S; Khmelevskiĭ, Iu I

    1983-01-01

    During the expedition to the North Pole, the food consumption rates were calculated on a regular basis. The mean daily energy losses of the participants of the expedition, the energy losses during skiing with a rucksack across the drifting ice were estimated and the energy metabolism curve by days was built up. The body weight of the participants averaged 78 +/- 5 kg. This made it possible to perform an overall calculation per whole group. The total energy supply with food was appraised from the total amount of the food consumed during the expedition. The total body weight loss of the participants was 11.5 kg, the energy consumption being 100.000 kkal. The total (for 7 men) energy consumption during skiing without a rucksack was calculated according to the formula: [(2,770 kkal X 28.5 days)]+ +[(2,385 kkal X 35.5 days)]. It was thus found to be equal to 1.145.300 kkal. The total energy consumption during skiing with a rucksack was calculated according to the formula: (7 men X X 449 h) and was found to be equal to 1.883.200 kkal. The total energy consumption during the expedition amounted to 3.237.500 kkal. During the expedition, the daily energy deficiency per man was 1.300-1.500 kkal. This deficiency was compensated for during rest. The maintenance of such an energy supply pattern made it possible to preserve a high level of work fitness.

  20. Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method.

    PubMed

    Otsuka, Takao; Okimoto, Noriaki; Taiji, Makoto

    2015-11-15

    In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics-based force fields, although they cannot fully describe protein-ligand interactions. A noteworthy computational method in development involves large-scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large-scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange-correlation functionals, and solvation effects) on the binding energies of the FK506-binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2-MP2/6-31G(d), is suitable for evaluating the protein-ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure-activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein-ligand interaction distance. Our acceleration scheme, which uses FMO2-HF/STO-3G:MP2/6-31G(d) at R(int) = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy.

  1. Infinite dilution activity coefficients from ab initio solvation calculations

    SciTech Connect

    Lin, S.T.; Sandler, S.I.

    1999-12-01

    A Group Contribution Solvation (GCS) model was developed to calculate infinite dilution activity coefficients ({gamma}{sup {chi}}) based on modern computational chemistry. The GCS model results in an average error of 7% in {gamma}{sup {chi}} for the limited number of data points among water, n-hexane, acetonitrile and n-octanol, whereas the errors are 47% and 52% with the UNIFAC model and the modified UNIFAC model, respectively. GCS was also used to calculate infinite dilution partition coefficients, which can be used to determine how a dilute solute partitions between two solvents. Solutes were examined in three different liquid-liquid systems: water/n-hexane, water/acetonitrile, and water/n-octanol. With GCS, the average errors are 22% (for 18 solutes), 18% (for 14 solutes) and 14% (for 15 solutes) for these solvent systems, while comparable errors are 237%, 286% and 226% with UNIFAC; and 342%, 414% and 306% with modified UNIFAC. The GCS model is a powerful new tool to predict the octanol-water partition coefficients.

  2. 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…

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

    PubMed

    Michalski; Hardy; Saramago

    1998-12-01

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

  4. 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.

  5. 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

  6. Microscopic Calculation of Fission Fragment Energies for the 239Pu(nth,f) Reaction

    SciTech Connect

    Younes, W; Gogny, D

    2011-10-03

    We calculate the total kinetic and excitation energies of fragments produced in the thermal-induced fission of {sup 239}Pu. This result is a proof-of-principle demonstration for a microscopic approach to the calculation of fission-fragment observables for applied data needs. In addition, the calculations highlight the application of a fully quantum mechanical description of scission, and the importance of exploring scission configurations as a function of the moments of the fragments, rather than through global constraints on the moments of the fissioning nucleus. Using a static microscopic calculation of configurations at and near scission, we have identified fission fragments for the {sup 239}Pu (n{sub th}, f) reaction and extracted their total kinetic and excitation energies. Comparison with data shows very good overall agreement between theory and experiment. Beyond their success as a proof of principle, these calculations also highlight the importance of local constraints on the fragments themselves in microscopic calculations.

  7. Formation and migration energies of the vacancy in Si calculated using the HSE06 range-separated hybrid functional

    NASA Astrophysics Data System (ADS)

    Śpiewak, Piotr; Kurzydłowski, Krzysztof J.

    2013-11-01

    To overcome deficiencies of conventional density functional theory (DFT) utilizing the standard approximation for the exchange-correlation, the revised Heyd-Scuseria-Ernzerhof screened hybrid functional (HSE06) has been used for calculating the formation and migration energies of the vacancy in Si. It is demonstrated that the hybrid approach gives a much more accurate electronic description of the bulk and the vacancy. The correct description of the band gap and the donor transition levels obtained with the HSE06 functional builds confidence in predictions of the vacancy acceptor states. The calculated migration energies of the vacancy with different charge states agree well with low-temperature annealing measurements and, together with formation energies, provide an excellent estimate of the activation energy of vacancy-mediated self-diffusion in silicon.

  8. On the consequences of the energy imbalance for calculating surface conductance to water vapour

    PubMed Central

    Wohlfahrt, Georg; Haslwanter, Alois; Hörtnagl, Lukas; Jasoni, Richard L.; Fenstermaker, Lynn F.; Arnone, John A.; Hammerle, Albin

    2014-01-01

    The Penman-Monteith combination equation, which is most frequently used to derive the surface conductance to water vapour (Gs), implicitly assumes the energy balance to be closed. Any energy imbalance (positive or negative) will thus affect the calculated Gs. Using eddy covariance energy flux data from a temperate grassland and a desert shrub ecosystem we explored five possible approaches of closing the energy imbalance and show that calculated Gs may differ considerably between these five approaches depending on the relative magnitudes of sensible and latent heat fluxes, and the magnitude and sign of the energy imbalance. Based on our limited understanding of the nature of the energy imbalance, we tend to favour an approach which preserves the Bowen-ratio and closes the energy balance on a larger time scale. PMID:24465070

  9. Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies.

    PubMed

    Boström, Jonas; Delcey, Mickaël G; Aquilante, Francesco; Serrano-Andrés, Luis; Pedersen, Thomas Bondo; Lindh, Roland

    2010-03-09

    The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.

  10. 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.

  11. Quantum mechanical method of fragment's angular and energy distribution calculation for binary and ternary fission

    SciTech Connect

    Kadmensky, S. G. Titova, L. V.; Pen'kov, N. V.

    2006-08-15

    In the framework of quantum-mechanical fission theory, the method of calculation for partial fission width amplitudes and asymptotic behavior of the fissile nucleus wave function with strong channel coupling taken into account has been suggested. The method allows one to solve the calculation problem of angular and energy distribution countation for binary and ternary fission.

  12. 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)

  13. 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.

  14. First principles calculation of the activity of cytochrome P450

    NASA Astrophysics Data System (ADS)

    Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.; Boyes, R. N.

    1998-04-01

    The cytochrome P450 superfamily of enzymes is of enormous interest in the biological sciences due to the wide range of endogenous and xenobiotic compounds which it metabolises, including many drugs. We describe the use of first principles quantum mechanical modeling techniques, based on density functional theory, to determine the outcome of interactions between an enzyme and a number of compounds. Specifically, we calculate the spin state of an Fe3+ ion present in a haem moiety at the active site of these enzymes. The spin state of this ion indicates if the catalytic reaction will proceed. The computational results obtained compare favorably with experimental data. Only the principle components of the active site of the enzyme are included in the computational models, demonstrating that only a small fragment of the protein needs to be included in the models in order to accurately reproduce this aspect of the enzymes' function. These results open the way for further investigation of this superfamily of enzymes using the methods detailed in this paper.

  15. 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.

  16. 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)

  17. Solar and internal gain adjustments in calculation of energy conservation savings

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Wortman, D.

    1983-07-01

    Heating degree days are often used as a climatic measure in building energy calculations. To account for the effects of solar and internal gains, degree days at a lower base temperature are sometimes used, or the number of degree days is adjusted downward by a degree-day correction factor. A theoretical derivation which demonstrates that ASHRAE (American Society of Heating, Refrigerating, and Air-Conditioning Engineers) C sub d factors are not the appropriate correction factors for calculation of energy savings from envelope conservation measures is presented. The results of this derivation can be used to develop new correlation factors appropriate for savings calculations.

  18. 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 ...

  19. 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...

  20. 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…

  1. 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}

  2. 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...

  3. Zero-point energy constraint in quasi-classical trajectory calculations.

    PubMed

    Xie, Zhen; Bowman, Joel M

    2006-04-27

    A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.

  4. 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)

  5. Calculation of energy deposition, photon and neutron production in proton therapy of thyroid gland using MCNPX.

    PubMed

    Mowlavi, Ali Asghar; Fornasie, Maria Rosa; de Denaro, Mario

    2011-01-01

    In this study, the MCNPX code has been used to simulate a proton therapy in thyroid gland, in order to calculate the proton energy deposition in the target region. As well as, we have calculated the photon and neutron production spectra due to proton interactions with the tissue. We have considered all the layers of tissue, from the skin to the thyroid gland, and an incident high energy pencil proton beam. The results of the simulation show that the best proton energy interval, to cover completely the thyroid tissue, is from 42 to 54 MeV, assuming that the thyroid gland has a 14 mm thickness and is located 11.2mm under the skin surface. The most percentage of deposited energy (78%) is related to the 54 MeV proton energy beam. Total photon and neutron production are linear and polynomial second order functions of the proton energy, respectively.

  6. A universal method to calculate the surface energy density of spherical surfaces in crystals

    NASA Astrophysics Data System (ADS)

    Wang, Jian; Bian, Jianjun; Niu, Xinrui; Wang, Gangfeng

    2017-02-01

    Surface energy plays an important role in the mechanical performance of nanomaterials; however, determining the surface energy density of curved surfaces remains a challenge. In this paper, we conduct atomic simulations to calculate the surface energy density of spherical surfaces in various crystalline metals. It is found that the average surface energy density of spherical surfaces remains almost constant once its radius exceeds 5 nm. Then, using a geometrical analysis and the scaling law, we develop an analytical approach to estimate the surface energy density of spherical surfaces through that of planar surfaces. The theoretical prediction agrees well with the direct atomic simulations, and thus provides a simple and general method to calculate the surface energy density in crystals.

  7. Comparison of stress and total energy methods for calculation of elastic properties of semiconductors.

    PubMed

    Caro, M A; Schulz, S; O'Reilly, E P

    2013-01-16

    We explore the calculation of the elastic properties of zinc-blende and wurtzite semiconductors using two different approaches: one based on stress and the other on total energy as a function of strain. The calculations are carried out within the framework of density functional theory in the local density approximation, with the plane wave-based package VASP. We use AlN as a test system, with some results also shown for selected other materials (C, Si, GaAs and GaN). Differences are found in convergence rate between the two methods, especially in low symmetry cases, where there is a much slower convergence for total energy calculations with respect to the number of plane waves and k points used. The stress method is observed to be more robust than the total energy method with respect to the residual error in the elastic constants calculated for different strain branches in the systems studied.

  8. 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;…

  9. The calculations of small molecular conformation energy differences by density functional method

    NASA Astrophysics Data System (ADS)

    Topol, I. A.; Burt, S. K.

    1993-03-01

    The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Chen, Z. J.; Xiao, H. Y.; Zu, X. T.; Gao, F.

    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 Γ point in the Brillouin zone.

  12. 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.

  13. 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.

  14. Calculation of Raman optical activity spectra for vibrational analysis.

    PubMed

    Mutter, Shaun T; Zielinski, François; Popelier, Paul L A; Blanch, Ewan W

    2015-05-07

    By looking back on the history of Raman Optical Activity (ROA), the present article shows that the success of this analytical technique was for a long time hindered, paradoxically, by the deep level of detail and wealth of structural information it can provide. Basic principles of the underlying theory are discussed, to illustrate the technique's sensitivity due to its physical origins in the delicate response of molecular vibrations to electromagnetic properties. Following a short review of significant advances in the application of ROA by UK researchers, we dedicate two extensive sections to the technical and theoretical difficulties that were overcome to eventually provide predictive power to computational simulations in terms of ROA spectral calculation. In the last sections, we focus on a new modelling strategy that has been successful in coping with the dramatic impact of solvent effects on ROA analyses. This work emphasises the role of complementarity between experiment and theory for analysing the conformations and dynamics of biomolecules, so providing new perspectives for methodological improvements and molecular modelling development. For the latter, an example of a next-generation force-field for more accurate simulations and analysis of molecular behaviour is presented. By improving the accuracy of computational modelling, the analytical capabilities of ROA spectroscopy will be further developed so generating new insights into the complex behaviour of molecules.

  15. 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.

  16. 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)

  17. 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.

  18. 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

  19. The activation energy for dislocation nucleation at a crack

    NASA Astrophysics Data System (ADS)

    Rice, James R.; Beltz, Glenn E.

    1994-02-01

    T HE ACTIVATION energy for dislocation nucleation from a stressed crack tip is calculated within the Peierls framework, in which a periodic shear stress vs displacement relation is assumed to hold on a slip plane emanating from the crack tip. Previous results have revealed that the critical G (energy release rate corresponding to the "screened" crack tip stress field) for dislocation nucleation scales with γ us (the unstable stacking energy), in an analysis which neglects any coupling between tension and shear along the slip plane. That analysis represents instantaneous nucleation and takes thermal effects into account only via the weak temperature dependence of the elastic constants. In this work, the energy required to thermally activate a stable, incipient dislocation into its unstable "saddle-point" configuration is directly calculated for loads less than that critical value. We do so only with the simplest case, for which the slip plane is a prolongation of the crack plane. A first calculation reported is 2D in nature, and hence reveals an activation energy per unit length. A more realistic scheme for thermal activation involves the emission of a dislocation loop, an inherently 3D phenomenon. Asymptotic calculations of the activation energy for loads close to the critical load are performed in 2D and in 3D. It is found that the 3D activation energy generally corresponds to the 2D activation energy per unit length multiplied by about 5-10 Burgers vectors (but by as many as 17 very near to the critical loading). Implications for the emission of dislocations in copper, α-iron, and silicon at elevated temperature are discussed. The effects of thermal activation are very significant in lowering the load for emission. Also, the appropriate activation energy to correspond to molecular dynamics simulations of crack tips is discussed. Such simulations, as typically carried out with only a few atomic planes in a periodic repeat direction parallel to the crack tip, are

  20. 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.

  1. First-principle Calculations of Equation of State for Metals at High Energy Density

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel; Khishchenko, Konstantin

    2012-02-01

    In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and isentropic sound velocity behind the shock front for aluminum. Also we perform similar calculations for nickel and iron. We use the VASP code with ultrasoft and PAW pseudopotentials and GGA exchange-correlation functional. Up to 512 particles have been used in calculations. To calculate Hugoniots we solve the Hugoniot equation numerically. To obtain release isentropes, we use Zel'dovich's approach and integrate an ordinary differential equation for the temperature thus restoring all thermodynamic parameters. Isentropic sound velocity is calculated by differentiation of pressure along isentropes. The results of our calculations are in good agreement with experimental data at densities both higher and lower than the normal one. Thus, quantum molecular dynamics results can be effectively used for verification or calibration of semiempirical equations of state under conditions of lack of experimental information at high energy densities.

  2. 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.

  3. Atomic scale calculations of tungsten surface binding energy and beryllium-induced tungsten sputtering

    NASA Astrophysics Data System (ADS)

    Yang, Xue; Hassanein, Ahmed

    2014-02-01

    Tungsten surface binding energy is calculated using classical molecular dynamic simulations with three many-body potentials. We present the consistency in tungsten sputtering yield by beryllium bombardment between molecular dynamic LAMMPS code and binary collision approximation ITMC code using the new surface binding energy (11.75 eV). The commonly used heat of sublimation value (8.68 eV) could lead to overestimated sputtering yield results. The analysis of the sputtered tungsten angular distributions show that molecular dynamic accurately reproduced the [1 1 1] most prominent preferential ejection directions in bcc tungsten, while the distinct shapes by typical MC codes such as ITMC code is caused by the treatment of amorphous target. The ITMC calculated emitted tungsten energy profile matches the Thompson energy spectrum, while the molecular dynamic results generally follow the Falcone energy spectrum.

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

    PubMed

    Chen, Changjun

    2016-03-31

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

  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. Calculation of Liquid-Solid Interfacial Free Energy in Pb-Cu Binary Immiscible System

    NASA Astrophysics Data System (ADS)

    Li, Hong-shan; Zhou, Sheng-gang; Cao, Yong

    2016-11-01

    Based on the solid-liquid interfacial free energy theory of the complex Warren binary & pseudo-binary system and through the simplification of it by taking Pb-Cu binary system as an example, the physical model for it in binary immiscible system can be obtained. Next, its thermodynamic formula is derived to obtain a theoretical formula that only contains two parameters, and comparisons are made with regard to γSL calculated values and experimental values of MPE (multiphase equilibrium method) under several kinds of temperatures. As manifested in the outcomes, the improved physical model and theoretical formula will become not only easy to understand but also simple for calculation (the calculated value of γSL depends on two parameters, i.e. temperature and percentage composition of Cu atom). It can be treated as the foundation of application for the γSL calculation of liquid-solid interfacial free energy in other immiscible systems.

  7. 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.

  8. Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

    NASA Astrophysics Data System (ADS)

    Chen, Xi H.; Zhang, John Z. H.

    2004-06-01

    In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.

  9. 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.

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

    PubMed

    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 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.

  11. 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.

  12. Energy Conservation Activities, Grades 1-6.

    ERIC Educational Resources Information Center

    Northern Colorado Educational Board of Cooperative Services, Boulder.

    This publication is a collection of energy education activities for grades 1-6. The activities were written or selected to be used with daily lesson plans and the existing school curriculum. Activities are classified by: (1) content area (fine arts, mathematics, physical education, reading and language arts, science, and social studies; and (2)…

  13. DFT calculations of magnetic anisotropy energy of Ge(1-x)Mn(x)Te ferromagnetic semiconductor.

    PubMed

    Łusakowski, A; Bogusławski, P; Story, T

    2015-06-10

    Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge(1-x)Mn(x)Te were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge(1-x)Mn(x)Te (1 1 1) thin layers.

