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Sample records for adsorption energies calculated

  1. 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.

  2. Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

    PubMed Central

    Wang, Feng; Stuart, Steven J.; Latour, Robert A.

    2009-01-01

    The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized surface is of fundamental importance for a broad range of applications in biotechnology. The adsorption free energy for these types of interactions can be determined from a molecular dynamics simulation using the partitioning between adsorbed and nonadsorbed states, provided that sufficient sampling of both states is obtained. However, if interactions between the solute and the surface are strong, the solute will tend to be trapped near the surface during the simulation, thus preventing the adsorption free energy from being calculated by this method. This situation occurs even when using an advanced sampling algorithm such as replica-exchange molecular dynamics (REMD). In this paper, the authors demonstrate the fundamental basis of this problem using a model system consisting of one sodium ion (Na+) as the solute positioned over a surface functionalized with one negatively charged group (COO−) in explicit water. With this simple system, the authors show that sufficient sampling in the coordinate normal to the surface cannot be obtained by conventional REMD alone. The authors then present a method to overcome this problem through the use of an adaptive windowed-umbrella sampling technique to develop a biased-energy function that is combined with REMD. This approach provides an effective method for the calculation of adsorption free energy for solute-surface interactions. PMID:19768127

  3. Potential of mean force calculation of the free energy of adsorption of Type I winter flounder antifreeze protein on ice

    NASA Astrophysics Data System (ADS)

    Battle, Keith; Alan Salter, E.; Wesley Edmunds, R.; Wierzbicki, Andrzej

    2010-04-01

    Antifreeze proteins (AFPs) are a unique class of proteins that inhibit ice growth without changing the melting point of ice. In this work, we study the detailed molecular mechanism of interactions between the hydrophobic side of the winter flounder (WF) AFP and two mutants, AAAA and SSSS, in which threonine residues are substituted by serines and alanines, respectively. Umbrella sampling molecular dynamics simulations of the separation of the proteins from the (2 0 1) surface in an explicit water box is carried out to calculate the potential of mean force free energies of adsorption using AMBER10i. We estimate wild-type WF's free energy of adsorption to ice to be about -12.0 kcal/mol. Gas-phase pseudopotential plane-wave calculations of methane adsorption onto select surfaces of ice are also carried out under periodic boundary conditions to address the possible enthalpic role of WF's methyl groups in binding. The contributions of hydrophobic residues to the free energy of adsorption are discussed.

  4. Adsorption energies of mercury-containing species on CaO and temperature effects on equilibrium constants predicted by density functional theory calculations.

    PubMed

    Kim, Bo Gyeong; Li, Xinxin; Blowers, Paul

    2009-03-03

    The adsorption of Hg, HgCl, and HgCl2 on the CaO surface was investigated theoretically so the fundamental interactions between Hg species and this potential sorbent can be explored. Surface models of a 4 x 4 x 2 cluster, a 5 x 5 x 2 cluster, and a periodic structure using density functional theory calculations with LDA/PWC and GGA/BLYP functionals, as employed in the present work, offer a useful description for the thermodynamic properties of adsorption on metal oxides. The effect of temperature on the equilibrium constant for the adsorption of mercury-containing species on the CaO (0 0 1) surface was investigated with GGA/BLYP calculations in the temperature range of 250-600 K. Results show that, at low coverage of elemental mercury, adsorption on the surface is physisorption while the two forms of oxidized mercury adsorption undergo stronger adsorption. The adsorption energies decrease with increasing coverage for elemental mercury on the surfaces. The chlorine atom enhances the adsorption capacity and adsorbs mercury to the CaO surface more strongly. The adsorption energy is changed as the oxidation state varies, and the equilibrium constant decreases as the temperature increases, in good agreement with data for exothermic adsorption systems.

  5. Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials Using Force Field Calculations Based on Energy Decomposed Density Functional Theory.

    PubMed

    Heinen, Jurn; Burtch, Nicholas C; Walton, Krista S; Fonseca Guerra, Célia; Dubbeldam, David

    2016-12-12

    For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions.

  6. Methane Adsorption on Aggregates of Fullerenes: Site-Selective Storage Capacities and Adsorption Energies

    PubMed Central

    Kaiser, Alexander; Zöttl, Samuel; Bartl, Peter; Leidlmair, Christian; Mauracher, Andreas; Probst, Michael; Denifl, Stephan; Echt, Olof; Scheier, Paul

    2013-01-01

    Methane adsorption on positively charged aggregates of C60 is investigated by both mass spectrometry and computer simulations. Calculated adsorption energies of 118–281 meV are in the optimal range for high-density storage of natural gas. Groove sites, dimple sites, and the first complete adsorption shells are identified experimentally and confirmed by molecular dynamics simulations, using a newly developed force field for methane–methane and fullerene–methane interaction. The effects of corrugation and curvature are discussed and compared with data for adsorption on graphite, graphene, and carbon nanotubes. PMID:23744834

  7. Methane adsorption on aggregates of fullerenes: site-selective storage capacities and adsorption energies.

    PubMed

    Kaiser, Alexander; Zöttl, Samuel; Bartl, Peter; Leidlmair, Christian; Mauracher, Andreas; Probst, Michael; Denifl, Stephan; Echt, Olof; Scheier, Paul

    2013-07-01

    Methane adsorption on positively charged aggregates of C60 is investigated by both mass spectrometry and computer simulations. Calculated adsorption energies of 118-281 meV are in the optimal range for high-density storage of natural gas. Groove sites, dimple sites, and the first complete adsorption shells are identified experimentally and confirmed by molecular dynamics simulations, using a newly developed force field for methane-methane and fullerene-methane interaction. The effects of corrugation and curvature are discussed and compared with data for adsorption on graphite, graphene, and carbon nanotubes.

  8. Computation of Adsorption Energies of Some Interstellar Species

    NASA Astrophysics Data System (ADS)

    Sil, Milan; Chakrabarti, Sandip Kumar; Das, Ankan; Majumdar, Liton; Gorai, Prasanta; Etim, Emmanuel; Arunan, Elangannan

    2016-07-01

    Adsorption energies of surface species are most crucial for chemical complexity of interstellar grain mantle. Aim of this work is to study the variation of the adsorption energies depending upon the nature of adsorbent. We use silicate and carbonaceous grains for the absorbents. For silicate grains, we use very simple crystalline ones, namely, Enstatite (MgSiO_3)_n, Ferrosilite (FeSiO_3)_n, Forsterite (Mg_2SiO_4)_n and Fayalite (Fe_2SiO_4)_n. We use n=1, 2, 4, 8 to study the variation of adsorption energies with the increase in cluster size. For carbonaceous grain, we use Coronene (polyaromatic hydrocarbon surface). Adsorption energy of all these species are calculated by means of quantum chemical calculation using self consistent density functional theory (DFT). MPWB1K hybrid meta-functional is employed since it has been proven useful to study the systems with weak interactions such as van der Waals interactions. Optimization are also carried out with MPWB1K/6-311g(d) and MPWB1K/6311g(d,p) and a comparison of adsorption energies are discussed for these two different basis sets. We use crystalline structure of the adsorbent. The adsorbate is placed in the different site of the grain with a suitable distance. The energy of adsorption for a species on the grain surface is defined as follows: E_a_d_s = E_s_s - (E_s_u_r_f_a_c_e + E_s_p_e_c_i_e_s), where E_a_d_s is the adsorption energy, E_s_s is the optimized energy for species placed in a suitable distance from the grain surface, E_s_u_r_f_a_c_e and E_s_p_e_c_i_e_s respectively are the optimized energies of the surface and species separately.

  9. Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces.

    PubMed

    Qin, Wu; Li, Xin; Bian, Wen-Wen; Fan, Xiu-Juan; Qi, Jing-Yao

    2010-02-01

    There is increasing attention in the unique biological and medical properties of graphene, and it is expected that biomaterials incorporating graphene will be developed for the graphene-based drug delivery systems and biomedical devices. Despite the importance of biomolecules-graphene interactions, a detailed understanding of the adsorption mechanism and features of biomolecules onto the surfaces of graphene is lacking. To address this, we have performed density functional theory (DFT) and molecular dynamics (MD) methods exploring the adsorption geometries, adsorption energies, electronic band structures, adsorption isotherms, and adsorption dynamics of l-leucine (model biomolecule)/graphene composite system. DFT calculations confirmed the energetic stability of adsorption model and revealed that electronic structure of graphene can be controlled by the adsorption direction of l-leucine. MD simulations further investigate the potential energy and van der Waals energy for the interaction processes of l-leucine/graphene system at different temperatures and pressures. We find that the van der Waals interaction between the l-leucine and the graphene play a dominant role in the adsorption process under a certain range of temperature and pressure, and the l-leucine molecule could be adsorbed onto graphene spontaneously in aqueous solution.

  10. 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.

  11. 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

  12. Numerical estimation of adsorption energy distributions from adsorption isotherm data with the expectation-maximization method

    SciTech Connect

    Stanley, B.J.; Guiochon, G. |

    1993-08-01

    The expectation-maximization (EM) method of parameter estimation is used to calculate adsorption energy distributions of molecular probes from their adsorption isotherms. EM does not require prior knowledge of the distribution function or the isotherm, requires no smoothing of the isotherm data, and converges with high stability towards the maximum-likelihood estimate. The method is therefore robust and accurate at high iteration numbers. The EM algorithm is tested with simulated energy distributions corresponding to unimodal Gaussian, bimodal Gaussian, Poisson distributions, and the distributions resulting from Misra isotherms. Theoretical isotherms are generated from these distributions using the Langmuir model, and then chromatographic band profiles are computed using the ideal model of chromatography. Noise is then introduced in the theoretical band profiles comparable to those observed experimentally. The isotherm is then calculated using the elution-by-characteristic points method. The energy distribution given by the EM method is compared to the original one. Results are contrasted to those obtained with the House and Jaycock algorithm HILDA, and shown to be superior in terms of robustness, accuracy, and information theory. The effect of undersampling of the high-pressure/low-energy region of the adsorption is reported and discussed for the EM algorithm, as well as the effect of signal-to-noise ratio on the degree of heterogeneity that may be estimated experimentally.

  13. Determination of the Surface Energy of Sand Using Adsorption Isotherm

    NASA Astrophysics Data System (ADS)

    Ma, Lianxi; Holste, James; Hall, Kenneth

    2003-03-01

    The BET isotherm equation for multiplayer adsorption was applied to hexane, methyl propyl ketone, and water adsorption by sand (particle size > 75 mm) at 25¡ãC and accordingly, specific surface area of sand was obtained. Spreading pressures and surface energies of sand were calculated from adsorption isotherms. Hysteresis loops were observed in all isotherms but desorption isotherms approach to original points at low vapor pressure. A modified Toth-Freundlich equation was developed, which agrees with experimental data well over a wider p/p0 range. Plots of Dubinin-Radushkevich show that at low-pressure linear relation was obtained therefore our sand sample can be treated as microporous materials.

  14. Surface study of gallium- and aluminum- doped graphenes upon adsorption of cytosine: DFT calculations

    NASA Astrophysics Data System (ADS)

    Shokuhi Rad, Ali; Zareyee, Daryoush; Peyravi, Majid; Jahanshahi, Mohsen

    2016-12-01

    The adsorption of cytosine molecule on Al- and Ga- doped graphenes is studied using first-principles density functional theory (DFT) calculations. The energetically most stable geometries of cytosine on both Al- and Ga- doped graphenes are determined and the adsorption energies are calculated. The net charge of transfer as well as local charge of doped atoms upon adsorption of cytosine are studied by natural bond orbitals (NBO) analysis. Orbital hybridizing of complexes was searched by frontier molecular orbital theory (FMO), and density of states (DOS). Depending on the side of cytosine, there are four possible sites for its adsorption on doped graphene; denoted as P1, P2, P3, and P4, respectively. The order of binding energy in the case of Al-doped graphene is found as P1 ˃ P4 ˃ P3 ˃ P2. Interestingly, the order in the case of Ga-doped graphene changes to: P4 ∼ P1˃ P3˃ P2. Both surfaces show superior adsorbent property, resulting chemisorption of cytosine, especially at P1 and P4 position configurations. The NBO charge analysis reveals that the charge transfers from Al- and Ga- doped graphene sheets to cytosine. The electronic properties of both surfaces undertake important changes after cytosine adsorption, which indicates notable change in its electrical conductivity.

  15. CO2 adsorption and separation from natural gason phosphorene surface: Combining DFT and GCMC calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Yayun; Liu, Chao; Hao, Feng; Xiao, Hang; Zhang, Shiwei; Chen, Xi

    2017-03-01

    We have examined the performance of phosphorene-based material, phosphorene slit pores (PSP), in CO2 adsorption and separation from natural gas by using Density Function Theory (DFT) calculation and Grand Canonical Monte Carlo (GCMC) simulations. First, the adsorption of CH4 and CO2molecules on phosphorene sheet were conducted by DFT study. Then, adsorption performances of natural gas components as well as their binary CO2/CH4 gas mixture were investigated at 300 K with the pressure up to 3.0 MPa. The effects of slit pore width, H, and mole ratio of CO2/CH4in the gas phase on the separation of CO2 from mixtures of CO2/CH4 were also investigated. Our DFT calculation results show that the CO2 moleculehas higher adsorption energy than that of CH4, which implies that it can be easily adsorbed to the phosphorene surface than CH4. Detailed GCMC simulations reveal that the phosphorene slit pore has a high performance in separating CO2fromnature gas and achieves the highest gas selectivity at H = 1.0 nm at pressures lower than 0.1 MPa. Moreover, the selectivity of CO2 overCO2/CH4gas mixture increases with increasing the mole ratio of CO2/CH4due to the enhanced adsorbate-adsorbent interactions for the favorable component. Therefore, it is suggested that the phosphorene is a promising candidate for natural gas purification and possessing practical potential applications in gas adsorption.

  16. First-principles calculations of H, O and OH adsorption on metallic layered supported thin films

    NASA Astrophysics Data System (ADS)

    Pereira, Aline O.; Miranda, Caetano R.

    2013-05-01

    In this work, the adsorption of hydrogen, oxygen and hydroxyl on metallic thin films is studied through first-principles calculations. We explore how the structural and electronic properties of palladium, platinum and gold thin films change with respect to the type of substrate. As a major result we find that Pd/Au(111) and Pt/Au(111) thin films present enhanced adsorption properties for H, O and OH. This improvement is a result of the induced tensile strain on the film due to the misfit between the lattice parameters of the film and the substrate. For these systems, the tensile strain results in a shift of the d-band center position towards to the Fermi level, with implications for the enhancement of adsorption properties. Our results suggest that the location of the unadsorbed d-band center for Pd/Au(111), Pt/Au(111) and Au thin films is a good parameter to predict the reactivity between these surfaces and H, O and OH. However, when considering different numbers of atomic monolayers, changes in adsorption energy are observed and there is no correlation for Pd/Au(111) and Au/Pt(111) films. For Pd/Pt(111) and Pt/Pd(111) films the difference between lattice parameters is relatively small, and no correlation is found, since no considerable strain is induced. In addition, our results support that a compressive strain will always lead to weaker adsorption. We also observe that the work function is strongly affected by adsorption. In particular, H adsorption results in an expansion of the interlayer distance between the topmost layers of the film. Furthermore, after atomic insertion, the interlayer distance of Pd/Pt(111) films is similar to the interlayer distance for bulk PdH0.6, which indicates that these thin films can act as precursor states for hydride formation.

  17. The Calculation of Adsorption Isotherms from Chromatographic Peak Shapes

    ERIC Educational Resources Information Center

    Neumann, M. G.

    1976-01-01

    Discusses the relationship between adsorption isotherms and elution peak shapes in gas chromatography, and describes a laboratory experiment which involves the adsorption of hexane, cyclohexane, and benzene on alumina at different temperatures. (MLH)

  18. Free energy of adsorption of supported lipid bilayers from molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Schneemilch, M.; Quirke, N.

    2016-11-01

    A novel method is presented for the calculation of adhesion energies of lipid bilayers on solid surfaces from molecular dynamics simulation. We illustrate the method with a fully atomistic model comprising a gold surface and an adsorbed lipid bilayer. We use our technique to scale the lipid-surface interactions to reproduce the experimental value for adsorption of DMPC bilayers on gold surfaces. Finally we estimate the entropic contribution to the free energy change on adsorption of the bilayer.

  19. Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations.

    PubMed

    Wang, Xinye; Huang, Yaji; Pan, Zhigang; Wang, Yongxing; Liu, Changqi

    2015-09-15

    Kaolinite can be used as the in-furnace sorbent/additive to adsorb lead (Pb) vapor at high temperature. In this paper, the adsorptions of Pb atom, PbO molecule and PbCl2 molecule on kaolinie surfaces were investigated by density functional theory (DFT) calculation. Si surface is inert to Pb vapor adsorption while Al surfaces with dehydroxylation are active for the unsaturated Al atoms and the O atoms losing H atoms. The adsorption energy of PbO is much higher than that of Pb atom and PbCl2. Considering the energy barriers, it is easy for PbO and PbCl2 to adsorb on Al surfaces but difficult to escape. The high energy barriers of de-HCl process cause the difficulties of PbCl2 to form PbO·Al2O3·2SiO2 with kaolinite. Considering the inertia of Si atoms and the activity of Al atoms after dehydroxylation, calcination, acid/alkali treatment and some other treatment aiming at amorphous silica producing and Al activity enhancement can be used as the modification measures to improve the performance of kaolinite as the in-furnace metal capture sorbent.

  20. First-principles calculations of the indigo encapsulation and adsorption by MgO nanotubes

    SciTech Connect

    Sánchez-Ochoa, F. Cocoletzi, Gregorio H.; Canto, Gabriel I.; Takeuchi, Noboru

    2014-06-07

    We have performed ab-initio calculations to investigate the structural and electronic properties of (m,m) chiral magnesium oxide nanotubes, (m,m)MgONTs, to explore the encapsulation, inclusion, and adsorption of dyes (organic molecules) such as Indigo (IND). Studies start by determining the structural parameters of the MgO nanotubes with different diameters and the IND. The indigo encapsulation into the MgONT is studied considering four (m,m) chiralities which yield 4 different NT diameters. In the endohedral functionalization, the indigo is within the NT at a tilt angle as in previous theoretical studies of organic molecules inside carbon and boron-nitride nanotubes. Results show that the encapsulation is a strong exothermic process with the m = 6 case exhibiting the largest encapsulation energy. It is also explored the indigo adsorption on the NT surface in the parallel and perpendicular configurations. The perpendicular configuration of the IND adsorption on the (8,8)MgONT exhibits the largest energy. The indigo inclusion within the NTs meets a potential barrier when m < 6, however this barrier diminishes as the index increases. Additionally, we have determined the total density of states (DOS), partial DOS, electron charge redistributions, and the highest occupied molecular orbital–lowest unoccupied molecular orbital levels for the NTs with m = 6. Very strong binding energies and electron charge transfer from the IND to NTs is present in the atomic structures.

  1. Formulating the bonding contribution equation in heterogeneous catalysis: a quantitative description between the surface structure and adsorption energy.

    PubMed

    Wang, Ziyun; Hu, P

    2017-02-15

    The relation between the surface structure and adsorption energy of adsorbates is of great importance in heterogeneous catalysis. Based on density functional theory calculations, we propose an explicit equation with three chemically meaningful terms, namely the bonding contribution equation, to quantitatively account for the surface structures and the adsorption energies. Successful predictions of oxygen adsorption energies on complex alloy surfaces containing up to 4 components are demonstrated, and the generality of this equation is also tested using different surface sizes and other adsorbates. This work may not only offer a powerful tool to understand the structure-adsorption relation, but may also be used to inversely design novel catalysts.

  2. Lithium adsorption on graphite from density functional theory calculations.

    PubMed

    Valencia, Felipe; Romero, Aldo H; Ancilotto, Francesco; Silvestrelli, Pier Luigi

    2006-08-03

    The structural, energetic, and electronic properties of the Li/graphite system are studied through density functional theory (DFT) calculations using both the local spin density approximation (LSDA), and the gradient-corrected Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation energy. The calculations were performed using plane waves basis, and the electron-core interactions are described using pseudopotentials. We consider a disperse phase of the adsorbate comprising one Li atom for each 16 graphite surface cells, in a slab geometry. The close contact between the Li nucleus and the graphene plane results in a relatively large binding energy (larger than 1.1 eV). A detailed analysis of the electronic charge distribution, density difference distribution, and band structures indicates that one valence electron is entirely transferred from the atom to the surface, which gives rise to a strong interaction between the resulting lithium ion and the cloud of pi electrons in the substrate. We show that it is possible to explain the differences in the binding of Li, Na, and K adatoms on graphite considering the properties of the corresponding cation/aromatic complexes.

  3. Statistical thermodynamics of adsorption of dye DR75 onto natural materials and its modifications: double-layer model with two adsorption energies.

    PubMed

    Khalfaoui, M; Nakhli, A; Aguir, Ch; Omri, A; M'henni, M F; Ben Lamine, A

    2014-02-01

    In this article, adsorption modelling was presented to describe the sorption of textile dye, Direct Red 75 (DR75), from coloured wastewater onto the natural and modified adsorbent, Posidonia oceanica. The formulation of the double-layer model with two energy levels was based on statistical physics and theoretical considerations. Thanks to the grand canonical ensemble in statistical physics some physico-chemical parameters related to the adsorption process were introduced in the analytical model expression. Fitting results show that the dye molecules are adsorbed in parallel position to the adsorbent surface. The magnitudes of the calculated adsorption energies show that the DR75 dye is physisorbed onto Posidonia. Both Van der Waals and hydrogen interactions are implicated in the adsorption process. Despite its simplicity, the model fits a wide range of experimental data, thereby supporting the underlying data that the grafted groups facilitate the parallel anchorage of the anionic dye molecule. Thermodynamic parameters, such as adsorption energy, entropy, Gibbs free adsorption energy and internal energy were calculated according to the double-layer model. Results suggested that the DR75 adsorption onto Posidonia was a spontaneous and exothermic process.

  4. A benchmark database for adsorption bond energies to transition metal surfaces and comparison to selected DFT functionals

    NASA Astrophysics Data System (ADS)

    Wellendorff, Jess; Silbaugh, Trent L.; Garcia-Pintos, Delfina; Nørskov, Jens K.; Bligaard, Thomas; Studt, Felix; Campbell, Charles T.

    2015-10-01

    We present a literature collection of experimental adsorption energies over late transition metal surfaces for systems where we believe the energy measurements are particularly accurate, and the atomic-scale adsorption geometries are particularly well established. We propose that this could become useful for benchmarking theoretical methods for calculating adsorption processes. We compare the experimental results to six commonly used electron density functionals, including some (RPBE, BEEF-vdW) which were specifically developed to treat adsorption processes. The comparison shows that there is ample room for improvements in the theoretical descriptions.

  5. Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes

    SciTech Connect

    Liu, Kexi; Lei, Yinkai; Wang, Guofeng

    2013-11-28

    Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O{sub 2} adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N{sub 4} chelation, as well as the molecular and electronic structures for the O{sub 2} adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O{sub 2} on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d{sub z{sup 2}}, d{sub xy}, d{sub xz}, and d{sub yz}) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O{sub 2} adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

  6. Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes.

