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Sample records for energy deposition calculations

  1. 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.

  2. Calculation of energy deposition distributions for simple geometries

    NASA Technical Reports Server (NTRS)

    Watts, J. W., Jr.

    1973-01-01

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

  3. 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)

  4. 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.

  5. Calculations of heat deposition in a target system bombarded by high energy charged particles

    NASA Astrophysics Data System (ADS)

    Nishida, Takahiko; Nakahara, Yasuaki

    1984-09-01

    At the Japan Atomic Energy Research Institute (JAERI), with the use of the Monte Carlo code NMTC/JAERI and the analysis code NMTA, studies have been performed of the feasibility of an emerging new technology such as an accelerator nuclear fuel producer or a radioactive waste transmuter, which utilizes abundant neutrons emitted by the spallation and fission reactions in a proton accelerator target. New subroutines were added to the NMTA code calculating the total heat deposition and the spatial distribution of heat deposition density in a target. A new subroutine is provided also for estimating the mean excitation energy of recoiling residual nuclei after the particle evaporation ceased to occur. The NMTC/JAERI flow for a fission event was also modified. The processes that account for the heat producing energy in the range greater than 15 MeV are mainly (a) ionization loss by charged particles through transport and (b) the kinetic energy of recoil nuclei after intranuclear cascades and fissions. Preliminary calculations of the heat deposition are carried out for small bare targets of Pb, Nat. U and molten salts for some combinations of incident particle energy, beam radius, target material and size. The new computational routines are explained in detail and discussions are done on the calculated results.

  6. 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.

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

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cicinotta, Francis A.

    2012-01-01

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

  8. Monte Carlo calculation of energy deposition in ionization chambers for tritium measurements

    NASA Astrophysics Data System (ADS)

    Zhilin, Chen; Shuming, Peng; Dan, Meng; Yuehong, He; Heyi, Wang

    2014-10-01

    Energy deposition in ionization chambers for tritium measurements has been theoretically studied using Monte Carlo code MCNP 5. The influence of many factors, including carrier gas, chamber size, wall materials and gas pressure, has been evaluated in the simulations. It is found that β rays emitted by tritium deposit much more energy into chambers flowing through with argon than with deuterium in them, as much as 2.7 times higher at pressure 100 Pa. As chamber size gets smaller, energy deposition decreases sharply. For an ionization chamber of 1 mL, β rays deposit less than 1% of their energy at pressure 100 Pa and only 84% even if gas pressure is as high as 100 kPa. It also indicates that gold plated ionization chamber results in the highest deposition ratio while aluminum one leads to the lowest. In addition, simulations were validated by comparison with experimental data. Results show that simulations agree well with experimental data.

  9. Comparison of energy deposition calculations by the LAHET Code System with experimental results

    SciTech Connect

    Beard, C.A.; Lisowski, P.W.; Russell, G.J.; Waters, L.S.

    1993-08-01

    A comparison was performed between the energy deposition predicted by the LAHET Code System (LCS) with experimental values determined by Belyakov-Bodin et al. for 800, 1000, and 1200 MeV protons on targets composed of lead, bismuth, beryllium, carbon, and aluminum. The lead and bismuth showed agreement within approximately 10% at locations throughout the targets, and the agreement of the total energy deposited over the axial length of the targets ranged from 1% to 25%. For the lead and bismuth cases, the LCS predictions were always greater than the experimental results. For the lighter materials, the agreement at locations throughout the target only agreed within approximately 20%. No definable trend could be determined for the lighter materials since some LCS predictions were greater than the experimental results, some were less than the experimental results, and some showed very good agreement. The total energy deposited over the axial length of the targets was not compared for the lighter materials since it was not explicitly given with the experimental data.

  10. Energy-Deposition and Damage Calculations in Core-Vessel Inserts at the Spallation Neutron Source

    SciTech Connect

    Murphy, B.D.

    2002-06-25

    Heat-deposition and damage calculations are described for core-vessel inserts in the target area of the Spallation Neutron Source. Two separate designs for these inserts (or neutron beam tubes) were studied; a single-unit insert and a multi-unit insert. The single unit contains a neutron guide; the multi unit does not. Both units are constructed of stainless steel. For the single unit, separate studies were carried out with the guide composed of stainless steel, glass, and aluminum. Results are also reported for an aluminum window on the front of the insert, a layer of nickel on the guide, a cadmium shield surrounding the guide, and a stainless steel plug in the beam-tube opening. The locations of both inserts were the most forward positions to be occupied by each design respectively thus ensuring that the calculations are conservative.

  11. 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.

  12. BMAP dipole magnetic field analysis and orbit tracking/calculations of energy deposition in GaAs WHEBY detectors

    NASA Astrophysics Data System (ADS)

    Humphries, S., Jr.; Baltrusaitis, R. M.; Ekdahl, C.; Young, C.; Warn, C.

    This report contains two separate papers. The first paper discusses BMAP which is a versatile program for field analysis and orbit tracking in dipole magnets. The program was created to aid the design of charged-particle magnetic spectrometers. BMAP is written in Pascal and runs on any IBM-PC computer or compatible. The second paper covers a study on energy deposition in GaAS WHEBY detectors. The study was done for two purposes: (1) to set up a three-dimensional electron-photon transport problem using the ACCEPT computer code; and (2) to calculate energy deposition in GaAs detectors in the WHEBY for a given flux of electrons.

  13. Intercomparison measurements with energy deposition spectrometer Liulin and TEPC Hawk at HIMAC, and related calculations with PHITS

    NASA Astrophysics Data System (ADS)

    Ploc, Ondrej; Uchihori, Yukio; Kitamura, H.; Kodaira, S.; Dachev, Tsvetan; Spurny, Frantisek; Jadrnickova, Iva; Mrazova, Zlata; Kubancak, Jan

    Liulin type detectors are recently used in a wide range of cosmic radiation measurements, e.g. at alpine observatories, onboard aircrafts and spacecrafts. They provide energy deposition spectra up to 21 MeV, higher energy deposition events are stored in the last (overflow) channel. Their main advantages are portability (about the same size as a pack of cigarettes) and ability to record spectra as a function of time, so they can be used as personal dosimeters. Their well-known limitations are: (i) the fact that they are not tissue equivalent, (ii) they can be used as LET spectrometer only under specific conditions (e.g. broad parallel beam), and (iii) that the energy deposition event from particles of LETH20¿35 keV/µm is stored in the overflow bin only so the spectral information is missing. Tissue equivalent proportional counter (TEPC) Hawk has no of these limitations but on the other hand, it cannot be used as personal dosimeter because of its big size (cylinder of 16 cm diameter and 34 cm long). An important fraction of dose equivalent onboard spacecrafts is caused by heavy ions. This contribution presents results from intercomparison measurements with Liulin and Hawk at Heavy Ion Medical Accelerator in Chiba (HIMAC) and cyclotron beams, and related calculations with PHITS (Particle and Heavy-ion Transport code System). Following particles/ions and energies were used: protons 70 MeV, He 150 MeV, Ne 400 MeV, C 135 MeV, C 290 MeV, and Fe 500 MeV. Calculations of LET spectra by PHITS were performed for both, Liulin and Hawk. In case of Liulin, the dose equivalent was calculated using simulations in which several tissue equivalent materials were used as active volume instead of the silicon diode. Dose equivalents calculated in such way was compared with that measured with Hawk. LET spectra measured with Liulin and Hawk were compared for each ion at several points behind binary filters along the Brag curve. Good agreement was observed for some configurations; for

  14. Heat Deposit Calculation in Spallation Unit

    NASA Astrophysics Data System (ADS)

    Karmanov, F. I.; Travleev, A. A.; Latysheva, L. N.; Vecchi, M.

    2001-11-01

    The present study concerns the calculation of the heat deposition in one of the EAP-80 basic units - the spallation module including the beam window, lead-bismuth spallation target and primary liquid metal cooling system. It is assumed that the model of sub-critical reactor under investigation is based on ANSALDO-INFN-ENEA-CRS4 reference configuration1. The calculation have been done by means of a couple computer codes: INCC 2 and GEANT3.21 3. These codes have been preliminary tested on the experimental data obtained in 4 for the case of interaction of proton beam and lead-bismuth targets at the energy Ep= 800MeV which is close to energy range relevant for ADS configuration.

  15. Diagnostic and Impact Estimation of Nuclear Data Inconsistencies on Energy Deposition Calculations in Coupled Neutron-Photon Monte-Carlo Simulation, with TRIPOLI-4®

    NASA Astrophysics Data System (ADS)

    Péron, A.; Malouch, F.; Zoia, A.; Diop, C. M.

    2014-06-01

    Nuclear heating evaluation by Monte-Carlo simulation requires coupled neutron-photon calculation so as to take into account the contribution of secondary photons. Nuclear data are essential for a good calculation of neutron and photon energy deposition and for secondary photon generation. However, a number of isotopes of the most common nuclear data libraries happen to be affected by energy and/or momentum conservation errors concerning the photon production or inaccurate thresholds for photon emission sections. In this paper, we perform a comprehensive survey of the three evaluations JEFF3.1.1, JEFF3.2T2 (beta version) and ENDF/B-VII.1, over 142 isotopes. The aim of this survey is, on the one hand, to check the existence of photon production data by neutron reaction and, on the other hand, to verify the consistency of these data using the kinematic limits method recently implemented in the TRIPOLI-4 Monte-Carlo code, developed by CEA (Saclay center). Then, the impact of these inconsistencies affecting energy deposition scores has been estimated for two materials using a specific nuclear heating calculation scheme in the context of the OSIRIS Material Testing Reactor (CEA/Saclay).

  16. Energy deposition in STARFIRE reactor components

    SciTech Connect

    Gohar, Y.; Brooks, J.N.

    1985-04-01

    The energy deposition in the STARFIRE commercial tokamak reactor was calculated based on detailed models for the different reactor components. The heat deposition and the 14 MeV neutron flux poloidal distributions in the first wall were obtained. The poloidal surface heat load distribution in the first wall was calculated from the plasma radiation. The Monte Carlo method was used for the calculation to allow an accurate modeling for the reactor geometry.

  17. Model calculates was deposition for North Sea oils

    SciTech Connect

    Majeed, A.; Bringedal, B.; Overa, S. )

    1990-06-18

    A model for calculation of wax formation and deposition in pipelines and process equipment has been developed along with a new method for wax-equilibrium calculations using input from TBP distillation cuts. Selected results from the wax formation and deposition model have been compared with laboratory data from wax equilibrium and deposition experiments, and there have been some field applications of the model.

  18. Tokomak disruption runaway electron beam energy deposition

    NASA Astrophysics Data System (ADS)

    Lei, Yian

    2012-10-01

    Disruption is one of the major concerns in magnetic confinement fusion (MCF) research. People believe the energetic runaway electron beam can damage the first wall by depositing most of its energy to certain region as heat, melting the wall. However, as the energy of the beam electron is very high (up to 50 MeV), most of the beam energy should be converted as gamma radiation and escape, and the fraction of thermal energy deposition is relatively small. We will calculate the runaway electron energy deposition in typical first wall configurations in ITER disruption scenario, and give the temperature profile of the wall. We will also calculate the bremsstrahlung gamma ray spectra of the beam and discuss the consequences.