  14. DFT calculations of magnetic anisotropy energy of Ge1-xMnxTe ferromagnetic semiconductor

    NASA Astrophysics Data System (ADS)

    Łusakowski, A.; Bogusławski, P.; Story, T.

    2015-06-01

    Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge1-xMnxTe were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge1-xMnxTe (1 1 1) thin layers.

  15. Monte Carlo calculations of energy deposition distributions of electrons below 20 keV in protein.

    PubMed

    Tan, Zhenyu; Liu, Wei

    2014-05-01

    The distributions of energy depositions of electrons in semi-infinite bulk protein and the radial dose distributions of point-isotropic mono-energetic electron sources [i.e., the so-called dose point kernel (DPK)] in protein have been systematically calculated in the energy range below 20 keV, based on Monte Carlo methods. The ranges of electrons have been evaluated by extrapolating two calculated distributions, respectively, and the evaluated ranges of electrons are compared with the electron mean path length in protein which has been calculated by using electron inelastic cross sections described in this work in the continuous-slowing-down approximation. It has been found that for a given energy, the electron mean path length is smaller than the electron range evaluated from DPK, but it is large compared to the electron range obtained from the energy deposition distributions of electrons in semi-infinite bulk protein. The energy dependences of the extrapolated electron ranges based on the two investigated distributions are given, respectively, in a power-law form. In addition, the DPK in protein has also been compared with that in liquid water. An evident difference between the two DPKs is observed. The calculations presented in this work may be useful in studies of radiation effects on proteins.

  16. A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.

    PubMed

    Woods, Christopher J; Malaisree, Maturos; Hannongbua, Supot; Mulholland, Adrian J

    2011-02-07

    The accurate prediction of absolute protein-ligand binding free energies is one of the grand challenge problems of computational science. Binding free energy measures the strength of binding between a ligand and a protein, and an algorithm that would allow its accurate prediction would be a powerful tool for rational drug design. Here we present the development of a new method that allows for the absolute binding free energy of a protein-ligand complex to be calculated from first principles, using a single simulation. Our method involves the use of a novel reaction coordinate that swaps a ligand bound to a protein with an equivalent volume of bulk water. This water-swap reaction coordinate is built using an identity constraint, which identifies a cluster of water molecules from bulk water that occupies the same volume as the ligand in the protein active site. A dual topology algorithm is then used to swap the ligand from the active site with the identified water cluster from bulk water. The free energy is then calculated using replica exchange thermodynamic integration. This returns the free energy change of simultaneously transferring the ligand to bulk water, as an equivalent volume of bulk water is transferred back to the protein active site. This, directly, is the absolute binding free energy. It should be noted that while this reaction coordinate models the binding process directly, an accurate force field and sufficient sampling are still required to allow for the binding free energy to be predicted correctly. In this paper we present the details and development of this method, and demonstrate how the potential of mean force along the water-swap coordinate can be improved by calibrating the soft-core Coulomb and Lennard-Jones parameters used for the dual topology calculation. The optimal parameters were applied to calculations of protein-ligand binding free energies of a neuraminidase inhibitor (oseltamivir), with these results compared to experiment. These

  17. Accuracy and precision of free-energy calculations via molecular simulation

    NASA Astrophysics Data System (ADS)

    Lu, Nandou

    A quantitative characterization of the methodologies of free-energy perturbation (FEP) calculations is presented, and optimal implementation of the methods for reliable and efficient calculation is addressed. Some common misunderstandings in the FEP calculations are corrected. The two opposite directions of FEP calculations are uniquely defined as generalized insertion and generalized deletion, according to the entropy change along the perturbation direction. These two calculations are not symmetric; they produce free-energy results differing systematically due to the different capability of each to sample the important phase-space in a finite-length simulation. The FEP calculation errors are quantified by characterizing the simulation sampling process with the help of probability density functions for the potential energy change. While the random error in the FEP calculation is analyzed with a probabilistic approach, the systematic error is characterized as the most-likely inaccuracy, which is modeled considering the poor sampling of low-probability energy distribution tails. Our analysis shows that the entropy difference between the perturbation systems plays a key role in determining the reliability of FEP results, and the perturbation should be carried out in the insertion direction in order to ensure a good sampling and thus a reliable calculation. Easy-to-use heuristics are developed to estimate the simulation errors, as well as the simulation length that ensures a certain accuracy level of the calculation. The fundamental understanding obtained is then applied to tackle the problem of multistage FEP optimization. We provide the first principle of optimal staging: For each substage FEP calculation, the higher entropy system should be used as the reference to govern the sampling, i.e., the calculation should be conducted in the generalized insertion direction for each stage of perturbation. To minimize the simulation error, intermediate states should be

  18. 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)

  19. Calculating the rate of exothermic energy release for catalytic converter efficiency monitoring

    SciTech Connect

    Hepburn, J.S.; Meitzler, A.H.

    1995-12-31

    This paper reports on the development of a new methodology for OBD-II catalyst efficiency monitoring. Temperature measurements taken from the center of the catalyst substrate or near the exterior surface of the catalyst brick were used in conjunction with macroscopic energy balances to calculate the instantaneous rate of exothermic energy generation within the catalyst. The total calculated rate of exothermic energy release over the FTP test cycle was within 10% of the actual or theoretical value and provided a good indicator of catalyst light-off for a variety of aged catalytic converters. Normalization of the rate of exothermic energy release in the front section of the converter by the mass flow rate of air inducted through the engine was found to provide a simple yet practical means of monitoring the converter under both FTP and varying types of road driving.

  20. 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.

  1. Approximate method of free energy calculation for spin system with arbitrary connection matrix

    NASA Astrophysics Data System (ADS)

    Kryzhanovsky, Boris; Litinskii, Leonid

    2015-01-01

    The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with long-range interaction, where large coordination number q ensures the correctness of the central limit theorem application. However, the method provides good results also for systems with short-range interaction when the number q is not so large.

  2. The calculation of bond dissociation energies of transition metal complexes using isostructural reactions

    NASA Astrophysics Data System (ADS)

    Dapprich, S.; Pidun, U.; Ehlers, A. W.; Frenking, G.

    1995-08-01

    The metal-ligand bond dissociation energies (CO) nM-L are theoretically predicted at the HF, MP2 and CCSD(T) levels of theory using effective core potentials for the metals for M = Cr, Mo, W, Ni, Pd, Pt and for L = CO, NO +, CN -, NC -, CS, SiO, N 2. The bond energies at the HF level are too low and the MP2 values are too high, while the CCSD(T) results are in good agreement with experimental data. The bond energies at MP2 show the same trend as the CCSD(T) values and may therefore be used for the prediction of relative bond dissociation energies. The absolute values for the bond energies calculated at MP2 are significantly improved when they are corrected using the energies of isostructural reactions M(CO) n + L → M(CO) n-1 L + CO.

  3. A novel method for calculating relative free energy of similar molecules in two environments

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2017-03-01

    Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy, simple implementation, robustness and efficiency, which prevent the calculations from being automated and limit their use. Here we present an exact and complete decoupling analysis in which the partition functions of the compared systems decompose into the partition functions of the common and different subsystems. This decoupling analysis is applicable to submolecules with coupled degrees of freedom such as the methyl group and to any potential function (including the typical dihedral potentials), enabling to remove less terms in the transformation which results in a more efficient calculation. Then we show mathematically, in the context of partition function decoupling, that the two compared systems can be simulated separately, eliminating the need to design a composite system. We demonstrate the decoupling analysis and the separate transformations in a relative free energy calculation using MD simulations for a general force field and compare to another calculation and to experimental results. We present a unified soft-core technique that ensures the monotonicity of the numerically integrated function (analytical proof) which is important for the selection of intermediates. We show mathematically that in this soft-core technique the numerically integrated function can be non-steep only when we transform the systems separately, which can simplify the numerical integration. Finally, we show that when the systems have rugged energy landscape they can be equilibrated without introducing another sampling dimension which can also enable to use the simulation results for other free energy calculations.

  4. Energy intake, physical activity, energy balance, and cancer: epidemiologic evidence.

    PubMed

    Pan, Sai Yi; DesMeules, Marie

    2009-01-01

    Energy intake, physical activity, and obesity are modifiable lifestyle factors. This chapter reviews and summarizes the epidemiologic evidence on the relation of energy intake, physical activity, and obesity to cancer. High energy intake may increase the risk of cancers of colon-rectum, prostate (especially advanced prostate cancer), and breast. However, because physical activity, body size, and metabolic efficiency are highly related to total energy intake and expenditure, it is difficult to assess the independent effect of energy intake on cancer risk. There are sufficient evidences to support a role of physical activity in preventing cancers of the colon and breast, whereas the association is stronger in men than in women for colon cancer and in postmenopausal than in premenopausal women for breast cancer. The evidence also suggests that physical activity likely reduces the risk of cancers of endometrium, lung, and prostate (to a lesser extent). On the other hand, there is little or no evidence that the risk of rectal cancer is related to physical activity, whereas the results have been inconsistent regarding the association between physical activity and the risks of cancers of pancreas, ovary and kidney. Epidemiologic studies provide sufficient evidence that obesity is a risk factor for both cancer incidence and mortality. The evidence supports strong links of obesity with the risk of cancers of the colon, rectum, breast (in postmenopausal women), endometrium, kidney (renal cell), and adenocarcinoma of the esophagus. Epidemiologic evidence also indicates that obesity is probably related to cancers of the pancreas, liver, and gallbladder, and aggressive prostate cancer, while it seems that obesity is not associated with lung cancer. The role of obesity in other cancer risks is unclear.

  5. 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.

  6. 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.

  7. Activation Energies of Fragmentations of Disaccharides by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kuki, Ákos; Nagy, Lajos; Szabó, Katalin E.; Antal, Borbála; Zsuga, Miklós; Kéki, Sándor

    2014-03-01

    A simple multiple collision model for collision induced dissociation (CID) in quadrupole was applied for the estimation of the activation energy (Eo) of the fragmentation processes for lithiated and trifluoroacetated disaccharides, such as maltose, cellobiose, isomaltose, gentiobiose, and trehalose. The internal energy-dependent rate constants k(Eint) were calculated using the Rice-Ramsperger-Kassel-Marcus (RRKM) or the Rice-Ramsperger-Kassel (RRK) theory. The Eo values were estimated by fitting the calculated survival yield (SY) curves to the experimental ones. The calculated Eo values of the fragmentation processes for lithiated disaccharides were in the range of 1.4-1.7 eV, and were found to increase in the order trehalose < maltose < isomaltose < cellobiose < gentiobiose.

  8. 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.

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

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... cost indexes? 591.220 Section 591.220 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ALLOWANCES AND DIFFERENTIALS Cost-of-Living Allowance and Post Differential-Nonforeign Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a)...

  10. 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.

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

    DOE PAGES

    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.

  12. Calculating Interaction Energies Using First Principle Theories: Consideration of Basis Set Superposition Error and Fragment Relaxation

    ERIC Educational Resources Information Center

    Bowen, J. Philip; Sorensen, Jennifer B.; Kirschner, Karl N.

    2007-01-01

    The analysis explains the basis set superposition error (BSSE) and fragment relaxation involved in calculating the interaction energies using various first principle theories. Interacting the correlated fragment and increasing the size of the basis set can help in decreasing the BSSE to a great extent.

  13. 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)

  14. Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine.

    PubMed

    Suzuki, Masayo; Kino, Katsuhito; Morikawa, Masayuki; Kobayashi, Takanobu; Komori, Rie; Miyazawa, Hiroshi

    2012-06-01

    DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H)-oxazolone (Oz), guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiro-imino-dihydantoin (Sp) are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.

  15. The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.

    ERIC Educational Resources Information Center

    Castano, F.; And Others

    1983-01-01

    The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)

  16. First-principles Calculations of Twin-boundary and Stacking-fault Energies in Magnesium

    DTIC Science & Technology

    2010-01-01

    The interfacial energies of twin boundaries and stacking faults in metal magnesium have been calculated using first-principles supercell approach...Four types of twin boundaries and two types of stacking faults are investigated, namely, those due to the mirror reflection, the mirror glide and the

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. Density functional calculation of core-electron binding energies of transition metal carbonyl and nitrosyl complexes

    NASA Astrophysics Data System (ADS)

    Hu, Ching-Han; Chong, Delano P.

    1996-11-01

    Our recent procedure of the unrestricted generalized transition state (uGTS) model for density functional calculations of core-electron binding energies has been applied to seven carbonyl and nitrosyl inorganic complexes: Fe(CO) 5, Ni(CO) 4, Mn(CO) 4NO, Co(CO) 3NO, Fe(CO) 2(NO) 2, Mn(NO) 3CO and Cr(NO) 4. The exchange-correlation potential is based on a combined functional of Becke's exchange (B88) and Perdew's correlation (P86). The cc-pVTZ basis set was used for the calculation of neutral molecules, while for the partial cation created in the uGTS approach we scaled the cc-pVTZ basis set using a procedure based on Clementi and Raimondi's rules for atomic screening. The average absolute deviation of the calculated core-electron binding energy from experiment is 0.28 eV.

  3. 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.

  4. Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

    PubMed

    Ellingson, Benjamin A; Geballe, Matthew T; Wlodek, Stanislaw; Bayly, Christopher I; Skillman, A Geoffrey; Nicholls, Anthony

    2014-03-01

    Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson-Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5-2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors.

  5. A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles

    PubMed Central

    Zhang, Yong; Voth, Gregory A.

    2011-01-01

    Free energy calculations are one of the most useful methods for the study of ion transport mechanisms through confined spaces such as protein ion channels. Their reliability depends on a correctly defined reaction coordinate (RC). A straight line is usually not a proper RC for such complicated processes so in this work a combined metadynamics/umbrella sampling (MTD/US) method is proposed. In the combined method, the ion transport pathway is first identified by the MTD method and then the free energy profile or potential of mean force (PMF) along the path is calculated using umbrella sampling. This combined method avoids the discontinuity problem often associated with normal umbrella sampling calculations that assume a straight line RC and it provides a more physically accurate PMF for such processes. The method is demonstrated for the proton transport process through the protein channel of aquaporin-1. PMID:25100923

  6. High-energy cosmic-ray fluxes in the Earth atmosphere: Calculations vs experiments

    NASA Astrophysics Data System (ADS)

    Kochanov, A. A.; Sinegovskaya, T. S.; Sinegovsky, S. I.

    2008-12-01

    A new calculation of the atmospheric fluxes of cosmic-ray hadrons and muons in the energy range 10-105 GeV has been performed for the set of hadron production models, EPOS 1.6, QGSJET II-03, SIBYLL 2.1, and others that are of interest to cosmic-ray physicists. The fluxes of secondary cosmic rays at several levels in the atmosphere are computed using directly data of the ATIC-2, GAMMA experiments, and the model proposed recently by Zatsepin and Sokolskaya as well as the parameterization of the primary cosmic-ray spectrum by Gaisser and Honda. The calculated energy spectra of the hadrons and muon flux as a function of zenith angle are compared with measurements as well as other calculations. The effect of uncertainties both in the primary cosmic-ray flux and hadronic model predictions on the spectra of atmospheric hadrons and muons is considered.

  7. Resonance energies, lifetimes and complex energy potential curves from standard wave-packet calculations

    NASA Astrophysics Data System (ADS)

    Goldzak, Tamar; Gilary, Ido; Moiseyev, Nimrod

    2012-05-01

    We show here for a simple model system that the wavepacket dynamics in the interaction region can be described by a superposition of the non-Hermitian exponential divergent eigenfunctions of the physical Hamiltonian. We demonstrate how it is possible to obtain the complex eigenvalues and also the corresponding resonance eigenfunctions from the propagation of the wavepacket within the framework of the standard formalism of quantum mechanics. The general results demonstrated here for a simple model can lead to two different types of computational applications: (i) for systems where one can obtain the resonance energies and lifetimes as well as their corresponding eigenfunctions it is possible to study the evolution of the physical properties solely based on the initially populated resonance states without the need to propagate the wavepacket; (ii) for molecular systems where it is quite difficult to solve the non-Hermitian time-independent Schrödinger equation and obtain molecular resonance energies and functions. For this type of problem, the methods presented here enable one to evaluate the topology of complex potential energy surfaces from the wavepacket propagation and facilitate the study of the nuclear dynamics of ionizing molecular systems.

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

    SciTech Connect

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

    2014-05-14

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

  9. Radial dose distributions from protons of therapeutic energies calculated with Geant4-DNA.

    PubMed

    Wang, He; Vassiliev, Oleg N

    2014-07-21

    Models based on the amorphous track structure approximation have been successful in predicting the biological effects of heavy charged particles. Development of such models remains an active area of research that includes applications to hadrontherapy. In such models, the radial distribution of the dose deposited by delta electrons and directly by the particle is the main characteristic of track structure. We calculated these distributions with Geant4-DNA Monte Carlo code for protons in the energy range from 10 to 100 MeV. These results were approximated by a simple formula that combines the well-known inverse square distance dependence with two factors that eliminate the divergence of the radial dose integral at both small and large distances. A clear physical interpretation is given to the asymptotic behaviour of the radial dose distribution resulting from these two factors. The proposed formula agrees with the Monte Carlo data within 10% for radial distances of up to 10 μm, which corresponds to a dose range covering over eight orders of magnitude. Differences between our results and those of previously published analytical models are discussed.

  10. Radial dose distributions from protons of therapeutic energies calculated with Geant4-DNA

    NASA Astrophysics Data System (ADS)

    Wang, He; Vassiliev, Oleg N.

    2014-07-01

    Models based on the amorphous track structure approximation have been successful in predicting the biological effects of heavy charged particles. Development of such models remains an active area of research that includes applications to hadrontherapy. In such models, the radial distribution of the dose deposited by delta electrons and directly by the particle is the main characteristic of track structure. We calculated these distributions with Geant4-DNA Monte Carlo code for protons in the energy range from 10 to 100 MeV. These results were approximated by a simple formula that combines the well-known inverse square distance dependence with two factors that eliminate the divergence of the radial dose integral at both small and large distances. A clear physical interpretation is given to the asymptotic behaviour of the radial dose distribution resulting from these two factors. The proposed formula agrees with the Monte Carlo data within 10% for radial distances of up to 10 μm, which corresponds to a dose range covering over eight orders of magnitude. Differences between our results and those of previously published analytical models are discussed.