    PubMed

    Liu, Kexi; Lei, Yinkai; Wang, Guofeng

    2013-11-28

    Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O2 adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N4 chelation, as well as the molecular and electronic structures for the O2 adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O2 on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d(z(2)), d(xy), d(xz), and d(yz)) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O2 adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

  7. Adsorption energies and prefactor determination for CH3OH adsorption on graphite.

    PubMed

    Doronin, M; Bertin, M; Michaut, X; Philippe, L; Fillion, J-H

    2015-08-28

    In this paper, we have studied adsorption and thermal desorption of methanol CH3OH on graphite surface, with the specific aim to derive from experimental data quantitative parameters that govern the desorption, namely, adsorption energy Eads and prefactor ν of the Polanyi-Wigner law. In low coverage regime, these two values are interconnected and usually the experiments can be reproduced with any couple (Eads, ν), which makes intercomparison between studies difficult since the results depend on the extraction method. Here, we use a method for determining independently the average adsorption energy and a prefactor value that works over a large range of incident methanol coverage, from a limited set of desorption curves performed at different heating rates. In the low coverage regime the procedure is based on a first order kinetic law, and considers an adsorption energy distribution which is not expected to vary with the applied heating rate. In the case of CH3OH multilayers, Eads is determined as 430 meV with a prefactor of 5 × 10(14) s(-1). For CH3OH submonolayers on graphite, adsorption energy of 470 ± 30 meV and a prefactor of (8 ± 3) × 10(16) s(-1) have been found. These last values, which do not change between 0.09 ML and 1 ML initial coverage, suggest that the methanol molecules form island-like structure on the graphite even at low coverage.

  8. Importance of the accuracy of experimental data in the nonlinear chromatographic determination of adsorption energy distributions

    SciTech Connect

    Stanley, B.J.; Guiochon, G. Oak Ridge National Lab., TN )

    1994-11-01

    Adsorption energy distributions (AEDs) are calculated from the classical, fundamental integral equation of adsorption using adsorption isotherms and the expectation-maximization method of parameter estimation. The adsorption isotherms are calculated from nonlinear elution profiles obtained from gas chromatographic data using the characteristic points method of finite concentration chromatography. Porous layer open tubular capillary columns are used to support the adsorbent. The performance of these columns is compared to that of packed columns in terms of their ability to supply accurate isotherm data and AEDs. The effect of the finite column efficiency and the limited loading factor on the accuracy of the estimated energy distributions is presented. This accuracy decreases with decreasing efficiency, and approximately 5000 theoretical plates are needed when the loading factor, L[sub f], equals 0.56 for sampling of a unimodal Gaussian distribution. Increasing L[sub f] further increases the contribution of finite efficiency to the AED and causes a divergence at the low-energy endpoint if too high. This occurs as the retention time approaches the holdup time. Data are presented for diethyl ether adsorption on porous silica and its C-18-bonded derivative. 36 refs., 8 figs., 2 tabs.

  9. Adsorption of nitrogen oxides on graphene and graphene oxides: insights from density functional calculations.

    PubMed

    Tang, Shaobin; Cao, Zexing

    2011-01-28

    The interactions of nitrogen oxides NO(x) (x = 1,2,3) and N(2)O(4) with graphene and graphene oxides (GOs) were studied by the density functional theory. Optimized geometries, binding energies, and electronic structures of the gas molecule-adsorbed graphene and GO were determined on the basis of first-principles calculations. The adsorption of nitrogen oxides on GO is generally stronger than that on graphene due to the presence of the active defect sites, such as the hydroxyl and carbonyl functional groups and the carbon atom near these groups. These active defect sites increase the binding energies and enhance charge transfers from nitrogen oxides to GO, eventually leading to the chemisorption of gas molecules and the doping character transition from acceptor to donor for NO(2) and NO. The interaction of nitrogen oxides with GO with various functional groups can result in the formation of hydrogen bonds OH⋅⋅⋅O (N) between -OH and nitrogen oxides and new weak covalent bonds C⋅⋅⋅N and C⋅⋅⋅O, as well as the H abstraction to form nitrous acid- and nitric acidlike moieties. The spin-polarized density of states reveals a strong hybridization of frontier orbitals of NO(2) and NO(3) with the electronic states around the Fermi level of GO, and gives rise to the strong acceptor doping by these molecules and remarkable charge transfers from molecules to GO, compared to NO and N(2)O(4) adsorptions on GO. The calculated results show good agreement with experimental observations.

  10. Adsorption and diffusion of Ru adatoms on Ru(0001)-supported graphene: Large-scale first-principles calculations

    SciTech Connect

    Han, Yong; Evans, James W.

    2015-10-28

    Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C{sub 6}-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ∼0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. This in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001)

  11. Adsorption and diffusion of Ru adatoms on Ru(0001)-supported graphene: Large-scale first-principles calculations

    DOE PAGES

    Han, Yong; Evans, James W.

    2015-10-27

    Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom inmore » the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).« less

  12. Adsorption and diffusion of Ru adatoms on Ru(0001)-supported graphene: Large-scale first-principles calculations

    SciTech Connect

    Han, Yong; Evans, James W.

    2015-10-27

    Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).

  13. Water adsorption in SAPO-34: elucidating the role of local heterogeneities and defects using dispersion-corrected DFT calculations.

    PubMed

    Fischer, Michael

    2015-10-14

    The chabazite-type silicoaluminophosphate SAPO-34 is a promising adsorbent for applications in thermal energy storage using water adsorption-desorption cycles. In order to develop a microscopic understanding of the impact of local heterogeneities and defects on the water adsorption properties, the interaction of different models of SAPO-34 with water was studied using dispersion-corrected density-functional theory (DFT-D) calculations. In addition to SAPO-34 with isolated silicon atoms, the calculations considered models incorporating two types of heterogeneities (silicon islands, aluminosilicate domains), and two defect-containing (partially and fully desilicated) systems. DFT-D optimisations were performed for systems with small amounts of adsorbed water, in which all H2O molecules can interact with framework protons, and systems with large amounts of adsorbed water (30 H2O molecules per unit cell). At low loadings, the host-guest interaction energy calculated for SAPO-34 with isolated Si atoms amounts to approximately -90 kJ mol(-1). While the presence of local heterogeneities leads to the creation of some adsorption sites that are energetically slightly more favourable, the interaction strength is drastically reduced in systems with defects. At high water loadings, energies in the range of -70 kJ mol(-1) are obtained for all models. The DFT-D interaction energies are in good agreement with experimentally measured heats of water adsorption. A detailed analysis of the equilibrium structures was used to gain insights into the binding modes at low coverages, and to assess the extent of framework deprotonation and changes in the coordination environment of aluminium atoms at high water loadings.

  14. Copper(II) adsorption on the kaolinite(001) surface: Insights from first-principles calculations and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kong, Xiang-Ping; Wang, Juan

    2016-12-01

    The adsorption behavior of Cu(II) on the basal hydroxylated kaolinite(001) surface in aqueous environment was investigated by first-principles calculations and molecular dynamics simulations. Structures of possible monodentate and bidentate inner-sphere adsorption complexes of Cu(II) were examined, and the charge transfer and bonding mechanism were analyzed. Combining the binding energy of complex, the radial distribution function of Cu(II) with oxygen and the extended X-ray absorption fine structure data, monodentate complex on site of surface oxygen with "upright" hydrogen and bidentate complex on site of two oxygens (one with "upright" hydrogen and one with "lying" hydrogen) of single Al center have been found to be the major adsorption species of Cu(II). Both adsorption species are four-coordinated with a square planar geometry. The distribution of surface hydroxyls with "lying" hydrogen around Cu(II) plays a key role in the structure and stability of adsorption complex. Upon the Mulliken population analysis and partial density of states, charge transfer occurs with Cu(II) accepting some electrons from both surface oxygens and aqua oxygens, and the bonding Cu 3d-O 2p state filling is primarily responsible for the strong covalent interaction of Cu(II) with surface oxygen.

  15. Adsorption, dissociation, penetration, and diffusion of N2 on and in bcc Fe: first-principles calculations.

    PubMed

    Yeo, Sang Chul; Han, Sang Soo; Lee, Hyuck Mo

    2013-04-14

    We report first-principles calculations of adsorption, dissociation, penetration, and diffusion for the complete nitridation mechanism of nitrogen molecules on a pure Fe surface (bcc, ferrite phase). The mechanism of the definite reaction path was calculated by dividing the process into four steps. We investigated various reaction paths for each step including the energy barrier based on the climb image nudged elastic band (CI-NEB) method, and the complete reaction pathway was computed as the minimum energy path (MEP). The adsorption characteristics of nitrogen (N) and molecular nitrogen (N2) indicate that nitrogen atoms and molecules are energetically favorable at the hollow sites on pure Fe(100) and (110). The dissociation of the nitrogen molecule (N2) was theoretically supported by electronic structure calculations. The penetration of nitrogen from the surface to the sub-surface has a large energy barrier compared with the other steps. The activation energy calculated for nitrogen diffusion in pure bcc Fe was in good agreement with the experimental results. Finally, we confirmed the rate-determining step for the full nitridation reaction pathway. This study provides fundamental insight into the nitridation mechanism for nitrogen molecules in pure bcc Fe.

  16. Adsorption/desorption process of formaldehyde onto iron doped graphene: a theoretical exploration from density functional theory calculations.

    PubMed

    Cortés-Arriagada, Diego; Villegas-Escobar, Nery; Miranda-Rojas, Sebastián; Toro-Labbé, Alejandro

    2017-02-08

    The interaction of formaldehyde (H2CO) onto Fe-doped graphene (FeG) was studied in detail from density functional theory calculations and electronic structure analyses. Our aim was to obtain insights into the adsorption, desorption and sensing properties of FeG towards H2CO, a hazardous organic compound. The adsorption of H2CO was shown to be energetically stable onto FeG, with adsorption energies of up to 1.45 eV and favored in different conformations. This interaction was determined to be mostly electrostatic in nature, where the oxygen plays an important role in this contribution; besides, our quantum molecular dynamics results showed the high stability of the FeG-H2CO interaction at ambient temperature (300 K). All the interactions were determined to be accompanied by an increase in the HOMO-LUMO energy gap with respect to the isolated adsorbent, indicating that FeG is highly sensitive to H2CO with respect to pristine graphene. Finally, it was found that external electric fields of 0.04-0.05 a.u. were able to induce the pollutant desorption from the adsorbent, allowing the adsorbent reactivation for repetitive applications. These results indicate that FeG could be a promising candidate for adsorption/sensing platforms of H2CO.

  17. Density functional calculation of transition metal adatom adsorption on graphene.

    PubMed

    Mao, Yuliang; Yuan, Jianmei; Zhong, Jianxin

    2008-03-19

    The functionalization of graphene (a single graphite layer) by the addition of transition metal atoms of Mn, Fe and Co to its surface has been investigated computationally using density functional theory. In the calculation, the graphene surface supercell was constructed from a single layer of graphite (0001) surface separated by vertical vacuum layers 2 nm thick. We found that the center of the hexagonal ring formed by carbon from graphene is the most stable site for Mn, Fe, Co to stay after optimization. The calculated spin-polarized band structures of the graphene encapsulating the Mn adatom indicate that the conduction bands are modified and move down due to the coupling between the Mn atom and graphene. For Fe adsorbed on the graphene surface, it is semi-half-metallic, and the spin polarization P is found to be 100%. The system of Co adatom on graphene exhibits metallic electronic structure due to the density of states (DOS) peak at the band center with both majority and minority spins. Local density of states analyses indicate a larger promotion of 4s electrons into the 3d state in Fe and Co, resulting in lower local moments compared to an Mn adatom on the graphite surface.

  18. 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.

  19. Estimation of adsorption energy for water molecules on a multi-walled carbon nanotube thin film by measuring electric resistance

    NASA Astrophysics Data System (ADS)

    Kokabu, Takuya; Inoue, Shuhei; Matsumura, Yukihiko

    2016-11-01

    Gas sensors based on carbon nanotube (CNT) films have attracted attention owing to their low power consumption. For further development of these sensors, we need to understand the surface interaction of the films with gas molecules. In our previous research, we investigated the influence of water molecules on the electrical conductance of multi-walled CNT films and explained this phenomenon using a two-layer adsorption model. This work motivated us to measure the adsorption energy of CNT-H2O. In this study, we focused on the first-layer adsorption and investigated the sheet resistance to water vapor pressure at various temperatures using the transmission line method (TLM). The results were fitted to Langmuir adsorption model and the adsorption equilibrium constant was determined. The temperature dependence of the sheet resistance followed a model of fluctuation induced tunneling (FIT), in which the energy barrier at the CNT junction is regarded as the main factor influencing the electrical conductance of the CNT film. The sheet resistance and equilibrium constant decreased as temperature increased. This result was consistent with the adsorption phenomenon. Finally, the adsorption energy was determined to be 0.22-0.31 eV, which is larger than the previously calculated value. It was also reported that the adsorption energy of the gas molecules in the interstitial site between two carbon nanotubes was larger than that on the CNT surface. These results indicate that the CNT junction plays a key role in the detection of gas molecules.

  20. 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.

  1. 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.

  2. Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold.

    PubMed

    Hughes, Zak E; Wright, Louise B; Walsh, Tiffany R

    2013-10-29

    The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively

  3. Adsorption of energy in photocatalytic reactors

    SciTech Connect

    Somorjai, G.A.

    1985-07-01

    The dissociation of water to hydrogen and oxygen requires energy ..delta..G/sub 298/ = 228 kJ/mole. By irradiating a semiconductor with light of energy greater than this amount, one may produce electrons in the excited state and electron vacancies at the surface that can perform the photochemical reduction (2H/sup +/ + 2e/sup -/ ..-->.. 2H ..-->.. H/sub 2/) and oxidation (20H/sup -/ + 2/sup +/ ..-->.. H/sub 2/O/sub 2/ ..-->.. H/sub 2/O + (1/2)O/sub 2/). There are several semiconductors, SrTiO/sub 3/, TiO/sub 2/, CdS, and Fe/sub 2/O/sub 3/ among them, that can photodissociate water. Some possess sites for both reduction and oxidation, while others carry out the two processes at different surfaces. A reversible solid state reaction that involves changes in the transition metal and ion oxidation state must accompany the splitting of water. Platinum, rhodium, and ruthenium oxide, when deposited on the semiconductor, serve as catalysts that accelerate the water photodissociation. These additives accelerate the recombination of hydrogen and oxygen atoms, shift the semiconductor Fermi level to a more favorable position that improves the thermodynamic feasibility for the process, accelerate electron transport, and inhibit side reactions like the photoreduction of oxygen. Many of the elementary reaction steps leading to photoproduction of hydrogen and oxygen over SrTiO/sub 3/ and Fe/sub 2/O/sub 3/ have been identified and will be discussed.

  4. Classical dynamics of dissociative adsorption for a nonactivated system: The role of zero point energy

    NASA Astrophysics Data System (ADS)

    Busnengo, H. F.; Crespos, C.; Dong, W.; Rayez, J. C.; Salin, A.

    2002-05-01

    We present dissociative adsorption probabilities of H2 on Pd(111) computed with the classical trajectory method. We perform both classical (C) and quasiclassical (QC) calculations, the latter including, by contrast with the former, the initial zero point energy (ZPE) of H2. We analyze in detail the role played by the ZPE and demonstrate the strong and weak points of both C and QC calculations. We show that ZPE is crucial in accelerating the molecules toward the surface through vibrational softening. However, at low energies, dynamic trapping is quenched in QC calculations by processes of vibration to rotation energy transfer that would be associated with closed channels in a quantum approach. In this study we use a new representation of the H2/Pd(111) potential energy surface (obtained by interpolation of ab initio data) with a significantly better accuracy in the entrance channel region which plays a decisive role in the dissociation dynamics.

  5. 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.

  6. 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.

  7. Hydrogen adsorption and storage on Palladium - functionalized graphene with NH-dopant: A first principles calculation

    NASA Astrophysics Data System (ADS)

    Faye, Omar; Szpunar, Jerzy A.; Szpunar, Barbara; Beye, Aboubaker Chedikh

    2017-01-01

    We conducted a detailed theoretical investigation of the structural and electronic properties of single and double sided Pd-functionalized graphene and NH-doped Pd-functionalized graphene, which are shown to be efficient materials for hydrogen storage. Nitrene radical dopant was an effective addition required for enhancing the Pd binding on the graphene sheet as well as the storage of hydrogen. We found that up to eight H2 molecules could be adsorbed by double-sided Pd-functionalized graphene at 0 K with an average binding energy in the range 1.315-0.567 eVA gravimetric hydrogen density of 3.622 wt% was reached in the Pd-functionalized graphene on both sides. The binding mechanism of H2 molecules came not only the polarization mechanism between Pd and H atoms but also from the binding of the Pd atoms on the graphene sheet and the orbital hybridization. The most crucial part of our work is measuring the effect of nitrene radical on the H2 adsorption on Pd-functionalized graphene. Our calculations predicted that the addition of NH radicals on Pd-functionalized graphene enhance the binding of H2 molecules, which helps also to avoid the desorption of Pd(H2)n (n = 1-5) complexes from graphene sheet. Our results also predict Pd-functionalized NH-doped graphene is a potential hydrogen storage medium for on-board applications.

  8. Surface complexation modeling calculation of Pb(II) adsorption onto the calcined diatomite

    NASA Astrophysics Data System (ADS)

    Ma, Shu-Cui; Zhang, Ji-Lin; Sun, De-Hui; Liu, Gui-Xia

    2015-12-01

    Removal of noxious heavy metal ions (e.g. Pb(II)) by surface adsorption of minerals (e.g. diatomite) is an important means in the environmental aqueous pollution control. Thus, it is very essential to understand the surface adsorptive behavior and mechanism. In this work, the Pb(II) apparent surface complexation reaction equilibrium constants on the calcined diatomite and distributions of Pb(II) surface species were investigated through modeling calculations of Pb(II) based on diffuse double layer model (DLM) with three amphoteric sites. Batch experiments were used to study the adsorption of Pb(II) onto the calcined diatomite as a function of pH (3.0-7.0) and different ionic strengths (0.05 and 0.1 mol L-1 NaCl) under ambient atmosphere. Adsorption of Pb(II) can be well described by Freundlich isotherm models. The apparent surface complexation equilibrium constants (log K) were obtained by fitting the batch experimental data using the PEST 13.0 together with PHREEQC 3.1.2 codes and there is good agreement between measured and predicted data. Distribution of Pb(II) surface species on the diatomite calculated by PHREEQC 3.1.2 program indicates that the impurity cations (e.g. Al3+, Fe3+, etc.) in the diatomite play a leading role in the Pb(II) adsorption and dominant formation of complexes and additional electrostatic interaction are the main adsorption mechanism of Pb(II) on the diatomite under weak acidic conditions.

  9. Thermodynamic investigations using molecular dynamics simulations with potential of mean force calculations for cardiotoxin protein adsorption on mixed self-assembled monolayers.

    PubMed

    Hung, Shih-Wei; Hsiao, Pai-Yi; Lu, Ming-Chang; Chieng, Ching-Chang

    2012-10-25

    Understanding protein adsorption onto solid surfaces is of critical importance in the field of bioengineering, especially for applications such as medical implants, diagnostic biosensors, drug delivery systems, and tissue engineering. This study proposed the use of molecular dynamics simulations with potential of mean force (PMF) calculations to identify and characterize the mechanisms of adsorption of a protein molecule on a designed surface. A set of model systems consisting of a cardiotoxin (CTX) protein and mixed self-assembled monolayer (SAM) surfaces were used as examples. The set of mixed SAM surfaces with varying topographies were created by mixing alkanethiol chains of different lengths. The results revealed that CTX proteins underwent similar conformal changes upon adsorption onto the various mixed SAMs but showed distinctive characteristics in free energy profiles. Enhancement of the adsorption affinity, i.e., the change in free energy of adsorption, for mixed SAMs was demonstrated by using atomic force microscopic measurements. A component analysis conducted to quantify the physical mechanisms that promoted CTX adsorption revealed contributions from both SAMs and the solvent. Further component analyses of thermodynamic properties, such as the free energy, enthalpy, and entropy, indicated that the contribution from SAMs was driven by enthalpy, and the contribution from the solvent was driven by entropy. The results indicated that CTX adsorption was an entropy-driven process, and the entropic component from the solvent, i.e., the hydrophobic interaction, was the major driving force for CTX adsorption onto SAMs. The study also concluded that the surfaces composed of mixtures of SAMs with different chain lengths promoted the adsorption of CTX protein.

  10. 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).

  11. 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…

  12. Verification of selected relationships for fractally porous solids by using adsorption isotherms calculated from density functional theory

    NASA Astrophysics Data System (ADS)

    Jaroniec, Mietek; Kruk, Michal; Olivier, James

    1995-11-01

    Methods of calculating the fractal dimension (D) on the basis of single adsorption isotherms were critically tested by using argon composite adsorption isotherms for fractally porous solids. These isotherms were obtained from adsorption data for homogeneous slit-like pores calculated by employing the density functional theory (DFT). The composite adsorption isotherms were used to test the validity of the method based on the Frenkel-Halsey-Hill equation and so called "thermodynamic method" proposed by Neimark. The applicability of these methods was confirmed. However, our studies reveal new aspects of practical usage of both approaches, which need to be taken into consideration in analysis of experimental data.

  13. 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)

  14. 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.

  15. Zero energy scattering calculation in Euclidean space

    NASA Astrophysics Data System (ADS)

    Carbonell, J.; Karmanov, V. A.

    2016-03-01

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

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

    SciTech Connect

    Jia, Juanjuan; Kara, Abdelkader E-mail: vladimir.esaulov@u-psud.fr; Pasquali, Luca; Bendounan, Azzedine; Sirotti, Fausto; Esaulov, Vladimir A. E-mail: vladimir.esaulov@u-psud.fr

    2015-09-14

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

  17. Energy-efficient recovery of butanol from model solutions and fermentation broth by adsorption.

    PubMed

    Qureshi, N; Hughes, S; Maddox, I S; Cotta, M A

    2005-07-01

    This article discusses the separation of butanol from aqueous solutions and/or fermentation broth by adsorption. Butanol fermentation is also known as acetone butanol ethanol (ABE) or solvent fermentation. Adsorbents such as silicalite, resins (XAD-2, XAD-4, XAD-7, XAD-8, XAD-16), bone charcoal, activated charcoal, bonopore, and polyvinylpyridine have been studied. Use of silicalite appears to be the more attractive as it can be used to concentrate butanol from dilute solutions (5 to 790-810 g L(-1)) and results in complete desorption of butanol (or ABE). In addition, silicalite can be regenerated by heat treatment. The energy requirement for butanol recovery by adsorption-desorption processes has been calculated to be 1,948 kcal kg(-1) butanol as compared to 5,789 kcal kg(-1) butanol by steam stripping distillation. Other techniques such as gas stripping and pervaporation require 5,220 and 3,295 kcal kg(-1) butanol, respectively.

  18. Understanding the Adsorption Mechanism of Xe and Kr in a Metal-Organic Framework from X-ray Structural Analysis and First- Principles Calculations

    SciTech Connect

    Ghose, Sanjit K.; Li, Yan; Yakovenko, Andrey; Dooryhee, Eric; Ehm, Lars; Ecker, Lynne E.; Dippel, Ann-Christin; Halder, Gregory J.; Strachan, Denis M.; Thallapally, Praveen K.

    2015-04-16

    Enhancement of adsorption capacity and separation of radioactive Xe/Kr at room temperature and above is a challenging problem. Here, we report a detailed structural refinement and analysis of the synchrotron X-ray powder diffraction data of Ni-DODBC metal organic framework with in situ Xe and Kr adsorption at room temperature and above. Our results reveal that Xe and Kr adsorb at the open metal sites, with adsorption geometries well reproduced by DFT calculations. The measured temperature-dependent adsorption capacity of Xe is substantially larger than that for Kr, indicating the selectivity of Xe over Kr and is consistent with the more negative adsorption energy (dominated by van der Waals dispersion interactions) predicted from DFT. Our results reveal critical structural and energetic information about host–guest interactions that dictate the selective adsorption mechanism of these two inert gases, providing guidance for the design and synthesis of new MOF materials for the separation of environmentally hazardous gases from nuclear reprocessing applications.