  19. 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

  20. Calculation of wet deposition from radioactive plumes

    SciTech Connect

    Brenk, H.D.; Vogt, K.J.

    1981-05-01

    A reevaluation of the current wet deposition models for radioactive plumes of the Gaussian type is presented. The application of the methodology to routine and accidental activity releases from nuclear facilities is discussed. A set of washout parameters for a simplified model has been included.

  1. Energy deposition of thermal tides

    NASA Astrophysics Data System (ADS)

    Becker, E.

    2015-12-01

    The main role of vertically propagating waves in the general circulation is to transfer pseudo momentum from the region of generation to the region of wave breaking. The most prominent examples in atmospheric dynamics are planetary Rossby waves forced in the troposphere, which drive a poleward residual circulation in the winter stratosphere, and mesoscale gravity waves with tropospheric origin, which drive a summer-to-winter-pole circulation in the mesopasue region. In addition, the role of energy deposition by gravity waves has long been recognized to contribute substantially to the energy budget above the stratopause. In atmospheric circulation models, gravity waves are usually parameterized. Their energy deposition can be computed along with the momentum deposition and the turbulent diffusivity associated with wave breaking. In particular, the energy deposition is expressed in terms of secondary moments of the parameterized waves. Therefore, one is tempted to assume that the energy deposition of waves that are resolved in circulation models, e.g., Rossby waves and thermal tides, is automatically taken into account. This assumption is, however, flawed. We show that the energy deposition by resolved waves corresponds to the shear production (frictional heating) of the subgrid-scale turbulence model by which these waves are damped. Computational results from an atmospheric circulation model with energetically consistent treatment of momentum diffusion and frictional heating show that the energy deposition of thermal tides is substantial above the mesopause. This effect is either incomplete or even ignored in conventional atmospheric models that resolve the mesopause region. An idealized sensitivity experiment furthermore shows that thermal tides lead to a significant downward shift of gravity-wave breaking in the upper mesosphere.

  2. Comparison of energy calculation procedures

    SciTech Connect

    Kusuda, T.

    1981-08-01

    ASHRAE has developed a simplified energy-calculation procedure suitable for small calculators that applied to nonresidential buildings and includes all the essential calculation elements - climatic data, buildings construction, operational characteristics, utility system and equipment performance, and internal heat gain due to lighting, occupancy, cooking, etc. A comparison of the results predicted by the proposed method for four typical HVAC (heating, ventilation, and air conditioning) systems in an office building in Washington, DC, against the predictions of seven detailed computer-simulation programs - AXCESS, BLAST, BLDSIM, DOE-2, E-CUBE, ESAS, and TRACE - revealed that the similarity of the results depended more on which analyst employed the methods than on which methods were used.

  3. Calorimetric sensors for energy deposition measurements

    SciTech Connect

    Langenbrunner, J.; Cooper, R.; Morgan, G.

    1998-12-31

    A calorimetric sensor with several novel design features has been developed. These sensors will provide an accurate sampling of thermal power density and energy deposition from proton beams incident on target components of accelerator-based systems, such as the Accelerator Production of Tritium Project (APT) and the Spallation Neutron Source (SNS). A small, solid slug (volume = 0.347 cc) of target material is suspended by kevlar fibers and surrounded by an adiabatic enclosure in an insulating vacuum canister of stainless steel construction. The slug is in thermal contact with a low-mass, calibrated, 100-k{Omega} thermistor. Power deposition caused by the passage of radiation through the slug is calculated from the rate of temperature rise of the slug. The authors have chosen slugs composed of Pb, Al, and LiAl.

  4. Monte Carlo Techniques for Calculations of Charge Deposition and Displacement Damage from Protons in Visible and Infrared Sensor Arrays

    NASA Technical Reports Server (NTRS)

    Marshall, Paul; Reed, Robert; Fodness, Bryan; Jordan, Tom; Pickel, Jim; Xapsos, Michael; Burke, Ed

    2004-01-01

    This slide presentation examines motivation for Monte Carlo methods, charge deposition in sensor arrays, displacement damage calculations, and future work. The discussion of charge deposition sensor arrays includes Si active pixel sensor APS arrays and LWIR HgCdTe FPAs. The discussion of displacement damage calculations includes nonionizing energy loss (NIEL), HgCdTe NIEL calculation results including variance, and implications for damage in HgCdTe detector arrays.

  5. Modeling Atmospheric Energy Deposition (by energetic ions)

    NASA Astrophysics Data System (ADS)

    Parkinson, C. D.; Brain, D. A.; Lillis, R. J.; Liemohn, M. W.; Bougher, S. W.

    2011-12-01

    The structure, dynamics, chemistry, and evolution of planetary upper atmospheres are in large part determined by the available sources of energy. In addition to the solar EUV flux, the solar wind and solar energetic particle (SEP) events are also important sources. Both of these particle populations can significantly affect an atmosphere, causing atmospheric loss and driving chemical reactions. Attention has been paid to these sources from the standpoint of the radiation environment for humans and electronics, but little work has been done to evaluate their impact on planetary atmospheres. At unmagnetized planets or those with crustal field anomalies, in particular, the solar wind and SEPs of all energies have direct access to the atmosphere and so provide a more substantial energy source than at planets having protective global magnetic fields. Additionally, solar wind and energetic particle fluxes should be more significant for planets orbiting more active stars, such as is the case in the early history of the solar system for paleo-Venus and Mars. Therefore quantification of the atmospheric energy input from the solar wind and SEP events is an important component of our understanding of the processes that control their state and evolution. Such modeling has been previously done for Earth, Mars and Jupiter using a guiding center precipitation model with extensive collisional physics. Currently, this code is only valid for particles with small gyroradii in strong uniform magnetic fields. There is a clear necessity for a Lorentz formulation that can perform calculations for cases where there is only a weak or nonexistent magnetic field that includes detailed physical interaction with the atmosphere (i.e. collisional physics). We show initial efforts to apply a full Lorentz motion particle transport model to study the effects of particle precipitation in the upper atmospheres of Venus, Mars, and Titan. A systematic study of the ionization, excitation, and energy

  6. Localized flow control with energy deposition

    NASA Astrophysics Data System (ADS)

    Adelgren, Russell Gene

    A series of experiments with energy deposition via laser-induced optical breakdown of air, i.e., a laser spark, have been performed. These experiments have demonstrated the possibility of using a laser spark for supersonic flow control. In the first of these experiments, Rayleigh scattering flow visualization was taken for energy deposition into quiescent air. A time sequence of images showed the post breakdown fluid motion created by the laser spark for different laser energy levels. Blast wave radius and wave speed measurements were made and correlated to five different laser energy deposition levels. Laser energy was deposited upstream of a sphere in Mach 3.45 flow. The energy was deposited one sphere diameter and 0.6 diameters upstream of the front of the sphere. The frontal surface pressure on the sphere was recorded as the laser spark perturbed region interacted with the flow about the sphere. Tests for three different energy levels and two different incident laser beam diameters were completed. It has been demonstrated that the peak surface pressure associated with the Edney IV interaction can be momentarily reduced by 30% by the interaction with the thermal spot created by the laser spark. The effects of laser energy deposition on another shock interaction phenomena were studied. Laser energy deposition was used to modify the shock structure formed by symmetric wedges at Mach 3.45 within the dual solution domain. It was demonstrated experimentally that the Mach reflection could be reduced by 80% momentarily. The numerical simulations show a transition from the stable Mach reflection to a stable regular reflection. Two energy deposition methods (electric arcing and laser energy deposition) were used to force and control compressible mixing layers of axisymmetric jets. The energy deposition forcing methods have been experimentally investigated with the schlieren technique, particle image velocimetry, Mie scattering, and static pressure probe diagnostic

  7. Neutron absorbed dose determination by calculations of recoil energy.

    PubMed

    Wrobel, F; Benabdesselam, M; Iacconi, P; Lapraz, D

    2004-01-01

    The aim of this work is to calculate the absorbed dose to matter due to neutrons in the 5-150 MeV energy range. Materials involved in the calculations are Al2O3, CaSO4 and CaS, which may be used as dosemeters and have already been studied for their luminescent properties. The absorbed dose is assumed to be mainly due to the energy deposited by the recoils. Elastic reactions are treated with the ECIS code while for the non-elastic ones, a Monte Carlo code has been developed and allowed to follow the nucleus decay and to determine its characteristics (nature and energy). Finally, the calculations show that the absorbed dose is mainly due to non-elastic process and that above 20 MeV this dose decreases slightly with the neutron energy. PMID:15353750

  8. Global Auroral Energy Deposition Compared with Magnetic Indices

    NASA Technical Reports Server (NTRS)

    Brittnacher, M. J.; Fillingim, M. O.; Elsen, R.; Parks, G. K.; Germany, G. A.; Spann, J. F., Jr.

    1997-01-01

    Measurement of the global rate of energy deposition in the ionosphere via auroral particle precipitation is one of the primary goals of the Polar UVI program and is an important component of the ISTP program. The instantaneous rate of energy deposition for the entire month of January 1997 has been calculated by applying models to the UVI images and is presented by Fillingim et al. in this session. Magnetic indices, such as Kp, AE, and Dst, which are sensitive to variations in magnetospheric current systems have been constructed from ground magnetometer measurements and employed as measures of activity. The systematic study of global energy deposition raises the possibility of constructing a global magnetospheric activity index explicitly based on particle precipitation to supplement magnetic indices derived from ground magnetometer measurements. The relationship between global magnetic activity as measured by these indices and the rate of total global energy loss due to precipitation is not known at present. We study the correlation of the traditional magnetic index of Kp for the month of January 1997 with the energy deposition derived from the UVI images. We address the question of whether the energy deposition through particle precipitation generally matches the Kp and AE indices, or the more exciting, but distinct, possibility that this particle-derived index may provide an somewhat independent measure of global magnetospheric activity that could supplement traditional magnetically-based activity indices.