  11. Origin of activation energy in a superionic conductor.

    PubMed

    Kamishima, O; Kawamura, K; Hattori, T; Kawamura, J

    2011-06-08

    The characteristics of cation diffusion with many-body effects are discussed using Ag β-alumina as an example of a superionic conductor. Polarized Raman spectra of Ag β-alumina have been measured at room temperature. The interatomic potentials were determined by a non-linear least square fitting between the phonon eigenvalues from the Raman observations and a dynamical matrix calculation based on a rigid-ion model. The obtained potential parameters for the model crystal of Ag β-alumina successfully reproduce the macroscopic properties with respect to the heat capacity, isothermal compressibility and self-diffusion constant. A molecular dynamics (MD) calculation has been carried out using the model crystal of Ag β-alumina to understand the many-body effects for the fast ionic diffusion. It was found that the Ag-Ag repulsion by excess Ag defects significantly reduced the cost of the energy difference of the occupancy between the stable and metastable sites. It is possible for the system to take various configurations of the mobile ions through defects easily, and then the fast ionic diffusion will appear. On the other hand, the Ag-Ag repulsion changes the dynamics of the Ag ions from a random hopping to a cooperative motion. In the cooperative motion, the ionic transport becomes difficult due to the additional energy required for the structural relaxation of the surrounding Ag ions. We propose a new insight into the superionic conduction, that is, the activation energy for the ionic transport is composed of two kinds of elements: a 'static' activation energy and a 'dynamic' one. The static activation energy is the cost of the averaged energy difference in the various structural configurations in the equilibrium state. The dynamic activation energy is the additional energy required for the structural relaxation induced by the jump process.

  12. 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.

  13. 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.

  14. 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.

  15. Calculation of Energy Diagram of Asymmetric Graded-Band-Gap Semiconductor Superlattices.

    PubMed

    Monastyrskii, Liubomyr S; Sokolovskii, Bogdan S; Alekseichyk, Mariya P

    2017-12-01

    The paper theoretically investigates the peculiarities of energy diagram of asymmetric graded-band-gap superlattices with linear coordinate dependences of band gap and electron affinity. For calculating the energy diagram of asymmetric graded-band-gap superlattices, linearized Poisson's equation has been solved for the two layers forming a period of the superlattice. The obtained coordinate dependences of edges of the conduction and valence bands demonstrate substantial transformation of the shape of the energy diagram at changing the period of the lattice and the ratio of width of the adjacent layers. The most marked changes in the energy diagram take place when the period of lattice is comparable with the Debye screening length. In the case when the lattice period is much smaller that the Debye screening length, the energy diagram has the shape of a sawtooth-like pattern.

  16. The simplest method for calculating energy output and Gurney velocity of explosives.

    PubMed

    Keshavarz, Mohammad Hossein; Semnani, Abolfazl

    2006-04-17

    Two correlations are introduced for calculating Gurney velocity as a useful parameter for thermochemical estimation of explosive energy output. For CaHbNcOd explosives, only the chemical composition of high explosive as well as its condensed or estimated gas phase heat of formation, which later is calculated by group additivity rules, is needed for calculating Gurney velocity. The introduced simple correlations in the present work may be applied to any explosive that contains the elements of carbon, hydrogen, nitrogen and oxygen with no difficulties at any loading density. There is no need to use any assumed decomposition reaction in present work. Gurney velocity are calculated for different pure and explosive formulations and compared with measured Gurney velocity at specified loading density. The results show that the agreement is good for present method as compared to previous correlations.

  17. 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.

  18. 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.

  19. 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

  20. Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

    NASA Astrophysics Data System (ADS)

    Gallicchio, Emilio; Deng, Nanjie; He, Peng; Wickstrom, Lauren; Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Olson, Arthur J.; Levy, Ronald M.

    2014-04-01

    As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization.

  1. Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

    PubMed Central

    Gallicchio, Emilio; Deng, Nanjie; He, Peng; Wickstrom, Lauren; Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Olson, Arthur J.; Levy, Ronald M.

    2014-01-01

    As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization. PMID:24504704

  2. 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.

  3. Light absorption and excitation energy transfer calculations in primitive photosynthetic bacteria

    NASA Astrophysics Data System (ADS)

    Komatsu, Yu; Kayanuma, Megumi; Shoji, Mitsuo; Yabana, Kazuhiro; Shiraishi, Kenji; Umemura, Masayuki

    2015-06-01

    In photosynthetic organisms, light energy is converted into chemical energy through the light absorption and excitation energy transfer (EET) processes. These processes start in light-harvesting complexes, which contain special photosynthetic pigments. The exploration of unique mechanisms in light-harvesting complexes is directly related to studies, such as artificial photosynthesis or biosignatures in astrobiology. We examined, through ab initio calculations, the light absorption and EET processes using cluster models of light-harvesting complexes in purple bacteria (LH2). We evaluated absorption spectra and energy transfer rates using the LH2 monomer and dimer models to reproduce experimental results. After the calibration tests, a LH2 aggregation model, composed of 7 or 19 LH2s aligned in triangle lattice, was examined. We found that the light absorption is red shifted and the energy transfer becomes faster as the system size increases. We also found that EET is accelerated by exchanging the central pigments to lower energy excited pigments. As an astrobiological application, we calculated light absorptions efficiencies of the LH2 in different photoenvironments.

  4. A local framework for calculating coupled cluster singles and doubles excitation energies (LoFEx-CCSD)

    DOE PAGES

    Baudin, Pablo; Bykov, Dmytro; Liakh, Dmitry I.; ...

    2017-02-22

    Here, the recently developed Local Framework for calculating Excitation energies (LoFEx) is extended to the coupled cluster singles and doubles (CCSD) model. In the new scheme, a standard CCSD excitation energy calculation is carried out within a reduced excitation orbital space (XOS), which is composed of localised molecular orbitals and natural transition orbitals determined from time-dependent Hartree–Fock theory. The presented algorithm uses a series of reduced second-order approximate coupled cluster singles and doubles (CC2) calculations to optimise the XOS in a black-box manner. This ensures that the requested CCSD excitation energies have been determined to a predefined accuracy compared tomore » a conventional CCSD calculation. We present numerical LoFEx-CCSD results for a set of medium-sized organic molecules, which illustrate the black-box nature of the approach and the computational savings obtained for transitions that are local compared to the size of the molecule. In fact, for such local transitions, the LoFEx-CCSD scheme can be applied to molecular systems where a conventional CCSD implementation is intractable.« less

  5. Strain and Cohesive Energy of TiN Deposit on Al(001) Surface: Density Functional Calculation

    NASA Astrophysics Data System (ADS)

    Ren, Yuan; Liu, Xuejie

    2016-07-01

    To apply the high hardness of TiN film to soft and hard multilayer composite sheets, we constructed a new type of composite structural material with ultra-high strength. The strain of crystal and cohesive energy between the atoms in the eight structures of N atom, Ti atom, 2N2Ti island and TiN rock salt deposited on the Al(001) surface were calculated with the first-principle ultra-soft pseudopotential approach of the plane wave based on the density functional theory. The calculations of the cohesive energy showed that N atoms could be deposited in the face-centered-cubic vacancy position of the Al(001) surface and results in a cubic structure AlN surface. The TiN film could be deposited on the interface of β-AlN. The calculations of the strains showed that the strain in the TiN film deposited on the Al(001) surface was less than that in the 2N2Ti island deposited on the Al(001) surface. The diffusion behavior of interface atom N was investigated by a nudged elastic band method. Diffusion energy calculation showed that the N atom hardly diffused to the substrate Al layer.

  6. 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.

  7. Grid-based steered thermodynamic integration accelerates the calculation of binding free energies.

    PubMed

    Fowler, Philip W; Jha, Shantenu; Coveney, Peter V

    2005-08-15

    The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differences using thermodynamic integration can be significantly reduced: potentially from weeks or months to days of wall-clock time. To be able to perform such accelerated calculations requires the ability to both run concurrently and control in realtime several parallel simulations on a computational Grid. We describe how the RealityGrid computational steering system, in conjunction with a scalable classical MD code, can be used to dramatically reduce the time to achieve a result. This is necessary to improve the adoption of this technique and further allows more detailed investigations into the accuracy and precision of thermodynamic integration. Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.

  8. 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.

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

    PubMed

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

    2016-01-01

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

  10. Application of ab-initio calculations to modeling of nanoscale diffusion and activation in silicon

    NASA Astrophysics Data System (ADS)

    Diebel, Milan

    As ULSI devices enter the nanoscale, ultra-shallow and highly electrically active junctions become necessary. New materials and 3D device structures as well as new process technologies are under exploration to meet the requirements of future devices. A detailed understanding of the atomistic mechanisms of point-defect/dopant interactions which govern diffusion and activation behavior is required to overcome the challenges in building these devices. This dissertation describes how ab-initio calculations can be used to develop physical models of diffusion and activation in silicon. A hierarchy of approaches (ab-initio, kinetic lattice Monte Carlo, continuum) is used to bridge the gaps in time scale and system size between atomistic calculations and nanoscale devices. This modeling approach is demonstrated by investigating two very different challenges in process technology: F co-implantation and stress effects on dopant diffusion/activation. In the first application, ab-initio calculations are used to understand anomalous F diffusion behavior. A set of strongly bound fluorine vacancy complexes (FnVm ) were found. The decoration of vacancies/dangling silicon bonds by fluorine leads to fluorine accumulating in vacancy rich regions, which explains the fluorine redistribution behavior reported experimentally. The revealed interactions of F with point-defects explain the benefits of F co-implantation for B and P activation and diffusion. Based on the insight gained, a simplified F diffusion model at the continuum level (50--100 nm scale) is extracted that accounts for co-implantation effects on B and P for various implant energies and doses. The second application addresses the effect of stress on point-defect/dopant equilibrium concentration, diffusion, and activation. A methodology is developed to extract detailed stress effects from ab-initio calculations. The approach is used to extract induced strains and elasticity tensors for various defects and impurities in order

  11. 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.

  12. FreeSolv: A database of experimental and calculated hydration free energies, with input files

    PubMed Central

    Mobley, David L.; Guthrie, J. Peter

    2014-01-01

    This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz. PMID:24928188

  13. FreeSolv: a database of experimental and calculated hydration free energies, with input files.

    PubMed

    Mobley, David L; Guthrie, J Peter

    2014-07-01

    This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz .

  14. 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.

  15. Calculation of excess interfacial entropy, stress and energy for solid-liquid interfaces

    NASA Astrophysics Data System (ADS)

    Laird, Brian B.; Davidchack, Ruslan L.; Asta, Mark; Yang, Yang

    2009-03-01

    The solid-liquid interfacial free energy, γsl, governs a number of important phenomena, e.g., crystal nucleation and growth, and wetting. For an equilibrium crystal-melt interface, γsl can be calculated via simulation using thermodynamic integration or capillary fluctuations [Phys. Chem. B 109, 17802 (2005)]. The calculation of γsl away from coexistence requires the temperature and strain dependence of γsl, which can be determined from the excess interfacial entropy, ηsl, and stress tensor, τsl. We determine ηsl and τsl for a system of Lennard-Jones particles and for particles with an inverse-power interaction [φ(r) = ɛ(σ/r)^n] for n = 6, 8 (fcc and bcc) and 12, 20 (fcc). We determine ηsl and τsl for the (100), (110) and (111) orientations. We calculate ηsl using two methods, both using the Gibbs dividing surface defined so that the excess interfacial particle number is zero. In the first, we calculate ηsl from the temperature dependence of γsl, τsl and the number density, ρ, along the coexistence curve. In the second, we calculate the excess interfacial energy, esl, and use the equation γsl= esl- T ηsl. The results agree within estimated errors. One surprising observation is that ηsl, esl and τsl are significantly more anisotropic than γsl.

  16. Empirical free energy calculations: a blind test and further improvements to the method.

    PubMed

    Novotny, J; Bruccoleri, R E; Davis, M; Sharp, K A

    1997-05-02

    Empirical Gibbs functions estimate free energies of non-covalent reactions (deltaG) from atomic coordinates of reaction products (e.g. antibody-antigen complexes). The function previously developed by us has four terms that quantify the effects of hydrophobic, electrostatic and entropy changes (conformational, association) upon complexation. The function was used to calculate delta deltaG of ten lysozyme mutants affecting the stability of the HyHEL-10 antibody-lysozyme complex. The mutants were computer-modeled from the X-ray structure of the wild-type, and free energy calculations produced a correlation coefficient of 0.5 with the experimental delta deltaG data (average absolute error +/-3 kcal). The following changes were then introduced into the Gibbs function: (1) the hydrophobic force was made proportional to the molecular surface, as calculated by the GEPOL93 algorithm, with the scaling constant of 70 cal/mol/A2; (2) calculation of the electrostatics of binding was carried out by the finite difference Poisson-Boltzmann algorithm, which employed uniform grid charging, dielectric boundary smoothing and charge anti-aliasing; and (3) side-chain conformational entropy was estimated from the CONGEN sampling of torsional degrees of freedom. In the new calculations, correlation with experimental data improved to 0.6 or 0.8 if a single outlying mutant, K96M, was neglected. Analysis of the errors remaining in our calculations indicated that molecular mechanics-based modeling of the mutants, rather than the form of our amended Gibbs function, was the main factor limiting the accuracy of the free energy estimates.

  17. Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation.

    PubMed

    Genheden, Samuel; Ryde, Ulf

    2012-04-10

    We have studied whether the efficiency of alchemical free-energy calculations with the Bennett acceptance ratio method of protein-ligand binding energies can be improved by simulating only part of the protein. To this end, we solvated the full protein in a spherical droplet with a radius of 46 Å, surrounded by a vacuum. Then, we systematically reduced the size of the droplet and at the same time ignored protein residues that were outside the droplet. Radii of 40-15 Å were tested. Ten inhibitors of the blood clotting factor Xa were studied, and the results were compared to an earlier study in which the protein was solvated in a periodic box, showing complete agreement between the two sets of calculations within statistical uncertainty. We then show that the simulated system can be truncated down to 15 Å, without changing the calculated affinities by more than 0.5 kJ/mol on average (maximum difference of 1.4 kJ/mol). Moreover, we show that reducing the number of intermediate states in the calculations from eleven to three gave deviations that, on average, were only 0.5 kJ/mol (maximum of 1.4 kJ/mol). Together, these results show that truncation is an appropriate way to improve the efficiency of free-energy calculations for small mutations that preserve the net charge of the ligand. In fact, each calculation of a relative binding affinity requires only six simulations, each of which takes ∼15 CPU h of computation on a single processor.

  18. Calculation and modeling of the energy released in result of water freezing process (WFP)

    NASA Astrophysics Data System (ADS)

    Ghodsi Hassanabad, M.; Mehrbadi, A. Dehghani

    Process of water freezing in different pressures has been studied with appropriate accuracy and freezing phenomenon has been tested in variety conditions. The effects of pressure on volume change in constant volume and constant pressure have also been reviewed. Calculation of these changes has been done by using the finite difference. Therefore, experimental model has been designed and built to validate these calculations and this experimental model has been studied the power of freezing water during the freezing process in different conditions. Finally, the results were used to design a machine that has an ability to control the power of freezing and turn it into a new clean energy. In this machine, some water is frozen due to temperature difference that is exerting between day and night and energy which is produced by this reaction consumes for creating electrical energy. The amount of extractable power from the temperature difference between day and night were calculated in different temperatures. As an overall result, the most energy extracted from freezing in one cubic meters water with a temperature below -22 °C during the night is 12.8 MJ, the equivalent of using 356 W for 10 h.

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

    PubMed

    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 -1.03 kcal/mol at a geometry where H2O is the proton donor, HO-H...CH4, with the O-H-C angle of 165 degrees, while the secondary minimum, with an energy of -0.72 kcal/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 -1.06 kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653 K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.

  20. 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.

  1. 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.

  2. Collapsed cone convolution of radiant energy for photon dose calculation in heterogeneous media.

    PubMed

    Ahnesjö, A

    1989-01-01

    A method for photon beam dose calculations is described. The primary photon beam is raytraced through the patient, and the distribution of total radiant energy released into the patient is calculated. Polyenergetic energy deposition kernels are calculated from the spectrum of the beam, using a database of monoenergetic kernels. It is shown that the polyenergetic kernels can be analytically described with high precision by (A exp( -ar) + B exp( -br)/r2, where A, a, B, and b depend on the angle with respect to the impinging photons and the accelerating potential, and r is the radial distance. Numerical values of A, a, B, and b are derived and used to convolve energy deposition kernels with the total energy released per unit mass (TERMA) to yield dose distributions. The convolution is facilitated by the introduction of the collapsed cone approximation. In this approximation, all energy released into coaxial cones of equal solid angle, from volume elements on the cone axis, is rectilinearly transported, attenuated, and deposited in elements on the axis. Scaling of the kernels is implicitly done during the convolution procedure to fully account for inhomogeneities present in the irradiated volume. The number of computational operations needed to compute the dose with the method is proportional to the number of calculation points. The method is tested for five accelerating potentials; 4, 6, 10, 15, and 24 MV, and applied to two geometries; one is a stack of slabs of tissue media, and the other is a mediastinum-like phantom of cork and water. In these geometries, the EGS4 Monte Carlo system has been used to generate reference dose distributions with which the dose computed with the collapsed cone convolution method is compared. Generally, the agreement between the methods is excellent. Deviations are observed in situations of lateral charged particle disequilibrium in low density media, however, but the result is superior compared to that of the generalized Batho method.

  3. 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}.