  19. Adsorption energies of H and H2: a quantum-chemical study1

    NASA Astrophysics Data System (ADS)

    Sil, Milan; Gorai, Prasanta; Das, Ankan; Sahu, Dipen; Chakrabarti, Sandip K.

    2017-02-01

    The chemical composition of interstellar grain mantle is mostly dependent on adsorption energies of the surface species. Since hydrogen is widespread either in atomic or in molecular form, our aim in this work is to review (by quantum chemical calculations) the variation of the adsorption energies of H and H2 depending on the nature of the adsorbents. Choice of absorbents was based on relative abundances of interstellar materials. Since carbonaceous and silicate grains are very abundant, we used them as our absorbents. To save computational time, benzene (smallest structure sample of PAHs) is employed as carbonaceous material and for silicate grain, simple cluster of silicon dioxide (silica) (SiO2)3 is used. Around dense cloud regions, water is the major constituent of a grain mantle, therefore, usage of binding energies with bare grains is immaterial. To mimic the water as the adsorbents, we use a water-cluster ((H2O)6). We found that, for all types of adsorbents considered here, binding energies of H are always lower than those of H2, whereas, some of the experimental values are just the other way around. Assuming a steady state solution to the rate equation method, we also present the H2 formation efficiency window in various cases. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic and B. Sivaraman.

  20. Fermi level pinning and the charge transfer contribution to the energy of adsorption at semiconducting surfaces

    SciTech Connect

    Krukowski, Stanisław; Kempisty, Paweł; Strak, Paweł; Sakowski, Konrad

    2014-01-28

    It is shown that charge transfer, the process analogous to formation of semiconductor p-n junction, contributes significantly to adsorption energy at semiconductor surfaces. For the processes without the charge transfer, such as molecular adsorption of closed shell systems, the adsorption energy is determined by the bonding only. In the case involving charge transfer, such as open shell systems like metal atoms or the dissociating molecules, the energy attains different value for the Fermi level differently pinned. The Density Functional Theory (DFT) simulation of species adsorption at different surfaces, such as SiC(0001) or GaN(0001) confirms these predictions: the molecular adsorption is independent on the coverage, while the dissociative process adsorption energy varies by several electronvolts.

  1. 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.

  2. Optimal smoothing of site-energy distributions from adsorption isotherms

    SciTech Connect

    Brown, L.F.; Travis, B.J.

    1983-01-01

    The equation for the adsorption isotherm on a heterogeneous surface is a Fredholm integral equation. In solving it for the site-energy distribution (SED), some sort of smoothing must be carried out. The optimal amount of smoothing will give the most information that is possible without introducing nonexistent structure into the SED. Recently, Butler, Reeds, and Dawson proposed a criterion (the BRD criterion) for choosing the optimal smoothing parameter when using regularization to solve Fredholm equations. The BRD criterion is tested for its suitability in obtaining optimal SED's. This criterion is found to be too conservative. While using it never introduces nonexistent structure into the SED, significant information is often lost. At present, no simple criterion for choosing the optimal smoothing parameter exists, and a modeling approach is recommended.

  3. The S(2p) Core Level Binding Energies for Alternative Adsorption Sites and the Example of Thiol Self Assembly

    NASA Astrophysics Data System (ADS)

    Jia, Juanjuan; Esaulov, Vladimir; Kara, Abdelkader

    2015-03-01

    Results of an investigation of the characteristics of thiol SAMs obtained by vacuum evaporative adsorption, useful for reactive substrates, are presented along with core level binding energy (BE) calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) are obtained by evaporation on Au. They display an unconventional BE structure at about 161 eV, which is close to a known BE of an S atom on Au. S(2p) core level BE calculations for molecules chemisorbed on hollow, bridge and atop sites are reported and suggest that the 161 eV peak is indeed due to an alternative adsorption site, which can be associated to an atop configuration. This must therefore not be confused with atomic sulfur and dissociation processes with S-C bond scission. Work partially supported by the U.S. Department of Energy Basic Energy Science under Contract No DE-FG02-11ER16243.

  4. Accurate Evaluation of the Dispersion Energy in the Simulation of Gas Adsorption into Porous Zeolites.

    PubMed

    Fraccarollo, Alberto; Canti, Lorenzo; Marchese, Leonardo; Cossi, Maurizio

    2017-03-07

    The force fields used to simulate the gas adsorption in porous materials are strongly dominated by the van der Waals (vdW) terms. Here we discuss the delicate problem to estimate these terms accurately, analyzing the effect of different models. To this end, we simulated the physisorption of CH4, CO2, and Ar into various Al-free microporous zeolites (ITQ-29, SSZ-13, and silicalite-1), comparing the theoretical results with accurate experimental isotherms. The vdW terms in the force fields were parametrized against the free gas densities and high-level quantum mechanical (QM) calculations, comparing different methods to evaluate the dispersion energies. In particular, MP2 and DFT with semiempirical corrections, with suitable basis sets, were chosen to approximate the best QM calculations; either Lennard-Jones or Morse expressions were used to include the vdW terms in the force fields. The comparison of the simulated and experimental isotherms revealed that a strong interplay exists between the definition of the dispersion energies and the functional form used in the force field; these results are fairly general and reproducible, at least for the systems considered here. On this basis, the reliability of different models can be discussed, and a recipe can be provided to obtain accurate simulated adsorption isotherms.

  5. 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.

  6. Adsorption energy distribution of carbon tetrachloride on carbon nanofiber arrays prepared by template synthesis

    NASA Astrophysics Data System (ADS)

    Wu, Chi-Hsin; Shr, Jin-Fang; Wu, Chu-Fu; Hsieh, Chien-Te

    2008-02-01

    The influence of pore size distribution on adsorption energy distributions (AEDs) of aligned carbon nanofiber (CNF) arrays in vapor phase was conducted in the present study. A template-assisted synthesis was employed to fabricate aligned CNF arrays with different pore size distributions (PSDs). Adsorption isotherms of CCl 4 onto the CNF arrays were investigated within an entire pressure of 0.05-0.18 atm at 30 °C. The adsorptive surface coverage was found to decrease with the average pore size, indicating the presence of heterogeneity for gas adsorption. An AED model was postulated to describe the heterogeneous surface consisting of numerous surface pitchwises that obey a localized Langmuir model. It was found that all CNF arrays exhibit a similar Gaussian-type AED, in where the peak adsorption energy shifts to a higher energy with decreasing the pore size of CNFs. This finding can be ascribed to a fact that micropores are major providers of adsorption sites, whereas in mesopores only weaker adsorption is observed, thus resulting in the shift of energy distribution. An excellent prediction to the adsorption isotherms of CCl 4 by the AED model indicates that the PSD of CNFs acts a crucial factor in affecting the adsorptive coverage.

  7. Predicting hydrogen and methane adsorption in carbon nanopores for energy storage

    NASA Astrophysics Data System (ADS)

    Ihm, Yungok; Morris, James; Cooper, Valentino; Morris Lab, U. tennessee Collaboration; Advanced material Group, ORNL Collaboration

    2013-03-01

    There are increasing demands for alternate fuels for transportation, which requires safe, high energy density, lightweight storage materials. Experimental measurements and theoretical predictions show relatively low hydrogen storage capacities in various porous materials, limiting hydrogen as a viable alternative for automobiles. In this work, we use a continuum model based on van der Waals density functional (vdW-DF) calculations to elucidate the role that long-range interactions play in the hydrogen adsorption properties of model slit nanopores in carbon. The proper treatment of long-range interactions gives an optimal pore size for hydrogen storage of 8-9 Å (larger than previously predicted). Remarkably, we find a peak hydrogen density close to that of liquid H2 at ambient temperatures, in agreement with recent experimental results on pore-size dependent adsorption in nanoporous carbon. We then show that such nanopores would be better suited to storing methane, possibly providing an alternative to fill the gap between the capacity required by DOE goals and that attainable with current hydrogen storage technology. Research supported by the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division.

  8. Large adsorption energies for CO on Scn (n = 2-8, 13) nanoclusters

    NASA Astrophysics Data System (ADS)

    Meng, Jiang

    2016-12-01

    In order to seek a transition metal cluster with high ability to adsorb CO molecule, the author performs a density function theory calculation on COScn (n = 2-8, 13) clusters. The results demonstrate that COScn (n = 2-8, 13) clusters have the large adsorption energies of which the values are over 3.6 eV, and the elongations of C-O bond length exceed 20% in most calculated sizes. Adsorbing CO contributes to the improvement of the chemical activity, but reduces the magnetic moment of corresponding Scn cluster. Project supported by the Natural Science Foundation of Tibet Autonomous Region, China (Grant No. 2016-ZR-15-23), the Fund from the Key Laboratory of Optical Information Processing and Visualization Technology, Tibet Autonomous Region, China, the Young Talent Cultivation Plan of Xizang (Tibet) Minzu University, China (Grant No. 14myQP05), and the Important Cultivate Plan of Xizang Minzu University (Grant No. 12myZP02).

  9. An improved single crystal adsorption calorimeter for determining gas adsorption and reaction energies on complex model catalysts

    NASA Astrophysics Data System (ADS)

    Fischer-Wolfarth, Jan-Henrik; Hartmann, Jens; Farmer, Jason A.; Flores-Camacho, J. Manuel; Campbell, Charles T.; Schauermann, Swetlana; Freund, Hans-Joachim

    2011-02-01

    A new ultrahigh vacuum microcalorimeter for measuring heats of adsorption and adsorption-induced surface reactions on complex single crystal-based model surfaces is described. It has been specifically designed to study the interaction of gaseous molecules with well-defined model catalysts consisting of metal nanoparticles supported on single crystal surfaces or epitaxial thin oxide films grown on single crystals. The detection principle is based on the previously described measurement of the temperature rise upon adsorption of gaseous molecules by use of a pyroelectric polymer ribbon, which is brought into mechanical/thermal contact with the back side of the thin single crystal. The instrument includes (i) a preparation chamber providing the required equipment to prepare supported model catalysts involving well-defined nanoparticles on clean single crystal surfaces and to characterize them using surface analysis techniques and in situ reflectivity measurements and (ii) the adsorption/reaction chamber containing a molecular beam, a pyroelectric heat detector, and calibration tools for determining the absolute reactant fluxes and adsorption heats. The molecular beam is produced by a differentially pumped source based on a multichannel array capable of providing variable fluxes of both high and low vapor pressure gaseous molecules in the range of 0.005-1.5 × 1015 molecules cm-2 s-1 and is modulated by means of the computer-controlled chopper with the shortest pulse length of 150 ms. The calorimetric measurements of adsorption and reaction heats can be performed in a broad temperature range from 100 to 300 K. A novel vibrational isolation method for the pyroelectric detector is introduced for the reduction of acoustic noise. The detector shows a pulse-to-pulse standard deviation ≤15 nJ when heat pulses in the range of 190-3600 nJ are applied to the sample surface with a chopped laser. Particularly for CO adsorption on Pt(111), the energy input of 15 nJ (or 120 nJ cm

  10. Volumetric interpretation of protein adsorption: Partition coefficients, interphase volumes, and free energies of adsorption to hydrophobic surfaces.

    PubMed

    Noh, Hyeran; Vogler, Erwin A

    2006-12-01

    The solution-depletion method of measuring protein adsorption is implemented using SDS gel electrophoresis as a separation and quantification tool. Experimental method is demonstrated using lysozyme (15kDa), alpha-amylase (51kDa), human serum albumin (66kDa), prothrombin (72kDa), immunoglobulin G (160kDa), and fibrinogen (341kDa) adsorption from aqueous-buffer solution to hydrophobic octyl-sepharose and silanized-glass particles. Interpretive mass-balance equations are derived from a model premised on the idea that protein reversibly partitions from bulk solution into a three-dimensional (3D) interphase volume separating the physical-adsorbent surface from bulk solution. Theory both anticipated and accommodated adsorption of all proteins to the two test surfaces, suggesting that the underlying model is descriptive of the essential physical chemistry of protein adsorption. Application of mass balance equations to experimental data quantify partition coefficients P, interphase volumes V(I), and the number of hypothetical layers M occupied by protein adsorbed within V(I). Partition coefficients quantify protein-adsorption avidity through the equilibrium ratio of interphase and bulk-solution-phase w/v (mg/mL) concentrations W(I) and W(B), respectively, such that P identical withW(I)/W(B). Proteins are found to be weak biosurfactants with 45energy-of-adsorption -6RT<(DeltaG(adsphobic)(0)=-RTlnP)<-4RT. These measurements corroborate independent estimates obtained from interfacial energetics of adsorption (tensiometry) and are in agreement with thermochemical measurements for related proteins by hydrophobic-interaction chromatography. Proteins with molecular weight MW<100kDa occupy a single layer at surface saturation whereas the larger proteins IgG and fibrinogen required two layers.

  11. Accurate prediction of adsorption energies on graphene, using a dispersion-corrected semiempirical method including solvation.

    PubMed

    Vincent, Mark A; Hillier, Ian H

    2014-08-25

    The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can predict the adsorption energies of unsaturated hydrocarbons and the effect of substitution on these values to an accuracy comparable to DFT values and in good agreement with the experiment. The adsorption energies of TCNE, TCNQ, and a number of sulfonated pyrenes are also predicted, along with the effect of hydration using the COSMO model.

  12. Organic molecules on metal and oxide semiconductor substrates: Adsorption behavior and electronic energy level alignment

    NASA Astrophysics Data System (ADS)

    Ruggieri, Charles M.

    Modern devices such as organic light emitting diodes use organic/oxide and organic/metal interfaces for crucial processes such as charge injection and charge transfer. Understanding fundamental physical processes occurring at these interfaces is essential to improving device performance. The ultimate goal of studying such interfaces is to form a predictive model of interfacial interactions, which has not yet been established. To this end, this thesis focuses on obtaining a better understanding of fundamental physical interactions governing molecular self-assembly and electronic energy level alignment at organic/metal and organic/oxide interfaces. This is accomplished by investigating both the molecular adsorption geometry using scanning tunneling microscopy, as well as the electronic structure at the interface using direct and inverse photoemission spectroscopy, and analyzing the results in the context of first principles electronic structure calculations. First, we study the adsorption geometry of zinc tetraphenylporphyrin (ZnTPP) molecules on three noble metal surfaces: Au(111), Ag(111), and Ag(100). These surfaces were chosen to systematically compare the molecular self-assembly and adsorption behavior on two metals of the same surface symmetry and two surface symmetries of one metal. From this investigation, we improve the understanding of self-assembly at organic/metal interfaces and the relative strengths of competing intermolecular and molecule-substrate interactions that influence molecular adsorption geometry. We then investigate the electronic structure of the ZnTPP/Au(111), Ag(111), and Ag(100) interfaces as examples of weakly-interacting systems. We compare these cases to ZnTPP on TiO2(110), a wide-bandgap oxide semiconductor, and explain the intermolecular and molecule-substrate interactions that determine the electronic energy level alignment at the interface. Finally we study tetracyanoquinodimethane (TCNQ), a strong electron acceptor, on TiO2

  13. Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

    SciTech Connect

    Nakano, C. Masato; Ma, Heng; Wei, Tao

    2015-04-13

    Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

  14. 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.

  15. Optimization of adsorption processes for climate control and thermal energy storage

    SciTech Connect

    Narayanan, S; Yang, S; Kim, H; Wang, EN

    2014-10-01

    Adsorption based heat-pumps have received significant interest owing to their promise of higher efficiencies and energy savings when coupled with waste heat and solar energy compared to conventional heating and cooling systems. While adsorption systems have been widely studied through computational analysis and experiments, general design guidelines to enhance their overall performance have not been proposed. In this work, we identified conditions suitable for the maximum utilization of the adsorbent to enhance the performance of both intermittent as well as continuously operating adsorption systems. A detailed computational model was developed based on a general framework governing adsorption dynamics in a single adsorption layer and pellet. We then validated the computational analysis using experiments with a model system of zeolite 13X-water for different operating conditions. A dimensional analysis was subsequently carried out to optimize adsorption performance for any desired operating condition, which is determined by the choice of adsorbent-vapor pair, adsorption duration, operational pressure, intercrystalline porosity, adsorbent crystal size, and intracrystalline vapor diffusivity. The scaling analysis identifies the critical dimensionless parameters and provides a simple guideline to determine the most suitable geometry for the adsorbent particles. Based on this selection criterion, the computational model was used to demonstrate maximum utilization of the adsorbent for any given operational condition. By considering a wide range of parametric variations for performance optimization, these results offer important insights for designing adsorption beds for heating and cooling systems. (C) 2014 Elsevier Ltd. All rights reserved.

  16. 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.

  17. Comparisons of multilayer H2O adsorption onto the (110) surfaces of alpha-TiO2 and SnO2 as calculated with density functional theory.

    PubMed

    Bandura, Andrei V; Kubicki, James D; Sofo, Jorge O

    2008-09-18

    Mono- and bilayer adsorption of H2O molecules on TiO2 and SnO 2 (110) surfaces has been investigated using static planewave density functional theory (PW DFT) simulations. Potential energies and structures were calculated for the associative, mixed, and dissociative adsorption states. The DOS of the bare and hydrated surfaces has been used for the analysis of the difference between the H2O interaction with TiO2 and SnO 2 surfaces. The important role of the bridging oxygen in the H2O dissociation process is discussed. The influence of the second layer of H2O molecules on relaxation of the surface atoms was estimated.

  18. Rb+ adsorption at the quartz(101)-aqueous interface: comparison of resonant anomalous x-ray reflectivity with ab initio calculations

    DOE PAGES

    Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; ...

    2015-01-29

    We study adsorption of Rb+ to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb+ distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights of 1.8 ±more » 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb+ between these two conditions. At pH 7, the lowest energy structure shows that Rb+ adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb+ coverage was -0.11 C/m2, in good agreement with the range of the surface charge magnitudes reported in the literature.« less

  19. Virial expansion of the second layer in physical adsorption - An ab initio calculation for helium on argon crystal

    NASA Technical Reports Server (NTRS)

    Oh, B. K.; Kim, S. K.

    1974-01-01

    A model of helium adsorption on an argon crystal is built up from the premise that local adsorption predominates in the first layer and nonlocal adsorption in the second. Application of the virial expansion theorem to the second layer gives a series in which the first term represents the motion of a single molecule in the external potential field and the second a two-body interaction under this field. The thermodynamic functions of the adsorbed phase are calculated ab initio, the gas-solid interaction potential being derived from lattice summation and the partition function from an appropriate choice of a site-spacing polynomial to describe the periodic potential. The mutual interaction of adsorbed molecules is calculated with a two-dimensional Lennard-Jones potential. The second virial coefficient is calculated and its dependence on temperature and choice of potential is studied. It is found that the second virial coefficient is very well approximated by a two-dimensional gas in free space. The adsorption isotherm, isosteric heat, and specific heat are obtained and compared with the results of Ross and Steele, giving excellent agreement.

  20. 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.

  1. Periodic density-functional calculations on work-function change induced by adsorption of halogens on Cu(111).

    PubMed

    Roman, Tanglaw; Groß, Axel

    2013-04-12

    Using periodic density-functional theory calculations, we address the work-function change induced by the adsorption of chlorine and iodine on Cu(111) which are shown to change the work function in opposite ways, contrary to what one may expect for these two electron acceptors. In contrast to previous studies, we demonstrate that substrate effects play only a minor role in work-function changes brought about by halogen adsorption on metals. Instead, polarization on the adsorbate not only explains the sign of the work-function change as a contributor to a positive surface dipole moment, but it is also the decisive factor in the dependence of adsorption-induced work-function changes on the coverage of halogens on metal surfaces.

  2. 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.

  3. 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.

  4. 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.

  5. Predicting Enzyme Adsorption to Lignin Films by Calculating Enzyme Surface Hydrophobicity*

    PubMed Central

    Sammond, Deanne W.; Yarbrough, John M.; Mansfield, Elisabeth; Bomble, Yannick J.; Hobdey, Sarah E.; Decker, Stephen R.; Taylor, Larry E.; Resch, Michael G.; Bozell, Joseph J.; Himmel, Michael E.; Vinzant, Todd B.; Crowley, Michael F.

    2014-01-01

    The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production. PMID:24876380

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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.

  12. 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.

  13. 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

  14. Ammonia adsorption on Cl/Si(0 0 1): First-principles calculations

    NASA Astrophysics Data System (ADS)

    Lange, B.; Schmidt, W. G.

    2008-03-01

    Motivated by recent experiments [C.C. Finstad, A.G. Thorsness, A.J. Muscat, Surf. Sci. 600 (2006) 3363], the interaction between ammonia and the Cl-terminated Si(0 0 1) surface is studied using density functional theory (DFT). The reaction NH 3 (gas) + Si(0 0 1):Cl → Si(0 0 1):NH 2 + HCl (gas) is endothermic, even if temperature effects are included in the calculation. We find that the formation of ionic bonds between surface-bonded NH3+ and nearby Cl - rather than the desorption of HCl corresponds to a local energy minimum.

  15. 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.

  16. 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.

  17. Adsorption of inert gases including element 118 on noble metal and inert surfaces from ab initio Dirac-Coulomb atomic calculations.

    PubMed

    Pershina, V; Borschevsky, A; Eliav, E; Kaldor, U

    2008-10-14

    The interaction of the inert gases Rn and element 118 with various surfaces has been studied on the basis of fully relativistic ab initio Dirac-Coulomb CCSD(T) calculations of atomic properties. The calculated polarizability of element 118, 46.3 a.u., is the largest in group 18, the ionization potential is the lowest at 8.91 eV, and the estimated atomic radius is the largest, 4.55 a.u. These extreme values reflect, in addition to the general trends in the Periodic Table, the relativistic expansion and destabilization of the outer valence 7p(3/2) orbital. Van der Waals coefficients C(3) and adsorption enthalpies DeltaH(ads) of Ne through element 118 on noble metals and inert surfaces, such as quartz, ice, Teflon, and graphite, were calculated in a physisorption model using the atomic properties obtained. The C(3) coefficients were shown to steadily increase in group 18, while the increase in DeltaH(ads) from Ne to Rn does not continue to element 118: The large atomic radius of the latter element is responsible for a decrease in the interaction energy. We therefore predict that experimental distinction between Rn and 118 by adsorption on these types of surfaces will not be feasible. A possible candidate for separating the two elements is charcoal; further study is needed to test this possibility.

  18. 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

  19. Experimental approach to the anion problem in DFT calculation of the partial charge transfer during adsorption at electrochemical interfaces

    NASA Astrophysics Data System (ADS)

    Marichev, V. A.

    2005-08-01

    In DFT calculation of the charge transfer (Δ N), anions pose a special problem since their electron affinities are unknown. There is no method for calculating reasonable values of the absolute electronegativity ( χA) and chemical hardness ( ηA) for ions from data of species themselves. We propose a new approach to the experimental measurement of χA at the condition: Δ N = 0 at which η values may be neglected and χA = χMe. Electrochemical parameters corresponding to this condition may be obtained by the contact electric resistance method during in situ investigation of anion adsorption in the particular system anion-metal.

  20. Establishing and Understanding Adsorption-Energy Scaling Relations with Negative Slopes.

    PubMed

    Su, Hai-Yan; Sun, Keju; Wang, Wei-Qi; Zeng, Zhenhua; Calle-Vallejo, Federico; Li, Wei-Xue

    2016-12-15

    Adsorption-energy scaling relations are widely used for the design of catalytic materials. To date, only linear scaling relations are known in which the slopes are positive. Considering the adsorption energies of F, O, N, C, and B on transition metals, we show here that scaling relations with negative slopes also exist between certain adsorbates. The origin of such unconventional scaling relations is analyzed in terms of common descriptors such as d-band center, work function, number of outer electrons, electronic charge on the adsorbates, integrated crystal orbital overlap populations, and crystal orbital Hamilton populations. Conventional scaling relations are formed between adsorbates such as F, O, N, and C, which create ionic-like bonds with surfaces. Conversely, anomalous scaling relations are established between those and covalently bound adsorbates such as B. This widens the theory of adsorption-energy scaling relations and opens new avenues in physical chemistry and catalysis, for instance, in direct borohydride fuel cells.