  9. Calculation of Dose Deposition in 3D Voxels by Heavy Ions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2010-01-01

    The biological response to high-LET radiation is very different from low-LET radiation, and can be partly attributed to the energy deposition by the radiation. Several experiments, notably detection of gamma-H2AX foci by immunofluorescence, has revealed important differences in the nature and in the spatial distribution of double-strand breaks (DSB) induced by low- and high-LET radiations. Many calculations, most of which are based on amorphous track models with radial dose, have been combined with chromosome models to calculate the number and distribution of DSB within nuclei and chromosome aberrations. In this work, the Monte-Carlo track structure simulation code RITRACKS have been used to calculate directly the energy deposition in voxels (3D pixels). A cubic volume of 5 micrometers of side was irradiated by 1) 450 (1)H+ ions of 300 MeV (LET is approximately 0.3 keV/micrometer) and 2) by 1 (56)Fe26+ ion of 1 GeV/amu (LET is approximately 150 keV/micrometer). In both cases, the dose deposited in the volume is approximately 1 Gy. All energy deposition events are recorded and dose is calculated in voxels of 20 micrometers of side. The voxels are then visualized in 3D by using a color scale to represent the intensity of the dose in a voxel. This simple approach has revealed several important points which may help understand experimental observations. In both simulations, voxels which receive low dose are the most numerous, and those corresponding to electron track ends received a dose which is in the higher range. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. The distribution of the voxels shows major differences for the (56)Fe26+ ion. The track structure can still be seen, and voxels with much higher dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and may be responsible for DSB that are more difficult to

  10. Calculation of Dose Deposition in Nanovolumes and Simulation of gamma-H2AX Experiments

    NASA Technical Reports Server (NTRS)

    Plante, Ianik

    2010-01-01

    Monte-Carlo track structure simulations can accurately simulate experimental data: a) Frequency of target hits. b) Dose per event. c) Dose per ion. d) Radial dose. The dose is uniform in micrometers sized voxels; at the nanometer scale, the difference in energy deposition between high and low-LET radiations appears. The calculated 3D distribution of dose voxels, combined with chromosomes simulated by random walk is very similar to the distribution of DSB observed with gamma-H2AX experiments. This is further evidenced by applying a visualization threshold on dose.

  11. Reactivity of adducts relevant to the deposition of hexagonal BN from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Freitas, R. R. Q.; Gueorguiev, G. K.; de Brito Mota, F.; de Castilho, C. M. C.; Stafström, S.; Kakanakova-Georgieva, A.

    2013-09-01

    First-principles calculations, which also implement the nudged elastic band (NEB) code, are performed to investigate (i) the stability of the (C2H5)3B:NH3 adduct formed by the initial precursor molecules triethylborane (C2H5)3B and ammonia NH3 in the metal-chemical-vapor-deposition (MOCVD) of hexagonal BN, and (ii) the energy barrier to the first ethane elimination through consistent unimolecular, ammonia-assisted, and adduct-assisted reaction pathways. Comparison is done with the reference case of the (CH3)3Al:NH3 adduct, notoriously known for its high degree of stability and reactivity, which determines an overall severe parasitic gas-phase chemical reaction mechanism in the deposition of AlN.

  12. Accurate free energy calculation along optimized paths.

    PubMed

    Chen, Changjun; Xiao, Yi

    2010-05-01

    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  13. 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.

  14. 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.

  15. Monte-Carlo Simulation of Radiation Track Structure and Calculation of Dose Deposition in Nanovolumes

    NASA Technical Reports Server (NTRS)

    Plante, I.; Cucinotta, F. A.

    2010-01-01

    INTRODUCTION: The radiation track structure is of crucial importance to understand radiation damage to molecules and subsequent biological effects. Of a particular importance in radiobiology is the induction of double-strand breaks (DSBs) by ionizing radiation, which are caused by clusters of lesions in DNA, and oxidative damage to cellular constituents leading to aberrant signaling cascades. DSB can be visualized within cell nuclei with gamma-H2AX experiments. MATERIAL AND METHODS: In DSB induction models, the DSB probability is usually calculated by the local dose obtained from a radial dose profile of HZE tracks. In this work, the local dose imparted by HZE ions is calculated directly from the 3D Monte-Carlo simulation code RITRACKS. A cubic volume of 5 micron edge (Figure 1) is irradiated by a (Fe26+)-56 ion of 1 GeV/amu (LET approx.150 keV/micron) and by a fluence of 450 H+ ions, 300 MeV/amu (LET approx. 0.3 keV/micron). In both cases, the dose deposited in the volume is approx.1 Gy. The dose is then calculated into each 3D pixels (voxels) of 20 nm edge and visualized in 3D. RESULTS AND DISCUSSION: The dose is deposited uniformly in the volume by the H+ ions. The voxels which receive a high dose (orange) corresponds to electron track ends. The dose is deposited differently by the 56Fe26+ ion. Very high dose (red) is deposited in voxels with direct ion traversal. Voxels with electron track ends (orange) are also found distributed around the path of the track. In both cases, the appearance of the dose distribution looks very similar to DSBs seen in gammaH2AX experiments, particularly when the visualization threshold is applied. CONCLUSION: The refinement of the dose calculation to the nanometer scale has revealed important differences in the energy deposition between high- and low-LET ions. Voxels of very high dose are only found in the path of high-LET ions. Interestingly, experiments have shown that DSB induced by high-LET radiation are more difficult to

  16. Total energy calculations and bonding at interfaces

    SciTech Connect

    Louie, S.G.

    1984-08-01

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

  17. 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.

  18. Calculations of turbidite deposits and tsunamis from submarine landslides

    SciTech Connect

    Gisler, Galen R; Weaver, Robert P; Gittings, Michael L

    2009-01-01

    Great underwater landslides like Storegga off the Norwegian coast leave massive deposits on the seafloor and must produce enormous tsunamis. Such events have occurred on continental slopes worldwide, and continue to do so. Triggers for such slides include earthquakes, gas hydrate releases, and underwater volcanos. We have petformed a numerical study of such landslides using the multi-material compressible hydrocode Sage in order to understand the relationship between the rheology of the slide material, the configuration of the resulting deposits on the seafloor, and the tsunami that is produced. Instabilities in the fluid-fluid mixing between slide material and seawater produce vortices and swirls with sizes that depend on the rheology of the slide material. These dynamical features of the flow may be preserved as ridges when the sliding material finally stops. Thus studying the configuration of the ridges in prehistoric slides may give us measures of the circumstances under which the slide was initiated. As part of this study, we have also done a convergence test showing that the slide velocity is sensitive to the resolution adopted in the simulation, but that extrapolation to infinite resolution is possible, and can yield good velocities. We will present two-dimensional simulations of schematic underwater slides for our study of rheology, and a three-dimensional simulation in bathymetric conditions that resemble the pre-Storegga Norwegian margin.

  19. 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.

  20. Surface free energy and microarray deposition technology.

    PubMed

    McHale, Glen

    2007-03-01

    Microarray techniques use a combinatorial approach to assess complex biochemical interactions. The fundamental goal is simultaneous, large-scale experimentation analogous to the automation achieved in the semiconductor industry. However, microarray deposition inherently involves liquids contacting solid substrates. Liquid droplet shapes are determined by surface and interfacial tension forces, and flows during drying. This article looks at how surface free energy and wetting considerations may influence the accuracy and reliability of spotted microarray experiments.

  1. Energy deposition rates by charged particles. [in upper atmosphere

    NASA Technical Reports Server (NTRS)

    Torkar, K. M.; Urban, A.; Bjordal, J.; Lundblad, J. A.; Soraas, F.; Smith, L. G.; Dumbs, A.; Grandal, B.; Ulwick, J. C.; Vancour, R. P.

    1985-01-01

    A summary of measurements of the precipitation of electrons and positive ions (in the keV-MeV range) detected aboard eight rockets launched within the Energy Budget Campaign from Northern Scandinavia is given, together with corresponding satellite data. In some cases strong temporal variations of the downgoing integral fluxes were observed. The fluxes provide the background for the calculated ion production rates and altitude profiles of the energy deposition into the atmosphere at different levels of geomagnetic disturbance and cosmic noise absorption. The derived ion production rates by eneretic particles are compared to other night-time ionisation sources.

  2. 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…

  3. Energy Deposition and Radiological Studies for the LBNF Hadron Absorber

    SciTech Connect

    Rakhno, I. L.; Mokhov, N. V.; Tropin, I. S.; Eidelman, Y. I.

    2015-06-25

    Results of detailed Monte Carlo energy deposition and radiological studies performed for the LBNF hadron absorber with the MARS15 code are described. The model of the entire facility, that includes a pion-production target, focusing horns, target chase, decay channel, hadron absorber system – all with corresponding radiation shielding – was developed using the recently implemented ROOT-based geometry option in the MARS15 code. Both normal operation and accidental conditions were studied. Results of detailed thermal calculations with the ANSYS code helped to select the most viable design options.

  4. The DEPOSIT computer code: Calculations of electron-loss cross-sections for complex ions colliding with neutral atoms

    NASA Astrophysics Data System (ADS)

    Litsarev, Mikhail S.

    2013-02-01

    A description of the DEPOSIT computer code is presented. The code is intended to calculate total and m-fold electron-loss cross-sections (m is the number of ionized electrons) and the energy T(b) deposited to the projectile (positive or negative ion) during a collision with a neutral atom at low and intermediate collision energies as a function of the impact parameter b. The deposited energy is calculated as a 3D integral over the projectile coordinate space in the classical energy-deposition model. Examples of the calculated deposited energies, ionization probabilities and electron-loss cross-sections are given as well as the description of the input and output data. Program summaryProgram title: DEPOSIT Catalogue identifier: AENP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 8726 No. of bytes in distributed program, including test data, etc.: 126650 Distribution format: tar.gz Programming language: C++. Computer: Any computer that can run C++ compiler. Operating system: Any operating system that can run C++. Has the code been vectorised or parallelized?: An MPI version is included in the distribution. Classification: 2.4, 2.6, 4.10, 4.11. Nature of problem: For a given impact parameter b to calculate the deposited energy T(b) as a 3D integral over a coordinate space, and ionization probabilities Pm(b). For a given energy to calculate the total and m-fold electron-loss cross-sections using T(b) values. Solution method: Direct calculation of the 3D integral T(b). The one-dimensional quadrature formula of the highest accuracy based upon the nodes of the Yacobi polynomials for the cosθ=x∈[-1,1] angular variable is applied. The Simpson rule for the φ∈[0,2π] angular variable is used. The Newton-Cotes pattern of the seventh order

  5. PDB ligand conformational energies calculated quantum-mechanically.

    PubMed

    Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C

    2012-03-26

    We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient

  6. 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.

  7. A simple model for calculating tsunami flow speed from tsunami deposits

    USGS Publications Warehouse

    Jaffe, B.E.; Gelfenbuam, G.

    2007-01-01

    This paper presents a simple model for tsunami sedimentation that can be applied to calculate tsunami flow speed from the thickness and grain size of a tsunami deposit (the inverse problem). For sandy tsunami deposits where grain size and thickness vary gradually in the direction of transport, tsunami sediment transport is modeled as a steady, spatially uniform process. The amount of sediment in suspension is assumed to be in equilibrium with the steady portion of the long period, slowing varying uprush portion of the tsunami. Spatial flow deceleration is assumed to be small and not to contribute significantly to the tsunami deposit. Tsunami deposits are formed from sediment settling from the water column when flow speeds on land go to zero everywhere at the time of maximum tsunami inundation. There is little erosion of the deposit by return flow because it is a slow flow and is concentrated in topographic lows. Variations in grain size of the deposit are found to have more effect on calculated tsunami flow speed than deposit thickness. The model is tested using field data collected at Arop, Papua New Guinea soon after the 1998 tsunami. Speed estimates of 14??m/s at 200??m inland from the shoreline compare favorably with those from a 1-D inundation model and from application of Bernoulli's principle to water levels on buildings left standing after the tsunami. As evidence that the model is applicable to some sandy tsunami deposits, the model reproduces the observed normal grading and vertical variation in sorting and skewness of a deposit formed by the 1998 tsunami.