  4. Multireference coupled-cluster calculation of the dissociation energy profile of triplet ketene

    NASA Astrophysics Data System (ADS)

    Ogihara, Yusuke; Yamamoto, Takeshi; Kato, Shigeki

    2011-07-01

    Triplet ketene exhibits a steplike structure in the experimentally observed photodissociation rates, but its mechanism is still unknown despite many theoretical efforts. Here we revisit this problem by calculating the potential energy profile of triplet ketene with the Adamowicz and Mukherjee multireference coupled-cluster (MRCC) theories. At the MRCCSD level, the imaginary frequency of the dissociation barrier is calculated to be about 300i cm-1, which is slightly smaller than the previous estimates but is still much greater than the expected maximum value for reproducing the observed steps (100i cm-1). This implies that other types of mechanisms (including nonadiabatic ones) may be more plausible for the observed steps.

  5. Surface energy calculation - metals with 1 and 2 delocalized electrons per atom

    NASA Astrophysics Data System (ADS)

    Halas, S.; Durakiewicz, T.; Joyce, J. J.

    2002-05-01

    In this paper we calculate surface energy (SE) of monovalent, divalent and some trivalent metals. For these metals for which SE can be solely expressed by dimensionless Wigner-Seitz density parameter, rs, of delocalized electrons: SE=C 1r s-5+C 2r s-3.5-C 3r s-4, where constants C1, C2 and C3 have been calculated on the basis of Sommerfeld's free electron and surface plasma models. Excellent agreement with experimental data was obtained. On the basis of our model SE values for Fr and Ra have been predicted as well.

  6. 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.

  7. Modeling reaction pathways of low energy particle deposition on thiophene via ab initio calculations

    NASA Astrophysics Data System (ADS)

    Crenshaw, Jasmine D.; Phillpot, Simon R.; Iordanova, Nedialka; Sinnott, Susan B.

    2011-07-01

    Chemical reactions of thiophene with organic molecules are of interest to modify thermally deposited coatings of conductive polymers. Here, energy barriers for reactions involving thiophene and small hydrocarbon radicals are identified. Enthalpies of formation involving reactants are also calculated using the B3LYP, BMK, and B98 hybrid functionals within the G AUSSIAN03 program. Experimental values, G3, and CBS-QB3 calculations are used as standards, due to their accurate thermochemistry parameters. The BMK functional is found to perform best for the selected organic molecules. These results provide insights into the reactivity of several polymerization and deposition processes.

  8. First-principles calculations of free energies of unstable phases: the case of fcc W.

    PubMed

    Ozolins, V

    2009-02-13

    Ab initio molecular dynamics simulations are used to solve the long-standing problem of calculating the free energies of unstable phases, such as fcc W. We find that fcc W is mechanically unstable with respect to long-wavelength shear at all temperatures considered (T>2500 K), while the short-wavelength phonon modes are anharmonically stabilized. The calculated fcc-bcc enthalpy and entropy differences at T=3500 K (308 meV and 0.74k_{B} per atom, respectively) agree well with the recent values derived from analysis of experimental data.

  9. 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.

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

    PubMed

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

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange.

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

    PubMed

    Ceriotti, Michele; Manolopoulos, David E

    2012-09-07

    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.

  12. 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

  13. New parametrization of Skyrme's interaction for regularized multireference energy density functional calculations

    NASA Astrophysics Data System (ADS)

    Washiyama, K.; Bennaceur, K.; Avez, B.; Bender, M.; Heenen, P.-H.; Hellemans, V.

    2012-11-01

    Background: Symmetry restoration and configuration mixing in the spirit of the generator coordinate method based on energy density functionals have become widely used techniques in low-energy nuclear structure physics. Recently, it has been pointed out that these techniques are ill defined for standard Skyrme functionals, and a regularization procedure has been proposed to remove the resulting spuriosities from such calculations. This procedure imposes an integer power of the density for the density-dependent terms of the functional. At present, only dated parametrizations of the Skyrme interaction fulfill this condition.Purpose: To construct a set of parametrizations of the Skyrme energy density functional for multireference energy density functional calculations with regularization using the state-of-the-art fitting protocols.Method: The parametrizations were adjusted to reproduce ground-state properties of a selected set of doubly magic nuclei and properties of nuclear matter. Subsequently, these parameter sets were validated against properties of spherical and deformed nuclei.Results: Our parameter sets successfully reproduce the experimental binding energies and charge radii for a wide range of singly magic nuclei. Compared to the widely used SLy5 and to the SIII parametrization that has integer powers of the density, a significant improvement of the reproduction of the data is observed. Similarly, a good description of the deformation properties at A˜80 was obtained.Conclusions: We have constructed new Skyrme parametrizations with integer powers of the density and validated them against a broad set of experimental data for spherical and deformed nuclei. These parametrizations are tailor-made for regularized multireference energy density functional calculations and can be used to study correlations beyond the mean field in atomic nuclei.

  14. Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution.

    PubMed

    Fogarty, Heather A; Ottosson, Henrik; Michl, Josef

    2006-12-21

    The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.

  15. A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies.

    PubMed

    Cave-Ayland, Christopher; Skylaris, Chris-Kriton; Essex, Jonathan W

    2017-02-14

    Hybrid free energy methods allow estimation of free energy differences at the quantum mechanics (QM) level with high efficiency by performing sampling at the classical mechanics (MM) level. Various approaches to allow the calculation of QM corrections to classical free energies have been proposed. The single step free energy perturbation approach starts with a classically generated ensemble, a subset of structures of which are postprocessed to obtain QM energies for use with the Zwanzig equation. This gives an estimate of the free energy difference associated with the change from an MM to a QM Hamiltonian. Owing to the poor numerical properties of the Zwanzig equation, however, recent developments have produced alternative methods which aim to provide access to the properties of the true QM ensemble. Here we propose an approach based on the resampling of MM structural ensembles and application of a Monte Carlo acceptance test which in principle, can generate the exact QM ensemble or intermediate ensembles between the MM and QM states. We carry out a detailed comparison against the Zwanzig equation and recently proposed non-Boltzmann methods. As a test system we use a set of small molecule hydration free energies for which hybrid free energy calculations are performed at the semiempirical Density Functional Tight Binding level. Equivalent ensembles at this level of theory have also been generated allowing the reverse QM to MM perturbations to be performed along with a detailed analysis of the results. Additionally, a previously published nucleotide base pair data set simulated at the QM level using ab initio molecular dynamics is also considered. We provide a strong rationale for the use of the Monte Carlo Resampling and non-Boltzmann approaches by showing that configuration space overlaps can be estimated which provide useful diagnostic information regarding the accuracy of these hybrid approaches.

  16. Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations.

    PubMed

    Shen, Mingyun; Zhou, Shunye; Li, Youyong; Pan, Peichen; Zhang, Liling; Hou, Tingjun

    2013-03-01

    Rho-associated protein kinases (ROCK1 and ROCK2) are promising targets for a number of diseases, including cardiovascular disorders, nervous system diseases, cancers, etc. Recently, we have successfully identified a ROCK1 inhibitor (1) with the triazine core. In order to gain a deeper insight into the microscopic binding of this inhibitor with ROCK1 and design derivatives with improved potency, the interactions between ROCK1 and a series of triazine/pyrimidine-based inhibitors were studied by using an integrated computational protocol that combines molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and binding energy decomposition analysis. First, three docking protocols, rigid receptor docking, induced fit docking, QM-polarized ligand docking, were used to determine the binding modes of the studied inhibitors in the active site of ROCK1. The results illustrate that rigid receptor docking achieves the best performance to rank the binding affinities of the studied inhibitors. Then, based on the predicted structures from molecular docking, MD simulations and MM/GBSA free energy calculations were employed to determine the dynamic binding process and compare the binding modes of the inhibitors with different activities. The binding free energies predicted by MM/GBSA are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. In addition, the residue-inhibitor interaction spectra were obtained by the MM/GBSA free energy decomposition analysis, and the important residues for achieving strong binding were highlighted, which affords important guidance for the rational design of novel ROCK inhibitors. Finally, a variety of derivatives of inhibitor 1 were designed and four of them showed promising potency according to the predictions. We expect that our study can provide significant insight into the

  17. 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

  18. Energy Consumption Calculation of Permanent Magnet Synchronous Motor for Railway Vehicle Traction Using Equivalent Circuit

    NASA Astrophysics Data System (ADS)

    Kondo, Minoru; Kawamura, Junya; Terauchi, Nobuo

    We are developing a new high performance traction motor for railway vehicle using interior permanent magnet synchronous motor (IPMSM) and expecting it can reduce energy consumption. To estimate the losses and energy consumption of IPMSM, a simple motor model is needed. In this paper, We propose a simple equivalent circuit and loss model for IPMSM, the constants of which can be obtained from several simple test results. The calculation results using them show that the total loss of the IPMSM becomes about 60% of that of the induction motor when used as a traction motor for a typical commuter train.

  19. 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.

  20. Calculated self-energy contributions for an ns valence electron using the multiple-commutator method

    NASA Astrophysics Data System (ADS)

    Labzowsky, Leonti; Goidenko, Igor; Tokman, Maria; Pyykkö, Pekka

    1999-04-01

    The self-energy (SE) correction is evaluated for a single valence ns electron of heavy and superheavy atoms with n up to 8 and the nuclear charge Z up to 119. The recently developed approach based on the commutator expansion is employed. Various Dirac-Slater one-electron local potentials with extended nuclei are used. The Lamb shifts were calculated by adding the average values of the Uehling potential to the SE contributions. The results confirm the earlier estimates for the quantum electrodynamical effects on the valence energies of heavy and superheavy atoms.

  1. A New Internal Energy Calculation for the HELP Code and Its Implications to Conical Shaped Charge Simulations

    DTIC Science & Technology

    1979-06-01

    TECHNICAL REPORT ARBRL-TR-02168 d’ A NEtJ INTFRNAL ENERGY CALCULATION FOR THE HELP CODE AND ITS IMPLICATIONS TO CONICAL SHAPED CHARGE SIMULATIONS...Energy Calculation for the HELP Code and Its Implications to Conical Shaped Cha Simulat.ions S. PERFORMING ORG. REPORT NUMBER 7- AUTHOIR,&) 8. CONTRACT...terms of the order of the truncation errrlr in the kinetic energy calculation . A corrcc- tion is given and qualitative the.-mal agreement is achieved, for

  2. New Method for Calculating the Potential Energy of Deformed Nuclei within the Liquid-Drop Model

    SciTech Connect

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

    2004-11-01

    The method that we previously developed for going over from double volume integrals to double surface integrals in calculating the Coulomb energy of nuclei that have a sharp surface is generalized to the case of nuclei where the range of nuclear forces is finite and where the nuclear surface is diffuse. New formulas for calculating the Coulomb and the nuclear energy of deformed nuclei are obtained within this approach. For a spherically symmetric nucleus, in which case there is an analytic solution to the problem in question, the results are compared with those that are quoted in the literature, and it is shown that the respective results coincide identically. A differential formulation of the method developed previously by Krappe, Nix, and Sierk for going over from double volume integrals to double surface integrals is proposed here on the basis of the present approach.

  3. Estimation of nitrogen ion energy calculated using distribution for nitrogen in Si implanted by PBII

    NASA Astrophysics Data System (ADS)

    Tanaka, T.; Watanabe, S.; Takagi, T.

    2006-01-01

    Plasma-based ion implantation (PBII) using N2 gas is examined as a sterilization technique for three-dimensional targets. The application of a pulsed negative voltage (5 μs pulse width, 300 pulses/s, -800 V to -13 kV) at an N2 gas pressure of 2.4 Pa is shown to reduce the number of Bacillus pumilus survivors by up to 105 times after just 5 min of exposure. The energy of nitrogen ions is calculated based on the depth profile of nitrogen concentration in Si implanted by PBII, and it is revealed that the actual nitrogen ion energy is much lower than that calculated based on the voltage applied during processing.

  4. Electronic Couplings for Resonance Energy Transfer from CCSD Calculations: From Isolated to Solvated Systems.

    PubMed

    Caricato, Marco; Curutchet, Carles; Mennucci, Benedetta; Scalmani, Giovanni

    2015-11-10

    Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study of resonance energy transfer (RET). However, most of these calculations rely on approximate QM methods due to the computational limitations imposed by the size of typical donor-acceptor systems. In this work, we present a novel implementation that allows computing electronic couplings at the coupled cluster singles and doubles (CCSD) level of theory. Solvent effects are also taken into account through the polarizable continuum model (PCM). As a test case, we use a dimer of indole, a common model system for tryptophan, which is routinely used as an intrinsic fluorophore in Förster resonance energy transfer studies. We consider two bright π → π* states, one of which has charge transfer character. Lastly, the results are compared with those obtained by applying TD-DFT in combination with one of the most popular density functionals, B3LYP.

  5. 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.

  6. 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.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    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.

  9. Methods for calculating dietary energy density in a nationally representative sample.

    PubMed

    Vernarelli, Jacqueline A; Mitchell, Diane C; Rolls, Barbara J; Hartman, Terryl J

    2013-01-01

    There has been a growing interest in examining dietary energy density (ED, kcal/g) as it relates to various health outcomes. Consuming a diet low in ED has been recommended in the 2010 Dietary Guidelines, as well as by other agencies, as a dietary approach for disease prevention. Translating this recommendation into practice; however, is difficult. Currently there is no standardized method for calculating dietary ED; as dietary ED can be calculated with foods alone, or with a combination of foods and beverages. Certain items may be defined as either a food or a beverage (e.g., meal replacement shakes) and require special attention. National survey data are an excellent resource for evaluating factors that are important to dietary ED calculation. The National Health and Nutrition Examination Survey (NHANES) nutrient and food database does not include an ED variable, thus researchers must independently calculate ED. The objective of this study was to provide information that will inform the selection of a standardized ED calculation method by comparing and contrasting methods for ED calculation. The present study evaluates all consumed items and defines foods and beverages based on both USDA food codes and how the item was consumed. Results are presented as mean EDs for the different calculation methods stratified by population demographics (e.g. age, sex). Using United State Department of Agriculture (USDA) food codes in the 2005-2008 NHANES, a standardized method for calculating dietary ED can be derived. This method can then be adapted by other researchers for consistency across studies.

  10. Precise calculations in simulations of the interaction of low energy neutrons with nano-dispersed media

    SciTech Connect

    Artem’ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.

    2016-01-15

    We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2–5 nm and for neutron energies 3 × 10{sup -7}–10{sup -3} eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.

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

    PubMed

    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.

  12. 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.

  13. Precise calculations in simulations of the interaction of low energy neutrons with nano-dispersed media

    NASA Astrophysics Data System (ADS)

    Artem'ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.

    2016-01-01

    We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2-5 nm and for neutron energies 3 × 10-7-10-3 eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.

  14. 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.

  15. 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.

  16. Fully Relativistic Calculations on the Potential Energy Surfaces of the Lowest 23 States of Molecular Chlorine

    SciTech Connect

    Luiz Guilherme M. de Macedo; de Jong, Wibe A.

    2008-01-24

    The electronic structure and spectroscopic properties (Re, ωexe, βe, Te ) of the ground state and the 22 lowest excited states of chlorine molecule were studied within a four component relativistic framework using the MOLFDIR program package. The potential energy curves of all possible 23 covalent states were calculated using relativistic complete open shell configuration interaction (COSCI) approach. In addition, four component multi-reference configuration interaction with singles and doubles excitations (MRCISD) calculations were performed in order to infer the effects due to dynamical correlation in vertical excitations. The calculated properties are in good agreement with the available experimental data.

  17. 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.

  18. Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculation.

    PubMed

    Pak, Alireza; Lesage, Denis; Gimbert, Yves; Vékey, Károly; Tabet, Jean-Claude

    2008-04-01

    The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values () carried by desolvated ions. These mean internal energy values seem to be slightly dependent on the size of the studied ion. ESI mass spectra and CID spectra were then simulated using the MassKinetics software to propose an empirical equation for the mean internal energy () versus cone voltage (V(c)) for different source temperatures (T): < E(int) > = [405 x 10(-6) - 480 x 10(-9) (DOF)] V(c)T + E(therm)(T). In this equation, the E(therm)(T) parameter is the mean internal energy due to the source temperature at 0 V(c).

  19. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

    PubMed Central

    Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew

    2013-01-01

    Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license. PMID:24185531

  20. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

    SciTech Connect

    Larriba, Carlos Hogan, Christopher J.

    2013-10-15

    The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas

  1. Ab initio calculation of optical constants from visible to x-ray energies

    NASA Astrophysics Data System (ADS)

    Prange, M. P.; Rivas, G.; Ankudinov, A. L.; Rehr, J. J.

    2004-03-01

    We present a semi-automated approach for ab initio calculations of optical constants of materials from the visible to the hard x-ray energies. The approach is based on a generalization of the real space Green's formalism implemented in the FEFF8 spectroscopy code to include optical spectra. The method includes self-consistent potentials, core-hole and self-energy effects, inelastic losses and a full- or high order multiple-scattering. The procedure is based on calculations of the imaginary part of the dielectric function ɛ2 summed over all edges, from which other optical constants are derived using Kramers-Kronig transforms and analytical relations. These constants include the complex index of refraction, the real part of the dielectric function, and energy loss spectra. In contrast to standard atomic tables, the calculations include solid-state corrections, such as fine structure, Debye-Waller factors, lifetime broadening, etc. Typical results for several materials are presented and compared with experiment.

  2. Total energy magnetic anisotropy calculations for free-standing transition-metal monolayers.

    NASA Astrophysics Data System (ADS)

    Shick, A. B.; Blügel, S.

    1997-03-01

    A self-consistent relativistic spin-polarized version of the full potential linearized augmented planewave (FLAPW) method (E. Wimmer, H. Krakauer, M. Weinert and A.J. Freeman, Phys. Rev. B 24), 864 (1981). is developed on the basis of a second variation treatment of the spin-orbit (SOC) interaction. The method is applied to the study of the magnetic anisotropy energy (MAE) of free-standing transition-metal monolayers (Fe, Rh, Ir). The total energy results are compared with different theoretical models used to calculate the MAE, e.g. those based on the "local force" theorem for SOC interaction or rotation of the magnetization direction. The anisotropy of the orbital magnetic moment is calculated to be in qualitative agreement with previous theoretical predictions. For Fe and Rh monolayers, the self-consistently determined MAE and the results based on the "local force" theorem are in good agreement, but the approaches fail to agree for the case of Ir. On the basis of self-consistent total energy calculations we show that an Ir monolayer shows a large in-plane magnetic anisotropy and a large anisotropy for the spin and orbital magnetic moments.