  1. 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.

  2. 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.

  3. Adsorption and structure of water on kaolinite surfaces: possible insight into ice nucleation from grand canonical monte carlo calculations.

    PubMed

    Croteau, T; Bertram, A K; Patey, G N

    2008-10-30

    Grand canonical Monte Carlo calculations are used to determine water adsorption and structure on defect-free kaolinite surfaces as a function of relative humidity at 235 K. This information is then used to gain insight into ice nucleation on kaolinite surfaces. Results for both the SPC/E and TIP5P-E water models are compared and demonstrate that the Al-surface [(001) plane] and both protonated and unprotonated edges [(100) plane] strongly adsorb at atmospherically relevant relative humidities. Adsorption on the Al-surface exhibits properties of a first-order process with evidence of collective behavior, whereas adsorption on the edges is essentially continuous and appears dominated by strong water lattice interactions. For the protonated and unprotonated edges no structure that matches hexagonal ice is observed. For the Al-surface some of the water molecules formed hexagonal rings. However, the a o lattice parameter for these rings is significantly different from the corresponding constant for hexagonal ice ( Ih). A misfit strain of 14.0% is calculated between the hexagonal pattern of water adsorbed on the Al-surface and the basal plane of ice Ih. Hence, the ring structures that form on the Al-surface are not expected to be good building-blocks for ice nucleation due to the large misfit strain.

  4. Calorimetric measurement of adsorption and adhesion energies of Cu on Pt(111)

    NASA Astrophysics Data System (ADS)

    James, Trevor E.; Hemmingson, Stephanie L.; Sellers, Jason R. V.; Campbell, Charles T.

    2017-03-01

    The adsorption energies of submonolayer amounts of one metal on the surface of another metal have been measured for decades by temperature programmed desorption. However, that method fails for metals that alloy. We report here the first measurement of the adsorption energy for any such metal-on-metal combination that forms a bulk alloy. The adsorption and interfacial energetics of vapor deposited Cu onto Pt(111) at 300 K has been studied using single crystal adsorption calorimetry (SCAC) and X-ray photoelectron spectroscopy (XPS). The Cu grows as 2D pseudomorphic islands in the first layer and its heat of adsorption decreased linearly from 358 to 339 kJ/mol. This is attributed to increasing lattice strain with island size, associated with the small lattice mismatch (8%). It adsorbs 2 kJ/mol more weakly in the 2nd layer than above 3 ML, where it reaches the bulk heat of sublimation of Cu(solid), 337 kJ/mol. The adhesion energy of multilayer Cu onto Pt(111) is 3.76 J/m2. The extra stability of the first Cu monolayer compared to bulk Cu measured here is 12 kJ/mol, compared to a difference of 83 kJ/mol for underpotential deposition of Cu on a Pt(111) electrode, with the difference attributed to stronger bonding of Cu to the solvent and double layer compared to Pt.

  5. 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.

  6. Insights into the Mechanism of Fe(II) Adsorption and Oxidation at Fe-Clay Mineral Surfaces from First-Principles Calculations

    SciTech Connect

    Alexandrov, Vitali Y.; Rosso, Kevin M.

    2013-10-02

    Interfacial reactivity of redox-active iron-bearing mineral surfaces plays a crucial role in many environmental processes including biogeochemical cycling of various elements and contaminants. Herein, we apply density-functional-theory (DFT) calculations to provide atomistic insights into the heterogeneous reaction between aqueous Fe(II) and the Fe-bearing clay mineral nontronite Fe2Si4O10(OH)2 by studying its adsorption mechanism and interfacial Fe(II)-Fe(III) electron transfer (ET) at edge and basal surfaces. We find that edge-bound Fe(II) adsorption complexes at different surface sites (ferrinol, silanol and mixed) may coexist on both (010) and (110) edge facets, with complexes at ferrinol FeO(H) sites being the most energetically favorable and coupled to proton transfer. Calculation of the ET activation energy suggests that interfacial ET into dioctahedral Fe(III) sheets is probable at the clay edges and occurs predominantly but not exclusively through the complexes adsorbed at ferrinol sites and might also involve mixed sites. No clear evidence is found for complexes on basal surface that are compatible with ET through the basal sheet despite this experimentally hypothesized ET interface. This study suggests a strong pH-dependence of Fe(II) surface complexation at basal versus edge facets and highlights the importance of the protonation state of bridging ligands and proton coupled electron transfer to facilitate ET into Fe-rich clay minerals.

  7. Adsorption free energy of variable-charge nanoparticles to a charged surface in relation to the change of the average chemical state of the particles.

    PubMed

    Weng, Liping; Van Riemsdijk, Willem H; Hiemstra, Tjisse

    2006-01-03

    Variable-charge nanoparticles such as proteins and humics can adsorb strongly to charged macroscopic surfaces such as silica and iron oxide minerals. To model the adsorption of variable-charge particles to charged surfaces, one has to be able to calculate the adsorption free energy involved. It has been shown that the change in the free energy of variable-charge particles is related to the change in their average chemical state upon adsorption, which is commonly described using surface complexation models. In this work, expressions for the free-energy change in variable-charge particles due to changes in chemical binding are derived for three ion-binding models (i.e., the Langmuir, Langmuir-Freundlich, and NICA models) and for changes due to nonspecific binding for the Donnan model. The expressions for the adsorption free energy of the variable-charge particles to a charged surface are derived on the basis of the equality of the (electro)chemical potential of the particles in the bulk solution and adsorption phase. The expressions derived are general in the sense that they account for the competition between charge-determining ions that bind chemically to the particles, and they also apply in case of the formation of chemical bonds between particle ligands and surface sites. The derived expressions can be applied in the future to model the adsorption of variable-charge nanoparticles to charged surfaces. The results obtained for the NICA-Donnan model make it possible to apply this advanced surface complexation model to describe the adsorption of humics to minerals.

  8. 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.

  9. Atomic properties of element 113 and its adsorption on inert surfaces from ab initio Dirac-Coulomb calculations.

    PubMed

    Pershina, V; Borschevsky, A; Eliav, E; Kaldor, U

    2008-12-25

    Fully relativistic ab initio Dirac-Coulomb Fock-space coupled cluster calculations were performed on Tl and element 113. The calculated polarizabilty of element 113, 29.85 au, is the smallest in group 13, except for B. The estimated atomic and van der Waals radii of element 113 are also the smallest among these elements. Using the calculated atomic properties and an adsorption model, adsorption enthalpies of elements Al through 113 on inert surfaces, such as Teflon and polyethylene, are predicted. The trends in the atomic properties and DeltaH(ads) in group 13 were found to reverse from In to element 113, reflecting the strong relativistic contraction and stabilization of the outer np(1/2) orbital, which are largest for element 113. The small values of DeltaH(ads) for element 113 on Teflon (14 kJ/mol) and polyethylene (16 kJ/mol) guarantee its transport from the target chamber to the chemistry set up, and the 6 kJ/mol difference relative to Tl values makes possible the separation and identification of the superheavy element on the inert surfaces.

  10. Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane

    NASA Astrophysics Data System (ADS)

    Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.

    2008-03-01

    Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.

  11. 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.

  12. 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.

  13. 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.

  14. First-principles calculations of the adsorption of nitromethane and 1,1-diamino-2,2-dinitroethylene (FOX-7) molecules on the alpha-Al2O3(0001) surface.

    PubMed

    Sorescu, Dan C; Boatz, Jerry A; Thompson, Donald L

    2005-02-03

    First-principles calculations based on density functional theory (DFT) and the generalized gradient approximation (GGA) have been used to study the adsorption of nitromethane (NM) and 1,1-diamino-2,2-dinitroethylene (FOX-7) molecules on the basal plane of an alpha-Al(2)O(3) crystal. The calculations employ a (2 x 2) supercell slab model and 3D periodic boundary conditions. On the basis of these calculations, we have determined that both NM and FOX-7 molecules can adsorb nondissociatively on the surface with the most stable adsorption configurations parallel to the surface. The binding energies are in the range 25.3-26.0 kcal/mol for NM and 35.6-48.3 kcal/mol for FOX-7 depending on the relative molecular orientation and the surface sites. The minimum energy pathways for NM dissociation have been determined, and a low-energy pathway leading to H-atom elimination with formation of adsorbed CH(2)NO(2) and hydroxyl species has been identified. Additional calculations have focused on adsorption properties of aci-nitromethane tautomers and on description of the energetic pathways connecting adsorbed nitromethane molecule with these tautomers.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Quantum Dynamics Study on the Effects of Vibration, Translational Energy and Incident Angle on H2 Adsorption on a Defective Pt(111) Surface

    NASA Astrophysics Data System (ADS)

    Natividad, Michelle T.; Arboleda, Nelson B.; Kasai, Hideaki

    2014-12-01

    Quantum dynamics calculations via the local reflection matrix method are performed to investigate the effects of the vibration and initial translational energy on the dissociative adsorption of H2 approaching a defective Pt(111) surface at different incident angles and adsorption sites. The sticking probability plot for H2 incident on the top site at 15° shows that as the translational energy is increased, the probability rapidly rises to unity which suggests that H2 is easily adsorbed on the Pt surface. The plot also shows that even though the adsorption process is non-activated, there is a probability that H2 will not be adsorbed on the Pt surface at low translational energies due to quantum mechanical effects. For the rest of the configurations, an S-shaped region is observed in the plots suggesting an activated adsorption process. The plots show that when the initial translational energy (Et) is less that the barrier, H2 sticks to the Pt surface by tunneling through the barrier and when Et is greater than the barrier, H2 sticks on the Pt surface by using its available energy to overcome the barrier. The plots also show significant vibration assisted sticking (VAS) effect for all cases. VAS effect is most prominent for H2 approaching the vacant site at incident angles 15 and 30°.

  20. 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.

  1. CO2 adsorption on Fe-doped graphene nanoribbons: First principles electronic transport calculations

    NASA Astrophysics Data System (ADS)

    Berdiyorov, G. R.; Abdullah, H.; Al Ezzi, M.; Rakhmatullaeva, G. V.; Bahlouli, H.; Tit, N.

    2016-12-01

    Decoration of graphene with metals and metal-oxides is known to be one of the effective methods to enhance gas sensing and catalytic properties of graphene. We use density functional theory in combination with the nonequilibrium Green's function formalism to study the conductance response of Fe-doped graphene nanoribbons to CO2 gas adsorption. A single Fe atom is either adsorbed on graphene's surface (aFe-graphene) or it substitutes the carbon atom (sFe-graphene). Metal atom doping reduces the electronic transmission of pristine graphene due to the localization of electronic states near the impurities. The reduction in the transmission is more pronounced in the case of aFe-graphene. In addition, the aFe-graphene is found to be less sensitive to the CO2 molecule attachment as compared to the sFe-graphene system. Pristine graphene is also found to be less sensitive to the molecular adsorption. Since the change in the conductivity is one of the main outputs of sensors, our findings will be useful in developing graphene-based solid-state gas sensors.

  2. 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.

  3. Insights into the adsorption and energy transfer of Ag clusters on the AgCl(100) surface.

    PubMed

    Ma, Xiangchao; Dai, Ying; Guo, Meng; Zhu, Yingtao; Huang, Baibiao

    2013-06-14

    It is fundamental to uncover the real adsorption properties of Ag clusters on an AgCl surface and the energy transfer mechanisms at the interface to understand the highly active photocatalytic performance and the stability of the plasmonic photocatalyst Ag@AgCl. Based on density functional theory calculations we provide valuable insights into the binding nature of Ag clusters on AgCl surface, where the binding between Ag atoms in the cluster and on the surface plays a decisive role in determining the most stable adsorption configurations. Our results demonstrate that there is energy transfer from the plasmonic metals to substrate. The hot holes excited by the decay of surface plasmon resonance on the metals can diffuse into the Cl ions in the outermost two layers of the surface producing highly oxidative Cl atoms. The dipole-dipole interaction between the plasmonic metal clusters and substrate Cl ions can also generate electron-hole pairs in the surface layers. It is deduced that the positively charged nature of adsorbed clusters acting as electron trapping centers and reduction sites plays a crucial role in keeping the stability of the Ag@AgCl system during the photocatalytic process. Finally, the validity of the cluster adsorption model for energy transfer is verified with respect to the nucleation and aggregation process of Ag atoms on the AgCl surface and a detailed description of the formation and evolution of Ag nanoparticles on an AgCl surface is provided. The present study may be helpful for understanding and designing this novel plasmonic photocatalyst and can be useful for investigating other relevant photocatalysts as well.

  4. Energy of adhesion of human T cells to adsorption layers of monoclonal antibodies measured by a film trapping technique.

    PubMed Central

    Ivanov, I B; Hadjiiski, A; Denkov, N D; Gurkov, T D; Kralchevsky, P A; Koyasu, S

    1998-01-01

    A novel method for studying the interaction of biological cells with interfaces (e.g., adsorption monolayers of antibodies) is developed. The method is called the film trapping technique because the cell is trapped within an aqueous film of equilibrium thickness smaller than the cell diameter. A liquid film of uneven thickness is formed around the trapped cell. When observed in reflected monochromatic light, this film exhibits an interference pattern of concentric bright and dark fringes. From the radii of the fringes one can restore the shape of interfaces and the cell. Furthermore, one can calculate the adhesive energy between the cell membrane and the aqueous film surface (which is covered by a layer of adsorbed proteins and/or specific ligands), as well as the disjoining pressure, representing the force of interaction per unit area of the latter film. The method is applied to two human T cell lines: Jurkat and its T cell receptor negative (TCR-) derivative. The interaction of these cells with monolayers of three different monoclonal antibodies adsorbed at a water-air interface is studied. The results show that the adhesive energy is considerable (above 0.5 mJ/m2) when the adsorption monolayer contains antibodies acting as specific ligands for the receptors expressed on the cell surface. In contrast, the adhesive energy is close to zero in the absence of such a specific ligand-receptor interaction. In principle, the method can be applied to the study of the interaction of a variety of biological cells (B cells, natural killer cells, red blood cells, etc.) with adsorption monolayers of various biologically active molecules. In particular, film trapping provides a tool for the gentle micromanipulation of cells and for monitoring of processes (say the activation of a T lymphocyte) occurring at the single-cell level. PMID:9649417

  5. First-Principles Calculation Study of Mechanism of Cation Adsorption Selectivity of Zeolites: A Guideline for Effective Removal of Radioactive Cesium

    NASA Astrophysics Data System (ADS)

    Nakamura, Hiroki; Okumura, Masahiko; Machida, Masahiko

    2013-02-01

    Zeolites have attracted attention in the reprocessing of radioactive nuclear waste because of their high selective affinity for radioisotopes of Cs. Very recently, their useful properties have been widely utilized in decontamination after the accident at the Fukushima Daiichi Nuclear Power Plants. In this study, we study the high selectivity in the Cs adsorption of zeolites using first-principles calculations and clarify the mechanism of the cation selectivity of zeolites. We obtain energy surfaces on all capture locations for Cs/Na ions inside the micropores of a zeolite, ``mordenite'', and find three crucial conditions for the highly ion-selective exchange of Na for Cs: i) micropores with a radius of ˜3 Å, ii) a moderate Al/Si ratio, and iii) a uniform distribution of Al atoms around each micropore. These insights suggest a guideline for developing zeolites with high Cs selectivity and for enhancing the cation selectivity in more general situations.

  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. A thermodynamic analysis of gas adsorption on microporous materials: evaluation of energy heterogeneity.

    PubMed

    Llorens, Joan; Pera-Titus, Marc

    2009-03-15

    This paper presents a thermodynamic isotherm derived from solution thermodynamics principles to describe gas adsorption on microporous materials. This isotherm relies on a potential relationship between the integral free energy of adsorption relative to saturation, Psi/RT, expressed by the Kiselev equation, and the variable Z = 1/-Ln(Pi), being Pi the relative pressure. A mathematical analysis reveals that the adsorption energy heterogeneity in the micropores is collected in a characteristic parameter of the isotherm, m, that can be related to the alpha parameter of the Dubinin-Astakhov isotherm in a simple way (m = alpha + 1). The isotherm also predicts a plateau in Psi/RT at extremely low pressures (Pi < 10(-7)). Neimark's thermodynamic equation accounting for gas adsorption on mesoporous solids is found to be a particular case of the isotherm presented in this study. The Langmuir isotherm only shows consistency with the thermodynamic isotherm for a reduced combination of values of the relevant parameters, not usually found in common adsorbents. The suitability of the thermodynamic isotherm is experimentally assessed by testing a collection of microporous materials, including activated carbons, carbon nanotubes, and zeolites.

  8. Densely-packed ZnTPPs Monolayer on the Rutile TiO2(110)-(1×1) Surface: Adsorption Behavior and Energy Level Alignment.

    PubMed

    Rangan, Sylvie; Ruggieri, Charles; Bartynski, Robert; Martínez, José Ignacio; Flores, Fernando; Ortega, José

    2016-03-03

    The adsorption of a densely packed Zinc(II) tetraphenylporphyrin monolayer on a rutile TiO2(110)-(1×1) surface has been studied using a combination of experimental and theoretical methods, aimed at analyzing the relation between adsorption behavior and barrier height formation. The adsorption configuration of ZnTPP was determined from scanning tunnel microscopy (STM) imaging, density functional theory (DFT) calculations and STM image simulation. The corresponding energy alignment was experimentally determined from X-ray and UV-photoemission spectroscopies and inverse photoemission spectroscopy. These results were found in good agreement with an appropriately corrected DFT model, pointing to the importance of local bonding and intermolecular interactions in the establishment of barrier heights.

  9. Densely-packed ZnTPPs Monolayer on the Rutile TiO2(110)-(1×1) Surface: Adsorption Behavior and Energy Level Alignment

    PubMed Central

    Rangan, Sylvie; Ruggieri, Charles; Bartynski, Robert; Martínez, José Ignacio; Flores, Fernando; Ortega, José

    2016-01-01

    The adsorption of a densely packed Zinc(II) tetraphenylporphyrin monolayer on a rutile TiO2(110)-(1×1) surface has been studied using a combination of experimental and theoretical methods, aimed at analyzing the relation between adsorption behavior and barrier height formation. The adsorption configuration of ZnTPP was determined from scanning tunnel microscopy (STM) imaging, density functional theory (DFT) calculations and STM image simulation. The corresponding energy alignment was experimentally determined from X-ray and UV-photoemission spectroscopies and inverse photoemission spectroscopy. These results were found in good agreement with an appropriately corrected DFT model, pointing to the importance of local bonding and intermolecular interactions in the establishment of barrier heights. PMID:26998188

  10. The role of vdW interactions in coverage dependent adsorption energies of atomic adsorbates on Pt(111) and Pd(111)

    NASA Astrophysics Data System (ADS)

    Thirumalai, Hari; Kitchin, John R.

    2016-08-01

    Adsorption, a fundamental process in heterogeneous catalysis is known to be dependent on the adsorbate-adsorbate and surface-adsorbate bonds. van der Waals (vdW) interactions are one of the types of interactions that have not been examined thoroughly as a function of adsorbate coverage. In this work we quantify the vdW interactions for atomic adsorbates on late transition metal surfaces, and determine how these long range forces affect the coverage dependent adsorption energies. We calculate the adsorption energies of carbon, nitrogen, oxygen, sulfur, fluorine, bromine and chlorine species on Pt(111) and Pd(111) at coverages ranging from 1/4 to 1 ML using the BEEF-vdW functional. We observe that adsorption energies remain coverage dependent, and this coverage dependence is shown to be statistically significant. vdW interactions are found to be coverage dependent, but more significantly, they are found to be dependent on molecular properties such as adsorbate size, and consequently, correlate with the adsorbate effective nuclear charge. We observe that these interactions account for a reduction in the binding energy of the system, due to the destabilizing attractive interactions between the adsorbates which weaken its bond with the surface.

  11. 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.

  12. 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.

  13. 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.

  14. 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)

  15. A Initio Calculations Performed on Carbon Monoxide Adsorption on the IRON(100) Surface and Complementing Theoretical Techniques

    NASA Astrophysics Data System (ADS)

    Meehan, Timothy Erickson

    1992-01-01

    Unrestricted Hartree-Fock calculations were performed on Fe_{x}CO clusters to model the CO(alpha_1), CO(alpha_2), and CO( alpha_3) adsorptions on the Fe(100) surface. Clusters of FeCO(C_{4v}) and a multiplicity of 5, Fe_2 CO(C_{2v}) and a multiplicity of 7, and Fe_2CO(C _{s}) and a multiplicity of 7, were constructed to model, respectively, the adsorption for the on top site, bridging site, and tilted CO structure at the 4-fold site. The CO position was optimized with respect to the Fe bulk distances using gradient techniques and the partial geometry optimization. CO stretching frequencies were calculated for each optimized geometry, and we find no evidence supporting CO adsorption in the bridging site. Using a full basis set the calculated CO stretching frequencies for the FeCO(C_{4v}), Fe_2CO(C_ {2v}), and the Fe_2 CO(C_{s}) clusters are 1992, 1767, and 771 cm^{ -1}, respectively. The CSOV analysis was executed to analyze the major orbital interactions between the CO and Fe_{x} clusters. For both Fe_2CO clusters, the CO pi^* perpendicular to the Fe _2 axis had a more significant contribution involving the pi backdonation from the Fe_2 clusters. Furthermore, the spin minority d electrons are mainly responsible for the pi backdonation. Due to problems with SCF convergence incurred during the Fe_{x}CO studies, we were forced to investigate a number of different techniques to achieve SCF convergence. Therefore, techniques that generate starting guesses of the eigenvectors for the SCF procedure and techniques used to accelerate SCF convergence are reviewed. The standard guesses of H _{core} and charge build -up are examined, and we introduce a new incremental cluster method for generating starting guesses for large clusters. The standard techniques of extrapolation, DIIS, damping, level shifting, restrict, and symmetry blocking are examined, and we also developed the hacker method and partial geometry optimization as new techniques to achieve SCF convergence. Results

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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).

  1. 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

  2. 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.

  3. A comparative study of surface energies and water adsorption on Ce-bastnäsite, La-bastnäsite, and calcite via density functional theory and water adsorption calorimetry.

    PubMed

    Goverapet Srinivasan, Sriram; Shivaramaiah, Radha; Kent, Paul R C; Stack, Andrew G; Riman, Richard; Anderko, Andre; Navrotsky, Alexandra; Bryantsev, Vyacheslav S

    2017-03-06

    Bastnäsite, a fluoro-carbonate mineral, is the single largest mineral source of light rare earth elements (REE), La, Ce and Nd. Enhancing the efficiency of separation of the mineral from gangue through froth flotation is the first step towards meeting an ever increasing demand for REE. To design and evaluate collector molecules that selectively bind to bastnäsite, a fundamental understanding of the structure and surface properties of bastnäsite is essential. In our earlier work (J. Phys. Chem. C, 2016, 120, 16767), we carried out an extensive study of the structure, surface stability and water adsorption energies of La-bastnäsite. In this work, we make a comparative study of the surface properties of Ce-bastnäsite, La-bastnäsite, and calcite using a combination of density functional theory (DFT) and water adsorption calorimetry. Spin polarized DFT+U calculations show that the exchange interaction between the electrons in Ce 4f orbitals is negligible and that these orbitals do not participate in bonding with the oxygen atom of the adsorbed water molecule. In agreement with calorimetry, DFT calculations predict larger surface energies and stronger water adsorption energies on Ce-bastnäsite than on La-bastnäsite. The order of stabilities for stoichiometric surfaces is as follows: [101[combining macron]0] > [101[combining macron]1] > [101[combining macron]2] > [0001] > [112[combining macron]2] > [101[combining macron]4] and the most favorable adsorption sites for water molecules are the same as for La-bastnäsite. In agreement with water adsorption calorimetry, at low coverage water molecules are strongly stabilized via coordination to the surface Ce(3+) ions, whereas at higher coverage they are adsorbed less strongly via hydrogen bonding interaction with the surface anions. Due to similar water adsorption energies on bastnäsite [101[combining macron]1] and calcite [101[combining macron]4] surfaces, the design of collector molecules that selectively bind to

  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. Kinetic and geometric isotope effects originating from different adsorption potential energy surfaces: cyclohexane on Rh(111).