  8. X-ray amplifier energy deposition scaling with channeled propagation

    SciTech Connect

    Boyer, K.; Luk, T.S.; McPherson, A.

    1991-12-31

    The spatial control of the energy deposited for excitation of an x-ray amplifier plays an important role in the fundamental scaling relationship between the required energy, the gain and the wavelength. New results concerning the ability to establish confined modes of propagation of sort pulse radiation of sufficiently high intensity in plasmas lead to a sharply reduced need for the total energy deposited, since the concentration of deposited power can be very efficiently organized.

  9. [Calculating critical loads of acid deposition with different percentiles in China].

    PubMed

    Duan, Lei; Hao, Jiming; Zhou, Zhongping; Xie, Shaodong

    2002-09-01

    While mapping critical loads of acid deposition in China, the 1 degree (latitude) x 1 degree (longitude) resolution was always adopted in critical load calculation. However, the results of mapping can not show the difference of sensitivity of ecosystems to acid deposition within a 1 degree x 1 degree grid. For the convenience of policy-makers to formulate acid deposition control strategies based on critical loads, and to improve the representation and practicability of 1 degree x 1 degree results, a series of critical load maps with different percentiles were compiled, which may be accordance with a given economic or technological level, and allows some degree of damage. Based on the cumulative distribution function, the critical load exceedance maps with different percentiles and the maximum allowable deposition of each province was also derived.

  10. Energy Deposition Processes in Titan's Upper Atmosphere

    NASA Technical Reports Server (NTRS)

    Sittler, Edward C., Jr.; Bertucci, Cesar; Coates, Andrew; Cravens, Tom; Dandouras, Iannis; Shemansky, Don

    2008-01-01

    Most of Titan's atmospheric organic and nitrogen chemistry, aerosol formation, and atmospheric loss are driven from external energy sources such as Solar UV, Saturn's magnetosphere, solar wind and galactic cosmic rays. The Solar UV tends to dominate the energy input at lower altitudes of approximately 1100 km but which can extend down to approximately 400 km, while the plasma interaction from Saturn's magnetosphere, Saturn's magnetosheath or solar wind are more important at higher altitudes of approximately 1400 km, but the heavy ion plasma [O(+)] of approximately 2 keV and energetic ions [H(+)] of approximately 30 keV or higher from Saturn's magnetosphere can penetrate below 950km. Cosmic rays with energies of greater than 1 GeV can penetrate much deeper into Titan's atmosphere with most of its energy deposited at approximately 100 km altitude. The haze layer tends to dominate between 100 km and 300 km. The induced magnetic field from Titan's interaction with the external plasma can be very complex and will tend to channel the flow of energy into Titan's upper atmosphere. Cassini observations combined with advanced hybrid simulations of the plasma interaction with Titan's upper atmosphere show significant changes in the character of the interaction with Saturn local time at Titan's orbit where the magnetosphere displays large and systematic changes with local time. The external solar wind can also drive sub-storms within the magnetosphere which can then modify the magnetospheric interaction with Titan. Another important parameter is solar zenith angle (SZA) with respect to the co-rotation direction of the magnetospheric flow. Titan's interaction can contribute to atmospheric loss via pickup ion loss, scavenging of Titan's ionospheric plasma, loss of ionospheric plasma down its induced magnetotail via an ionospheric wind, and non-thermal loss of the atmosphere via heating and sputtering induced by the bombardment of magnetospheric keV ions and electrons. This

  11. Energy deposition and microstructural modification in dynamically consolidated metal powders

    SciTech Connect

    Gourdin, W.H.

    1984-01-01

    A model is presented for the deposition of energy at powder particle surfaces during dynamic consolidation. The average energy flux incident on the surface of a powder particle is estimated to be E/tauA where E is the specific energy deposited by the shock, tau is the shock rise time, and A the measured powder specific surface area. This flux is assumed to be constant over the rise time of the shock, falling abruptly to zero for times longer than tau. Solution of the thermal transport equation subject to this boundary condition yields the thermal history within a powder particle having the area-equivalent diameter D = 6/rho/sub 0/A, where rho/sub 0/ is the solid density. The magnitude of the temperatures and the heating and cooling rates indicate likely material transformations. The penetration of a given isotherm provides an estimate of the volume fraction of material transformed. Good agreement is found between model calculations and measurements of the extent of local martensite formation in consolidated 4330V steel powder and of local melting in consolidated aluminum-6% silicon and copper powders. The general implications of the model are discussed.

  12. Effect of Embolization Material in the Calculation of Dose Deposition in Arteriovenous Malformations

    SciTech Connect

    De la Cruz, O. O. Galvan; Moreno-Jimenez, S.; Larraga-Gutierrez, J. M.; Celis-Lopez, M. A.

    2010-12-07

    In this work it is studied the impact of the incorporation of high Z materials (embolization material) in the dose calculation for stereotactic radiosurgery treatment for arteriovenous malformations. A statistical analysis is done to establish the variables that may impact in the dose calculation. To perform the comparison pencil beam (PB) and Monte Carlo (MC) calculation algorithms were used. The comparison between both dose calculations shows that PB overestimates the dose deposited. The statistical analysis, for the quantity of patients of the study (20), shows that the variable that may impact in the dose calculation is the volume of the high Z material in the arteriovenous malformation. Further studies have to be done to establish the clinical impact with the radiosurgery result.

  13. Effect of Embolization Material in the Calculation of Dose Deposition in Arteriovenous Malformations

    NASA Astrophysics Data System (ADS)

    De la Cruz, O. O. Galván; Lárraga-Gutiérrez, J. M.; Moreno-Jiménez, S.; Célis-López, M. A.

    2010-12-01

    In this work it is studied the impact of the incorporation of high Z materials (embolization material) in the dose calculation for stereotactic radiosurgery treatment for arteriovenous malformations. A statistical analysis is done to establish the variables that may impact in the dose calculation. To perform the comparison pencil beam (PB) and Monte Carlo (MC) calculation algorithms were used. The comparison between both dose calculations shows that PB overestimates the dose deposited. The statistical analysis, for the quantity of patients of the study (20), shows that the variable that may impact in the dose calculation is the volume of the high Z material in the arteriovenous malformation. Further studies have to be done to establish the clinical impact with the radiosurgery result.

  14. A generalized framework for in-line energy deposition during steady-state Monte Carlo radiation transport

    SciTech Connect

    Griesheimer, D. P.; Stedry, M. H.

    2013-07-01

    A rigorous treatment of energy deposition in a Monte Carlo transport calculation, including coupled transport of all secondary and tertiary radiations, increases the computational cost of a simulation dramatically, making fully-coupled heating impractical for many large calculations, such as 3-D analysis of nuclear reactor cores. However, in some cases, the added benefit from a full-fidelity energy-deposition treatment is negligible, especially considering the increased simulation run time. In this paper we present a generalized framework for the in-line calculation of energy deposition during steady-state Monte Carlo transport simulations. This framework gives users the ability to select among several energy-deposition approximations with varying levels of fidelity. The paper describes the computational framework, along with derivations of four energy-deposition treatments. Each treatment uses a unique set of self-consistent approximations, which ensure that energy balance is preserved over the entire problem. By providing several energy-deposition treatments, each with different approximations for neglecting the energy transport of certain secondary radiations, the proposed framework provides users the flexibility to choose between accuracy and computational efficiency. Numerical results are presented, comparing heating results among the four energy-deposition treatments for a simple reactor/compound shielding problem. The results illustrate the limitations and computational expense of each of the four energy-deposition treatments. (authors)

  15. Energy deposition studies for the LBNE beam absorber

    SciTech Connect

    Rakhno, Igor L.; Mokhov, Nikolai V.; Tropin, Igor S.

    2015-01-29

    Results of detailed Monte Carlo energy deposition studies performed for the LBNE absorber core and the surrounding shielding with the MARS15 code are described. The model of the entire facility, that includes a pion-production target, focusing horns, target chase, decay channel, hadron absorber system – all with corresponding radiation shielding – was developed using the recently implemented ROOT-based geometry option in the MARS15 code. This option provides substantial flexibility and automation when developing complex geometry models. Both normal operation and accidental conditions were studied. Various design options were considered, in particular the following: (i) filling the decay pipe with air or helium; (ii) the absorber mask material and shape; (iii) the beam spoiler material and size. Results of detailed thermal calculations with the ANSYS code helped to select the most viable absorber design options.

  16. Low-energy calculations for nuclear photodisintegration

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  17. Comparison of mineral resources calculation methods for different genetic types of gravel and sand deposits

    NASA Astrophysics Data System (ADS)

    Patashova, T.

    2009-04-01

    Calculation of mineral resources and their proper assessment is relevant, since the stock of resources determines the economic independence of the state. I would like present the work wherein discusses gravel and sand deposits of different genetic type (kames, eskers, marginal glaciofluvial ridges, sandurs, glaciofluvial deltas and redrifted glaciofluvial aeolian formations). Their geological structure and formation conditions have been assessed; quality characteristics of mineral resources have been analysed; calculation of resources has been performed by applying most popular resources calculating methods used in Lithuania up to now, such as those of geological blocks, profiles and isolines, as well as the up-to-date GRID method created on the basis of triangle method in GIS environment. Comparison of resources assessed by different methods has revealed their advantages and disadvantages, their availability subject to deposits‘genetic types.

  18. Modeling Atmospheric Energy Deposition (by energetic ions): New Results

    NASA Astrophysics Data System (ADS)

    Parkinson, C.; Brain, D. A.; Lillis, R. J.; Liemohn, M. W.; Bougher, S. W.

    2012-12-01

    The structure, dynamics, chemistry, and evolution of planetary upper atmospheres are in large part determined by the available sources of energy. In addition to the solar EUV flux, the solar wind and solar energetic particle (SEP) events are also important sources. Both of these particle populations can significantly affect an atmosphere, causing atmospheric loss and driving chemical reactions. Attention has been paid to these sources from the standpoint of the radiation environment for humans and electronics, but little work has been done to evaluate their impact on planetary atmospheres. At unmagnetized planets or those with crustal field anomalies, in particular, the solar wind and SEPs of all energies have direct access to the atmosphere and so provide a more substantial energy source than at planets having protective global magnetic fields. Additionally, solar wind and energetic particle fluxes should be more significant for planets orbiting more active stars, such as is the case in the early history of the solar system for paleo-Venus and Mars. Therefore quantification of the atmospheric energy input from the solar wind and SEP events is an important component of our understanding of the processes that control their state and evolution. Such modeling has been previously done for Earth, Mars and Jupiter using a guiding center precipitation model with extensive collisional physics. Currently, this code is only valid for particles with small gyroradii in strong uniform magnetic fields. There is a clear necessity for a Lorentz formulation that can perform calculations for cases where there is only a weak or nonexistent magnetic field that includes detailed physical interaction with the atmosphere (i.e. collisional physics). We show initial efforts to apply a full Lorentz motion particle transport model to study the effects of particle precipitation in the upper atmospheres of Venus, Mars, and Titan. A systematic study of the ionization, excitation, and energy

  19. Free energy calculations of gramicidin dimer dissociation.

    PubMed

    Wanasundara, Surajith N; Krishnamurthy, Vikram; Chung, Shin-Ho

    2011-11-24

    Molecular dynamics simulations, combined with umbrella sampling, is used to study how gramicidin A (gA) dimers dissociate in the lipid bilayer. The potential of mean force and intermolecular potential energy are computed as functions of the distance between center of masses of the two gA monomers in two directions of separation: parallel to the bilayer surface and parallel to the membrane normal. Results from this study show that the dissociation of gA dimers occurs via lateral displacement of gA monomers followed by tilting of dimers with respect to the lipid bilayer normal. It is found that the dissociation energy of gA dimers in the dimyristoylphosphatidylcholine bilayer is 14 kcal mol(-1) (~22 kT), which is approximately equal to the energy of breaking six intermolecular hydrogen bonds that stabilize the gA channel dimer.