  3. 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.

  4. 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.

  5. How to calculate financial information for home energy raters, lenders and savvy home buyers

    SciTech Connect

    Vieira, R.K.; Cummings, J.E.; Fairey, P.W.; Hannani, K.

    1998-07-01

    Home ratings and energy-efficient mortgages are becoming the key vehicles in the process of moving more buyers and builders to energy efficiency that exceed minimum code limits. The energy-efficient mortgages industry requires both the projected savings of energy-conservation measures and other key financial information for builders, realtors, buyers and lenders. This paper presents the methodology used by the one state's home rating software for calculating and reporting key financial information and for selecting the most cost-effective upgrades automatically through an optimization process. Historically, many statistics have been calculated based on two pieces of information--the cost of the energy conservation measures and the projected savings from the measures. Unfortunately, when attempting to upgrade an existing or code-minimum new home up to more efficient level, such as EPA's Energy Star Home program level, a number of measures interact. The savings of a package of upgrades can be determined, but a methodology was required for attributing the savings due to each measure as required for certain national mortgage products. When examining the cash flow of measures there are a host of other factors - the amount of the upgrade that will be borrowed, the income tax rate used for deducting interest, any increase to the property that will result in higher property tax and insurance rates and the maintenance on the upgrade. The reporting of the financial analysis is of significant importance to the lending industry. This paper presents many report options contained in the Florida software, Energy Gauge, and its ability to meet the requirements of HUD, Fannie Mae, and the national HERS guidelines.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

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

    2016-09-01

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

  8. Calculation of Coster-Kronig energies and transition probabilities by linear interpolation method

    NASA Astrophysics Data System (ADS)

    Trivedi, R. K.; Shrivastava, Uma; Hinge, V. K.; Shrivastava, B. D.

    2016-10-01

    The X-ray emission spectrum consists of two types of spectral lines heaving different origins. The diagram lines originate because of transitions in singly ionized atom, while the nondiagram lines or satellites originate due to transitions in doubly or multiply ionized atom. The X- ray satellite energy is the difference between the energies of initial and final states which are both doubly or multiply ionized. Thus, the satellite has a different energy than the energy of the X-ray diagram line. Once the singly ionized state has been created, it is the probability of a particular subsequent process that will lead to the formation of two-hole state. The single hole may get converted through a Coster-Kronig transition to a double hole state. The probability of formation of double hole state via this process is written as σ.σ', where σ is the probability of creation of single hole state and σ' is the probability of the Coster-Kronig transition. The value of σ' can be taken from the tables of Chen et al. [1], who have presented the calculated values of σ' for almost all possible Coster-Kronig transitions in some elements. The energies of the satellites can be calculated by using the tables of Parente et al. [2]. Both of these tables do not give values for all the elements. The aim of the present work is to show that the values for other elements, for which values are not listed by Chen et al. and Parente et al., can be calculated by linear interpolation method.

  9. 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

  10. 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

  11. 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…

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    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, 10-23m3 ), 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.

  14. 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.

  15. QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.

    PubMed

    Martí, Sergio; Moliner, Vincent; Tuñón, Iñaki; Williams, Ian H

    2003-02-07

    Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P calculations using the GRACE program, with full gradient relaxation of the position of > 5200 atoms for the enzymic simulations, and with a box containing 711 water molecules for the corresponding reaction in aqueous solution. Comparison of these results, and of gas phase calculations, with experimental data has shown that the chemical rearrangement is largely rate-determining for the enzyme mechanism. Inclusion of the chorismate conformational pre-equilibrium step in the modelled kinetic scheme leads to better agreement between recent experimental data and theoretical predictions. These results provide new information on an important enzymatic transformation, and the key factors responsible for the kinetics of its molecular mechanism are clarified. Treatment of the enzyme and/or solvent environment by means of a large and flexible model is absolutely essential for prediction of kinetic isotope effects.

  16. Raman active high energy excitations in URu2Si2

    NASA Astrophysics Data System (ADS)

    Buhot, Jonathan; Gallais, Yann; Cazayous, Maximilien; Sacuto, Alain; Piekarz, Przemysław; Lapertot, Gérard; Aoki, Dai; Méasson, Marie-Aude

    2017-02-01

    We have performed Raman scattering measurements on URu2Si2 single crystals on a large energy range up to ∼1300 cm-1 and in all the Raman active symmetries as a function of temperature down to 15 K. A large excitation, active only in the Eg symmetry, is reported. It has been assigned to a crystal electric field excitation on the Uranium site. We discuss how this constrains the crystal electric field scheme of the Uranium ions. Furthermore, three excitations in the A1g symmetry are observed. They have been associated to double Raman phonon processes consistently with ab initio calculations of the phonons dispersion.

  17. 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.

  18. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

    PubMed

    Miao, Yinglong; McCammon, J Andrew

    Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

  19. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.

    PubMed

    Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew

    2011-06-02

    The independent trajectory thermodynamic integration (IT-TI) approach (Lawrenz et. al J. Chem. Theory. Comput. 2009, 5:1106-1116(1)) for free energy calculations with distributed computing is employed to study two distinct cases of protein-ligand binding: first, the influenza surface protein N1 neuraminidase bound to the inhibitor oseltamivir, and second, the M. tuberculosis enzyme RmlC complexed with the molecule CID 77074. For both systems, finite molecular dynamics (MD) sampling and varied molecular flexibility give rise to IT-TI free energy distributions that are remarkably centered on the target experimental values, with a spread directly related to protein, ligand, and solvent dynamics. Using over 2 μs of total MD simulation, alternative protocols for the practical, general implementation of IT-TI are investigated, including the optimal use of distributed computing, the total number of alchemical intermediates, and the procedure to perturb electrostatics and van der Waals interactions. A protocol that maximizes predictive power and computational efficiency is proposed. IT-TI outperforms traditional TI predictions and allows a straightforward evaluation of the reliability of free energy estimates. Our study has broad implications for the use of distributed computing in free energy calculations of macromolecular systems.

  20. 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.

  1. 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

  2. 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…

  3. 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.…

  4. Energy gap of extended states in SiC-doped graphene nanoribbon: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Liu, Xiaoshi; Wu, Yong; Li, Zhongyao; Gao, Yong

    2017-04-01

    The energy gap of extended states in zigzag graphene nanoribbons (ZGNRs) was examined on the basis of density-functional theory. In isolated ZGNRs, the energy gap is inversely proportional to the width of ribbon. It agrees well with the results from the Dirac equation in spin-unpolarized ZGNRs, although the considered ZGNRs have spin-polarized edges. However, the energy gap in SiC-doped ZGNRs cannot be modeled by effective width approximation. The doping also lifts the spin-degenerate of edge states and results in a metallic-like band structure near the Fermi level in SiC-doped ZGNRs. Our calculations may be helpful for understanding the origin of the reported single-channel ballistic transport in epitaxial graphene nanoribbons.

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

    DOE PAGES

    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

  6. 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.

  7. First-Principles Approach to Calculating Energy Level Alignment at Aqueous Semiconductor Interfaces

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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 the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.

  8. [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.

  9. 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.

  10. Including the relativistic kinetic energy in a spline-augmented plane-wave band calculation

    SciTech Connect

    Fehrenbach, G.M.; Schmidt, G.

    1997-03-01

    The first-order relativistic correction to the kinetic energy of an electron, the mass-velocity term, is not bounded from below. It can, therefore, not be used within a variational framework. To overcome this deficiency we developed a method to include the entire relativistic kinetic energy {radical}(p{sup 2}c{sup 2}+m{sub 0}{sup 2}c{sup 4}){minus}m{sub 0}c{sup 2} in a spline-augmented plane-wave band calculation. The first results for silver are quite promising, especially for d and p states: The analysis of the energies of the core states as well as of the valence band structure suggests that the energies of d bands are reproduced within 1 mRy. However, the combination of the relativistic kinetic energy with the Darwin term leads to energies which are too low for s-like valence states by 10 mRy. Therefore, the s and d valence band complex is spread out and the Fermi level is lowered by the same amount as the s states. We expect to overcome these deficiencies in future investigations by using a alternative form of the relativistic potential correction along the lines proposed by Douglas and Kroll. {copyright} {ital 1997} {ital The American Physical Society}

  11. Calculations of the free energy of dislocation defects in lamellae forming diblock copolymers using thermodynamic integration

    NASA Astrophysics Data System (ADS)

    Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

    2016-04-01

    State-of-the-art directed self-assembly (DSA) of block copolymer (BCP) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication. The defect free energy of a dislocation pair or jog defect, one of the most common defects found in BCP-DSA, is calculated via thermodynamic integration using a coarse-grained molecular dynamics model as a function of χ and the degree of polymerization (N). It is found that χN is not the best predictor of defect free energy and that a single χN value can yield vastly different free energies when χ and N are different. Defect free energy was highly dependent on defect location relative to the underlayer, and free energy differences ˜100 kT were found among the three possible defect locations on a 1:3 guiding pattern. It was found that increasing molar mass dispersity (Ð) significantly reduced defect free energy. Extrapolating from Ð up to 1.5 suggests that the defect will occur in equal proportions to the defect free state at a Ð of around 1.6 for this system. It was found that long chains tended to concentrate near the defect and stabilize the defect.

  12. 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.

  13. Calculation of electron affinities of polycyclic aromatic hydrocarbons and solvation energies of their radical anion.

    PubMed

    Betowski, Leon D; Enlow, Mark; Riddick, Lee; Aue, Donald H

    2006-11-30

    Electron affinities (EAs) and free energies for electron attachment (DeltaGo(a,298K)) have been directly calculated for 45 polynuclear aromatic hydrocarbons (PAHs) and related molecules by a variety of theoretical methods, with standard regression errors of about 0.07 eV (mean unsigned error = 0.05 eV) at the B3LYP/6-31 + G(d,p) level and larger errors with HF or MP2 methods or using Koopmans' Theorem. Comparison of gas-phase free energies with solution-phase reduction potentials provides a measure of solvation energy differences between the radical anion and neutral PAH. A simple Born-charging model approximates the solvation effects on the radical anions, leading to a good correlation with experimental solvation energy differences. This is used to estimate unknown or questionable EAs from reduction potentials. Two independent methods are used to predict DeltaGo(a,298K) values: (1) based upon DFT methods, or (2) based upon reduction potentials and the Born model. They suggest reassignments or a resolution of conflicting experimental EAs for nearly one-half (17 of 38) of the PAH molecules for which experimental EAs have been reported. For the antiaromatic molecules, 1,3,5-tri-tert-butylpentalene and the dithia-substituted cyclobutadiene 1, the reduction potentials lead to estimated EAs close to those expected from DFT calculations and provide a basis for the prediction of the EAs and reduction potentials of pentalene and cyclobutadiene. The Born model has been used to relate the electrostatic solvation energies of PAH and hydrocarbon radical anions, and spherical halide anions, alkali metal cations, and ammonium ions to effective ionic radii from DFT electron-density envelopes. The Born model used for PAHs has been successfully extended here to quantitatively explain the solvation energy of the C60 radical anion.

  14. Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor.

    PubMed

    Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

    2011-01-01

    We report a Quantum mechanics/Molecular Mechanics-Poisson-Boltzmann/ Surface Area (QM/MM-PB/SA) method to calculate the binding free energy of c-Abl human tyrosine kinase by combining the QM and MM principles where the ligand is treated quantum mechanically and the rest of the receptor by classical molecular mechanics. To study the role of entropy and the flexibility of the protein ligand complex in a solvated environment, molecular dynamics calculations are performed using a hybrid QM/MM approach. This work shows that the results of the QM/MM approach are strongly correlated with the binding affinity. The QM/MM interaction energy in our reported study confirms the importance of electronic and polarization contributions, which are often neglected in classical MM-PB/SA calculations. Moreover, a comparison of semi-empirical methods like DFTB-SCC, PM3, MNDO, MNDO-PDDG, and PDDG-PM3 is also performed. The results of the study show that the implementation of a DFTB-SCC semi-empirical Hamiltonian that is derived from DFT gives better results than other methods. We have performed such studies using the AMBER molecular dynamic package for the first time. The calculated binding free energy is also in agreement with the experimentally determined binding affinity for c-Abl tyrosine kinase complex with Imatinib.Electronic supplementary material The online version of this article (doi:10.1007/s10867-010-9199-z) contains supplementary material, which is available to authorized users.

  15. 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.

  16. An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

    NASA Astrophysics Data System (ADS)

    Woods, Christopher J.; Manby, Frederick R.; Mulholland, Adrian J.

    2008-01-01

    The combination of quantum mechanics (QM) with molecular mechanics (MM) offers a route to improved accuracy in the study of biological systems, and there is now significant research effort being spent to develop QM/MM methods that can be applied to the calculation of relative free energies. Currently, the computational expense of the QM part of the calculation means that there is no single method that achieves both efficiency and rigor; either the QM/MM free energy method is rigorous and computationally expensive, or the method introduces efficiency-led assumptions that can lead to errors in the result, or a lack of generality of application. In this paper we demonstrate a combined approach to form a single, efficient, and, in principle, exact QM/MM free energy method. We demonstrate the application of this method by using it to explore the difference in hydration of water and methane. We demonstrate that it is possible to calculate highly converged QM/MM relative free energies at the MP2/aug-cc-pVDZ/OPLS level within just two days of computation, using commodity processors, and show how the method allows consistent, high-quality sampling of complex solvent configurational change, both when perturbing hydrophilic water into hydrophobic methane, and also when moving from a MM Hamiltonian to a QM/MM Hamiltonian. The results demonstrate the validity and power of this methodology, and raise important questions regarding the compatibility of MM and QM/MM forcefields, and offer a potential route to improved compatibility.

  17. 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.

  18. Vibrational Energy Levels via Finite-Basis Calculations Using a Quasi-Analytic Form of the Kinetic Energy.

    PubMed

    Vázquez, Juana; Harding, Michael E; Stanton, John F; Gauss, Jürgen

    2011-05-10

    A variational method for the calculation of low-lying vibrational energy levels of molecules with small amplitude vibrations is presented. The approach is based on the Watson Hamiltonian in rectilinear normal coordinates and characterized by a quasi-analytic integration over the kinetic energy operator (KEO). The KEO beyond the harmonic approximation is represented by a Taylor series in terms of the rectilinear normal coordinates around the equilibrium configuration. This formulation of the KEO enables its extension to arbitrary order until numerical convergence is reached for those states describing small amplitude motions and suitably represented with a rectilinear system of coordinates. A Gauss-Hermite quadrature grid representation of the anharmonic potential is used for all the benchmark examples presented. Results for a set of molecules with linear and nonlinear configurations, i.e., CO2, H2O, and formyl fluoride (HFCO), illustrate the performance of the method and the versatility of our implementation.

  19. 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

  20. 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

  1. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.

    PubMed

    Pham, Tri T; Shirts, Michael R

    2011-07-21

    Improving the efficiency of free energy calculations is important for many biological and materials design applications, such as protein-ligand binding affinities in drug design, partitioning between immiscible liquids, and determining molecular association in soft materials. We show that for any pair potential, moderately accurate estimation of the radial distribution function for a solute molecule is sufficient to accurately estimate the statistical variance of a sampling along a free energy pathway. This allows inexpensive analytical identification of low statistical error free energy pathways. We employ a variety of methods to estimate the radial distribution function (RDF) and find that the computationally cheap two-body "dilute gas" limit performs as well or better than 3D-RISM theory and other approximations for identifying low variance free energy pathways. With a RDF estimate in hand, we can search for pairwise interaction potentials that produce low variance. We give an example of a search minimizing statistical variance of solvation free energy over the entire parameter space of a generalized "soft core" potential. The free energy pathway arising from this optimization procedure has lower curvature in the variance and reduces the total variance by at least 50% compared to the traditional soft core solvation pathway. We also demonstrate that this optimized pathway allows free energies to be estimated with fewer intermediate states due to its low curvature. This free energy variance optimization technique is generalizable to solvation in any homogeneous fluid and for any type of pairwise potential and can be performed in minutes to hours, depending on the method used to estimate g(r).

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Is the peptide bond formation activated by Cu(2+) interactions? Insights from density functional calculations.

    PubMed

    Rimola, A; Rodríguez-Santiago, L; Ugliengo, P; Sodupe, M

    2007-05-24

    The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.

  7. 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

  8. Variational Monte Carlo calculations for the binding energy of sub. Lambda. Lambda. sup 31 Si

    SciTech Connect

    Ahsan, M.H. ); Kaykobad, M. ); Ali, S. )

    1991-01-01

    The binding energy of the {Lambda}{Lambda} hypernucleus {sub {Lambda}{Lambda}}{sup 31}Si has been calculated variationally with a {sup 28}Si+{ital n}+{Lambda}+{Lambda} four-body model. The integrations have been carried out with the help of a Monte Carlo technique. Three different types of {Lambda}-{Lambda} and {Lambda}-{ital N} potentials have been used. {ital n}-{sup 28}Si and {Lambda}-{sup 28}Si potentials have been generated by folding the {ital N}-{ital N} and {Lambda}-{ital N} potentials into the harmonic-oscillator shell-model density distribution of {sup 28}Si. The calculated values of the binding energy for the three different potentials are 40.19, 46.30, and 39.90 MeV. These values are compared with the reported experimental value of 38.2{plus minus}6.3 MeV. The dependence of the binding energy on the depth of the {Lambda}-{Lambda} interaction has also been investigated.

  9. Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations.

    PubMed

    Slavícek, Petr; Winter, Bernd; Faubel, Manfred; Bradforth, Stephen E; Jungwirth, Pavel

    2009-05-13

    Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.

  10. Configurational space discretization and free energy calculation in complex molecular systems.

    PubMed

    Wang, Kai; Long, Shiyang; Tian, Pu

    2016-03-14

    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.

  11. 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.