    PubMed

    Koitaya, Takanori; Shimizu, Sumera; Mukai, Kozo; Yoshimoto, Shinya; Yoshinobu, Jun

    2012-06-07

    Novel isotope effects were observed in desorption kinetics and adsorption geometry of cyclohexane on Rh(111) by the use of infrared reflection absorption spectroscopy, temperature programmed desorption, photoelectron spectroscopy, and spot-profile-analysis low energy electron diffraction. The desorption energy of deuterated cyclohexane (C(6)D(12)) is lower than that of C(6)H(12). In addition, the work function change by adsorbed C(6)D(12) is smaller than that by adsorbed C(6)H(12). These results indicate that C(6)D(12) has a shallower adsorption potential than C(6)H(12) (vertical geometric isotope effect). The lateral geometric isotope effect was also observed in the two-dimensional cyclohexane superstructures as a result of the different repulsive interaction between interfacial dipoles. The observed isotope effects should be ascribed to the quantum nature of hydrogen involved in the C-H···metal interaction.

  11. 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.

  12. 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.

  13. Phenolic resin-based porous carbons for adsorption and energy storage applications

    NASA Astrophysics Data System (ADS)

    Wickramaratne, Nilantha P.

    The main objective of this dissertation research is to develop phenolic resin based carbon materials for range of applications by soft-templating and Stober-like synthesis strategies. Applications Studied in this dissertation are adsorption of CO2, bio-molecular and heavy metal ions, and energy storage devices. Based on that, our goal is to design carbon materials with desired pore structure, high surface area, graphitic domains, incorporated metal nanoparticles, and specific organic groups and heteroatoms. In this dissertation the organic-organic self-assembly of phenolic resins and triblock copolymers under acidic conditions will be used to obtain mesoporous carbons/carbon composites and Stober-like synthesis involving phenolic resins under basic condition will be used to prepare polymer/carbon particles and their composites. The structure of this dissertation consists of an introductory chapter (Chapter 1) discussing the general synthesis of carbon materials, particularly the soft-templating strategy and Stober-like carbon synthesis. Also, Chapter 1 includes a brief outline of applications namely adsorption of CO2, biomolecule and heavy metal ions, and supercapacitors. Chapter 2 discusses the techniques used for characterization of the carbon materials studied. This chapter starts with nitrogen adsorption analysis, which is used to measure the specific surface area, pore volume, distribution of pore sizes, and pore width. In addition to nitrogen adsorption, powder X-ray diffraction (XRD), transmission electron microscopy (TEM), high resolution thermogravimetric analysis (HR-TGA), cyclic voltammetry (CV) and CHNS elemental analysis (EA) are mentioned too. Chapter 3 is focused on carbon materials for CO2 adsorption. There are different types of porous solid materials such as silicate, MOFs, carbons, and zeolites studied for CO2 adsorption. However, the carbon based materials are considered to be the best candidates for CO 2 adsorption to the industrial point of

  14. 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.

  15. 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.

  16. 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.

  17. Dioxygen molecule adsorption and oxygen atom diffusion on clean and defective aluminum(111) surface using first principles calculations

    NASA Astrophysics Data System (ADS)

    Guiltat, Mathilde; Brut, Marie; Vizzini, Sébastien; Hémeryck, Anne

    2017-03-01

    First principles calculations are conducted to investigate kinetic behavior of oxygen species at the surface of clean and defective Al(111) substrate. Oxygen island, aluminum vacancy, aluminum sub-vacancy, aluminum ad-atom and aluminum terraces defects are addressed. Adsorption of oxygen molecule is first performed on all these systems resulting in dissociated oxygen atoms in main cases. The obtained adsorbed configurations are then picked to study the behavior of atomic oxygen specie and get a detailed understanding on the effect of the local environment on the ability of the oxygen atom to diffuse on the surface. We pointed out that local environment impacts energetics of oxygen atom diffusion. Close packed oxygen island, sub-vacancy and ad-atoms favor oxygen atom stability and decrease mobility of oxygen atom on the surface, to be seen as surface area for further nucleation of oxygen island.

  18. Galactose adsorption on Ru(0001)

    NASA Astrophysics Data System (ADS)

    Alatalo, Matti; Puisto, Mikko

    2014-03-01

    In order to understand the valorisation of biomass, it is essential to study the behavior of sugar molecules on catalytic surfaces. We have studied the adsorption of galactose molecules on the Ru(0001) surface using first principles calculations. We present results for the fully relaxed configurations of the molecule at different adsorption sites. We also compare the effect of the inclusion of the van der Waals interactions on both the energetics of the free galactose molecule and the adsorption energy of galactose on Ru(0001). We compare our results, obtained using periodically repeated supercells, to those obtained with cluster calculations.

  19. 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

  20. The adsorption of H2 on Fe(111) studied by thermal energy atom scattering

    NASA Astrophysics Data System (ADS)

    Jiang, P.; Zappone, M.; Bernasek, S. L.

    1993-11-01

    The interaction of H2 with Fe(111) has been studied by thermal energy atom scattering (TEAS). The specularly scattered He intensity as a function of hydrogen coverage exhibits a concave drop in scattered He intensity up to 30% coverage, followed by a plateau and another drop in intensity at 80% coverage. A model has been developed to account for this data which assumes three adsorption sites for H on Fe(111), in analogy with the three desorption peaks seen in temperature-programmed desorption (TPD). The adsorption sites have not been definitely assigned, but are labeled ``deep-hollow,'' ``shallow-hollow,'' and ``on-top.'' Competitive adsorption into the deep-hollow and shallow-hollow sites is assumed to account for the initial concavity of the data. Adsorption into on-top sites only becomes significant at 80% coverage. Effective cross sections and reflectivities for the three sites have been obtained for θi=60° and 40°. When a H saturated surface is heated, the scattered He intensity decreases upon heating from 173 to 240 K, at which point desorption has already begun. This drop in intensity is not completely explicable by a Debye-Waller attenuation. It is proposed to be due to a shift in population of the adsorbed H to more exposed, on-top sites, in accord with a Boltzmann distribution of adsorption sites. The scattered He intensity increases upon further heating from 240 to 400 K, corresponding to the desorption of recombined H2 from the surface. Comparison of the He/H/Fe(111) system is made with the He/H/Pt(111) and He/H/Fe(110) systems.

  1. 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

  2. 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.

  3. 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.

  4. Anharmonicity and confinement in zeolites: Structure, spectroscopy, and adsorption free energy of ethanol in H-ZSM-5

    DOE PAGES

    Alexopoulos, Konstantinos; Lee, Mal -Soon; Liu, Yue; ...

    2016-03-21

    Here, to account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Brønsted acid site of the H-ZSM-5 catalyst has been studied at different temperatures and ethanol loadings using ab initio molecular dynamics (AIMD) simulations, infrared (IR) spectroscopy and calorimetric measurements. At low temperatures (T ≤ 400 K) and ethanol loading, a single ethanol molecule adsorbed in H-ZSM-5 forms a Zundel-like structure where the proton is equally shared between the oxygen of the zeolite and the oxygen of the alcohol. At higher ethanol loading, a second ethanol molecule helpsmore » to stabilize the protonated ethanol at all temperatures by acting as a solvating agent. The vibrational density of states (VDOS), as calculated from the AIMD simulations, are in excellent agreement with measured IR spectra for C2H5OH, C2H5OD and C2D5OH isotopomers and support the existence of both monomers and dimers. A quasi-harmonic approximation (QHA), applied to the VDOS obtained from the AIMD simulations, provides estimates of adsorption free energy within ~10 kJ/mol of the experimentally determined quantities, whereas the traditional approach, employing harmonic frequencies from a single ground state minimum, strongly overestimates the adsorption free energy by at least ~30 kJ/mol. This discrepancy is traced back to the inability of the harmonic approximation to represent the contributions to the vibrational motions of the ethanol molecule upon confinement in the zeolite. KA, MFR, GBM were supported by the Long Term Structural Methusalem Funding by the Flemish Government – grant number BOF09/01M00409. MSL, VAG, RR and JAL were supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated for DOE by Battelle. Computational resources were provided at W. R. Wiley

  5. Anharmonicity and confinement in zeolites: Structure, spectroscopy, and adsorption free energy of ethanol in H-ZSM-5

    SciTech Connect

    Alexopoulos, Konstantinos; Lee, Mal -Soon; Liu, Yue; Zhi, Yuchun; Liu, Yuanshuai; Reyniers, Marie -Francoise; Marin, Guy B.; Glezakou, Vassiliki -Alexandra; Rousseau, Roger; Lercher, Johannes A.

    2016-03-21

    Here, to account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Brønsted acid site of the H-ZSM-5 catalyst has been studied at different temperatures and ethanol loadings using ab initio molecular dynamics (AIMD) simulations, infrared (IR) spectroscopy and calorimetric measurements. At low temperatures (T ≤ 400 K) and ethanol loading, a single ethanol molecule adsorbed in H-ZSM-5 forms a Zundel-like structure where the proton is equally shared between the oxygen of the zeolite and the oxygen of the alcohol. At higher ethanol loading, a second ethanol molecule helps to stabilize the protonated ethanol at all temperatures by acting as a solvating agent. The vibrational density of states (VDOS), as calculated from the AIMD simulations, are in excellent agreement with measured IR spectra for C2H5OH, C2H5OD and C2D5OH isotopomers and support the existence of both monomers and dimers. A quasi-harmonic approximation (QHA), applied to the VDOS obtained from the AIMD simulations, provides estimates of adsorption free energy within ~10 kJ/mol of the experimentally determined quantities, whereas the traditional approach, employing harmonic frequencies from a single ground state minimum, strongly overestimates the adsorption free energy by at least ~30 kJ/mol. This discrepancy is traced back to the inability of the harmonic approximation to represent the contributions to the vibrational motions of the ethanol molecule upon confinement in the zeolite. KA, MFR, GBM were supported by the Long Term Structural Methusalem Funding by the Flemish Government – grant number BOF09/01M00409. MSL, VAG, RR and JAL were supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated for DOE by Battelle

  6. 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.

  7. 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.

  8. Ab initio calculations for dissociative hydrogen adsorption on lithium oxide surfaces

    SciTech Connect

    Sutjianto, A. |; Tam, S.W.; Curtiss, L.A.; Johnson, C.E.; Pandey, R.

    1994-12-01

    Lithium ceramics are one class of materials being considered as tritium breeders for fusion technology,and hydrogen is known to enhance the release of tritium from lithium ceramic materials. Dissociative hydrogen chemisorption on the Li{sub 2}O surfaces of the (100), (110), and (111) planes has been investigated with ab initio Hartree-Fock calculations. Calculations for unrelaxed crystal Li{sub 2}O structures indicated that except for the (100) surface, the (110) and (111) surfaces are stable. Results on the heterolytic sites of n-layer (110) (where n {ge} 2) slabs and three-layer (111) slabs suggest that dissociative hydrogen chemisorption is endothermic. For a one-layer (110) slab at 100% surface coverage, the dissociative hydrogen chemisorption is exothermic, forming OH{sup {minus}} and Li{sup +}H{sup {minus}}Li{sup +}. The results also indicate that the low coordination environment in surface step structures, such as kinks and ledges, may plan an important role in the hydrogen chemisorption process. On the homolytic sites of the (110) and (111) surfaces, there is no hydrogen chemisorption.

  9. Adsorption of metal-phthalocyanine molecules onto the Si(111) surface passivated by δ doping: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Veiga, R. G. A.; Miwa, R. H.; McLean, A. B.

    2016-03-01

    We report first-principles calculations of the energetic stability and electronic properties of metal-phthalocyanine (MPc) molecules (M = Cr, Mn, Fe, Co, Ni, Cu, and Zn) adsorbed on the δ -doped Si(111)-B (√{3 }×√{3 }) reconstructed surface. (i) It can be seen that CrPc, MnPc, FePc, and CoPc are chemically anchored to the topmost Si atom. (ii) Contrastingly, the binding of the NiPc, CuPc, and ZnPc molecules to the Si (111 ) -B (√{3 }×√{3 }) surface is exclusively ruled by van der Waals interactions, the main implication being that these molecules may diffuse and rearrange to form clusters and/or self-organized structures on this surface. The electronic structure calculations reveal that in point (i), owing to the formation of the metal-Si covalent bond, the net magnetic moment of the molecule is quenched by 1 μB , remaining unchanged in point (ii). In particular, the magnetic moment of CuPc (1 μB ) is preserved after adsorption. Finally, we verify that the formation of ZnPc, CuPc, and NiPc molecular (self-assembled) arrangements on the Si(111)-B (√{3 }×√{3 } ) surface is energetically favorable, in good agreement with recent experimental findings.

  10. 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.

  11. Evaluation of the isosteric heat of adsorption at zero coverage for hydrogen on activated carbons

    NASA Astrophysics Data System (ADS)

    Dohnke, E.; Beckner, M.; Romanos, J.; Olsen, R.; Wexler, C.; Pfeifer, P.

    2011-03-01

    Activated carbons made from corn cob show promise as materials for high-capacity hydrogen storage. As part of our characterization of these materials, we are interested in learning how different production methods affect the adsorption energies. In this talk, we will show how hydrogen adsorption isotherms may be used to calculate these adsorption energies at zero coverage using Henry's law. We will additionally discuss differences between the binding energy and the isosteric heat of adsorption by applying this analysis at different temperatures.

  12. Ab Initio Density Funcitonal Calculations of Adsorption of Transiton Metal Atoms on theta-Al2O3 (010) Surface

    SciTech Connect

    Narula, Chaitanya Kumar; Stocks, George Malcolm

    2012-01-01

    The catalytic properties of metal clusters and particles depend on their environment, however, little is known so far about the subnanometer metal particles, smallest being single atoms, supported on metal oxide substrates, especially, the systems that can be experimentally synthesized. Employing first principles density functional theory approach, we have studied single metal atoms, Ni, Pt, Pd, Cu, Au, and Ag, adsorbed on a -Al2O3 (010) surface. We find that metal adsorption on a dry alumina surface follows the binding strength order of Pd>Pt>Ni>Cu>Au>Ag. Interestingly, Ni, Pt, and Pd atoms, supported on alumina, exhibit no magnetization whereas Cu, Ag, and Au exhibit unpaired electrons. The bonding picture that emerges from this study shows that Ni, Pt, and Pd, are d10 species with d-s hybrid character that are able to interact with the 2p orbital of surface oxygen. The interaction of Group 11 (Cu, Ag, Au) atoms with 010 surface of -Al2O3 is superficially similar to that of Group 10 metals. Group 11 metals with filled d orbitals have low tendency for d-s hybridization due to larger energy gaps than Group 10 metals. As a result of the overlap with O 2p, the d orbital shifts to lower energy. The magnetization of Group 11 metals is primarily due to single electrons in s orbitals.

  13. 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.

  14. 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.

  15. 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.

  16. Rb+ adsorption at the quartz(101)-aqueous interface: comparison of resonant anomalous x-ray reflectivity with ab initio calculations

    SciTech Connect

    Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; Bandura, Andrei V.; Zhang, Zhan; Wesolowski, David J.; Fenter, Paul

    2015-01-29

    We study adsorption of Rb+ to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb+ distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights of 1.8 ± 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb+ between these two conditions. At pH 7, the lowest energy structure shows that Rb+ adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb+ coverage was -0.11 C/m2, in good agreement with the range of the surface charge magnitudes reported in the literature.

  17. 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.

  18. 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

  19. Application of van der Waals functionals to the calculation of dissociative adsorption of N2 on W(110) for static and dynamic systems

    NASA Astrophysics Data System (ADS)

    Migliorini, Davide; Nattino, Francesco; Kroes, Geert-Jan

    2016-02-01

    The fundamental understanding of molecule-surface reactions is of great importance to heterogeneous catalysis, motivating many theoretical and experimental studies. Even though much attention has been dedicated to the dissociative chemisorption of N2 on tungsten surfaces, none of the existing theoretical models has been able to quantitatively reproduce experimental reaction probabilities for the sticking of N2 to W(110). In this work, the dissociative chemisorption of N2 on W(110) has been studied with both static electronic structure and ab initio molecular dynamics (AIMD) calculations including the surface temperature effects through surface atom motion. Calculations have been performed using density functional theory, testing functionals that account for the long range van der Waals (vdW) interactions, which were previously only considered in dynamical calculations within the static surface approximation. The vdW-DF2 functional improves the description of the potential energy surface for N2 on W(110), returning less deep molecular adsorption wells and a better ratio between the barriers for the indirect dissociation and the desorption, as suggested by previous theoretical work and experimental evidence. Using the vdW-DF2 functional less trapping-mediated dissociation is obtained compared to results obtained with standard semi-local functionals such as PBE and RPBE, improving agreement with experimental data at Ei = 0.9 eV. However, at Ei = 2.287 and off-normal incidence, the vdW-DF2 AIMD underestimates the experimental reaction probabilities, showing that also with the vdW-DF2 functional the N2 on W(110) interaction is not yet described with quantitative accuracy.

  20. 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.

  1. Dependence of single-walled carbon nanotube adsorption kinetics on temperature and binding energy.

    PubMed

    Rawat, D S; Krungleviciute, V; Heroux, L; Bulut, M; Calbi, M M; Migone, A D

    2008-12-02

    We present results for the isothermal adsorption kinetics of methane, hydrogen, and tetrafluoromethane on closed-ended single-walled carbon nanotubes. In these experiments, we monitor the pressure decrease as a function of time as equilibrium is approached, after a dose of gas is added to the cell containing the nanotubes. The measurements were performed at different fractional coverages limited to the first layer. The results indicate that, for a given coverage and temperature, the equilibration time is an increasing function of E/(k(B)T), where E is the binding energy of the adsorbate and k(B)T is the thermal energy. These findings are consistent with recent theoretical predictions and computer simulations results that we use to interpret the experimental measurements.

  2. Dissociative adsorption of H2 on Cu(100): Fixed-site calculations for impact at hollow and top sites

    NASA Astrophysics Data System (ADS)

    Mowrey, R. C.; Kroes, G. J.; Baerends, E. J.

    1998-04-01

    The reaction of H2 on Cu(100) is studied using a wave-packet method to solve a four-dimensional quantum mechanical model for impact on the high-symmetry hollow and top sites. The potential energy surface (PES) is a fit to the results of density functional calculations treating a periodic overlayer of H2 on a Cu slab. The dynamics calculations include motion in the azimuthal coordinate although the PES does not depend on φ for impact on the top and hollow sites. Large dissociation probabilities (˜0.9) are found for impact at the hollow site but those for impact at the top site are lower (˜0.3). Dissociation probabilities for molecules incident with "helicoptering" motion (mj=j) are larger than those for molecules with "cartwheeling" motion (mj=0). This differs from the results of previous calculations for impact at the azimuthally corrugated bridge site which predicted comparable probabilities for the two orientations of incident molecules. The dissociation probabilities from fixed-site calculations at the different impact sites are combined to yield an averaged probability which is compared with experiment and the results of six-dimensional quantum calculations. Vibrationally inelastic scattering is predicted to occur primarily for impact at the top site.

  3. Adsorption of Organic Compounds to Diesel Soot: Frontal Analysis and Polyparameter Linear Free-Energy Relationship.

    PubMed

    Lu, Zhijiang; MacFarlane, John K; Gschwend, Philip M

    2016-01-05

    Black carbons (BCs) dominate the sorption of many hydrophobic organic compounds (HOCs) in soils and sediments, thereby reducing the HOCs' mobilities and bioavailabilities. However, we do not have data for diverse HOCs' sorption to BC because it is time-consuming and labor-intensive to obtain isotherms on soot and other BCs. In this study, we developed a frontal analysis chromatographic method to investigate the adsorption of 21 organic compounds with diverse functional groups to NIST diesel soot. This method was precise and time-efficient, typically taking only a few hours to obtain an isotherm. Based on 102 soot-carbon normalized sorption coefficients (KsootC) acquired at different sorbate concentrations, a sorbate-activity-dependent polyparameter linear free-energy relationship was established: logKsootC = (3.74 ± 0.11)V + ((-0.35 ± 0.02)log ai)E + (-0.62 ± 0.10)A + (-3.35 ± 0.11)B + (-1.45 ± 0.09); (N = 102, R(2) = 0.96, SE = 0.18), where V, E, A, and B are the sorbate's McGowan's characteristic volume, excess molar refraction, and hydrogen acidity and basicity, respectively; and ai is the sorbate's aqueous activity reflecting the system's approach to saturation. The difference in dispersive interactions with the soot versus with the water was the dominant factor encouraging adsorption, and H-bonding interactions discouraged this process. Using this relationship, soot-water and sediment-water or soil-water adsorption coefficients of HOCs of interest (PAHs and PCBs) were estimated and compared with the results reported in the literature.

  4. 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…

  5. 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.

  6. 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

  7. 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.

  8. Energy gap modulation in V2O5 nanowires by gas adsorption

    NASA Astrophysics Data System (ADS)

    Kim, Byung Hoon; Kim, Ansoon; Oh, Soon-Young; Bae, Sung-Soo; Yun, Yong Ju; Yu, Han Young

    2008-12-01

    The current-voltage characteristics at various pressures (2-10 atm) and the scanning tunneling microscopy of vanadium pentoxide nanowires (VONs) with the inert gases (He, Ne, and Ar) and diatomic molecules (H2,N2, O2) have been investigated. The gas dependent conductance (G) is consistent with the inverse energy gap obtained from the scanning tunneling spectroscopy study for the gas-adsorbed single VON. The three possible interactions for gas adsorption of the VON have been discussed. Among them, we have found that the induced dipole-dipole interaction between adsorbed gases plays an important role in conductance variation in the gas adsorbed VON using the conductance per molecule (G /N).

  9. Phosphate adsorption on lanthanum loaded biochar.

    PubMed

    Wang, Zhanghong; Shen, Dekui; Shen, Fei; Li, Tianyu

    2016-05-01

    To attain a low-cost and high-efficient phosphate adsorbent, lanthanum (La) loaded biochar (La-BC) prepared by a chemical precipitation method was developed. La-BC and its pristine biochar (CK-BC) were comparatively characterized using zeta potential, BET surface area, scanning electron microscopy/energy dispersive spectrometer (SEM-EDS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FT-IR). The adsorption ability and the mechanisms during adsorption process for the La-BC samples were also investigated. La loaded on the surface of biochar can be termed as La-composites (such as LaOOH, LaONO3 and La(OH)3), leading to the decrease of negative charge and surface area of biochar. La-BC exhibited the high adsorption capacity to phosphate compared to CK-BC. Adsorption isotherm and adsorption kinetic studies showed that the Langmuir isotherm and second order model could well describe the adsorption process of La-BC, indicating that the adsorption was dominated by a homogeneous and chemical process. The calculated maximum adsorption capacity was as high as 46.37 mg g(-1) (computed in P). Thermodynamic analysis revealed that the adsorption was spontaneous and endothermic. SEM, XRD, XPS and FT-IR analysis suggested that the multi-adsorption mechanisms including precipitation, ligand exchange and complexation interactions can be evidenced during the phosphate adsorption process by La-composites in La-BC.