  20. Validation of model calculation of ammonia deposition in the neighbourhood of a poultry farm using measured NH 3 concentrations and N deposition

    NASA Astrophysics Data System (ADS)

    Sommer, S. G.; Østergård, H. S.; Løfstrøm, P.; Andersen, H. V.; Jensen, L. S.

    Substantial emission of ammonia (NH 3) from animal houses and the related high local deposition of NH 3-N are a threat to semi-natural nitrogen-deficient ecosystems situated near the NH 3 source. In Denmark, there are regulations limiting the level of NH 3 emission from livestock houses near N-deficient ecosystems that are likely to change due to nitrogen (N) enrichment caused by NH 3 deposition. The models used for assessing NH 3 emission from livestock production, therefore, need to be precise, as the regulation will affect both the nature of the ecosystem and the economy of the farmer. Therefore a study was carried out with the objective of validating the Danish model used to monitor NH 3 transport, dispersion and deposition from and in the neighbourhood of a chicken farm. In the study we measured NH 3 emission with standard flux measuring methods, NH 3 concentrations at increasing distances from the chicken houses using passive diffusion samplers and deposition using 15N-enriched biomonitors and field plot studies. The dispersion and deposition of NH 3 were modelled using the Danish OML-DEP model. It was also shown that model calculations clearly reflect the measured NH 3 concentration and N deposition. Deposition of N measured by biomonitors clearly reflected the variation in NH 3 concentrations and showed that deposition was not significantly different from zero ( P < 0.05) at distances greater than 150-200 m from these chicken houses. Calculations confirmed this, as calculated N deposition 320 m away from the chicken farm was only marginally affected by the NH 3 emission from the farm. There was agreement between calculated and measured deposition showing that the model gives true estimates of the deposition in the neighbourhood of a livestock house emitting NH 3.

  1. Global Auroral Energy Deposition Derived from Polar UVI Images

    NASA Technical Reports Server (NTRS)

    Fillingim, M. O.; Brittnacher, M. J.; Elsen, R.; Parks, G. K.; Spann, J. F., Jr.; Germany, G. A.

    1997-01-01

    Quantitative measurement of the transfer of energy and momentum to the ionosphere from the solar wind is one of the main objectives of the ISTP program. Global measurement of auroral energy deposition derived from observations of the longer wavelength LBH band emissions made by the Ultraviolet Imager on the Polar spacecraft is one of the key elements in this satellite and ground-based instrument campaign. These "measurements" are inferred by combining information from consecutive images using different filters and have a time resolution on the average of three minutes and are made continuously over a 5 to 8 hour period during each 18 hour orbit of the Polar spacecraft. The energy deposition in the ionosphere from auroral electron precipitation augments are due to Joule heating associated with field aligned currents. Assuming conjugacy of energy deposition between the two hemispheres the total energy input to the ionosphere through electron precipitation can be determined at high time resolution. Previously, precipitating particle measurements along the tracks of low altitude satellites provided only local measurements and the global energy precipitation could be inferred through models but not directly measured. We use the UVI images for the entire month of January 1997 to estimate the global energy deposition at high time resolution. We also sort the energy deposition into sectors to find possible trends, for example, on the dayside and nightside, or the dawn and dusk sides.

  2. Energetic particle energy deposition in Titan's upper atmosphere

    NASA Astrophysics Data System (ADS)

    Westlake, J. H.; Smith, H. T.; Mitchell, D. G.; Paranicas, C. P.; Rymer, A. M.; Bell, J. M.; Waite, J. H., Jr.; Mandt, K. E.

    2012-04-01

    Titan’s upper atmosphere has been observed to be variable on a pass-by-pass basis. During the nominal mission where the Cassini Ion and Neutral Mass Spectrometer (INMS) only sampled the northern hemisphere this variability was initially believed to be tied to solar drivers manifest in latitudinal variations in the thermal structure of the upper atmosphere. However, when Cassini delved into the southern hemisphere the latitudinal dependence was not present in the data. Recently, Westlake et al. (2011) showed that the pass-by-pass variability is correlated with the deviations in the plasma environment as identified by Rymer et al. (2009) and Simon et al. (2010). Furthermore, the studies of Westlake et al. (2011) and Bell et al. (2011) showed that Titan’s upper atmosphere responds to changes in the ambient magnetospheric plasma on timescales of roughly one Titan day (16 Earth days). We report on recent studies of energy deposition in Titan’s upper atmosphere. Previous studies by Smith et al. (2009), Cravens et al. (2008), Tseng et al. (2008), and Shah et al. (2009) reported on energetic proton and oxygen ion precipitation. Back of the envelope calculations by Sittler et al. (2009) showed that magnetospheric energy inputs are expected to be of the order of or greater than the solar processes. We report on further analysis of the plasma environment around Titan during the flybys that the INMS has good data. We utilize data from the Magnetospheric Imaging Instrument to determine how the magnetospheric particle population varies from pass to pass and how this influences the net magnetospheric energy input prior to the flyby. We also report on enhanced energetic neutral atom emissions during select highly energetic passes. References: Bell, J., et al.: “Simulating the time-dependent response of Titan's upper atmosphere to periods of magnetospheric forcing”. Geophys. Res. Lett., Vol. 38, L06202, 2011. Rymer, A. M., et al.: “Discrete classification and electron

  3. 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.

  4. Comparison of mineral resources calculation methods for different genetic types of gravel and sand deposits

    NASA Astrophysics Data System (ADS)

    Patašova, Tatjana; Jurgaitis, Algirdas

    2008-01-01

    Calculation of mineral resources and their proper assessment is relevant, since the stock of resources determines the economic independence of the state. The present work discusses gravel and sand deposits of different genetic type (kames, eskers, marginal glaciofluvial ridges, sandurs, glaciofluvial deltas and redrifted glaciofluvial aeolian formations). Their geological structure and formation conditions have been assessed; quality characteristics of mineral resources have been analysed; calculation of resources has been performed by applying old methods used in Lithuania up to now, such as those of geological blocks, profiles and isolines, as well as the up-to-date GRID method created on the basis of the triangle method in GIS environment. Comparison of resources assessed by different methods has revealed their advantages and disadvantages.

  5. Energy deposition in the earth's atmosphere due to impact of solar activity-generated disturbances

    NASA Technical Reports Server (NTRS)

    Wu, S. T.; Kan, L. C.; Tandberg-Hanssen, E.; Dryer, M.

    1979-01-01

    Energy deposition in and dynamic responses of the terrestrial atmosphere to solar flare-generated shocks and other physical processes - such as particle precipitation and local heating - are investigated self-consistently in the context of hydrodynamics, the problem being treated as an initial boundary-value problem. It is extremely difficult to construct a general model for the line solar activity-magnetosphere-atmosphere; however, a limited model for this link is possible. The paper describes such a model, and presents some results on energy deposition into the earth's atmosphere due to solar activity-generated disturbances. Results from the present calculations are presented and discussed.

  6. Heuristic control of kinetic energy in dynamic reaction coordinate calculations.

    PubMed

    Hellweg, Arnim

    2013-08-01

    For the understanding and prediction of chemical reactions, detailed knowledge of the minimum energy path between reactants and transition state is of utmost importance. Stewart et al. (J. Comput. Chem. 1987, 8, 1117) proposed the usage of molecular trajectories calculated from Newton's equations of motion for an efficient reaction path following. Two operational modes are possible thereby: intrinsic (IRC) and dynamic reaction coordinate calculations (DRC). The technical difference between these modes is that in an IRC calculation the kinetic energy of the nuclei is quenched while the total energy is conserved in DRC calculations. In this work, a heuristic control methodology of atomic kinetic energies in DRC calculations using fuzzy logic is proposed. A diversified test set of 10 reactions has been collected to examine the performance of this approach. Fuzzy rule-based models are found to be a convenient way to make the determination of accessible paths of chemical reactions computationally efficient.

  7. Energy deposition of single femtosecond filaments in the atmosphere.

    PubMed

    Rosenthal, E W; Jhajj, N; Larkin, I; Zahedpour, S; Wahlstrand, J K; Milchberg, H M

    2016-08-15

    We present spatially resolved measurements of energy deposition into atmospheric air by femtosecond laser filaments. Single filaments formed with varying laser pulse energy and pulsewidth were examined using longitudinal interferometry, sonographic probing, and direct energy loss measurements. We measure peak and average energy absorption of ∼4  μJ/cm and ∼1  μJ/cm for input pulse powers up to ∼6 times the critical power for self-focusing. PMID:27519120

  8. Guidelines for the analysis of free energy calculations

    PubMed Central

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

    2015-01-01

    Free energy calculations based on molecular dynamics (MD) simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical–analysis.py, freely available on GitHub at https://github.com/choderalab/pymbar–examples, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Perry, Jason

    2005-05-01

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

  11. 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...

  12. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

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

  13. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 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...

  14. 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...

  15. 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...

  16. An introduction to best practices in free energy calculations.

    PubMed

    Shirts, Michael R; Mobley, David L

    2013-01-01

    Free energy calculations are extremely useful for investigating small-molecule biophysical properties such as protein-ligand binding affinities and partition coefficients. However, these calculations are also notoriously difficult to implement correctly. In this chapter, we review standard methods for computing free energy via simulation, discussing current best practices and examining potential pitfalls for computational researchers performing them for the first time. We include a variety of examples and tips for how to set up and conduct these calculations, including applications to relative binding affinities and small-molecule solvation free energies.

  17. Simulation of proton-induced energy deposition in integrated circuits

    NASA Technical Reports Server (NTRS)

    Fernald, Kenneth W.; Kerns, Sherra E.

    1988-01-01

    A time-efficient simulation technique was developed for modeling the energy deposition by incident protons in modern integrated circuits. To avoid the excessive computer time required by many proton-effects simulators, a stochastic method was chosen to model the various physical effects responsible for energy deposition by incident protons. Using probability density functions to describe the nuclear reactions responsible for most proton-induced memory upsets, the simulator determines the probability of a proton hit depositing the energy necessary for circuit destabilization. This factor is combined with various circuit parameters to determine the expected error-rate in a given proton environment. An analysis of transient or dose-rate effects is also performed. A comparison to experimental energy-disposition data proves the simulator to be quite accurate for predicting the expected number of events in certain integrated circuits.