  12. Higher energy states in the CO dimer: millimeter-wave spectra and rovibrational calculations.

    PubMed

    Surin, Leonid A; Fourzikov, Dmitri N; Giesen, Thomas F; Schlemmer, Stephan; Winnewisser, Gisbert; Panfilov, Victor A; Dumesh, Boris S; Vissers, Gé W M; van der Avoird, Ad

    2007-12-13

    New extensive millimeter-wave measurements of the 12C16O dimer have been made, and more than 300 new spectral transitions have been observed in the frequency range 81-135 GHz. A joint analysis of these and previous millimeter-wave data yielded the precise location of 33 new energy levels of A+ symmetry and 20 levels of A- symmetry. These energy levels are located at 8-18 cm(-1) above the zero-point level. Some of them belong to already known stacks, and others make up 9 new stacks of the dimer. Newly determined stacks have K=0, 1, and, for the first time, 2, where K is the projection of the total angular momentum on the intermolecular axis. The energy levels from accompanying rovibrational calculations with the use of a recently developed hybrid CCSD(T)/DFT-SAPT potential are in very good agreement with experiment. Analysis of the calculated wave functions revealed that two new stacks of A+ symmetry with K=2 correspond to overall rotation of the dimer while the other newly observed stacks belong to the geared bend overtone modes. The ground vibrational states of the two "isomers" found are more or less localized at the two minima in the potential surface, whereas all the geared bend excited states show a considerable amount of delocalization.

  13. A simplified analytical dose calculation algorithm accounting for tissue heterogeneity for low-energy brachytherapy sources

    NASA Astrophysics Data System (ADS)

    Mashouf, Shahram; Lechtman, Eli; Beaulieu, Luc; Verhaegen, Frank; Keller, Brian M.; Ravi, Ananth; Pignol, Jean-Philippe

    2013-09-01

    The American Association of Physicists in Medicine Task Group No. 43 (AAPM TG-43) formalism is the standard for seeds brachytherapy dose calculation. But for breast seed implants, Monte Carlo simulations reveal large errors due to tissue heterogeneity. Since TG-43 includes several factors to account for source geometry, anisotropy and strength, we propose an additional correction factor, called the inhomogeneity correction factor (ICF), accounting for tissue heterogeneity for Pd-103 brachytherapy. This correction factor is calculated as a function of the media linear attenuation coefficient and mass energy absorption coefficient, and it is independent of the source internal structure. Ultimately the dose in heterogeneous media can be calculated as a product of dose in water as calculated by TG-43 protocol times the ICF. To validate the ICF methodology, dose absorbed in spherical phantoms with large tissue heterogeneities was compared using the TG-43 formalism corrected for heterogeneity versus Monte Carlo simulations. The agreement between Monte Carlo simulations and the ICF method remained within 5% in soft tissues up to several centimeters from a Pd-103 source. Compared to Monte Carlo, the ICF methods can easily be integrated into a clinical treatment planning system and it does not require the detailed internal structure of the source or the photon phase-space.

  14. [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.

  15. A simplified analytical dose calculation algorithm accounting for tissue heterogeneity for low-energy brachytherapy sources.

    PubMed

    Mashouf, Shahram; Lechtman, Eli; Beaulieu, Luc; Verhaegen, Frank; Keller, Brian M; Ravi, Ananth; Pignol, Jean-Philippe

    2013-09-21

    The American Association of Physicists in Medicine Task Group No. 43 (AAPM TG-43) formalism is the standard for seeds brachytherapy dose calculation. But for breast seed implants, Monte Carlo simulations reveal large errors due to tissue heterogeneity. Since TG-43 includes several factors to account for source geometry, anisotropy and strength, we propose an additional correction factor, called the inhomogeneity correction factor (ICF), accounting for tissue heterogeneity for Pd-103 brachytherapy. This correction factor is calculated as a function of the media linear attenuation coefficient and mass energy absorption coefficient, and it is independent of the source internal structure. Ultimately the dose in heterogeneous media can be calculated as a product of dose in water as calculated by TG-43 protocol times the ICF. To validate the ICF methodology, dose absorbed in spherical phantoms with large tissue heterogeneities was compared using the TG-43 formalism corrected for heterogeneity versus Monte Carlo simulations. The agreement between Monte Carlo simulations and the ICF method remained within 5% in soft tissues up to several centimeters from a Pd-103 source. Compared to Monte Carlo, the ICF methods can easily be integrated into a clinical treatment planning system and it does not require the detailed internal structure of the source or the photon phase-space.

  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. Review of some calculations of energy transport in a Garret-Munk ocean

    NASA Astrophysics Data System (ADS)

    Pomphrey, Neil

    1981-12-01

    A review of current understanding of energy redistribution processes within the ocean internal wave field will be given. Relaxation rates for ''test waves'' in a Garrett-Munk model ocean have mainly been calculated using Hasselmann transport theory or related methods. Computations show that GM76 is approximately a steady state spectrum for 3-wave interactions except for frequencies near the inertial frequency and at the lowest vertical mode-numbers. The lack of variation of the internal wave coupling coefficients allows discussion of results in terms of McComas and Bretherton's three limiting mechanisms; Induced Diffusion, Elastic Scattering and Parametric Subharmonic Instability. In the high vertical modenumber regime Induced Diffusion provides the most significant contribution. Transfer rates are high here and there has been concern for the validity of the Hasselmann theory. However, recent calculations by Meiss and Watson which relate Induced Diffusion to the Taylor Goldstein equation yield relaxation rates which are valid over a much extended domain.

  18. 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.

  19. 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.

  20. Density functional theory calculations of magnetocrystalline anisotropy energies for (Fe1-xCox)2B

    DOE PAGES

    Daene, Markus; Kim, Soo Kyung; Surh, Michael P.; ...

    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

  1. A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations.

    PubMed

    Li, Jue; Wei, Dong-Qing; Wang, Jing-Fang; Li, Yi-Xue

    2011-12-27

    Human cytochrome P450 2E1 (CYP2E1) participates in the metabolism of over 2% of all the oral drugs. A hallmark peculiar feature of this enzyme is that it exhibits a pronounced negative cooperativity in substrate binding. However the mechanism by which the negative cooperativity occurs is unclear. Here, we performed molecular dynamics simulations and free energy calculations on human CYP2E1 to examine the structural differences between the substrate-free and the enzymes with one and two aniline molecules bound. Our results indicate that although the effector substrate does not bind in the active site cavity, it still can directly interact with the active site residues of human CYP2E1. The interaction of the effector substrate with the active site leads to a reorientation of active site residues, which thereby weakens the interactions of the active substrate with this site. We also identify a conserved residue T303 that plays a crucial role in the negative cooperative binding on the short-range effects. This residue is a key factor in the positioning of substrates and in proton delivery to the active site. Additionally, a long-range effect of the effector substrate is identified in which F478 is proposed to play a key role. As located in the interface between the active and effector sites, this residue structurally links the active and effector sites and is found to play a significant role in affecting substrate access and ligand positioning within the active site. In the negative cooperative binding, this residue can decrease the interactions of the active substrate with the active site by π-π stacking which then lowers the hydroxylation activity for the active substrate. These findings are in agreement with previous experimental observations and thus provide detailed atomistic insight into the poorly understood mechanism of the negative cooperativity in human CYP2E1.

  2. 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.

  3. Activation energies of metal atomization and nitrate and sulfate decomposition in concentrated matrices (10 -1 M).

    NASA Astrophysics Data System (ADS)

    Le Bihan, A.; Le Garrec, H.; Cabon, J. Y.; Guern, Y.

    1998-08-01

    This paper reports on activation energies measured during copper and manganese atomization in a graphite furnace in the presence of large amounts of nitrate and sulfate matrices. It also deals with activation energies corresponding to the decomposition of these matrices and to the atomization of their metal, i.e. Na, Ca or Mg. These results were obtained from Arrhenius-type calculations carried out on specific and non-specific absorbance values. Atomization was achieved under a very high gas flow which allowed us to get to the source function. Some of the calculated energies were compared to reaction energies deduced from tables of thermodynamic data.

  4. 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.

  5. Calculation tool for transported geothermal energy using two-step absorption process

    SciTech Connect

    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"

  6. 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.

  7. 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

  8. A truncated quasiharmonic method for free energy calculations and finite-temperature applications

    NASA Astrophysics Data System (ADS)

    Chen, Yan Yu; Chen, Chuin Shan

    2012-12-01

    Harmonic-based finite-temperature calculation methods play an important role in the study of thermodynamic properties of materials. In this study, we propose a truncated quasiharmonic (TQH) method to approximate the Helmholtz free energy by truncating the high-order terms of finite-temperature vibrational energy. To evaluate the efficacy of the TQH method against other established finite-temperature methods, i.e. the quasiharmonic (QH), the modified local harmonic (MLH) and the local quasiharmonic (LQH) methods, analysis of a homogeneous and vacancy-containing atomic system is performed with each method and compared. We found that the TQH method provides improved accuracy over the MLH and LQH methods for a system containing defects while requiring less computational time than the QH method to achieve convergence.

  9. Calculation of energy relaxation rates of fast particles by phonons in crystals

    NASA Astrophysics Data System (ADS)

    Prange, Micah; Campbell, Luke; Wu, Dangxin; Kerisit, Sebastien

    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 moving 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 several important scintillators whose performance is affected by electron thermalization. We discuss the influence of the form assumed for quasiparticle dispersion on theoretical estimates of electron cooling rates. This research was supported by the National Nuclear Security Administration, Office of DNN R&D, of the DOE. PNNL is operated by Battelle Memorial Institute under Contract DE-AC0576RL01830.

  10. Calculation of fluence and absorbed dose in head tissues due to different photon energies.

    PubMed

    Azorín, C; Vega-Carrillo, H R; Rivera, T; Azorín, J

    2014-01-01

    Calculations of fluence and absorbed dose in head tissues due to different photon energies were carried out using the MCNPX code, to simulate two models of a patient's head: one spherical and another more realistic ellipsoidal. Both head models had concentric shells to describe the scalp skin, the cranium and the brain. The tumor was located at the center of the head and it was a 1 cm-radius sphere. The MCNPX code was run for different energies. Results showed that the fluence decreases as the photons pass through the different head tissues. It can be observed that, although the fluence into the tumor is different for both head models, absorbed dose is the same.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

    PubMed

    Mielke, Steven L; Truhlar, Donald G

    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(-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.

  15. Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Barclay, V. J.

    "Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations

  16. 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

  17. CASSCF and CASPT2 ab initio electronic structure calculations find singlet methylnitrene is an energy minimum

    SciTech Connect

    Kemnitz, C.R.; Ellison, G.B.; Karney, W.L.; Borden, W.T.

    2000-02-16

    (12/11)CASSCF and (12/11)CASPT2 ab initio electronic structure calculations with both the cc-pVDZ and cc-pVTZ basis sets find that there is a barrier to the very exothermic hydrogen shift that converts singlet methylnitrene, CH{sub 3}N, to methyleneimine, H{sub 2}C{double{underscore}bond}NH. These two energy minima are connected by a transition structure of C{sub s} symmetry, which is computed to lie 3.8 kcal/mol above the reactant at the (12/11)CASPT2/cc-pVTZ//(12/11)CASSCF/cc-pVTZ level of theory. The (12/11)CASSCF/cc-pVTZ value for the lowest frequency vibration in the transition structure is 854 cm{sup {minus}1}, and CASPT2 calculations concur that this a{double{underscore}prime} vibration does indeed have a positive force constant. Thus, there is no evidence that this geometry is actually a mountain top, rather than a transition structure, on the global potential energy surface or that a C{sub 1} pathway of lower energy connects the reactant to the product. Therefore, computational results indicate that the bands seen for singlet methylnitrene in the negative ion photoelectron spectrum of CH{sub 3}N{sup {minus}} are due to singlet methylnitrene being an energy minimum, rather than a transition state. These results also lead to the prediction that, at least in principle, singlet methylnitrene should be an observable intermediate in the formation of methyleneimine.

  18. 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.

  19. 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.

  20. 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.

  1. On the calculations of interaction energies and induced electric properties within the polarizable continuum model.

    PubMed

    Zawada, Agnieszka; Góra, Robert W; Mikołajczyk, Mikołaj M; Bartkowiak, Wojciech

    2012-05-03

    In this work we investigate the influence of a polarizable environment on the interaction energies and the interaction-induced (excess) static electric dipole properties for the selected model hydrogen-bonded complexes. The excess properties were estimated for water and hydrogen fluoride dimers using the supermolecular approach and assuming the polarizable continuum model (PCM) as a representation of the polarizable environment. We analyze in this context the performance of the counterpoise correction and the consequences of various possible monomer cavity choices. The polarizable environment reduces the absolute magnitudes of interaction energies and interaction-induced dipole moments, whereas an increase is observed for the absolute magnitudes of induced polarizabilities and first hyperpolarizabilities. Our results indicate that the use of either monomeric (MC) or dimeric (DC) cavities in calculations of monomer properties does not change qualitatively the resultant excess properties. We conclude that the DC scheme is more consistent with the definition of the interaction energy and consequently also the interaction-induced property, whereas the MC scheme corresponds to the definition of stabilization energy. Our results indicate also a good performance of the counterpoise correction scheme for the self-consistent methods in the case of all studied properties.

  2. Free-energy predictions and absorption spectra calculations for supramolecular nanocarriers and their photoactive cargo.

    PubMed

    Pietropaolo, Adriana; Tang, Sicheng; Raymo, Françisco M

    2017-04-13

    We reconstructed the free-energy landscape for supramolecular nanoparticles of amphiphilic methacrylated-based co-polymers. Their self-assembly in aqueous solution and encapsulation of borondipyrromethene (BODIPY) derivatives were enforced through atomistic free-energy simulations. The BODIPY binding modes detected in each of the free-energy basins were validated through a comparison of theoretical absorption spectra, calculated at the TD-DFT level, to their experimental counterparts. The nanoparticle distribution is controlled within a thermodynamic regime, with free-energy barriers approaching 8 kcal mol(-1), enabling the existence of different-sized nanoparticles in aqueous solution at room temperature. Two types of supramolecular morphologies were identified. One is compact and spherical in shape and the other is large and donut-like, with the former more stable than the latter by 4 kcal mol(-1). The morphology of the supramolecular host affects the binding mode of the BODIPY guests. Stacked BODIPY aggregates are encapsulated in the spherical nanocarriers, whereas isolated chromophores associate with the donut-shaped assemblies.

  3. Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations.

    PubMed

    Tomić, Antonija; Tomić, Sanja

    2014-11-07

    Multiple choices of the protein active conformations in flexible metalloenzymes complicate study of their catalytic mechanism. We used three different conformations of human dipeptidyl-peptidase III (DPP III) to investigate the influence of the protein environment on ligand binding and the Zn(2+) coordination. MD simulations followed by calculations of binding free energy components accomplished for a series of DPP III substrates, both synthetic and natural, revealed that binding of the β-strand shaped substrate to the five-stranded β-core of the compact DPP III form (in antiparallel fashion) is the preferred binding mode, in agreement with the experimentally determined structure of the DPP III inactive mutant-tynorphin complex (Bezerra et al., Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 6525). Previously it was proposed that the catalytic mechanism of DPP III is similar to that of thermolysin, which assumes exchange of five and four coordinated Zn(2+), and activation of Zn-bound water by a nearby Glu. Our QM/MM calculations, performed for a total of 18 protein structures with different zinc ion environments, revealed that the 5-coordinated metal ion is more favourable than the 6-coordinated one in only the most compact DPP III form. Besides, in this structure E451 is H-bonded to the metal ion coordinating water. Also, our study revealed two constraints for the broad substrate specificity of DPP III. One is the possibility of the substrate adopting the β-strand shape and the other is its charged N-terminus. Altogether, we assume that the human DPP III active conformation would be the most compact form, similar to the "closed X-ray" DPP III structure.

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin.

    PubMed

    Suess, Christian J; Hirst, Jonathan D; Besley, Nicholas A

    2017-04-01

    The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two-dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time-dependent density functional theory. Key intermediate residues between the donor and acceptor are identified, and in particular the residues Val68 and Ile75 play a critical role in calculations of the electron coupling matrix elements. Our calculations demonstrate how small changes in structure can have a large effect on the rates, and show that the different rates of electron transfer are dictated by the distance between the heme and tryptophan residues, while for excitation energy transfer the orientation of the tryptophan residues relative to the heme is important. © 2017 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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

    PubMed

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

    2017-04-07

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

  10. 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.

  11. 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.

  12. 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…

  13. 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…

  14. 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

  15. 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

  16. Identification of general linear relationships between activation energies and enthalpy changes for dissociation reactions at surfaces.

    PubMed

    Michaelides, Angelos; Liu, Z-P; Zhang, C J; Alavi, Ali; King, David A; Hu, P

    2003-04-02

    The activation energy to reaction is a key quantity that controls catalytic activity. Having used ab inito calculations to determine an extensive and broad ranging set of activation energies and enthalpy changes for surface-catalyzed reactions, we show that linear relationships exist between dissociation activation energies and enthalpy changes. Known in the literature as empirical Brønsted-Evans-Polanyi (BEP) relationships, we identify and discuss the physical origin of their presence in heterogeneous catalysis. The key implication is that merely from knowledge of adsorption energies the barriers to catalytic elementary reaction steps can be estimated.

  17. 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

  18. Quantitative analysis of weak interactions by Lattice energy calculation, Hirshfeld surface and DFT studies of sulfamonomethoxine

    NASA Astrophysics Data System (ADS)

    Patel, Kinjal D.; Patel, Urmila H.

    2017-01-01

    Sulfamonomethoxine, 4-Amino-N-(6-methoxy-4-pyrimidinyl) benzenesulfonamide (C11H12N4O3S), is investigated by single crystal X-ray diffraction technique. Pair of N-H⋯N and C-H⋯O intermolecular interactions along with π···π interaction are responsible for the stability of the molecular packing of the structure. In order to understand the nature of the interactions and their quantitative contributions towards the crystal packing, the 3D Hirshfeld surface and 2D fingerprint plot analysis are carried out. PIXEL calculations are performed to determine the lattice energies correspond to intermolecular interactions in the crystal structure. Ab initio quantum chemical calculations of sulfamonomethoxine (SMM) have been performed by B3LYP method, using 6-31G** basis set with the help of Schrodinger software. The computed geometrical parameters are in good agreement with the experimental data. The Mulliken charge distribution, calculated using B3LYP method to confirm the presence of electron acceptor and electron donor atoms, responsible for intermolecular hydrogen bond interactions hence the molecular stability.