  10. Adsorption dynamics of molecular nitrogen at an Fe(111) surface.

    PubMed

    Nosir, M A; Martin-Gondre, L; Bocan, G A; Díez Muiño, R

    2017-03-08

    We present an extensive theoretical study of N2 adsorption mechanisms on an Fe(111) surface. We combine the static analysis of a six-dimensional potential energy surface (6D-PES), based on ab initio density functional theory (DFT) calculations for the system, with quasi-classical trajectory (QCT) calculations to simulate the adsorption dynamics. There are four molecular adsorption states, usually called γ, δ, α, and ε, arising from our DFT calculations. We find that N2 adsorption in the γ-state is non-activated, while the threshold energy is associated with the entrance channel for the other three adsorption states. Our QCT calculations confirm that there are activated and nonactivated paths for the adsorption of N2 on the Fe(111) surface, which is in agreement with previous experimental investigations. Molecular dynamics at a surface temperature Ts = 300 K and impact energies Ei in the 0-5 eV range show the relative occupancy of the γ, δ, α, and ε states. The δ-state, however, is only marginally populated despite its adsorption energy being very similar to that of the γ-state. Our QCT calculations trace the dependence of molecular trapping on the surface temperature Ts and initial impact energy Ei and quantify the rates of the different competitive channels that eventually lead to molecular adsorption.

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

    PubMed

    Horn, Paul R; Head-Gordon, Martin

    2016-02-28

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

  12. 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.

  13. Energy dependent sticking coefficients of trimethylamine on Si(001)-Influence of the datively bonded intermediate state on the adsorption dynamics

    NASA Astrophysics Data System (ADS)

    Lipponer, M. A.; Reutzel, M.; Dürr, M.; Höfer, U.

    2016-11-01

    The adsorption dynamics of the datively bonded trimethylamine (TMA) on Si(001) was investigated by means of molecular beam techniques. The initial sticking probability s0 of TMA on Si(001) was measured as a function of kinetic energy at two different surface temperatures (230 and 550 K). At given surface temperature, s0 was found to decrease with increasing kinetic energy (0.1 to 0.6 eV) indicating a non-activated reaction channel. At increased surface temperature, s0 is reduced due to the onset of desorption into the gas phase. The energy dependence of s0 is compared to the results for the adsorption of tetrahydrofuran (THF) on Si(001), which reacts via a datively bonded intermediate into a covalently bound final state. As s0 follows the same energy dependence both for TMA and THF, the datively bonded intermediate state is concluded to dominate the reaction dynamics in the latter case as well.

  14. 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…

  15. Nanometer polymer surface features: the influence on surface energy, protein adsorption and endothelial cell adhesion

    NASA Astrophysics Data System (ADS)

    Carpenter, Joseph; Khang, Dongwoo; Webster, Thomas J.

    2008-12-01

    Current small diameter (<5 mm) synthetic vascular graft materials exhibit poor long-term patency due to thrombosis and intimal hyperplasia. Tissue engineered solutions have yielded functional vascular tissue, but some require an eight-week in vitro culture period prior to implantation—too long for immediate clinical bedside applications. Previous in vitro studies have shown that nanostructured poly(lactic-co-glycolic acid) (PLGA) surfaces elevated endothelial cell adhesion, proliferation, and extracellular matrix synthesis when compared to nanosmooth surfaces. Nonetheless, these studies failed to address the importance of lateral and vertical surface feature dimensionality coupled with surface free energy; nor did such studies elicit an optimum specific surface feature size for promoting endothelial cell adhesion. In this study, a series of highly ordered nanometer to submicron structured PLGA surfaces of identical chemistry were created using a technique employing polystyrene nanobeads and poly(dimethylsiloxane) (PDMS) molds. Results demonstrated increased endothelial cell adhesion on PLGA surfaces with vertical surface features of size less than 18.87 nm but greater than 0 nm due to increased surface energy and subsequently protein (fibronectin and collagen type IV) adsorption. Furthermore, this study provided evidence that the vertical dimension of nanometer surface features, rather than the lateral dimension, is largely responsible for these increases. In this manner, this study provides key design parameters that may promote vascular graft efficacy.

  16. 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.

  17. Adsorption site of c(2×2) O on Ni(0001): An off-normal-direction energy-dependent photoelectron-diffraction study

    NASA Astrophysics Data System (ADS)

    Mei, W. N.; Tong, S. Y.

    1986-01-01

    We have used the technique of energy-dependent photoelectron diffraction (EDPD) to study the pseudo-bridge-site model proposed by Demuth et al. for the adsorption of c(2×2) O on Ni(001). Calculated EDPD curves at the normal exit direction for the pseudo-bridge site, averaged over four domains, were compared with those for the fourfold hollow site. We found no significant differences in the EDPD curves for the two different structural models. However, the calculated EDPD curves at off-normal directions, such as those along the [011] direction, or along the O-Ni bond directions, were qualitatively different for the two sites. We therefore conclude that off-normal-direction EDPD curves, when compared with measured data, can effectively determine the lateral coordinates of the oxygen overlayer on Ni(001).

  18. 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.

  19. 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.

  20. 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).

  1. 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.

  2. Enhanced adsorption energy of Au1 and O2 on the stoichiometric TiO2(110) surface by coadsorption with other molecules

    NASA Astrophysics Data System (ADS)

    Chrétien, Steeve; Metiu, Horia

    2008-01-01

    During heterogeneous catalysis the surface is simultaneously covered by several adsorbed molecules. The manner in which the presence of one kind of molecule affects the adsorption of a molecule of another kind has been of interest for a long time. In most cases the presence of one adsorbate does not change substantially the binding energy of another adsorbate. The calculations presented here show that the stoichiometric rutile TiO2(110) surface, on which one of the compounds -OH, Au3, Au5, Au7, Na, K, or Cs or two different gold strips was preadsorbed, behaves differently: the binding energy of Au1 or O2 to such a surface is much stronger than the binding to the clean stoichiometric TiO2(110) surface. Moreover, the binding energy of Au1 or O2 and the amount of charge they take from the surface when they adsorb are the same, regardless of which of the above species is preadsorbed. The preadsorbed species donate electrons to the conduction band of the oxide, and these electrons are used by Au1 or O2 to make stronger bonds with the surface. This suggests that adding an electron to the conduction band of the clean stoichiometric TiO2(110) slab used in the calculation will affect similarly the adsorption energy of Au1 or O2. Our calculations show that it does. We have also studied how the preadsorption of Au4 or Au6 affects the binding of Au1 or O2 to the surface. These two gold clusters do not donate electrons to the surface when they bind to it and therefore should not influence substantially the binding energy of Au1 or O2 to the surface. However, adsorbing O2 or Au1 on the surface forces the clusters to change their structure into that of isomers that donate charge to the oxide. This charge is used by Au1 or O2 to bind to the surface and the energy of this bond exceeds the isomerization energy. As a result the surface with the isomerized cluster is the lowest energy state of the system. We believe that these results can be generalized as follows. The molecules that

  3. Experimental, density function theory calculations and molecular dynamics simulations to investigate the adsorption of some thiourea derivatives on iron surface in nitric acid solutions

    NASA Astrophysics Data System (ADS)

    Khaled, K. F.

    2010-09-01

    The effects of thiourea derivatives, namely N-methyl thiourea (MTU), N-propyl thiourea (PTU) and N-allyl thiourea (ATU) on the corrosion behaviour of iron in 1.0 M solution of HNO 3 have been investigated in relation to the concentration of thiourea derivatives. The experimental data obtained using the techniques of weight loss, Tafel polarization and electrochemical impedance spectroscopy, EIS. The results showed that these compounds revealed a good corrosion inhibition, (ATU) being the most efficient and (MTU) the least. Computational studies have been used to find the most stable adsorption sites for thiourea derivatives. This information help to gain further insight about corrosion system, such as the most likely point of attack for corrosion on iron (1 1 0), the most stable site for thiourea derivatives adsorption and the binding energy of the adsorbed layer. The efficiency order of the inhibitors obtained by experimental results was verified by theoretical analysis.

  4. 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.

  5. Adsorption of glucose, cellobiose, and cellotetraose onto cellulose model surfaces.

    PubMed

    Hoja, Johannes; Maurer, Reinhard J; Sax, Alexander F

    2014-07-31

    Reliable simulation of molecular adsorption onto cellulose surfaces is essential for the design of new cellulose nanocomposite materials. However, the applicability of classical force field methods to such systems remains relatively unexplored. In this study, we present the adsorption of glucose, cellobiose, and cellotetraose on model surfaces of crystalline cellulose Iα and Iβ. The adsorption of the two large carbohydrates was simulated with the GLYCAM06 force field. To validate this approach, quantum theoretical calculations for the adsorption of glucose were performed: Equilibrium geometries were studied with density functional theory (DFT) and dispersion-corrected DFT, whereas the adsorption energies were calculated with two standard density functional approximations and five dispersion-containing DFT approaches. We find that GLYCAM06 gives a good account of geometries and, in most cases, accurate adsorption energies when compared to dispersion-corrected DFT energies. Adsorption onto the (100) surface of cellulose Iα is, in general, stronger than onto the (100) surface of cellulose Iβ. Contrary to intuition, the adsorption energy is not directly correlated with the number of hydrogen bonds; rather, it is dominated by dispersion interactions. Especially for bigger adsorbates, a neglect of these interactions leads to a dramatic underestimation of adsorption energies.

  6. Facile synthesis of ultrahigh-surface-area hollow carbon nanospheres for enhanced adsorption and energy storage

    PubMed Central

    Xu, Fei; Tang, Zhiwei; Huang, Siqi; Chen, Luyi; Liang, Yeru; Mai, Weicong; Zhong, Hui; Fu, Ruowen; Wu, Dingcai

    2015-01-01

    Exceptionally large surface area and well-defined nanostructure are both critical in the field of nanoporous carbons for challenging energy and environmental issues. The pursuit of ultrahigh surface area while maintaining definite nanostructure remains a formidable challenge because extensive creation of pores will undoubtedly give rise to the damage of nanostructures, especially below 100 nm. Here we report that high surface area of up to 3,022 m2 g−1 can be achieved for hollow carbon nanospheres with an outer diameter of 69 nm by a simple carbonization procedure with carefully selected carbon precursors and carbonization conditions. The tailor-made pore structure of hollow carbon nanospheres enables target-oriented applications, as exemplified by their enhanced adsorption capability towards organic vapours, and electrochemical performances as electrodes for supercapacitors and sulphur host materials for lithium–sulphur batteries. The facile approach may open the doors for preparation of highly porous carbons with desired nanostructure for numerous applications. PMID:26072734

  7. 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.

  8. Tuning the work function of VO2(1 0 0) surface by Ag adsorption and incorporation: Insights from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Chen, Lanli; Wang, Xiaofang; Shi, Siqi; Cui, Yuanyuan; Luo, Hongjie; Gao, Yanfeng

    2016-03-01

    VO2 is an attractive material for application to thermochromic optoelectronic devices such as smart windows, and Ag/VO2 double-layered structure can effectively decrease the phase transition temperature (Tc) of VO2 thin film, which is very important for practical application of VO2. Previous works has shown that the decrease in phase transition temperature (Tc) seems to be relevant with the work function of VO2 in Ag/VO2 double-layered thin film, although the underlying mechanism of tuning its Tc by Ag incorporation and adsorption on the VO2(1 0 0) surface has been rarely investigated. Our first-principles calculations reveal that the adsorption of Ag atoms on the VO2(1 0 0) surface rather than incorporation of Ag exhibits a lower work function, which is ascribed to an integrated effect of charge transfer from Ag to VO2(1 0 0) surface and enhanced surface dipole moment. The results suggest that the decrease in work function of VO2 with Ag adsorption favors the reduction in Tc. The current findings are helpful to understand the fundamental mechanism for yielding high-efficiency VO2-based optoelectronic devices.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Crystal Structures, Surface Stability, and Water Adsorption Energies of La-Bastnäsite via Density Functional Theory and Experimental Studies

    SciTech Connect

    Srinivasan, Sriram Goverapet; Shivaramaiah, Radha; Kent, Paul R. C.; Stack, Andrew G.; Navrotsky, Alexandra; Riman, Richard; Anderko, Andre; Bryantsev, Vyacheslav S.

    2016-07-11

    Bastnasite is a fluoro-carbonate mineral that is the largest source of rare earth elements such as Y, La and Ce. With increasing demand for REE in many emerging technologies, there is an urgent need for improving the efficiency of ore beneficiation by froth flotation. In order to design improved flotation agents that can selectively bind to the mineral surface, a fundamental understanding of the bulk and surface properties of bastnasite is essential. Density functional theory calculations using the PBEsol exchange correlation functional and the DFT-D3 dispersion correction reveal that the most stable form of La bastnsite is isomorphic to the structure of Ce bastnasite belonging to the P2c space group, while the Inorganic Crystal Structure Database structure in the P2m space group is ca. 11.3 kJ/mol higher in energy per LaFCO3 formula unit. We report powder X-ray diffraction measurements on synthetic of La bastnasite to support these theoretical findings. Six different surfaces are studied by DFT, namely [100], [0001], [101], [102], [104] and [112]. Among these, the [100] surface is the most stable with a surface energy of 0.73 J/m2 in vacuum and 0.45 J/m2 in aqueous solution. We predicted the shape of a La bastnasite nanoparticle via thermodynamic Wulff construction to be a hexagonal prism with [100] and [0001] facets, chiseled at its ends by the [101] and [102] facets. The average surface energy of the nanoparticle in the gas phase is estimated to be 0.86 J/m2, in good agreement with a value of 1.11 J/m2 measured by calorimetry. The calculated adsorption energy of a water molecule varies widely with the surface plane and specific adsorption sites on a given surface. Moreover, the first layer of water molecules is predicted to adsorb strongly on the La-bastnasite surface, in agreement with water adsorption calorimetry experiments. Our work provides an important step towards a detailed atomistic understanding of

  20. Crystal Structures, Surface Stability, and Water Adsorption Energies of La-Bastnäsite via Density Functional Theory and Experimental Studies

    DOE PAGES

    Srinivasan, Sriram Goverapet; Shivaramaiah, Radha; Kent, Paul R. C.; ...

    2016-07-11

    Bastnasite is a fluoro-carbonate mineral that is the largest source of rare earth elements such as Y, La and Ce. With increasing demand for REE in many emerging technologies, there is an urgent need for improving the efficiency of ore beneficiation by froth flotation. In order to design improved flotation agents that can selectively bind to the mineral surface, a fundamental understanding of the bulk and surface properties of bastnasite is essential. Density functional theory calculations using the PBEsol exchange correlation functional and the DFT-D3 dispersion correction reveal that the most stable form of La bastnsite is isomorphic to themore » structure of Ce bastnasite belonging to the P2c space group, while the Inorganic Crystal Structure Database structure in the P2m space group is ca. 11.3 kJ/mol higher in energy per LaFCO3 formula unit. We report powder X-ray diffraction measurements on synthetic of La bastnasite to support these theoretical findings. Six different surfaces are studied by DFT, namely [100], [0001], [101], [102], [104] and [112]. Among these, the [100] surface is the most stable with a surface energy of 0.73 J/m2 in vacuum and 0.45 J/m2 in aqueous solution. We predicted the shape of a La bastnasite nanoparticle via thermodynamic Wulff construction to be a hexagonal prism with [100] and [0001] facets, chiseled at its ends by the [101] and [102] facets. The average surface energy of the nanoparticle in the gas phase is estimated to be 0.86 J/m2, in good agreement with a value of 1.11 J/m2 measured by calorimetry. The calculated adsorption energy of a water molecule varies widely with the surface plane and specific adsorption sites on a given surface. Moreover, the first layer of water molecules is predicted to adsorb strongly on the La-bastnasite surface, in agreement with water adsorption calorimetry experiments. Our work provides an important step towards a detailed atomistic understanding of the bastnasite water interface and designing

  1. Infrared absorption spectroscopic and DFT calculation studies on the adsorption structures of nitromethane on the single crystals of Cu and Ag

    NASA Astrophysics Data System (ADS)

    Itoh, K.; Iwa, A.; Uriu, Y.; Kadokura, K.

    2008-07-01

    The adsorption structures of nitromethane on Ag(1 1 0), Ag(1 1 1), Cu(1 1 0) and Cu(1 1 1) at 80 K were studied by using infrared reflection absorption spectroscopy (IRAS) and non-local density functional theory (DFT) calculation performed on nitromethane/Cu(1 1 0) and nitromethane/Cu(1 1 1) cluster models. Upon increasing exposure levels, the adsorbate on each substrate exhibits discrete spectral changes, characterizing sub-monolayer and/or monolayer, amorphous and multilayer (crystalline) states. The DFT calculation successively simulated the IRA spectra of nitromethane on the copper substrates, suggesting that nitromethane adsorbs on Cu(1 1 0) through an on-top coordination with one of the oxygen atom of the NO 2 group to the Cu atom and that nitromethane adsorbs on Cu(1 1 1) through a bridging coordination of the oxygen atom. In both states nitromethane takes an eclipsed form with the molecular plane perpendicular to the substrates surface and the hydrogen atom pointing to the surface in the molecular plane plays an important role in stabilizing the adsorption states in addition to the coordination interaction.

  2. 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.

  3. 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.

  4. 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.

  5. Electronic and magnetic properties of TM atoms adsorption on 2D silicon carbide by first-principles calculations

    NASA Astrophysics Data System (ADS)

    Luo, M.; Shen, Y. H.; Yin, T. L.

    2017-02-01

    The magnetic properties of different transition-metal (TM) atoms (TM=Co, Cu, Mn, Fe, and Ni) adsorption on SiC monolayer are investigated using density functional theory (DFT). Magnetism appears in the cases of Co, Cu, Mn, and Fe. Among all the magnetic cases, the Co-adsorbed system has the most stable structure. Therefore, we further study the interaction in the two-Co-adsorbed system. Our results show that the interaction between two Co atoms is always FM and the p-d hybridization mechanism results in such ferromagnetic states. However, the FM interaction is obviously depressed by the increasing Co-Co distance, which could be well explained by the Zener-RKKY theory. Moreover, different magnetic behavior is observed in the two-Mn-adsorbed system and a long-range AFM state is showing. Such multiple magnetic properties may suggest promising applications of TM-adsorbed SiC monolayer in the future.

  6. 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.

  7. The study of adsorption characteristics of electrospun polymer nanofibers for benzenes in water.

    PubMed

    Sun, Jing; Kang, Xue-Jun; Ma, Yu-Qin; Chen, Li-Qin; Wang, Yu; Gu, Zhong-Ze

    2011-01-01

    The adsorption properties of benzene, p-dichlorobenzene and nitrobenzene on polymer nanofibers were studied. Compared with polyacrylonitrile nanofiber, polystyrene (PS) nanofiber presented better adsorption performance. Langmuir and Freundlich adsorption models were used for the mathematical description of adsorption equilibria, and Freundlich isotherms fitted better. Kinetic studies showed that the adsorption of PS nanofiber followed pseudo first-order model. Various thermodynamic parameters such as standard free energy (delta G), enthalpy (delta H) and entropy (delta S) were calculated for predicting the adsorption nature of PS nanofiber for three benzenes, which indicated that the adsorption was spontaneous and a physical process. The regeneration efficiency maintains over 80% after five cycles of adsorption/desorption tests. It showed that PS nanofibers are promising candidates for adsorption and removal of aromatic hydrocarbons from water.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  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. [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.

  19. Ion-specific weak adsorption of salts and water/octanol transfer free energy of a model amphiphilic hexapeptide.

    PubMed

    Déjugnat, Christophe; Dufrêche, Jean-François; Zemb, Thomas

    2011-04-21

    An amphiphilic hexapeptide has been used as a model to quantify how specific ion effects induced by addition of four salts tune the hydrophilic/hydrophobic balance and induce temperature-dependant coacervate formation from aqueous solution. The hexapeptide chosen is present as a dimer with low transfer energy from water to octanol. Taking sodium chloride as the reference state in the Hofmeister scale, we identify water activity effects and therefore measure the free energy of transfer from water to octanol and separately the free energy associated to the adsorption of chaotropic ions or the desorption of kosmotropic ions for the same amphiphilic peptide. These effects have the same order of magnitude: therefore, both energies of solvation as well as transfer into octanol strongly depend on the nature of the electrolytes used to formulate any buffer. Model peptides could be used on separation processes based on criteria linked to "Hofmeister" but different from volume and valency.

  20. A new theoretical approach to adsorption desorption behavior of Ga on GaAs surfaces

    NASA Astrophysics Data System (ADS)

    Kangawa, Y.; Ito, T.; Taguchi, A.; Shiraishi, K.; Ohachi, T.

    2001-11-01

    We propose a new theoretical approach for studying adsorption-desorption behavior of atoms on semiconductor surfaces. The new theoretical approach based on the ab initio calculations incorporates the free energy of gas phase; therefore we can calculate how adsorption and desorption depends on growth temperature and beam equivalent pressure (BEP). The versatility of the new theoretical approach was confirmed by the calculation of Ga adsorption-desorption transition temperatures and transition BEPs on the GaAs (0 0 1) -(4×2) β2 Ga-rich surface. This new approach is feasible to predict how adsorption and desorption depend on the growth conditions.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Linear solvation energy relationship for the adsorption of synthetic organic compounds on single-walled carbon nanotubes in water.

    PubMed

    Ding, H; Chen, C; Zhang, X

    2016-01-01

    The linear solvation energy relationship (LSER) was applied to predict the adsorption coefficient (K) of synthetic organic compounds (SOCs) on single-walled carbon nanotubes (SWCNTs). A total of 40 log K values were used to develop and validate the LSER model. The adsorption data for 34 SOCs were collected from 13 published articles and the other six were obtained in our experiment. The optimal model composed of four descriptors was developed by a stepwise multiple linear regression (MLR) method. The adjusted r(2) (r(2)adj) and root mean square error (RMSE) were 0.84 and 0.49, respectively, indicating good fitness. The leave-one-out cross-validation Q(2) ([Formula: see text]) was 0.79, suggesting the robustness of the model was satisfactory. The external Q(2) ([Formula: see text]) and RMSE (RMSEext) were 0.72 and 0.50, respectively, showing the model's strong predictive ability. Hydrogen bond donating interaction (bB) and cavity formation and dispersion interactions (vV) stood out as the two most influential factors controlling the adsorption of SOCs onto SWCNTs. The equilibrium concentration would affect the fitness and predictive ability of the model, while the coefficients varied slightly.

  7. 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.

  8. 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.

  9. 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)

  10. 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.

  11. Effect of nitrogen doping of graphene oxide on hydrogen and hydroxyl adsorption

    NASA Astrophysics Data System (ADS)

    Min, Byeong June; Jeong, Hae Kyung

    2014-05-01

    We investigate how nitrogen-doping affects the hydrogen (H) and the hydroxyl (OH) adsorption on graphene oxide (GO) and on nitrogen-doped GO (NGO) via pseudopotential plane wave density functional calculations within the local spin density approximation. We find that the nitrogendoping brings about drastic changes in the hydrogen and the hydroxyl adsorption energetics, but its effects depend sensitively on the nitrogen configuration in NGO. The H and the OH adsorption energies are comparable only for pyrrolic NGO. In GO and quarternary NGO, the H adsorption energy is greater than the OH adsorption energy while the trend is reversed in pyridinic NGO. Also, the OH adsorption process is less affected by nitrogen-doping than the H adsorption is.