  18. A nuclear fragmentation energy deposition model

    NASA Technical Reports Server (NTRS)

    Ngo, D. M.; Wilson, J. W.; Fogarty, T. N.; Buck, W. W.; Townsend, L. W. (Principal Investigator)

    1991-01-01

    A formalism for target fragment transport is presented with application to energy loss spectra in thin silicon devices. A nuclear data base is recommended that agrees well with the measurements of McNulty et al. using surface barrier detectors. High-energy events observed by McNulty et al., which are not predicted by intranuclear cascade models, are well represented by the present work.

  19. Calculation of Dose Deposition in 3D Voxels by Heavy Ions and Simulation of gamma-H2AX Experiments

    NASA Technical Reports Server (NTRS)

    Plante, I.; Ponomarev, A. L.; Wang, M.; Cucinotta, F. A.

    2011-01-01

    The biological response to high-LET radiation is different from low-LET radiation due to several factors, notably difference in energy deposition and formation of radiolytic species. Of particular importance in radiobiology is the formation of double-strand breaks (DSB), which can be detected by -H2AX foci experiments. These experiments has revealed important differences in the spatial distribution of DSB induced by low- and high-LET radiations [1,2]. To simulate -H2AX experiments, models based on amorphous track with radial dose are often combined with random walk chromosome models [3,4]. In this work, a new approach using the Monte-Carlo track structure code RITRACKS [5] and chromosome models have been used to simulate DSB formation. At first, RITRACKS have been used to simulate the irradiation of a cubic volume of 5 m by 1) 450 1H+ ions of 300 MeV (LET 0.3 keV/ m) and 2) by 1 56Fe26+ ion of 1 GeV/amu (LET 150 keV/ m). All energy deposition events are recorded to calculate dose in voxels of 20 m. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. Many differences are found in the spatial distribution of dose voxels for the 56Fe26+ ion. The track structure can be distinguished, and voxels with very high dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and indicate clustered energy deposition, which may be responsible for complex DSB. In the second step, assuming that DSB will be found only in voxels where energy is deposited by the radiation, the intersection points between voxels with dose > 0 and simulated chromosomes were obtained. The spatial distribution of the intersection points is similar to -H2AX foci experiments. These preliminary results suggest that combining stochastic track structure and chromosome models could be a good approach to understand radiation-induced DSB and chromosome aberrations.

  20. System to quantify gamma-ray radial energy deposition in semiconductor detectors

    DOEpatents

    Kammeraad, Judith E.; Blair, Jerome J.

    2001-01-01

    A system for measuring gamma-ray radial energy deposition is provided for use in conjunction with a semiconductor detector. The detector comprises two electrodes and a detector material, and defines a plurality of zones within the detecting material in parallel with the two electrodes. The detector produces a charge signal E(t) when a gamma-ray interacts with the detector. Digitizing means are provided for converting the charge signal E(t) into a digitized signal. A computational means receives the digitized signal and calculates in which of the plurality of zones the gamma-ray deposited energy when interacting with the detector. The computational means produces an output indicating the amount of energy deposited by the gamma-ray in each of the plurality of zones.

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

    SciTech Connect

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

    2014-12-15

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

  2. 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.

  3. ENERGY DEPOSITION PROFILES AND ENTROPY IN GALAXY CLUSTERS

    SciTech Connect

    Chaudhuri, Anya; Majumdar, Subhabrata; Nath, Biman B. E-mail: subha@tifr.res.in

    2012-11-10

    We report the results of our study of fractional entropy enhancement in the intracluster medium (ICM) of the clusters from the representative XMM-Newton cluster structure survey. We compare the observed entropy profile of these clusters with that expected for the ICM without any feedback, as well as with the introduction of preheating and cooling. We make the first estimate of the total, as well as radial, non-gravitational energy deposition up to r {sub 500} for this large, nearly flux-limited, sample of clusters. We find that the total energy deposition corresponding to the entropy enhancement is proportional to the cluster temperature (and hence cluster mass). The energy deposition per particle scaled by T {sub sp}, {Delta}E/T {sub sp} has a similar profile in all clusters, and is more pronounced in the central regions. Our results support models of entropy enhancement through active galactic nucleus feedback.

  4. Protein thermostability calculations using alchemical free energy simulations.

    PubMed

    Seeliger, Daniel; de Groot, Bert L

    2010-05-19

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

  5. Deposition efficiency of fractal-like aggregates in fibrous filters calculated using Brownian dynamics method.

    PubMed

    Bałazy, Anna; Podgórski, Albert

    2007-07-15

    Nonspherical particles, such as fractal-like aggregates emitted by diesel engines, are commonly met in the ambient air. Some of them are believed to be carcinogenic to humans, thus their efficient removal is of crucial practical importance. A fibrous filter is the device commonly used for aerosol purification but the literature lacks experimental data concerning aggregates filtration. Effect of aggregates' parameters (fractal dimension, primary particle radius) as well as fiber diameter and air velocity on the filtration efficiency is investigated theoretically using the modified Brownian dynamics method. Three different expressions for the friction coefficient evaluation for the aggregates were examined. The results obtained indicate that structure of an aggregate, filter structure and process conditions strongly influence the aggregates deposition efficiency, which significantly differs from the values determined for mass-equivalent spherical particles. The results determined using the Brownian dynamics approach were compared with the values calculated using classical single fiber theory and noticeable discrepancy was observed for the most penetrating particles, while both approaches agree for the limiting cases of small or large particles. Peclet number based on the mobility radius and the interception parameter based on the outer radius are the proper criteria to describe diffusional and deterministic deposition of aggregates.

  6. Molecular modeling study of chiral drug crystals: lattice energy calculations.

    PubMed

    Li, Z J; Ojala, W H; Grant, D J

    2001-10-01

    The lattice energies of a number of chiral drugs with known crystal structures were calculated using Dreiding II force field. The lattice energies, including van der Waals, Coulombic, and hydrogen-bonding energies, of homochiral and racemic crystals of some ephedrine derivatives and of several other chiral drugs, are compared. The calculated energies are correlated with experimental data to probe the underlying intermolecular forces responsible for the formation of racemic species, racemic conglomerates, or racemic compounds, termed chiral discrimination. Comparison of the calculated energies among ephedrine derivatives reveals that a greater Coulombic energy corresponds to a higher melting temperature, while a greater van der Waals energy corresponds to a larger enthalpy of fusion. For seven pairs of homochiral and racemic compounds, correlation of the differences between the two forms in the calculated energies and experimental enthalpy of fusion suggests that the van der Waals interactions play a key role in the chiral discrimination in the crystalline state. For salts of the chiral drugs, the counter ions diminish chiral discrimination by increasing the Coulombic interactions. This result may explain why salt forms favor the formation of racemic conglomerates, thereby facilitating the resolution of racemates.

  7. Temporal and spatial characteristics of auroral energy deposition

    NASA Astrophysics Data System (ADS)

    Hampton, D. L.; Conde, M.

    2015-12-01

    Auroral electron precipitation forms a complex and dynamic energy input into the high-latitude ionosphere and thermopshere. Rapid changes in plasma density due to electron impact ionization create correspondingly rapid changes in conductivity which in turn change the magnitude and altitude profile of magnetospheric current closure in the E- and F-region. Modeling these changes in the ionosphere and their effects on the local or regional upper atmosphere requires detailed input over wide regions. In support of the AMISR PINOT campaign and several rocket campaigns (CASCADES-2, MICA, ASSP) we have developed and tested a method to determine the characteristics of auroral energy input using purely ground-based optical measurements in geometries away from magnetic zenith. Using the N2+ first negative emissions at 427.8 nm reproduces the total energy flux over a wide region, but alone does not indicate the altitude profile of this energy deposition. Using temperature maps of the E-region collected by a Scanning Doppler Imager (SDI) observing the auroral green-line emission is a proxy for the characteristic energy of the precipitating electrons. While in some cases the energy determination underestimates the average energy it still is a good proxy for understanding when the electron distribution changes. We examine two seasons worth of auroral observations and determine the spatial and temporal variability of auroral energy deposition in comparison to solar wind and geophysical activity parameters. We also compare the results with well-known empirical models of electron energy deposition and show that they underestimate the peak local energy deposition rates by as much as a factor of 30.

  8. The effect of calculated explosive energy output on blast design

    SciTech Connect

    Katsabanis, P.D.; Workman, L.

    1996-12-31

    The energy output of an explosive is typically calculated using an equation of state and computer applications. Results are reported as weight and bulk strength, either in absolute terms or relative to ANFO. The effect of the equation of state selected and the assumptions regarding the energy calculation are considered and interpreted for the purpose of blast design. It appears that variations in the heat of detonation which result from the selection of the equation of state and parameters associated with it are not sufficient to significantly affect blast patterns, explosive consumption and costs. However variations stemming from the use of available energy associated with a cut-off pressure are significant, suggesting in many cases large pattern expansions. The validity of the various approaches is discussed and blast design results based on the energy calculated by the different approaches are presented and evaluated.

  9. Abnormal energy deposition on the wall through plasma disruptions

    NASA Astrophysics Data System (ADS)

    Yamazaki, K.; Schmidt, G. L.

    1984-12-01

    The dissipation of plasma kinetic and magnetic energy during sawtooth oscillations and disruptions in tokamaks is analyzed using Kadomtsev's disruption model and the plasma-circuit equations. New simple scalings of several characteristic times are obtained for sawteeth and for thermal and magnetic energy quenches of disruptions. The abnormal energy deposition on the wall during major or minor disruptions, estimated from this analysis, is compared with bolometric measurements in the PDX tokamak. Especially, magnetic energy dissipation during the current termination period is shown to be reduced by the strong coupling of the plasma current with external circuits. These analyses are found to be useful to predict the phenomenological behavior of plasma disruptions in large future tokamaks, and to estimate abnormal heat deposition on the wall during plasma disruptions.

  10. Abnormal energy deposition on the wall through plasma disruptions

    NASA Astrophysics Data System (ADS)

    Yamazaki, K.; Schmidt, G. L.

    1984-06-01

    The dissipation of plasma kinetic and magnetic energy during sawtooth oscillations and disruptions in Tokamaks is analyzed using Kadomtsev's disruption model and the plasma-circuit equations. New simple scalings of several characteristic times are obtained for sawteeth and for thermal and magnetic energy quenches of disruptions. The abnormal energy deposition on the wall during major or minor disruptions, estimated from this analysis, is compared with bolometric measurements in the PDX Tokamak. Especially, magnetic energy dissipation during the current termination period is shown to be reduced by the strong coupling of the plasma current with external circuits. These analyses are found to be useful to predict the phenomenological behavior of plasma disruptions in large future Tokamaks, and to estimate abnormal heat deposition on the wall during plasma disruptions.

  11. Gamma-ray transfer and energy deposition in supernovae

    NASA Technical Reports Server (NTRS)

    Swartz, Douglas A.; Sutherland, Peter G.; Harkness, Robert P.