  19. Accurate Cross-section Calculations for Low-Energy Electron-Atom Collisions

    SciTech Connect

    Zatsarinny, Oleg; Bartschat, Klaus

    2011-05-11

    We describe a recently developed fully relativistic B-spline R-matrix method for atomic structure as well as calculations for electron and photon collision with atoms and ions. The method is based on the solution of the many-electron Fock-Dirac equation and allows to employ non-orthogonal sets of atomic orbitals. A B-spline basis is used to generate both the target description and the R-matrix basis functions in the inner region. Employing B-splines of different orders for the large and small components prevents the appearance of spurious states in the spectrum of the Dirac equation. Using term-dependent and thus nonorthogonal sets of one-electron functions enables us to generate accurate and flexible representations of the target states and the scattering function. Our method is based upon the Dirac-Coulomb Hamiltonian and thus may be employed for any complex atom or ion, without the use of phenomenological core potentials. Example results from recent applications of the method for accurate calculations of low-energy electron scattering from noble gases are presented. In most cases we obtained a substantial improvement over results obtained in previous Breit-Pauli R-matrix calculations.

  20. 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

  1. 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.

  2. An analytical ab initio potential surface and the calculated tunneling energies for the HCl dimer

    NASA Astrophysics Data System (ADS)

    Bunker, P. R.; Epa, V. C.; Jensen, Per; Karpfen, Alfred

    1991-03-01

    The six-dimensional potential energy surface of the HCl dimer has been calculated ab initio at 1654 nuclear geometries [A. Karpfen, P. R. Bunker and P. Jensen, Chem. Phys., in press]. In the present paper we have fitted an analytical function to these points; the analytical function is similar to that used previously by us for the potential surface of the HF dimer. The fitted function has 38 adjustable parameters and the standard deviation of the weighted fit is 19.0 cm -1. We have determined the minimum energy path for the trans-bending tunneling motion on this surface, and have calculated the tunneling and K-rotation energies and wavefunctions. Around equilibrium the path is qualitatively similar to that for the HF dimer in that there are two equivalent hydrogen-bonded structures of Cs symmetry (which are approximately L-shaped with a "bound" and a "free" H-atom) that can tunnel through a C2 h saddle point (the "closed" C2 h saddle point). However, away from equilibrium the path is qualitatively different from that found for the HF dimer since the HCl dimer never becomes linear along the path; in fact it passes through a second C2 h saddle point (the "open" C2 h saddle point). As a result the A-rotational constant only varies slightly along the path, and this explains the experimental observation that the tunneling splitting varies little with K-type rotation for the HCl dimer, in contrast to the situation for the HF dimer. Quantitatively it is clear that errors in the ab initio calculation, errors in the fitting of an analytic function to the points, the correction to the path that is caused by the zero point motion in the other vibrations, and the coupling between the four low-frequency modes, will all be relatively more significant than they were for the HF dimer because the full six-dimensional potential is much flatter; the ab initio dissociation energy is only ˜600 cm -1, and the ab initio tunneling barrier is only ˜70 cm -1. Therefore, we modify the

  3. Hydrogen Energy Storage (HES) Activities at NREL; NREL (National Renewable Energy Laboratory)

    SciTech Connect

    Eichman, J.

    2015-04-21

    This presentation provides an overview of hydrogen and energy storage, including hydrogen storage pathways and international power-to-gas activities, and summarizes the National Renewable Energy Laboratory's hydrogen energy storage activities and results.

  4. Controversial electronic structures and energies of Fe2, Fe_2^ +, and Fe_2^ - resolved by RASPT2 calculations

    NASA Astrophysics Data System (ADS)

    Hoyer, Chad E.; Manni, Giovanni Li; Truhlar, Donald G.; Gagliardi, Laura

    2014-11-01

    The diatomic molecule Fe2 was investigated using restricted active space second-order perturbation theory (RASPT2). This molecule is very challenging to study computationally because predictions about the ground state and excited states depend sensitively on the choice of the quantum chemical method. For Fe2 we show that one needs to go beyond a full-valence active space in order to achieve even qualitative agreement with experiment for the dissociation energy, and we also obtain a smooth ground-state potential curve. In addition we report the first multireference study of Fe_2^ +, for which we predict an 8Σ _u^ - ground state, which was not predicted by previous computational studies. By using an active space large enough to remove the most serious deficiencies of previous theoretical work and by explicitly investigating the interpretations of previous experimental results, this study elucidates previous difficulties and provides - for the first time - a qualitatively correct treatment of Fe2, Fe_2^ +, and Fe_2^ -. Moreover, this study represents a record in terms of the number or active electrons and active orbitals in the active space, namely 16 electrons in 28 orbitals. Conventional CASPT2 calculations can be performed with at most 16 electrons in 16 orbitals. We were able to overcome this limit by using the RASPT2 formalism.

  5. 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.

  6. Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole

    NASA Astrophysics Data System (ADS)

    Muthu, S.; Uma Maheswari, J.; Srinivasan, S.; Isac paulraj, E.

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-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.

  7. 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

  8. 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

  9. A Monte Carlo model for out-of-field dose calculation from high-energy photon therapy.

    PubMed

    Kry, Stephen F; Titt, Uwe; Followill, David; Pönisch, Falk; Vassiliev, Oleg N; White, R Allen; Stovall, Marilyn; Salehpour, Mohammad

    2007-09-01

    As cancer therapy becomes more efficacious and patients survive longer, the potential for late effects increases, including effects induced by radiation dose delivered away from the treatment site. This out-of-field radiation is of particular concern with high-energy radiotherapy, as neutrons are produced in the accelerator head. We recently developed an accurate Monte Carlo model of a Varian 2100 accelerator using MCNPX for calculating the dose away from the treatment field resulting from low-energy therapy. In this study, we expanded and validated our Monte Carlo model for high-energy (18 MV) photon therapy, including both photons and neutrons. Simulated out-of-field photon doses were compared with measurements made with thermoluminescent dosimeters in an acrylic phantom up to 55 cm from the central axis. Simulated neutron fluences and energy spectra were compared with measurements using moderated gold foil activation in moderators and data from the literature. The average local difference between the calculated and measured photon dose was 17%, including doses as low as 0.01% of the central axis dose. The out-of-field photon dose varied substantially with field size and distance from the edge of the field but varied little with depth in the phantom, except at depths shallower than 3 cm, where the dose sharply increased. On average, the difference between the simulated and measured neutron fluences was 19% and good agreement was observed with the neutron spectra. The neutron dose equivalent varied little with field size or distance from the central axis but decreased with depth in the phantom. Neutrons were the dominant component of the out-of-field dose equivalent for shallow depths and large distances from the edge of the treatment field. This Monte Carlo model is useful to both physicists and clinicians when evaluating out-of-field doses and associated potential risks.

  10. A Simple Method for the Calculation of Lattice Energies of Inorganic Ionic Crystals Based on the Chemical Hardness.

    PubMed

    Kaya, Savaş; Kaya, Cemal

    2015-09-08

    This paper presents a new technique for estimation of lattice energies of inorganic ionic compounds using a simple formula. This new method demonstrates the relationship between chemical hardness and lattice energies of ionic compounds. Here chemical hardness values of ionic compounds are calculated via our molecular hardness equation. The results obtained using the present method and comparisons made by considering experimental data and the results from other theoretical methods in the literature showed that the new method allows easy evaluation of lattice energies of inorganic ionic crystals without the need for ab initio calculations and complex calculations.

  11. 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.

  12. ERP Energy and Cognitive Activity Correlates

    NASA Astrophysics Data System (ADS)

    Schillaci, Michael Jay; Vendemia, Jennifer M. C.

    2014-03-01

    We propose a novel analysis approach for high-density event related scalp potential (ERP) data where the integrated channel-power is used to attain an energy density functional state for channel-clusters of neurophysiological significance. The method is applied to data recorded during a two-stimulus, directed lie paradigm and shows that deceptive responses emit between 8% and 10% less power. A time course analysis of these cognitive activity measures over posterior and anterior regions of the cortex suggests that neocortical interactions, reflecting the differing workload demands during executive and semantic processes, take about 50% longer for the case of deception. These results suggest that the proposed method may provide a useful tool for the analysis of ERP correlates of high-order cognitive functioning. We also report on a possible equivalence between the energy functional distribution and near-infrared signatures that have been measured with other modalities.

  13. Combining path-breaking with bidirectional nonequilibrium simulations to improve efficiency in free energy calculations

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

    An important limitation of unidirectional nonequilibrium simulations is the amount of realizations of the process necessary to reach suitable convergence of free energy estimates via Jarzynski's relationship [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. To this regard, an improvement of the method has been achieved by means of path-breaking schemes [R. Chelli et al., J. Chem. Phys. 138, 214109 (2013)] based on stopping highly dissipative trajectories before their normal end, under the founded assumption that such trajectories contribute marginally to the work exponential averages. Here, we combine the path-breaking scheme, called probability threshold scheme, to bidirectional nonequilibrium methods for free energy calculations [G. E. Crooks, Phys. Rev. E 61, 2361 (2000); R. Chelli and P. Procacci, Phys. Chem. Chem. Phys. 11, 1152 (2009)]. The method is illustrated and tested on a benchmark system, i.e., the helix-coil transition of deca-alanine. By using path-breaking in our test system, the computer time needed to carry out a series of nonequilibrium trajectories can be reduced up to a factor 4, with marginal loss of accuracy in free energy estimates.

  14. Energy of the interaction between membrane lipid domains calculated from splay and tilt deformations

    NASA Astrophysics Data System (ADS)

    Galimzyanov, T. R.; Molotkovsky, R. J.; Kheyfets, B. B.; Akimov, S. A.

    2013-01-01

    Specific domains, called rafts, are formed in cell membranes. Similar lipid domains can be formed in model membranes as a result of phase separation with raft size may remaining small (˜10-100 nm) for a long time. The characteristic lifetime of a nanoraft ensemble strongly depends on the nature of mutual raft interactions. The interaction energy between the boundaries of two rafts has been calculated under the assumption that the thickness of the raft bilayer is greater than that of the surrounding membrane, and elastic deformations appear in order to smooth the thickness mismatch at the boundary. When rafts approach each other, deformations from their boundaries overlap, making interaction energy profile sophisticated. It has been shown that raft merger occurs in two stages: rafts first merge in one monolayer of the lipid bilayer and then in another monolayer. Each merger stage requires overcoming of an energy barrier of about 0.08-0.12 k BT per 1 nm of boundary length. These results allow us to explain the stability of the ensemble of finite sized rafts.

  15. Calculations of bond dissociation energies. New select applications of an old method.

    PubMed

    Boudreaux, Edward A

    2011-03-10

    Application of Sanderson's definition of electronegativity as stability ratios (SRs), which BE = [E(i) + E(DA)] (IC) + E(cov) had been applied in the past to a wide variety of organic and nontransitional metal inorganic compounds with very good success, has been revived, modified so as to be applied to any types of molecules, including those containing transition metals, lanthanides, and actinides. This paper is limited to a demonstration of the method which is applied to a few metal cyclopentadienyl compounds, plus specific emphasis on the U(III) metallocene (CpSiMe(3))(3)U-AlCp* recently prepared by Arnold and co-workers having no experimental bond energies available. It is shown that computed bond energies of pertinent metallocyclopentadieneyls are in excellent agreement with the available experimental data. Calculated bond energies for all essential bonds in the uranium metallocene cited above are provided together with a further analysis of the bonding and magnetic properties of this unique compound.

  16. Free energy calculation provides insight into the action mechanism of selective PARP-1 inhibitor.

    PubMed

    Cao, Ran

    2016-04-01

    Selective poly (ADP-ribose) polymerase (PARP)-1 inhibitor represents promising therapy against cancers with a good balance between efficacy and safety. Owing to the conserved structure between PARP-1 and PARP-2, most of the clinical and experimental drugs show equivalent inhibition against both targets. Most recently, it's disclosed a highly selective PARP-1 inhibitor (NMS-P118) with promising pharmacokinetic properties. Herein, we combined molecular simulation with free energy calculation to gain insights into the selective mechanism of NMS-P118. Our results suggest the reduction of binding affinity for PARP-2 is attributed to the unfavorable conformational change of protein, which is accompanied by a significant energy penalty. Alanine-scanning mutagenesis study further reveals the important role for a tyrosine residue of donor loop (Tyr889(PARP-1) and Tyr455(PARP-2)) in contributing to the ligand selectivity. Retrospective structural analysis indicates the ligand-induced movement of Tyr455(PARP-2) disrupts the intra-molecule hydrogen bonding network, which partially accounts for the "high-energy" protein conformation in the presence of NMS-P118. Interestingly, such effect isn't observed in other non-selective PARP inhibitors including BMN673 and A861695, which validates the computational prediction. Our work provides energetic insight into the subtle variations in the crystal structures and could facilitate rational design of new selective PARP inhibitor.

  17. Energy- and Activity-Dependent Loss Timescales for Inner Magnetospheric keV-Energy Electrons

    NASA Astrophysics Data System (ADS)

    Liemohn, M. W.

    2011-12-01

    The Hot Electron and Ion Drift Integrator (HEIDI) inner magnetospheric drift physics model has recently been modified to include keV-energy electron scattering rates by VLF chorus and hiss waves, thus allowing for the calculation of the electron phase space distribution in the inner magnetosphere and electron precipitation to the upper atmosphere. Comparisons of calculated electron fluxes are made with low-Earth orbit electron precipitation data and dayside electron measurements to validate the scattering implementation procedure. The energy-dependent scattering rate coefficients are adjusted to take into account geomagnetic activity and plasmapause location, providing a scattering rate that best matches the simulations to the observed electron fluxes. In addition, the electron ring current intensities and spatio-temporal evolution are compared against simulation results for the hot ion species. While the electron total energy content is typically 10 times smaller than the ion total energy content in the inner magnetosphere, it can be significantly higher than this during the late main phase of magnetic storms.

  18. PLUMED: A portable plugin for free-energy calculations with molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni; Camilloni, Carlo; Provasi, Davide; Raiteri, Paolo; Donadio, Davide; Marinelli, Fabrizio; Pietrucci, Fabio; Broglia, Ricardo A.; Parrinello, Michele

    2009-10-01

    Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes. Program summaryProgram title: PLUMED Catalogue identifier: AEEE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Lesser GPL No. of lines in distributed program, including test data, etc.: 107 505 No. of bytes in distributed program, including test data, etc.: 2 052 759 Distribution format: tar.gz Programming language: ANSI-C Computer: Any computer capable of running an executable produced by GCC compiler Operating system: Linux/Unix RAM: Depending on the number of atoms, the method chosen and the collective variables used Classification: 23 External routines: Must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER). Nature of problem: Calculation of free-energy surfaces for biological and condensed matter systems. Solution method: Implementation of various enhanced sampling techniques. Unusual features: PLUMED is not a stand-alone program but it must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER) that needs to be recompiled. Each interface is provided in a patch form. Running time: Depending on the number of atoms, the method chosen and the

  19. Maximum-entropy calculation of free energy distributions for two forms of myoglobin.

    PubMed

    Poland, Douglas

    2002-03-01

    The temperature dependence of the heat capacity of myoglobin depends dramatically on pH. At low pH (near 4.5), there are two weak maxima in the heat capacity at low and intermediate temperatures, respectively, whereas at high pH (near 10.7), there is one strong maximum at high temperature. Using literature data for the low-pH form (Hallerbach and Hinz, 1999) and for the high-pH form (Makhatadze and Privalov, 1995), we applied a recently developed technique (Poland, 2001d) to calculate the free energy distributions for the two forms of the protein. In this method, the temperature dependence of the heat capacity is used to calculate moments of the protein enthalpy distribution function, which in turn, using the maximum-entropy method, are used to construct the actual distribution function. The enthalpy distribution function for a protein gives the fraction of protein molecules in solution having a given value of the enthalpy, which can be interpreted as the probability that a molecule picked at random has a given enthalpy value. Given the enthalpy distribution functions at several temperatures, one can then construct a master free energy function from which the probability distributions at all temperatures can be calculated. For the high-pH form of myoglobin, the enthalpy distribution function that is obtained exhibits bimodal behavior at the temperature corresponding to the maximum in the heat capacity (Poland, 2001a), reflecting the presence of two populations of molecules (native and unfolded). For this form of myoglobin, the temperature evolution of the relative probabilities of the two populations can be obtained in detail from the master free energy function. In contrast, the enthalpy distribution function for the low-pH form of myoglobin does not show any special structure at any temperature. In this form of myoglobin the enthalpy distribution function simply exhibits a single maximum at all temperatures, with the position of the maximum increasing to higher

  20. Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation.

    PubMed

    Hu, Guodong; Zhang, Qinggang; Chen, L Y

    2011-08-01

    Molecular dynamics simulations and free energy calculation have been performed to study how the single-chain variable fragment (scFv) binds methamphetamine (METH) and amphetamine (AMP). The structures of the scFv:METH and the scFv:AMP complexes are analyzed by examining the time-dependence of their RMSDs, by analyzing the distance between some key atoms of the selected residues, and by comparing the averaged structures with their corresponding crystallographic structures. It is observed that binding an AMP to the scFv does not cause significant changes to the binding pocket of the scFv:ligand complex. The binding free energy of scFv:AMP without introducing an extra water into the binding pocket is much stronger than scFv:METH. This is against the first of the two scenarios postulated in the experimental work of Celikel et al. (Protein Science 18, 2336 (2009)). However, adding a water to the AMP (at the position of the methyl group of METH), the binding free energy of the scFv:AMP-H2O complex, is found to be significantly weaker than scFv:METH. This is consistent with the second of the two scenarios given by Celikel et al. Decomposition of the binding energy into ligand-residue pair interactions shows that two residues (Tyr175 and Tyr177) have nearly-zero interactions with AMP in the scFv:AMP-H2O complex, whereas their interactions with METH in the scFv:METH complex are as large as -0.8 and -0.74 kcal mol(-1). The insights gained from this study may be helpful in designing more potent antibodies in treating METH abuse.