  12. 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.

  13. 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)

  14. 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.

  15. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111)

    NASA Astrophysics Data System (ADS)

    Geweke, Jan; Shirhatti, Pranav R.; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M.

    2016-08-01

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed—presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]—50 times smaller than those reported here—were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

  16. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111).

    PubMed

    Geweke, Jan; Shirhatti, Pranav R; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M

    2016-08-07

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed-presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]-50 times smaller than those reported here-were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

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

    ERIC Educational Resources Information Center

    Barbiric, Dora; Tribe, Lorena; Soriano, Rosario

    2015-01-01

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

  18. 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}

  19. 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...

  20. 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.

  1. 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)

  2. The effect of ligand substitution and water co-adsorption on the adsorption dynamics and energy level matching of amino-phenyl acid dyes on TiO2.

    PubMed

    Manzhos, Sergei; Segawa, Hiroshi; Yamashita, Koichi

    2012-02-07

    We perform a comparative theoretical analysis of adsorption of dyes NK1 (2E,4E-2-cyano-5-(4-dimethylaminophenyl)penta-2,4-dienoic acid) and NK7 (2E,4E-2-cyano-5-(4-diphenylaminophenyl)penta-2,4-dienoic acid) on clean and water-covered anatase (101) surfaces of TiO(2). Ligand substitution away from the anchoring group changes the energy level matching between the dye's LUMO and the oxide's conduction band. Monodentate binding and bidentate binding configurations of the dyes to TiO(2) are found to have similar adsorption energies even though the injection from the bidentate mode is found to dominate. Water has a strong effect on adsorption, inducing deprotonation and affecting strongly and differently between the dyes the energy level matching, leading to a shut-off of the injection from NK7 of bidentate adsorption configuration. Ab initio molecular dynamics simulations show a strong effect of nuclear motion on energy levels, specifically, increasing the driving force for injection in the monodentate regime.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

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

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

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

  9. 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.

  10. 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.

  11. 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.

  12. Computational Investigation of Conformational Changes in Proteins upon Adsorption

    NASA Astrophysics Data System (ADS)

    Sharma, Sumit; Anand, Gaurav; Belfort, Georges; Kumar, Sanat K.

    2009-03-01

    Amyloidogenic diseases, such as, Alzheimer's, are caused by adsorption and aggregation of partially unfolded proteins. Protein adsorption is often accompanied by conformational rearrangements, which are thought to affect many properties such as their adhesion strength to the surface, biological activity, and aggregation tendency. Experiments have shown that many proteins, upon adsorption to hydrophobic surfaces, undergo a helix to sheet or random coil secondary structural rearrangement. To better understand the equilibrium structural complexities of this phenomenon, we have performed Monte Carlo (MC) simulations and Single Chain Mean Field calculations of adsorption of different proteins, modeled as lattice chains, to study the adsorption behavior and equilibrium protein conformations at different temperatures, protein concentration and surface hydrophobicity. Free energy and entropic effects on adsorption have been studied by determining density of states using Weighted Histogram Analysis Method. Conformational transitions of proteins on surfaces will be discussed as a function of surface hydrophobicity.

  13. 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.

  14. The surface tension of a solid at the solid-vacuum interface, an evaluation from adsorption and wall potential calculations.

    PubMed

    Jakubov, Tim S; Mainwaring, David E

    2007-03-15

    A method for the evaluation of quantities that are experimentally inaccessible such as the surface tension at the solid-vacuum interface and the superficial tension of the fluid in contact with the solid is presented. The approach is based on consideration of an equilibrium of a fluid in solid capillary wherein a balance between surface and capillary forces has been replaced by conceptual alternative interfacial and centrifugal forces. This approach involves the simultaneous numerical solution one the special forms of the Gibbs equation for solid-fluid interface and a generalized Kelvin equation derived earlier. The latter equation takes into account interactions between the solid thick cylindrical wall and confined fluid, this body-body interaction potential has been primarily calculated using the Lennard-Jones (6-12) expression for the atom-atom pair potentials and expressed by hypergeometrical functions having good convergences. All numerical calculations shown here have been performed for the model graphite-argon system at 90 K. Finally, an analysis of the accuracy of the proposed method is considered.

  15. 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)

  16. 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

  17. Prediction of the adsorption behavior of elements 112 and 114 on inert surfaces from ab initio Dirac-Coulomb atomic calculations.

    PubMed

    Pershina, V; Borschevsky, A; Eliav, E; Kaldor, U

    2008-01-14

    The interaction of elements 112 and 114 with inert surfaces has been studied on the basis of fully relativistic ab initio Dirac-Coulomb CCSD(T) calculations of their atomic properties. The calculated polarizabilities of elements 112 and 114 are significantly lower than corresponding Hg and Pb values due to the relativistic contraction of the valence ns and np(12) orbitals, respectively, in the heavier elements. Due to the same reason, the estimated van der Waals radius of element 114 is smaller than that of Pb. The enthalpies of adsorption of Hg, Pb, and elements 112 and 114 on inert surfaces such as quartz, ice, and Teflon were predicted on the basis of these atomic calculations using a physisorption model. At the present level of accuracy, -DeltaH(ads) of element 112 on these surfaces is slightly (about 2 kJ/mol) larger than -DeltaH(ads)(Hg). The calculated -DeltaH(ads) of element 114 on quartz is about 7 kJ/mol and on Teflon is about 3 kJ/mol smaller than the respective values of -DeltaH(ads)(Pb). The trend of increasing -DeltaH(ads) in group 14 from C to Sn is thus reversed, giving decreasing values from Sn to Pb to element 114 due to the relativistic stabilization and contraction of the np(12) atomic orbitals. This is similar to trends shown by other atomic properties of these elements. The small difference in DeltaH(ads) of Pb and element 114 on inert surfaces obtained within a picture of physisorption contrasts with the large difference (more than 100 kJ/mol) in the chemical reactivity between these elements.

  18. 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).

  19. 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.

  20. 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.

  1. 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.

  2. Adsorption isotherms of some alkyl aromatic hydrocarbons and surface energies on partially dealuminated Y faujasite zeolite by inverse gas chromatography.

    PubMed

    Kondor, Anett; Dallos, András

    2014-10-03

    Adsorption isotherm data of some alkyl aromatic hydrocarbons (benzene, toluene, ethylbenzene, o-xylene, m-xylene and p-xylene) measured in the temperature range of 423-523K on a partially dealuminated faujasite type DAY F20 zeolite by inverse gas chromatography are presented in this work. The temperature dependent form of Tóth's equation has been fitted to the multiple temperature adsorption isotherms of benzene, toluene, ethylbenzene, o-xylene, m-xylene and p-xylene with standard deviations of 4.6, 5.0, 5.9, 4.3, 5.1 and 6.3mmolkg(-1) and coefficients of determinations (r(2)) of 0.977, 0.971, 0.974, 0.975, 0.991 and 0.991, respectively. The gas-solid equilibria and modeling were interpreted on the basis of the interfacial properties of the zeolite, by dispersive, specific and total surface energy heterogeneity profiles and distributions of the adsorbent measured by surface energy analysis.

  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. 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

  5. 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.

  6. 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.

  7. 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.

  8. Fast monolayer adsorption and slow energy transfer in CdSe quantum dot sensitized ZnO nanowires.

    PubMed

    Zheng, Kaibo; Žídek, Karel; Abdellah, Mohamed; Torbjörnsson, Magne; Chábera, Pavel; Shao, Shuyan; Zhang, Fengling; Pullerits, Tõnu

    2013-07-25

    A method for CdSe quantum dot (QD) sensitization of ZnO nanowires (NW) with fast adsorption rate is applied. Photoinduced excited state dynamics of the quantum dots in the case of more than monolayer coverage of the nanowires is studied. Transient absorption kinetics reveals an excitation depopulation process of indirectly attached quantum dots with a lifetime of ~4 ns. Photoluminescence and incident photon-to-electron conversion efficiency show that this process consists of both radiative e-h recombination and nonradiative excitation-to-charge conversion. We argue that the latter occurs via interdot energy transfer from the indirectly attached QDs to the dots with direct contact to the nanowires. From the latter, fast electron injection into ZnO occurs. The energy transfer time constant is found to be around 5 ns.

  9. Impact of interfacial high-density water layer on accurate estimation of adsorption free energy by Jarzynski's equality

    NASA Astrophysics Data System (ADS)

    Zhang, Zhisen; Wu, Tao; Wang, Qi; Pan, Haihua; Tang, Ruikang

    2014-01-01

    The interactions between proteins/peptides and materials are crucial to research and development in many biomedical engineering fields. The energetics of such interactions are key in the evaluation of new proteins/peptides and materials. Much research has recently focused on the quality of free energy profiles by Jarzynski's equality, a widely used equation in biosystems. In the present work, considerable discrepancies were observed between the results obtained by Jarzynski's equality and those derived by umbrella sampling in biomaterial-water model systems. Detailed analyses confirm that such discrepancies turn up only when the target molecule moves in the high-density water layer on a material surface. Then a hybrid scheme was adopted based on this observation. The agreement between the results of the hybrid scheme and umbrella sampling confirms the former observation, which indicates an approach to a fast and accurate estimation of adsorption free energy for large biomaterial interfacial systems.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Electrokinetic investigation of surfactant adsorption.

    PubMed

    Bellmann, C; Synytska, A; Caspari, A; Drechsler, A; Grundke, K

    2007-05-15

    Fuerstenau [D.W. Fuerstenau, in: M.L. Hair (Ed.), Dekker, New York, 1971, p. 143] has already discussed the role of hydrocarbon chain of surfactants, the effect of alkyl chain length, chain structure and the pH of the solution on the adsorption process of surfactants. Later Kosmulski [M. Kosmulski, Chemical Properties of Material Surfaces, Surfactant Science Series, vol. 102, Dekker, New York, Basel, 2001] included the effect of surfactant concentration, equilibration time, temperature and electrolyte in his approaches. Certainly, the character of the head groups of the surfactant and the properties of the adsorbent surface are the basis for the adsorption process. Different surfactants and adsorbents cause different adsorption mechanisms described firstly by Rosen [M.J. Rosen, Surfactants and Interfacial Phenomena, second ed., Wiley, New York, 1989]. These adsorption mechanisms and their influencing factors were studied by electrokinetic investigations. Here only changes of the charges at the surfaces could be detected. To control the results of electrokinetic investigations they were compared with results from ellipsometric measurements. In the case of surfactant adsorption the chain length was vitally important. It could be shown by the adsorption of alkyl trimethyl ammonium bromides onto polymer films spin coated at wafer surfaces. The influence of the chain length depending on surface properties of the polymer film was studied. Streaming potential measurements were applied for these investigations. The obtained results enabled us to calculate the molar cohesive free energy per mol of CH2-group in the alkaline chain of the surfactant if all other specific adsorption effects were neglected.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. A van der Waals density functional study of adenine on graphene: Single molecular adsorption and overlayer binding

    SciTech Connect

    Berland, Kristian; Cooper, Valentino R; Langreth, David C.; Schroder, Prof. Elsebeth; Chakarova-Kack, Svetla

    2011-01-01

    The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional (vdW-DF) [Dion et al., Phys. Rev. Lett. 92, 246401 (2004)]. The cohesive energy of an ordered adenine overlayer is also estimated. For the adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similar-sized naphthalene. Based on the single molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.

  2. 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.

  3. 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

  4. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  6. From single molecules to water networks: Dynamics of water adsorption on Pt(111)

    NASA Astrophysics Data System (ADS)

    Naderian, Maryam; Groß, Axel

    2016-09-01

    The adsorption dynamics of water on Pt(111) was studied using ab initio molecular dynamics simulations based on density functional theory calculations including dispersion corrections. Sticking probabilities were derived as a function of initial kinetic energy and water coverage. In addition, the energy distribution upon adsorption was monitored in order to analyze the energy dissipation process. We find that on the water pre-covered surface the sticking probability is enhanced because of the attractive water-water interaction and the additional effective energy dissipation channels to the adsorbed water molecules. The water structures forming directly after the adsorption on the pre-covered surfaces do not necessarily correspond to energy minimum structures.

  7. 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.

  8. 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.

  9. 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.

  10. Adsorption Refrigeration System

    SciTech Connect

    Wang, Kai; Vineyard, Edward Allan

    2011-01-01

    Adsorption refrigeration is an environmentally friendly cooling technology which could be driven by recovered waste heat or low-grade heat such as solar energy. In comparison with absorption system, an adsorption system has no problems such as corrosion at high temperature and salt crystallization. In comparison with vapor compression refrigeration system, it has the advantages of simple control, no moving parts and less noise. This paper introduces the basic theory of adsorption cycle as well as the advanced adsorption cycles such as heat and mass recovery cycle, thermal wave cycle and convection thermal wave cycle. The types, characteristics, advantages and drawbacks of different adsorbents used in adsorption refrigeration systems are also summarized. This article will increase the awareness of this emerging cooling technology among the HVAC engineers and help them select appropriate adsorption systems in energy-efficient building design.

  11. 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

  12. 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.

  13. 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.

  14. 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)...

  15. 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.

  16. 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.

  17. 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.

  18. 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)

  19. 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.

  20. 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)

  1. 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

  2. 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…

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Initial stages of CO2 adsorption on CaO: a combined experimental and computational study.

    PubMed

    Solis, Brian H; Cui, Yi; Weng, Xuefei; Seifert, Jan; Schauermann, Swetlana; Sauer, Joachim; Shaikhutdinov, Shamil; Freund, Hans-Joachim

    2017-02-08

    Room temperature adsorption of carbon dioxide (CO2) on monocrystalline CaO(001) thin films grown on a Mo(001) substrate was studied by infrared reflection-absorption spectroscopy (IRAS) and quantum chemical calculations. For comparison, CO2 adsorption was examined on poorly ordered, nanoparticulate CaO films prepared on Ru(0001). For both systems, CO2 readily adsorbs on the clean CaO surface. However, additional bands were observable on the CaO/Ru(0001) films compared with CaO/Mo(001), because the stricter IRAS surface selection rules do not apply to adsorption on the disordered thin films grown on Ru(0001). Spectral evolution with increasing exposure of the IRA bands suggested the presence of several adsorption sites which are consecutively populated by CO2. Density functional calculations showed that CO2 adsorption occurs as monodentate surface carbonate (CO3(2-)) species at monatomic step sites and other low-coordinated sites, followed by formation of carbonates on terraces, which dominate at increasing CO2 exposure. To explain the coverage-dependent IRAS results, we propose CO2 surface islanding from the onset, most likely in the form of pairs and other chain-like species, which were calculated as thermodynamically favorable. The calculated adsorption energy for isolated CO2 on the terrace sites (184 ± 10 kJ mol(-1)) is larger than the adsorption energy obtained by temperature programmed desorption (∼120-140 kJ mol(-1)) and heat of adsorption taken from microcalorimetry measurements at low coverage (∼125 kJ mol(-1)). However, the calculated adsorption energies become less favorable when carbonate chains intersect on CaO terraces, forming kinks. Furthermore, our assignments of the initial stages of CO2 adsorption are consistent with the observed coverage effect on the CO2 adsorption energy measured by microcalorimetry and the IRAS results.

  16. Adsorption characteristics of brilliant green dye on kaolin.

    PubMed

    Nandi, B K; Goswami, A; Purkait, M K

    2009-01-15

    Experimental investigations were carried out to adsorb toxic brilliant green dye from aqueous medium using kaolin as an adsorbent. Characterization of kaolin is done by measuring: (i) particle size distribution using particle size analyzer, (ii) BET surface area using BET surface analyzer, and (iii) structural analysis using X-ray diffractometer. The effects of initial dye concentration, contact time, kaolin dose, stirring speed, pH and temperature were studied for the adsorption of brilliant green in batch mode. Adsorption experiments indicate that the extent of adsorption is strongly dependent on pH of solution. Free energy of adsorption (DeltaG0), enthalpy (DeltaH0) and entropy (DeltaS0) changes are calculated to know the nature of adsorption. The calculated values of DeltaG0 at 299K and 323K indicate that the adsorption process is spontaneous. The estimated values of DeltaH0 and DeltaS0 both show the negative sign, which indicate that the adsorption process is exothermic and the dye molecules are organized on the kaolin surface in less randomly fashion than in solution. The adsorption kinetic has been described by first-order, pseudo-second-order and intra-particle-diffusion models. It was observed that the rate of dye adsorption follows pseudo-second-order model for the dye concentration range studied in the present case. Standard adsorption isotherms were used to fit the experimental equilibrium data. It was found that the adsorption of brilliant green on kaolin follows the Langmuir adsorption isotherm.

  17. Hydrogen adsorption on sulphur-doped SiC nanotubes

    NASA Astrophysics Data System (ADS)

    Sevak Singh, Ram

    2016-07-01

    Hydrogen (H2) is an energy carrier and clean fuel that can be used for a broad range of applications that include fuel cell vehicles. Therefore, development of materials for hydrogen storage is demanded. Nanotubes, in this context, are appropriate materials. Recently, silicon carbide nanotube (SiCNTs) have been predicted as potential nanomaterials for hydrogen storage, and atomic doping into the nanotubes improves the H2 adsorption. Here, we report H2 adsorption properties of sulphur-doped (S-doped) SiCNTs using first-principles calculations based on density functional theory. The H2 adsorption properties are investigated by calculations of energy band structures, density of states (DOS), adsorption energy and Mulliken charge population analysis. Our findings show that, compared to the intrinsic SiCNT, S-doped SiCNT is more sensitive to H2 adsorption. H2 gas adsorption on S-doped C-sites of SiCNT brings about significant modulation of the electronic structure of the nanotube, which results in charge transfer from the nanotube to the gas, and dipole-dipole interactions cause chemisorptions of hydrogen. However, in the case of H2 gas adsorption on S-doped Si-sites of the nanotube, lesser charge transfer from the nanotube to the gas results in physisorptions of the gas. The efficient hydrogen sensing properties of S-doped SiCNTs, studied here, may have potential for its practical realization for hydrogen storage application.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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 .

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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}.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Changes in the size of the apparent surface area and adsorption energy of the rye roots by low pH and the presence of aluminium ions induced

    NASA Astrophysics Data System (ADS)

    Szatanik-Kloc, Alicja

    2016-07-01

    The plant reactions on Al-stress include i.a. change of the surface area of the roots, which in the physicochemistry of plants characterizes the transport of water and ions through the root. The object of this study is the specific surface area of the roots of plants which are tolerant to aluminium, such as rye. Plants of rye were grown in a nutrient solution for 14 days at pH 4.5 in the presence of Al3+ ions of concentration 10, 20, and 40 mg dm-3. The control plants were grown continuously at pH 7 or pH 4.5 without Al3+. The apparent surface area and adsorption energy of the plants roots were determined from water vapour adsorption - desorption data. The apparent surface area of roots growing in the aluminium was (with respect to control) statistically significantly lower. There were no statistically significant differences in the apparent surface area of the roots which grew in pH 7, pH 4.5 without Al3+. The average water vapour adsorption energy of the root surface, under stress conditions decreased. In the roots grown in the presence of Al+3, there was a slight decrease in high energy adsorption centres and an increase in the amount of low-energy centres.

  14. The influence of the carbon surface chemical composition on Dubinin-Astakhov equation parameters calculated from SF6 adsorption data-grand canonical Monte Carlo simulation.

    PubMed

    Furmaniak, Sylwester; Terzyk, Artur P; Gauden, Piotr A; Kowalczyk, Piotr; Harris, Peter J F

    2011-10-05

    Using grand canonical Monte Carlo simulation we show, for the first time, the influence of the carbon porosity and surface oxidation on the parameters of the Dubinin-Astakhov (DA) adsorption isotherm equation. We conclude that upon carbon surface oxidation, the adsorption decreases for all carbons studied. Moreover, the parameters of the DA model depend on the number of surface oxygen groups. That is why in the case of carbons containing surface polar groups, SF(6) adsorption isotherm data cannot be used for characterization of the porosity.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Adsorption-driven translocation of polymer chain into nanopores

    NASA Astrophysics Data System (ADS)

    Yang, Shuang; Neimark, Alexander V.

    2012-06-01

    The polymer translocation into nanopores is generally facilitated by external driving forces, such as electric or hydrodynamic fields, to compensate for entropic restrictions imposed by the confinement. We investigate the dynamics of translocation driven by polymer adsorption to the confining walls that is relevant to chromatographic separation of macromolecules. By using the self-consistent field theory, we study the passage of a chain trough a small opening from cis to trans compartments of spherical shape with adsorption potential applied in the trans compartment. The chain transfer is modeled as the Fokker-Plank diffusion along the free energy landscape of the translocation pass represented as a sum of the free energies of cis and trans parts of the chain tethered to the pore opening. We investigate how the chain length, the size of trans compartment, the magnitude of adsorption potential, and the extent of excluded volume interactions affect the translocation time and its distribution. Interplay of these factors brings about a variety of different translocation regimes. We show that excluded volume interactions within a certain range of adsorption potentials can cause a local minimum on the free energy landscape, which is absent for ideal chains. The adsorption potential always leads to the decrease of the free energy barrier, increasing the probability of successful translocation. However, the translocation time depends non-monotonically of the magnitude of adsorption potential. Our calculations predict the existence of the critical magnitude of adsorption potential, which separates favorable and unfavorable regimes of translocation.

  2. 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

  3. 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.

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

    SciTech Connect

    Bentley, I.; Frauendorf, S.

    2011-06-15

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

  5. 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.

  6. Initial heats of H{sub 2}S adsorption on activated carbons: Effect of surface features

    SciTech Connect

    Bagreev, A.; Adib, F.; Bandosz, T.J.

    1999-11-15

    The sorption of hydrogen sulfide was studied on activated carbons of various origins by means of inverse gas chromatography at infinite dilution. The conditions of the experiment were dry and anaerobic. Prior to the experiments the surface of some carbon samples was oxidized using either nitric acid or ammonium persulfate. Then the structural parameters of carbons were evaluated from the sorption of nitrogen. From the IGC experiments at various temperatures, heats of adsorption were calculated. The results showed that the heat of H{sub 2}S adsorption under dry anaerobic conditions does not depend on surface chemistry. The dependence of the heat of adsorption on the characteristic energy of nitrogen adsorption calculated from the Dubinin-Raduskevich equation was found. This correlation can be used to predict the heat of H{sub 2}S adsorption based on the results obtained from nitrogen adsorption.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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).

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Enhanced fibronectin adsorption on carbon nanotube/poly(carbonate) urethane: independent role of surface nano-roughness and associated surface energy.

    PubMed

    Khang, Dongwoo; Kim, Sung Yeol; Liu-Snyder, Peishan; Palmore, G Tayhas R; Durbin, Stephen M; Webster, Thomas J

    2007-11-01

    The contribution of nanoscale surface roughness on the adsorption of one key cell adhesive protein, fibronectin, on carbon nanotube/poly(carbonate) urethane composites of different surface energies was evaluated. Systematic control of various surface energies by creating different nanosurface roughness features was performed by mixing two promising biomaterials: multi-wall carbon nanotubes and poly(carbonate) urethane. High ratios of carbon nanotubes coated with poly(carbonate) urethane provided for greater hydrophilic surfaces because of higher nanosurface roughness although pure carbon nanotube surfaces were extremely hydrophobic. Fabrication methods followed in this study generated various homogenous nanosurface roughness values (ranging from 2 to 20nm root mean square (RMS) AFM roughness). With the aid of such nanosurface roughness values in composites, a model was developed that linearly correlated nanosurface roughness and associated nanosurface energy to fibronectin adsorption. Specifically, independent contributions of surface chemistry (70%) and surface nano-roughness (30%) were found to mediate fibronectin adsorption. The results of the present study showed why carbon nanotube/poly(carbonate) urethane composites enhance cellular functions and tissue growth by delineating the importance of their physical nano-roughness on promoting the adsorption of a protein well known to be critical for mediating the adhesion of anchorage-dependent cells.