    1995-01-01

    Solutions to the energy-independent (gray) radiative transfer equations are compared to results of Monte Carlo simulations of the Ni-56 and Co-56 decay gamma-ray energy deposition in supernovae. The comparison shows that an effective, purely absorptive, gray opacity, kappa(sub gamma) approximately (0. 06 +/- 0.01)Y(sub e) sq cm/g, where Y is the total number of electrons per baryon, accurately describes the interaction of gamma-rays with the cool supernova gas and the local gamma-ray energy deposition within the gas. The nature of the gamma-ray interaction process (dominated by Compton scattering in the relativistic regime) creates a weak dependence of kappa(sub gamma) on the optical thickness of the (spherically symmetric) supernova atmosphere: The maximum value of kappa(sub gamma) applies during optically thick conditions when individual gamma-rays undergo multiple scattering encounters and the lower bound is reached at the phase characterized by a total Thomson optical depth to the center of the atmosphere tau(sub e) approximately less than 1. Gamma-ray deposition for Type Ia supernova models to within 10% for the epoch from maximum light to t = 1200 days. Our results quantitatively confirm that the quick and efficient solution to the gray transfer problem provides an accurate representation of gamma-ray energy deposition for a broad range of supernova conditions.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  13. 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.

  14. Energy deposition and primary chemical products in Titan’s upper atmosphere

    NASA Astrophysics Data System (ADS)

    Lavvas, P.; Galand, M.; Yelle, R. V.; Heays, A. N.; Lewis, B. R.; Lewis, G. R.; Coates, A. J.

    2011-05-01

    Cassini results indicate that solar photons dominate energy deposition in Titan's upper atmosphere. These dissociate and ionize nitrogen and methane and drive the subsequent complex organic chemistry. The improved constraints on the atmospheric composition from Cassini measurements demand greater precision in the photochemical modeling. Therefore, in order to quantify the role of solar radiation in the primary chemical production, we have performed detailed calculations for the energy deposition of photons and photoelectrons in the atmosphere of Titan and we validate our results with the Cassini measurements for the electron fluxes and the EUV/FUV emissions. We use high-resolution cross sections for the neutral photodissociation of N 2, which we present here, and show that they provide a different picture of energy deposition compared to results based on low-resolution cross sections. Furthermore, we introduce a simple model for the energy degradation of photoelectrons based on the local deposition approximation and show that our results are in agreement with detailed calculations including transport, in the altitude region below 1200 km, where the effects of transport are negligible. Our calculated, daytime, electron fluxes are in good agreement with the measured fluxes by the Cassini Plasma Spectrometer (CAPS), and the same holds for the measured FUV emissions by the Ultraviolet Imaging Spectrometer (UVIS). Finally, we present the vertical production profiles of radicals and ions originating from the interaction of photons and electrons with the main components of Titan's atmosphere, along with the column integrated production rates at different solar zenith angles. These can be used as basis for any further photochemical calculations.

  15. Heavy-ion fission probability calculations at high excitation energy

    SciTech Connect

    D'Arrigo, A.; Giardina, G.; Taccone, A. Istituto Nazionale di Fisica Nucleare, Gruppo Collegato di Messina, Messina Istituto di Tecniche Spettroscopiche del Consiglio Nazionale delle Ricerche, Messina )

    1991-12-01

    In the framework of the statistical theory of nuclear reactions we calculated the fission probability {ital P}{sub {ital f}} of the {sup 153}Tb, {sup 158}Er, {sup 159}Dy, {sup 175}Hf, {sup 179}Ta, {sup 186}Os, and {sup 188}Os nuclei with a mass number {ital A}=150--200 produced by heavy-ion reactions. Starting from the spectra of the single-particle levels as determined by Nix and Moeller, and utilizing a formalism we developed, we determined the excitation energy dependence of the effective level density parameters for the fission and the neutron emission channels. The agreement between the fission probability calculations and the experimental data was reached when a nonadiabatic estimate of the collective effects was used to calculate the nuclear level density. In the fission process at high excitation energies induced by ions heavier than the {alpha} particle, an energy dependence of the effective fission barrier has to be used.

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

    PubMed Central

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

    2013-01-01

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

  17. Energy Deposition and Redistribution in the Magnetosphere-Ionosphere System

    NASA Astrophysics Data System (ADS)

    Fok, M. H.; Khazanov, G. V.; Glocer, A.; Buzulukova, N.; Chen, S.

    2013-12-01

    The closed magnetic field region of the magnetosphere is extremely complicated and dynamic. The constituent populations of this region comprise a tightly coupled and interconnected system that must be considered in concert rather than independently. The major plasma components in this coupled system are: plasmasphere, superthermal electrons, ring current, and radiation belts. These components are moreover tightly tied to the ionosphere both through electrodynamic coupling and particle coupling. Each of these populations has distinctive features and contributes in a different way to the dynamic and energetic processes in the magnetosphere-ionosphere system. Energy from the Sun is deposited in these plasmas directly or indirectly through energy coupling mechanisms with surrounding plasma and electromagnetic fields. Our paper will focus on simulating energy deposition and redistribution in the magnetosphere-ionosphere system. Extensive data analysis and data-model comparison will be carried out to reconcile theory with measurements.

  18. 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.

  19. Calculating Ring Pucker Free Energy Surfaces From Reaction Coordinate Forces

    SciTech Connect

    Barnett, Christopher B.; Naidoo, Kevin J.

    2009-03-09

    We implemented the free energy from adaptive reaction coordinate forces (FEARCF) method and applied it to the conformational investigation of carbohydrate ring puckering. The method allows for significantly enhanced sampling of reaction coordinate space. The free energies associated with the ring pucker motion of {beta}-D-ribose (a furanose) and {beta}-D-glucose (a pyranose) were calculated. These can be used to interpret catalytic mechanisms of glycosylases.

  20. Removing the barrier to the calculation of activation energies

    NASA Astrophysics Data System (ADS)

    Mesele, Oluwaseun O.; Thompson, Ward H.

    2016-10-01

    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.

  1. Estimating the energy deposition in the mesosphere from anisotropic electron fluxes during REP events

    NASA Astrophysics Data System (ADS)

    Stadsnes, Johan; Sandanger, Marit; Nesse Tyssoy, Hilde; Odegaard, Linn-Kristine; Asnes, Arne

    Data from the MEPED particle spectrometers on the Polar Orbiting Operational Environmental Satellites (POES) are often used for estimating the energy deposition in the upper atmosphere from electrons in the energy range 30 keV - 2.5 MeV. MEPED includes two collimated electron detectors, which are pointing approximately towards zenith (0 degree detector) and in the horizontal plane (90 degree detector). At medium and high geomagnetic latitudes the 0 degree detector measures particles within a limited part of the bounce loss cone and the 90 degree detector measures particles outside or near the edge of the loss cone. The electron fluxes often show strong pitch angle anisotropy which causes large uncertainty in the estimate of energy deposition based on these measurements. An upper estimate is derived from the 90 degree detector and a lower estimate from the 0 degree detector. The electron anisotropy is to a large extent determined by wave-particle interactions causing pitch angle diffusion driving electrons into the bounce loss cone. The pitch angle anisotropy is dependent on the strength of the diffusion. We are developing a method for calculating the flux versus pitch angle in the loss cone based on the measured electron fluxes and modeled flux profiles from pitch angle scattering by whistler mode waves. We will present results from calculation of the energy deposition using the derived anisotropic flux distribution during a REP event in 2008.

  2. Distributions of deposited energy and ionization clusters around ion tracks studied with Geant4 toolkit

    NASA Astrophysics Data System (ADS)

    Burigo, Lucas; Pshenichnov, Igor; Mishustin, Igor; Hilgers, Gerhard; Bleicher, Marcus

    2016-05-01

    The Geant4-based Monte Carlo model for Heavy-Ion Therapy (MCHIT) was extended to study the patterns of energy deposition at sub-micrometer distance from individual ion tracks. Dose distributions for low-energy 1H, 4He, 12C and 16O ions measured in several experiments are well described by the model in a broad range of radial distances, from 0.5 to 3000 nm. Despite the fact that such distributions are characterized by long tails, a dominant fraction of deposited energy (∼80%) is confined within a radius of about 10 nm. The probability distributions of clustered ionization events in nanoscale volumes of water traversed by 1H, 2H, 4He, 6Li, 7Li, and 12C ions are also calculated. A good agreement of calculated ionization cluster-size distributions with the corresponding experimental data suggests that the extended MCHIT can be used to characterize stochastic processes of energy deposition to sensitive cellular structures.

  3. DEPDOSE: An interactive, microcomputer based program to calculate doses from exposure to radionuclides deposited on the ground

    SciTech Connect

    Beres, D.A.; Hull, A.P.

    1991-12-01

    DEPDOSE is an interactive, menu driven, microcomputer based program designed to rapidly calculate committed dose from radionuclides deposited on the ground. The program is designed to require little or no computer expertise on the part of the user. The program consisting of a dose calculation section and a library maintenance section. These selections are available to the user from the main menu. The dose calculation section provides the user with the ability to calculate committed doses, determine the decay time needed to reach a particular dose, cross compare deposition data from separate locations, and approximate a committed dose based on a measured exposure rate. The library maintenance section allows the user to review and update dose modifier data as well as to build and maintain libraries of radionuclide data, dose conversion factors, and default deposition data. The program is structured to provide the user easy access for reviewing data prior to running the calculation. Deposition data can either be entered by the user or imported from other databases. Results can either be displayed on the screen or sent to the printer.

  4. General method for calculating derivatives of the lattice electrostatic energy.

    NASA Technical Reports Server (NTRS)

    Macdonald, D. E.; Eftis, J.; Arkilic, G. M.

    1972-01-01

    A method for calculating the derivatives of lattice electrostatic strain energy is proposed. It offers a computation procedure that is more general, concise, and systematic than any of the procedures previously used by Fuchs (1936), Cousins (1967), and Suzuki et al. (1968). The method can also easily be extended to fourth- and higher-order derivatives without undue difficulty.

  5. On the calculation of classical vibrational energy exchange

    NASA Astrophysics Data System (ADS)

    Gibbons, John P.; Stettler, John D.

    1982-07-01

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

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

    PubMed

    Andersen, Torben B

    2015-09-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  8. The Calculation of Accurate Metal-Ligand Bond Energies

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  9. The theoretical shape of sucrose crystals from energy calculations

    NASA Astrophysics Data System (ADS)

    Saska, Michael; Myerson, Allan S.