  1. Torsional energy levels of CH₃OH⁺/CH₃OD⁺/CD₃OD⁺ studied by zero-kinetic energy photoelectron spectroscopy and theoretical calculations.

    PubMed

    Dai, Zuyang; Gao, Shuming; Wang, Jia; Mo, Yuxiang

    2014-10-14

    The torsional energy levels of CH3OH(+), CH3OD(+), and CD3OD(+) have been determined for the first time using one-photon zero kinetic energy photoelectron spectroscopy. The adiabatic ionization energies for CH3OH, CH3OD, and CD3OD are determined as 10.8396, 10.8455, and 10.8732 eV with uncertainties of 0.0005 eV, respectively. Theoretical calculations have also been performed to obtain the torsional energy levels for the three isotopologues using a one-dimensional model with approximate zero-point energy corrections of the torsional potential energy curves. The calculated values are in good agreement with the experimental data. The barrier height of the torsional potential energy without zero-point energy correction was calculated as 157 cm(-1), which is about half of that of the neutral (340 cm(-1)). The calculations showed that the cation has eclipsed conformation at the energy minimum and staggered one at the saddle point, which is the opposite of what is observed in the neutral molecule. The fundamental C-O stretch vibrational energy level for CD3OD(+) has also been determined. The energy levels for the combinational excitation of the torsional vibration and the fundamental C-O stretch vibration indicate a strong torsion-vibration coupling.

  2. Science. Iowa Developed Energy Activity Sampler, 6-12. Revised.

    ERIC Educational Resources Information Center

    Iowa State Dept. of Education, Des Moines. Div. of Instructional Services.

    The revised Iowa Developed Energy Activity Sampler (IDEAS) was compiled using the original IDEAS program and the Energy Conservation Activity Packets (ECAPS). This document is one of a series of revised IDEAS booklets, and provides activities for teaching science. The activities are intended to present energy principles in an interesting manner…

  3. Mathematics. Iowa Developed Energy Activity Sampler, 6-12. Revised.

    ERIC Educational Resources Information Center

    Iowa State Dept. of Education, Des Moines.

    The revised Iowa Developed Energy Activity Sampler (IDEAS) was compiled using the original IDEAS program and the Energy Conservation Activity Packets (ECAPS). This document is one of the series of revised IDEAS booklets, and provides activities for teaching mathematics. The activities are intended to present energy principles in an interesting…

  4. Science. Iowa Developed Energy Activity Sampler, 6-12. Revised.

    ERIC Educational Resources Information Center

    Iowa State Dept. of Education, Des Moines.

    The revised Iowa Developed Energy Activity Sampler (IDEAS) was compiled using the original IDEAS program and the Energy Conservation Activity Packets (ECAPS). This document is one of the series of revised IDEAS booklets, and provides activities for teaching science. The activities are intended to present energy principles in an interesting manner…

  5. Energy Adventure Center. Activity Book. Revised [and Expanded] Edition.

    ERIC Educational Resources Information Center

    Wichita Unified School District 259, KS.

    A variety of energy activities are provided, including instructions for and questions related to energy films. The activities are organized into five sections. Section 1 (work) includes an activity focusing on movement and change. Section 2 (forms of energy) includes activities related to mechanical (movement), radiant (light), chemical (burning),…

  6. Dynamics study of the OH + NH3 hydrogen abstraction reaction using QCT calculations based on an analytical potential energy surface.

    PubMed

    Monge-Palacios, M; Corchado, J C; Espinosa-Garcia, J

    2013-06-07

    To understand the reactivity and mechanism of the OH + NH3 → H2O + NH2 gas-phase reaction, which evolves through wells in the entrance and exit channels, a detailed dynamics study was carried out using quasi-classical trajectory calculations. The calculations were performed on an analytical potential energy surface (PES) recently developed by our group, PES-2012 [Monge-Palacios et al. J. Chem. Phys. 138, 084305 (2013)]. Most of the available energy appeared as H2O product vibrational energy (54%), reproducing the only experimental evidence, while only the 21% of this energy appeared as NH2 co-product vibrational energy. Both products appeared with cold and broad rotational distributions. The excitation function (constant collision energy in the range 1.0-14.0 kcal mol(-1)) increases smoothly with energy, contrasting with the only theoretical information (reduced-dimensional quantum scattering calculations based on a simplified PES), which presented a peak at low collision energies, related to quantized states. Analysis of the individual reactive trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) ≥ 6 kcal mol(-1)) all trajectories are direct, at low energies about 20%-30% of trajectories are indirect, i.e., with the mediation of a trapping complex, mainly in the product well. Finally, the effect of the zero-point energy constraint on the dynamics properties was analyzed.

  7. Calculation of smooth potential energy surfaces using local electron correlation methods

    NASA Astrophysics Data System (ADS)

    Mata, Ricardo A.; Werner, Hans-Joachim

    2006-11-01

    The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl- with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barrier heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.

  8. 3D calculation of Tucson-Melbourne 3NF effect in triton binding energy

    SciTech Connect

    Hadizadeh, M. R.; Tomio, L.; Bayegan, S.

    2010-08-04

    As an application of the new realistic three-dimensional (3D) formalism reported recently for three-nucleon (3N) bound states, an attempt is made to study the effect of three-nucleon forces (3NFs) in triton binding energy in a non partial wave (PW) approach. The spin-isospin dependent 3N Faddeev integral equations with the inclusion of 3NFs, which are formulated as function of vector Jacobi momenta, specifically the magnitudes of the momenta and the angle between them, are solved with Bonn-B and Tucson-Melbourne NN and 3N forces in operator forms which can be incorporated in our 3D formalism. The comparison with numerical results in both, novel 3D and standard PW schemes, shows that non PW calculations avoid the very involved angular momentum algebra occurring for the permutations and transformations and it is more efficient and less cumbersome for considering the 3NF.

  9. Calculation of smooth potential energy surfaces using local electron correlation methods

    SciTech Connect

    Mata, Ricardo A.; Werner, Hans-Joachim

    2006-11-14

    The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl{sup -} with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barrier heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.

  10. Applicability of n-vicinity method for calculation of free energy of Ising model

    NASA Astrophysics Data System (ADS)

    Kryzhanovsky, Boris; Litinskii, Leonid

    2017-02-01

    Here we apply the n-vicinity method of approximate calculation of the partition function to an Ising Model with the nearest neighbor interaction on D-dimensional hypercube lattice. We solve the equation of state for an arbitrary dimension D and analyze the behavior of the free energy. As expected, for large dimensions (D ≥ 3) the system demonstrates a phase transition of the second kind. In this case, we obtain a simple analytical expression for the critical value of the inverse temperature. When 3 ≤ D ≤ 7 this expression is in a very good agreement with the results of computer simulations. In the case of small dimensions (D = 1 , 2), there is a noticeable discrepancy with the known exact results.

  11. Calculation of the Frequency Distribution of the Energy Deposition in DNA Volumes by Heavy Ions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cicinotta, Francis A.

    2012-01-01

    Radiation quality effects are largely determined by energy deposition in small volumes of characteristic sizes less than 10 nm representative of short-segments of DNA, the DNA nucleosome, or molecules initiating oxidative stress in the nucleus, mitochondria, or extra-cellular matrix. On this scale, qualitatively distinct types of molecular damage are possible for high linear energy transfer (LET) radiation such as heavy ions compared to low LET radiation. Unique types of DNA lesions or oxidative damages are the likely outcome of the energy deposition. The frequency distribution for energy imparted to 1-20 nm targets per unit dose or particle fluence is a useful descriptor and can be evaluated as a function of impact parameter from an ions track. In this work, the simulation of 1-Gy irradiation of a cubic volume of 5 micron by: 1) 450 (1)H(+) ions, 300 MeV; 2) 10 (12)C(6+) ions, 290 MeV/amu and 3) (56)Fe(26+) ions, 1000 MeV/amu was done with the Monte-Carlo simulation code RITRACKS. Cylindrical targets are generated in the irradiated volume, with random orientation. The frequency distribution curves of the energy deposited in the targets is obtained. For small targets (i.e. <25 nm size), the probability of an ion to hit a target is very small; therefore a large number of tracks and targets as well as a large number of histories are necessary to obtain statistically significant results. This simulation is very time-consuming and is difficult to perform by using the original version of RITRACKS. Consequently, the code RITRACKS was adapted to use multiple CPU on a workstation or on a computer cluster. To validate the simulation results, similar calculations were performed using targets with fixed position and orientation, for which experimental data are available [5]. Since the probability of single- and double-strand breaks in DNA as function of energy deposited is well know, the results that were obtained can be used to estimate the yield of DSB, and can be extended

  12. Neutron spectra and dose equivalents calculated in tissue for high-energy radiation therapy

    PubMed Central

    Kry, Stephen F.; Howell, Rebecca M.; Salehpour, Mohammad; Followill, David S.

    2009-01-01

    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

  13. Influence of different approaches for calculating the athlete's mechanical energy on energetic parameters in the pole vault.

    PubMed

    Schade, F; Arampatzis, A; Brüggemann, G

    2000-10-01

    The purposes of this study were as follows: (1) To determine the differences between two- and three-dimensionally calculated energy of the athlete in the pole vault. (2) To determine the differences between CM energy and total body energy. (3) To examine the influence of these different approaches of calculating the athlete's energy on energetic parameter values during the pole vault. Kinematic data were gathered during the pole vault final of the track and field world championships in 1997. Two video cameras (50Hz) covered the last step of the approach including the pole plant and 2 cameras covered the pole phase up to bar clearance, respectively. Twenty successful jumps were analysed. The characteristics of the energy development is similar for the different approaches. Initial energy, energy at maximum pole bend and energy at pole release (primary parameters) show significant differences (p<0.05). The findings indicate that rotatory movements and movements relative to the CM have a larger influence on the primary parameters than movements apart from the main plane of movement. For analysing the energy exchange between the athlete and the elastic implement pole only the differences among the secondary parameters (initial energy minus energy at maximum pole bend, final energy minus energy at maximum pole bend) are needed (Arampatzis et al., 1997 Biomechanical Research Project at the Vth World Championships in Athletics, Athens 1997: Preliminary Report. New Studies in Athletics 13, 66-69). For those parameters the relative differences between the calculation approaches range only between 1.47 and 0.04%. This indicates that the influence of the different approaches for calculating the athlete's energy on the analysis of energy exchange is negligible.

  14. Bond dissociation energy of the phenol O sbnd H bond from ab initio calculations

    NASA Astrophysics Data System (ADS)

    da Silva, Gabriel; Chen, Chiung-Chu; Bozzelli, Joseph W.

    2006-06-01

    The phenol O sbnd H bond dissociation energy (BDE) is currently disputed, despite its importance in combustion chemistry and in the reactions of antioxidants such as vitamin E. We have studied this BDE using the computational methods G3, G3B3 and CBS-APNO, with bond-isodesmic work reactions. These calculations yield a BDE of 89.0 ± 1.0 kcal mol -1, which supports other recent calculations [B.J. Costa Cabral, S. Canuto, Chem. Phys. Lett. 406 (2005) 300]. From our BDE we determine the enthalpy of formation of the phenoxy radical to be 13.9 ± 1.0 kcal mol -1. Comparison of the phenol C sbnd H BDE with the vinyl alcohol H sbnd CH dbnd CHOH BDE reveals the bond in phenol to be around 3 kcal mol -1 stronger than that in vinyl alcohol. Replacement of a H atom with the OH group on benzene or ethylene strengthens the C sbnd H bonds on adjacent carbons by 3 to 4 kcal mol -1.

  15. On the partial wave method for self energy calculations for non-hydrogenic electrons

    NASA Astrophysics Data System (ADS)

    Hagelstein, Peter L.

    1994-07-01

    A method for computing the self-energy correction for highly-ionized and high-Z many electron atoms is proposed and developed. The method is based on a partical wave analysis, and is immediately applicable to general potentials and many-electron wavefunctions. In this work we discuss the general approach, develop a formalism amenable to practical anal- ysis, provide the angular momentum reduction for arbitrary one-electron orbitals, and describe the computation of the twdimensional integrals and their kernels required for the partial wave analysis. Analytical results allowing for a practical renormalization scheme are discussed. This work is exploratory and developmental, and the present document provides a status report of our eforts. To date we have obtained numerical evidence that the method successfully handles the renormalization, and we report on significant progress in numerical methods for evaluating and approximating the two-dimensional integrals which occur in the method. We believe that this method can ultimately achieve an accuracy which is competitive with that of modern Brown's method calculations. The methods discussed within this work for approximating the two-dimensional radial matrix eIements including the full retarded couIomb interaction can be applied to other relativistic atomic physics calculations as a practical way to obtain improvements over the coulomb and Breit approximations.

  16. Checking the Beam Energy Calculation from the June 14, 2000 $\\psi^\\prime$ Scan

    SciTech Connect

    Werkema, Steve; /Fermilab

    2000-06-14

    The Conclusions/Recommendations of this paper are: (1) It is very important to keep the orbit close to the reference orbit. (2) It is likely that BPMs are not perfectly calibrated. (3) The orbit length calculation with Quad Steering ON is more sensitive to errors in the BPM readout than with Quad Steering OFF. However, unless we are at the {psi}{prime}, Quad Steering should be ON. (4) Question: Should we use the BPM corrections derived from this scan? Answer: I don't know. I would prefer not to. If we keep the orbit close to the reference, we don't need the corrections. For cases where the orbit differs appreciably from the reference orbit, we should do the energy calculation both ways. (Perhaps with Quad steering ON and OFF too). (5) We should use the reference orbit derived from this scan. However, if there is the time and the man power, it would be desireable to do a proper scan of the {psi}{prime}.

  17. Surface energy budget and thermal inertia at Gale Crater: Calculations from ground-based measurements

    PubMed Central

    Martínez, G M; Rennó, N; Fischer, E; Borlina, C S; Hallet, B; de la Torre Juárez, M; Vasavada, A R; Ramos, M; Hamilton, V; Gomez-Elvira, J; Haberle, R M

    2014-01-01

    The analysis of the surface energy budget (SEB) yields insights into soil-atmosphere interactions and local climates, while the analysis of the thermal inertia (I) of shallow subsurfaces provides context for evaluating geological features. Mars orbital data have been used to determine thermal inertias at horizontal scales of ∼104 m2 to ∼107 m2. Here we use measurements of ground temperature and atmospheric variables by Curiosity to calculate thermal inertias at Gale Crater at horizontal scales of ∼102 m2. We analyze three sols representing distinct environmental conditions and soil properties, sol 82 at Rocknest (RCK), sol 112 at Point Lake (PL), and sol 139 at Yellowknife Bay (YKB). Our results indicate that the largest thermal inertia I = 452 J m−2 K−1 s−1/2 (SI units used throughout this article) is found at YKB followed by PL with I = 306 and RCK with I = 295. These values are consistent with the expected thermal inertias for the types of terrain imaged by Mastcam and with previous satellite estimations at Gale Crater. We also calculate the SEB using data from measurements by Curiosity's Rover Environmental Monitoring Station and dust opacity values derived from measurements by Mastcam. The knowledge of the SEB and thermal inertia has the potential to enhance our understanding of the climate, the geology, and the habitability of Mars. PMID:26213666

  18. Surface energy budget and thermal inertia at Gale Crater: Calculations from ground-based measurements.

    PubMed

    Martínez, G M; Rennó, N; Fischer, E; Borlina, C S; Hallet, B; de la Torre Juárez, M; Vasavada, A R; Ramos, M; Hamilton, V; Gomez-Elvira, J; Haberle, R M

    2014-08-01

    The analysis of the surface energy budget (SEB) yields insights into soil-atmosphere interactions and local climates, while the analysis of the thermal inertia (I) of shallow subsurfaces provides context for evaluating geological features. Mars orbital data have been used to determine thermal inertias at horizontal scales of ∼10(4) m(2) to ∼10(7) m(2). Here we use measurements of ground temperature and atmospheric variables by Curiosity to calculate thermal inertias at Gale Crater at horizontal scales of ∼10(2) m(2). We analyze three sols representing distinct environmental conditions and soil properties, sol 82 at Rocknest (RCK), sol 112 at Point Lake (PL), and sol 139 at Yellowknife Bay (YKB). Our results indicate that the largest thermal inertia I = 452 J m(-2) K(-1) s(-1/2) (SI units used throughout this article) is found at YKB followed by PL with I = 306 and RCK with I = 295. These values are consistent with the expected thermal inertias for the types of terrain imaged by Mastcam and with previous satellite estimations at Gale Crater. We also calculate the SEB using data from measurements by Curiosity's Rover Environmental Monitoring Station and dust opacity values derived from measurements by Mastcam. The knowledge of the SEB and thermal inertia has the potential to enhance our understanding of the climate, the geology, and the habitability of Mars.

  19. Effective approach for accurately calculating individual energy of polar heterojunction interfaces

    NASA Astrophysics Data System (ADS)

    Akiyama, Toru; Nakane, Harunobu; Nakamura, Kohji; Ito, Tomonori

    2016-09-01

    We propose a direct approach for calculating individual energy of polar semiconductor interfaces using density functional theory calculations. This approach is applied to polar interfaces between group-III nitrides (AlN and GaN) and SiC and clarifies the interplay of chemical bonding and charge neutrality at the interface, which is crucial for the stability and polarity of group-III nitrides on SiC substrates. The ideal interface is stabilized among various atomic arrangements over the wide range of the chemical potential on Si-face SiC, whereas those with intermixing are favorable on C-face SiC. The stabilization of the ideal interfaces resulting in Ga-polar GaN and Al-polar AlN films on Si-face SiC is consistent with experiments, suggesting that our approach is versatile to evaluate various polar heterojunction interfaces as well as group-III nitrides on semiconductor substrates.

  20. Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

    PubMed

    Várnai, Csilla; Bernstein, Noam; Mones, Letif; Csányi, Gábor

    2013-10-10

    We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.