  18. The different adsorption mechanism of methane molecule onto a boron nitride and a graphene flakes

    SciTech Connect

    Seyed-Talebi, Seyedeh Mozhgan; Neek-Amal, M.

    2014-10-21

    Graphene and single layer hexagonal boron-nitride are two newly discovered 2D materials with wonderful physical properties. Using density functional theory, we study the adsorption mechanism of a methane molecule over a hexagonal flake of single layer hexagonal boron-nitride (h-BN) and compare the results with those of graphene. We found that independent of the used functional in our ab-initio calculations, the adsorption energy in the h-BN flake is larger than that for graphene. Despite of the adsorption energy profile of methane over a graphene flake, we show that there is a long range behavior beyond minimum energy in the adsorption energy of methane over h-BN flake. This result reveals the higher sensitivity of h-BN sheet to the adsorption of a typical closed shell molecule with respect to graphene. The latter gives insight in the recent experiments of graphene over hexagonal boron nitride.

  19. Pyrite surface environment drives molecular adsorption: cystine on pyrite(100) investigated by X-ray photoemission spectroscopy and low energy electron diffraction.

    PubMed

    Sanchez-Arenillas, M; Mateo-Marti, E

    2016-10-05

    We have demonstrated that the annealing process for cleaning pyrite surfaces is a critical parameter in promoting ordering on the surface and driving surface reactivity. Furthermore, we describe a spectroscopic surface characterization of the presence or absence of the surface ordering, as indicated by the Low Energy Electron Diffraction (LEED) pattern, as a function of the surface annealing process. Complementary X-ray photoemission spectroscopy (XPS) results provide evidence that longer annealing processes of over 3 hours repair the sulfur vacancies in the pyrite, making FeS species partially disappear in favor of FeS2 species. These features play an important role in molecular adsorption. We show that in the case of the cystine amino acid on the (100) pyrite surface, the substrate structure is responsible for the chemical adsorption form. The presence of an ordered structure on the surface, as indicated by the LEED pattern, favors the cystine NH3(+) chemical form, whereas the absence of the surface ordering promotes cystine NH2 adsorption due to the sulfur-deficient surface. The cystine molecule could then act by changing its chemical functionalities to compensate for the iron surface coordination. The chemical molecular adsorption form can be selected by the surface annealing conditions, implying that environmental conditions could drive molecular adsorption on mineral surfaces. These findings are relevant in several surface processes, and they could play a possible role in prebiotic chemistry surface reactions and iron-sulfur scenarios.

  20. 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.

  1. 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.

  2. The adsorption of h-BN monolayer on the Ni(111) surface studied by density functional theory calculations with a semiempirical long-range dispersion correction

    SciTech Connect

    Sun, X.; Pratt, A.; Li, Z. Y.; Ohtomo, M.; Sakai, S.; Yamauchi, Y.

    2014-05-07

    The geometric and spin-resolved electronic structure of a h-BN adsorbed Ni(111) surface has been investigated by density functional theory calculations. Two energy minima (physisorption and chemisorption) are obtained when the dispersive van der Waals correction is included. The geometry of N atom on top site and B atom on fcc site is the most energetically favorable. Strong hybridization with the ferromagnetic Ni substrate induces considerable gap states in the h-BN monolayer. The induced π* states are spin-polarized.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Carbon dioxide adsorption in graphene sheets

    NASA Astrophysics Data System (ADS)

    Mishra, Ashish Kumar; Ramaprabhu, Sundara

    2011-09-01

    Control over the CO2 emission via automobiles and industrial exhaust in atmosphere, is one of the major concerns to render environmental friendly milieu. Adsorption can be considered to be one of the more promising methods, offering potential energy savings compared to absorbent systems. Different carbon nanostructures (activated carbon and carbon nanotubes) have attracted attention as CO2 adsorbents due to their unique surface morphology. In the present work, we have demonstrated the CO2 adsorption capacity of graphene, prepared via hydrogen induced exfoliation of graphitic oxide at moderate temperatures. The CO2 adsorption study was performed using high pressure Sieverts apparatus and capacity was calculated by gas equation using van der Waals corrections. Physical adsorption of CO2 molecules in graphene was confirmed by FTIR study. Synthesis of graphene sheets via hydrogen exfoliation is possible at large scale and lower cost and higher adsorption capacity of as prepared graphene compared to other carbon nanostructures suggests its possible use as CO2 adsorbent for industrial application. Maximum adsorption capacity of 21.6 mmole/g was observed at 11 bar pressure and room temperature (25 °C).

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. [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.

  14. Functionalized mesoporous silica materials for molsidomine adsorption: Thermodynamic study

    SciTech Connect

    Alyoshina, Nonna A.; Parfenyuk, Elena V.

    2013-09-15

    A series of unmodified and organically modified mesoporous silica materials was prepared. The unmodified mesoporous silica was synthesized via sol–gel synthesis in the presence of D-glucose as pore-forming agent. The functionalized by phenyl, aminopropyl and mercaptopropyl groups silica materials were prepared via grafting. The fabricated adsorbent materials were characterized by Fourier transform infrared spectroscopy (FTIR) analysis, N{sub 2} adsorption/desorption and elemental analysis methods. Then their adsorption properties for mesoionic dug molsidomine were investigated at 290–313 K and physiological pH value. Thermodynamic parameters of molsidomine adsorption on the synthesized materials have been calculated. The obtained results showed that the adsorption process of molsidomine on the phenyl modified silica is the most quantitatively and energetically favorable. The unmodified and mercaptopropyl modified silica materials exhibit significantly higher adsorption capacities and energies for molsidomine than the aminopropyl modified sample. The effects are discussed from the viewpoint of nature of specific interactions responsible for the adsorption. - Graphical abstract: Comparative analysis of the thermodynamic characteristics of molsidomine adsorption showed that the adsorption process on mesoporous silica materials is controlled by chemical nature of surface functional groups. Molsidomine adsorption on the phenyl modified silica is the most quantitatively and energetically favorable. Taking into account ambiguous nature of mesoionic compounds, it was found that molsidomine is rather aromatic than dipolar. Display Omitted - Highlights: • Unmodified and organically modified mesoporous silica materials were prepared. • Molsidomine adsorption on the silica materials was studied. • Phenyl modified silica shows the highest adsorption capacity and favorable energy. • Molsidomine exhibits the lowest affinity to aminopropyl modified silica.

  15. 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.

  16. 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}

  17. 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.

  18. 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.

  19. Theoretical investigations of the CO adsorption on ZnF2 surfaces

    NASA Astrophysics Data System (ADS)

    Kaawar, Zeinab; Müller, Carsten; Paulus, Beate

    2017-02-01

    Periodic density functional theory calculations were performed to investigate the Lewis acidity of unsaturated surface cations of ZnF2, using CO as probe molecule at different coverages. We have calculated adsorption energies for CO on all low index ZnF2 surfaces using DFT with the B3LYP functional and subsequent dispersion correction. Additionally local second order Møller-Plesset perturbation theory (LMP2) calculations were performed. In most of the cases, the adsorption of CO on different surfaces is described well using B3LYP. Dispersion correction to B3LYP is found to overestimate the adsorption energy. The interaction among adsorbed CO molecules appears to have a significant effect on the adsorption energies at full coverage.

  20. 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.

  1. 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.

  2. Enthalpy and entropy effects in hydrogen adsorption on carbon nanotubes.

    PubMed

    Efremenko, Irena; Sheintuch, Moshe

    2005-07-05

    Interaction energies and entropies associated with hydrogen adsorption on the inner and outer surfaces of zigzag single-wall carbon nanotubes (SWCNT) of various diameters are analyzed by means of molecular mechanics, density functional theory, and ab initio calculations. For a single molecule the strongest interaction, which is 3.5 greater than that with the planar graphite sheet, is found inside a (8,0) nanotube. Adsorption on the outer surfaces is weaker than that on graphite. Due to the steric considerations, both processes are accompanied by an extremely strong decline in entropy. Absence of specific adsorption sites and weak attractive interaction between hydrogen molecules within carbon nanotubes results in their close packing at low temperatures. Using the calculated geometric and thermodynamic parameters in Langmuir isotherms we predict the adsorption capacity of SWCNTs at room temperature to be smaller than 1 wt % even at 100 bar.

  3. Thermodynamic and kinetic investigations of PO3-4 adsorption on blast furnace slag.

    PubMed

    Oguz, Ensar

    2005-01-01

    The kinetics of adsorption of PO(3-)(4) by blast furnace slag were found to be fast, reaching equilibrium in 20 min and following a pseudo-second-order rate equation. The adsorption behavior of PO(3-)(4) on blast furnace slag has been studied as a function of the solution agitation speed, pH, and temperature. Results have been analyzed by Freundlich, Langmuir, BET, and Dubinin-Radushkevich (D-R) adsorption isotherms. The mean energy of adsorption, 10.31 kJ mol(-1), was calculated from the D-R adsorption isotherm. The rate constants were calculated for 293, 298, 303, and 308 K using a pseudo-second-order rate equation and the activation energy (E(a)) was derived using the Arrhenius equation. Thermodynamic parameters such as DeltaH(0), DeltaS(0), and DeltaG(0) were calculated from the slope and intercept of linear plot of lnK(D) against 1/T. The DeltaH(0) and DeltaG(0) values of PO(3-)(4) adsorption on the blast furnace slag show endothermic heat of adsorption. But there is a negative free energy value, indicating that the process of PO(3-)(4) adsorption is favored at high temperatures.

  4. 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.

  5. 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.

  6. Ab initio prediction of adsorption isotherms for small molecules in metal-organic frameworks: the effect of lateral interactions for methane/CPO-27-Mg.

    PubMed

    Sillar, Kaido; Sauer, Joachim

    2012-11-07

    A hybrid method that combines density functional theory for periodic structures with wave function-based electron correlation methods for finite-size models of adsorption sites is employed to calculate energies for adsorption of CH(4) onto different sites in the metal-organic framework (MOF) CPO-27-Mg (Mg-MOF-74) with chemical accuracy. The adsorption energies for the Mg(2+), linker, second layer sites are -27.8, -18.3, and -15.1 kJ/mol. Adsorbate-adsorbate interactions increase the average CH(4) adsorption energy by about 10% (2.4 kJ/mol). The free rotor-harmonic oscillator-ideal gas model is applied to calculate free energies/equilibrium constants for adsorption on the individual sites. This information is used in a multisite Langmuir model, augmented with a Bragg-Williams model for lateral interactions, to calculate adsorption isotherms. This ab initio approach yields the contributions of the individual sites to the final isotherms and also of the lateral interactions that contribute about 15% to the maximum excess adsorption capacity. Isotherms are calculated for both absolute amounts, for calculation of isosteric heats of adsorption as function of coverage, and excess amounts, for comparison with measured isotherms. Agreement with observed excess isotherms is reached if the experimentally determined limited accessibility of adsorption sites (78%) is taken into account.

  7. 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.

  8. First Principles and STM Studies of Cl Adsorption on TiO2 (110) Surfaces

    NASA Astrophysics Data System (ADS)

    Vogtenhuber, D.; Podloucky, R.; Redinger, J.; Hebenstreit, E. L. D.; Hebenstreit, W.; Diebold, U.

    2000-03-01

    Atomic Cl adsorption on reduced and stoichiometric TiO2 (110) surfaces was calculated by applying a Full Potential Linearized Augmented Plane Wave method (FLEUR), and the Tersoff-Hamann model for simulating STM images. The electronic structure results are compared to experimental ISS, STM and XPS data for dissociative adsorption of Cl_2. Adsorption on O-defect sites, which is favored from our results of the adsorption energies, is found experimentally at elevated T (> 200^circ C) only. According to measurements at low T, adsorption in registry with the bridging O seems to be kinetically hindered. Distinct differences between high- and low T adsoption types are found for ISS, STM, \\varphi and Cl-2p bonding energies, in excellent agreement between calculations and experiment.

  9. Periodic Density Functional Theory Study of Water Adsorption on the a-Quartz (101) Surface.

    SciTech Connect

    Bandura, Andrei V.; Kubicki, James D.; Sofo, Jorge O.

    2011-01-01

    Plane wave density functional theory (DFT) calculations have been performed to study the atomic structure, preferred H2O adsorption sites, adsorption energies, and vibrational frequencies for water adsorption on the R-quartz (101) surface. Surface energies and atomic displacements on the vacuum-reconstructed, hydrolyzed, and solvated surfaces have been calculated and compared with available experimental and theoretical data. By considering different initial positions of H2O molecules, the most stable structures of water adsorption at different coverages have been determined. Calculated H2O adsorption energies are in the range -55 to -65 kJ/mol, consistent with experimental data. The lowest and the highest O-H stretching vibrational bands may be attributed to different states of silanol groups on the watercovered surface. The dissociation energy of the silanol group on the surface covered by the adsorption monolayer is estimated to be 80 kJ/mol. The metastable states for the protonated surface bridging O atoms (Obr), which may lead to hydrolysis of siloxane bonds, have been investigated. The calculated formation energy of a Q2 center from a Q3 center on the (101) surface with 2/3 dense monolayer coverage is equal to 70 kJ/mol which is in the range of experimental activation energies for quartz dissolution.

  10. 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

  11. Adsorption of alkali metals on Ge(001)(2×1) surface

    SciTech Connect

    Xiao, H Y.; Zu, Xiaotao; Zhang, Yanfeng; Gao, Fei

    2006-01-09

    Ab initio total energy calculations have been performed for Na, K and Rb adsorption on Ge(001)(2?1) surface. It was found that the adsorption site of AM is AM size dependent. Structural analysis showed that the Ge-Ge dimer bond becomes stronger with increasing AM size. As the coverage increases from 0.5 to 1 ML it turns out that no depolarization effect occurs upon Na adsorption, while this effect become more important with increasing AM size. We also found that for all adsorption systems investigated the germanium surface is metallic and semiconducting for the coverage of 0.5 and 1 ML, respectively.

  12. Adsorption kinetics, isotherms and thermodynamics of atrazine on surface oxidized multiwalled carbon nanotubes.

    PubMed

    Chen, Guang-Cai; Shan, Xiao-Quan; Zhou, Yi-Quan; Shen, Xiu-e; Huang, Hong-Lin; Khan, Shahamat U

    2009-09-30

    The adsorption kinetics, isotherms and thermodynamic of atrazine on multiwalled carbon nanotubes (MWCNTs) containing 0.85%, 2.16%, and 7.07% oxygen was studied. Kinetic analyses were performed using pseudo-first-order, pseudo-second-order and intraparticle diffusion models. The regression results showed that the pseudo-second-order law fit the adsorption kinetics. The calculated thermodynamic parameters indicated that adsorption of atrazine on MWCNTs was spontaneous and exothermic. Standard free energy (DeltaG(0)) became less negative when the oxygen content of MWCNTs increased from 0.85% to 7.07% which is consistent with the low adsorption affinity of MWCNTs for atrazine.

  13. 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

  14. 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).

  15. 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.

  16. 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

  17. Van der Waals corrected DFT study of adsorption of groups VA and VIA hydrides on graphene monoxide

    NASA Astrophysics Data System (ADS)

    Notash, M. Yaghoobi; Ebrahimzadeh, A. Rastkar

    2016-06-01

    Adsorption properties of H2O, H2S, NH3 and PH3 on graphene monoxide (GMO) nano flack are investigated using density functional theory (DFT). Calculations were carried out by van der Waals correction and general gradient approximation. The adsorption energies and charge transfer between species are obtained and discussed for the considered positions of adsorbate molecules. Charge transfer analysis show that the gas molecules act as an electron acceptor in all cases. The analysis of the adsorption energies suggest GMO can be a good candidate for the adsorption of these molecules.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. [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.

  7. 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.

  8. Comparative isosteric ion adsorption for minerals

    NASA Technical Reports Server (NTRS)

    Omenyi, Samuel N.; Herren, Blair J.; Snyder, Robert S.; Seaman, Geoffrey V. F.

    1986-01-01

    A comparative isosteric ion adsorption study for minerals (kaolinite, rutile, and quartz) was performed in aqueous solutions of CaCl2, LaCl3, and Th(NO3)4 in the presence of the neutral salt NaCl. It was observed that the concentration of Ca(2+) ions required to produce a standard reduction in the electrophoretic mobility of mineral particles was always appreciably greater than the concentration required for the Th(4+) ions. The effectiveness of adsorption of the cations differed from particle to particle and showed that ion adsorption on a mineral surface depends, among other things, on the nature of the mineral surface and on the particular adsorbed cation. The number of cation binding sites on mineral surfaces and the electrochemical free energies of cation adsorption were calculated. It was found that the adsorption energy of La(3+) and Th(4+) ions on rutile, kaolinite, and quartz was greater than that of Ca(2+) on these minerals.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Applications of hierarchically structured porous materials from energy storage and conversion, catalysis, photocatalysis, adsorption, separation, and sensing to biomedicine.

    PubMed

    Sun, Ming-Hui; Huang, Shao-Zhuan; Chen, Li-Hua; Li, Yu; Yang, Xiao-Yu; Yuan, Zhong-Yong; Su, Bao-Lian

    2016-06-13

    Over the last decade, significant effort has been devoted to the applications of hierarchically structured porous materials owing to their outstanding properties such as high surface area, excellent accessibility to active sites, and enhanced mass transport and diffusion. The hierarchy of porosity, structural, morphological and component levels in these materials is key for their high performance in all kinds of applications. The introduction of hierarchical porosity into materials has led to a significant improvement in the performance of materials. Herein, recent progress in the applications of hierarchically structured porous materials from energy conversion and storage, catalysis, photocatalysis, adsorption, separation, and sensing to biomedicine is reviewed. Their potential future applications are also highlighted. We particularly dwell on the relationship between hierarchically porous structures and properties, with examples of each type of hierarchically structured porous material according to its chemical composition and physical characteristics. The present review aims to open up a new avenue to guide the readers to quickly obtain in-depth knowledge of applications of hierarchically porous materials and to have a good idea about selecting and designing suitable hierarchically porous materials for a specific application. In addition to focusing on the applications of hierarchically porous materials, this comprehensive review could stimulate researchers to synthesize new advanced hierarchically porous solids.

  14. 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.

  15. Study on the electronic properties and molecule adsorption of W18O49 nanowires as a catalyst support in the cathodes of direct methanol fuel cells

    NASA Astrophysics Data System (ADS)

    Karim, N. A.; Kamarudin, S. K.; Shyuan, L. K.; Yaakob, Z.; Daud, W. R. W.; Kadhum, A. A. H.

    2015-08-01

    Catalyst supports have been used to increase the catalytic activity of reactions in the cathode of Direct Methanol Fuel Cells (DMFCs). The properties of tungsten oxide (W18O49) nanowires were studied, and their adsorption capability was evaluated using density functional theory. The electronic properties of the bulk material and two different diameter nanowires were calculated. Moreover, the molecules involved in adsorption were carbon monoxide, methanol, oxygen and hydrogen peroxide. The results showed that the high adsorption energy produced is primarily the result of the adsorption of methanol, followed by that of hydrogen peroxide, carbon monoxide and oxygen. The negative adsorption energies obtained showed that the adsorption reactions were exothermic, and only oxygen was stable. Therefore, a new surface model was described where cobalt atoms were adsorbed on tungsten atoms on the surface of a 12 Å nanowire. In this new nanowire doped with cobalt atoms, the adsorption energy was reduced.

  16. 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.

  17. 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.

  18. 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"

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Adsorption of sulfur dioxide on ammonia-treated activated carbon fibers

    USGS Publications Warehouse

    Mangun, C.L.; DeBarr, J.A.; Economy, J.

    2001-01-01

    A series of activated carbon fibers (ACFs) and ammonia-treated ACFs prepared from phenolic fiber precursors have been studied to elucidate the role of pore size, pore volume, and pore surface chemistry on adsorption of sulfur dioxide and its catalytic conversion to sulfuric acid. As expected, the incorporation of basic functional groups into the ACFs was shown as an effective method for increasing adsorption of sulfur dioxide. The adsorption capacity for dry SO2 did not follow specific trends; however the adsorption energies calculated from the DR equation were found to increase linearly with nitrogen content for each series of ACFs. Much higher adsorption capacities were achieved for SO2 in the presence of oxygen and water due to its catalytic conversion to H2SO4. The dominant factor for increasing adsorption of SO2 from simulated flue gas for each series of fibers studied was the weight percent of basic nitrogen groups present. In addition, the adsorption energies calculated for dry SO2 were shown to be linearly related to the adsorption capacity of H2SO4 from this flue gas for all fibers. It was shown that optimization of this parameter along with the pore volume results in higher adsorption capacities for removal of SO2 from flue gases. ?? 2001 Elsevier Science Ltd. All rights reserved.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. A Method for the Calculation of Lattice Energies of Complex Crystals with Application to the Oxides of Molybdenum

    NASA Technical Reports Server (NTRS)

    Chaney, William S.

    1961-01-01

    A theoretical study has been made of molybdenum dioxide and molybdenum trioxide in order to extend the knowledge of factors Involved in the oxidation of molybdenum. New methods were developed for calculating the lattice energies based on electrostatic valence theory, and the coulombic, polarization, Van der Waals, and repulsion energie's were calculated. The crystal structure was examined and structure details were correlated with lattice energy.

  11. [Adsorption of Congo red from aqueous solution on hydroxyapatite].

    PubMed

    Zhan, Yan-Hui; Lin, Jian-Wei

    2013-08-01

    The adsorption of Congo red (CR) from aqueous solution on hydroxyapatite was investigated using batch experiments. The hydroxyapatite was effective for CR removal from aqueous solution. The adsorption kinetics of CR on hydroxyapatite well followed a pseudo-second-order model. The equilibrium adsorption data of CR on hydroxyapatite could be described by the Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherm models. Thermodynamic parameters such as Gibbs free energy change, enthalpy change and entropy change were calculated and showed that the adsorption of CR on hydroxyapatite was spontaneous and exothermic in nature. The CR adsorption capacity for hydroxyapatite decreased significantly with increasing pH from 8 to 10. Thermal regeneration showed that hydroxyapatite could be used for six desorption-adsorption cycles with high removal efficiency for CR in each cycle. The mechanisms for CR adsorption on hydroxyapatite with pH value below the pH at point of zero charge (pH(PZC)) include electrostatic attraction, hydrogen bonding and Lewis acid-base interaction. The mechanisms for CR adsorption on hydroxyapatite with pH value above its pH(PZC) include hydrogen bonding and Lewis acid-base interaction. Results of this work indicate that hydroxyapatite is a promising adsorbent for CR removal from aqueous solution.

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Improving iterative surface energy balance convergence for remote sensing based flux calculation

    NASA Astrophysics Data System (ADS)

    Dhungel, Ramesh; Allen, Richard G.; Trezza, Ricardo

    2016-04-01

    A modification of the iterative procedure of the surface energy balance was purposed to expedite the convergence of Monin-Obukhov stability correction utilized by the remote sensing based flux calculation. This was demonstrated using ground-based weather stations as well as the gridded weather data (North American Regional Reanalysis) and remote sensing based (Landsat 5, 7) images. The study was conducted for different land-use classes in southern Idaho and northern California for multiple satellite overpasses. The convergence behavior of a selected Landsat pixel as well as all of the Landsat pixels within the area of interest was analyzed. Modified version needed multiple times less iteration compared to the current iterative technique. At the time of low wind speed (˜1.3 m/s), the current iterative technique was not able to find a solution of surface energy balance for all of the Landsat pixels, while the modified v