    1983-05-01

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

  10. Solar Energy Deposition Rates in the Mesosphere Derived from Airglow Measurements: Implications for the Ozone Model Deficit Problem

    NASA Technical Reports Server (NTRS)

    Mlynczak, Martin G.; Garcia, Rolando R.; Roble, Raymond G.; Hagan, Maura

    2000-01-01

    We derive rates of energy deposition in the mesosphere due to the absorption of solar ultraviolet radiation by ozone. The rates are derived directly from measurements of the 1.27-microns oxygen dayglow emission, independent of knowledge of the ozone abundance, the ozone absorption cross sections, and the ultraviolet solar irradiance in the ozone Hartley band. Fifty-six months of airglow data taken between 1982 and 1986 by the near-infrared spectrometer on the Solar-Mesosphere Explorer satellite are analyzed. The energy deposition rates exhibit altitude-dependent annual and semi-annual variations. We also find a positive correlation between temperatures and energy deposition rates near 90 km at low latitudes. This correlation is largely due to the semiannual oscillation in temperature and ozone and is consistent with model calculations. There is also a suggestion of possible tidal enhancement of this correlation based on recent theoretical and observational analyses. The airglow-derived rates of energy deposition are then compared with those computed by multidimensional numerical models. The observed and modeled deposition rates typically agree to within 20%. This agreement in energy deposition rates implies the same agreement exists between measured and modeled ozone volume mixing ratios in the mesosphere. Only in the upper mesosphere at midlatitudes during winter do we derive energy deposition rates (and hence ozone mixing ratios) consistently and significantly larger than the model calculations. This result is contrary to previous studies that have shown a large model deficit in the ozone abundance throughout the mesosphere. The climatology of solar energy deposition and heating presented in this paper is available to the community at the Middle Atmosphere Energy Budget Project web site at http://heat-budget.gats-inc.com.

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

    NASA Technical Reports Server (NTRS)

    Lee, H.; Bludman, S. A.

    1985-01-01

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

  12. Calculation of energy for lighting using EN 15193

    NASA Astrophysics Data System (ADS)

    Mitsopoulou, Mairi

    The aim of this report is to investigate the impact of the application of the new European directive prEN 15193, concerning the Energy performance of buildings - Energy requirements for lighting on the design of artificial lighting in open plan office buildings. A study of the energy consequences of three different types of building and different types of lighting systems within the buildings was carried out. The result of the study helped understand how each type of building performs in terms of the amount of energy that is used in the lighting the study also helped to verify the calculation procedure LENI used in EN 15193 Energy Performance of Buildings - Energy Requirements for Lighting. The efficient use of energy for lighting can reduce operating costs by reducing the energy consumption for lighting. Besides direct savings, indirect energy savings can be found in buildings, with high cooling loads because of the reduced heat production and thus, the reduced energy consumption for air conditioning, a fact that in a worldwide scale will have important environmental benefits.

  13. Monte Carlo simulation of energy deposition by low-energy electrons in molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Heaps, M. G.; Furman, D. R.; Green, A. E. S.

    1975-01-01

    A set of detailed atomic cross sections has been used to obtain the spatial deposition of energy by 1-20-eV electrons in molecular hydrogen by a Monte Carlo simulation of the actual trajectories. The energy deposition curve (energy per distance traversed) is quite peaked in the forward direction about the entry point for electrons with energies above the threshold of the electronic states, but the peak decreases and broadens noticeably as the electron energy decreases below 10 eV (threshold for the lowest excitable electronic state of H2). The curve also assumes a very symmetrical shape for energies below 10 eV, indicating the increasing importance of elastic collisions in determining the shape of the curve, although not the mode of energy deposition.

  14. Composite electron propagator methods for calculating ionization energies

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  15. Composite electron propagator methods for calculating ionization energies.

    PubMed

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

    2016-06-14

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

  16. Validation of back-calculated body lengths and timing of growth mark deposition in Hawaiian green sea turtles.

    PubMed

    Goshe, Lisa R; Snover, Melissa L; Hohn, Aleta A; Balazs, George H

    2016-05-01

    Somatic growth rate data for wild sea turtles can provide insight into life-stage durations, time to maturation, and total lifespan. When appropriately validated, the technique of skeletochronology allows prior growth rates of sea turtles to be calculated with considerably less time and labor than required by mark--recapture studies. We applied skeletochronology to 10 dead, stranded green turtles Chelonia mydas that had previously been measured, tagged, and injected with OTC (oxytetracycline) during mark-recapture studies in Hawaii for validating skeletochronological analysis. We tested the validity of back-calculating carapace lengths (CLs) from diameters of LAGs (lines of arrested growth), which mark the outer boundaries of individual skeletal growth increments. This validation was achieved by comparing CLs estimated from measurements of the LAG proposed to have been deposited closest to the time of tagging to actual CLs measured at the time of tagging. Measureable OTC-mark diameters in five turtles also allowed us to investigate the time of year when LAGs are deposited. We found no significant difference between CLs measured at tagging and those estimated through skeletochronology, which supports calculation of somatic growth rates by taking the difference between CLs estimated from successive LAG diameters in humerus bones for this species. Back-calculated CLs associated with the OTC mark and growth mark deposited closest to tagging indicated that annual LAGs are deposited in the spring. The results of this validation study increase confidence in utilization of skeletochronology to rapidly obtain accurate age and growth data for green turtles.

  17. 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.

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

    PubMed Central

    Jorgensen, William L.; Thomas, Laura L.

    2009-01-01

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

  19. Energy deposited in the high luminosity inner triplets of the LHC by collision debris

    SciTech Connect

    Wildner, E.; Broggi, F.; Cerutti, F.; Ferrari, A.; Hoa, C.; Koutchouk, J.-P.; Mokhov, N.V.; /Fermilab

    2008-06-01

    The 14 TeV center of mass proton-proton collisions in the LHC produce not only debris interesting for physics but also showers of particles ending up in the accelerator equipment, in particular in the superconducting magnet coils. Evaluations of this contribution to the heat, that has to be transported by the cryogenic system, have been made to guarantee that the energy deposition in the superconducting magnets does not exceed limits for magnet quenching and the capacity of the cryogenic system. The models of the LHC base-line are detailed and include description of, for energy deposition, essential elements like beam-pipes and corrector magnets. The evaluations made using the Monte-Carlo code FLUKA are compared to previous studies using MARS. For the consolidation of the calculations, a dedicated comparative study of these two codes was performed for a reduced setup.

  20. Self-consistent calculations of alpha-decay energies

    SciTech Connect

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

    2013-06-15

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

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

    PubMed

    Janning, Jay D; Ball, David W

    2010-05-01

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

  2. Improved initial guess for minimum energy path calculations.

    PubMed

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

    2014-06-01

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

  3. 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.

  4. 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).

  5. 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

  6. REFLEX: An energy deposition code that models the effects of electron reflection during electron beam heating tests

    SciTech Connect

    Stone, C.A. IV; Croessmann, C.D.; Whitley, J.B.

    1988-01-01

    This report describes an energy coupling model that considers electron reflection losses during electron beam heating experiments. This model is embodied on the REFLEX computer code, written in standard FORTRAN 77. REFLEX currently models energy deposition phenomena in three different sample geometries. These configurations include flat, cylindrical shell, and hemispherical shell surfaces. Given the electron beam operating parameters, REFLEX calculates the heat flux profile over a sample's surface, the total amount of energy deposited into a sample, and the percentage of the electron beam energy that is transferred to a sample. This document describes the energy deposition equations used in the REFLEX code; the program is described and detailed instructions are given regarding the input. Results are given for each geometry and possible experimental applications are presented. 3 refs., 20 figs., 11 tabs.

  7. REFLEX: An energy deposition code that models the effects of electron reflection during electron beam heating tests

    NASA Astrophysics Data System (ADS)

    Stone, C. A., IV; Croessmann, C. D.; Whitley, J. B.

    1988-01-01

    This report describes an energy coupling model that considers electron reflection losses during electron beam heating experiments. This model is embodied on the REFLEX computer code, written in standard FORTRAN 77. REFLEX currently models energy deposition phenomena in three different sample geometries. These configurations include flat, cylindrical shell, and hemispherical shell surfaces. Given the electron beam operating parameters, REFLEX calculates the heat flux profile over a sample's surface, the total amount of energy deposited into a sample, and the percentage of the electron beam energy that is transferred to a sample. This document describes the energy deposition equations used in the REFLEX code; the program is described and detailed instructions are given regarding the input. Results are given for each geometry and possible experimental applications are presented.

  8. 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.

  9. Free energy calculations for a flexible water model.

    PubMed

    Habershon, Scott; Manolopoulos, David E

    2011-11-28

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

  10. Free energy calculations for a flexible water model.

    PubMed

    Habershon, Scott; Manolopoulos, David E

    2011-11-28

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

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

    PubMed

    Ruiza, F M; Grigera, J Raúl

    2005-09-01

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

  12. Basic ingredients of free energy calculations: a review.

    PubMed

    Christ, Clara D; Mark, Alan E; van Gunsteren, Wilfred F

    2010-06-01

    Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and their utility when applied in practice to biomolecular systems. A free energy calculation is comprised of three basic components: (i) a suitable model or Hamiltonian, (ii) a sampling protocol with which one can generate a representative ensemble of molecular configurations, and (iii) an estimator of the free energy difference itself. Alternative sampling protocols can be distinguished according to whether one or more states are to be sampled. In cases where only a single state is considered, six alternative techniques could be distinguished: (i) changing the dynamics, (ii) deforming the energy surface, (iii) extending the dimensionality, (iv) perturbing the forces, (v) reducing the number of degrees of freedom, and (vi) multi-copy approaches. In cases where multiple states are to be sampled, the three primary techniques are staging, importance sampling, and adiabatic decoupling. Estimators of the free energy can be classified as global methods that either count the number of times a given state is sampled or use energy differences. Or, they can be classified as local methods that either make use of the force or are based on transition probabilities. Finally, this overview of the available techniques and how they can be best used in a practical context is aimed at helping the reader choose the most appropriate combination of approaches for the biomolecular system, Hamiltonian and free energy difference of interest.

  13. Free energy calculation of permeation through aquaporin-5

    NASA Astrophysics Data System (ADS)

    Bastien, David

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

  14. Quantum calculations for rotational energy transfer in nitrogen molecule collisions

    NASA Astrophysics Data System (ADS)

    Huo, Winifred M.; Green, Sheldon

    1996-05-01

    Rotational energy transfer in collisions of nitrogen molecules has been studied theoretically, using the N2-N2 rigid-rotor potential of van der Avoird et al. [J. Chem. Phys. 84, 1629 (1986)]. For benchmarking purposes, converged close coupling (CC) calculations have been carried out to a total energy of about 200 cm-1. Coupled states (CS) approximation calculations have been carried out to a total energy of 680 cm-1, and infinite order sudden (IOS) approximation calculations have also been carried out. The CC and CS cross sections have been obtained both with and without identical molecule exchange symmetry, whereas exchange was neglected in the IOS calculations. The CS results track the CC cross sections rather well: between 113-219 cm-1 the average deviation is 14%, with accuracy improving at higher energy. Comparison between the CS and IOS cross sections at the high energy end of the CS calculations, 500-680 cm-1, shows that IOS is sensitive to the amount of inelasticity and the results for large ΔJ transitions are subject to larger errors. State-to-state cross sections with even and odd exchange symmetry agree to better than 2% and are well represented as a sum of direct and exchange cross sections for distinguishable molecules, an indication of the applicability of a classical treatment for this system. This result, however, does not apply to partial cross sections for given total J, but arises from a near cancellation of the interference terms between even and odd exchange symmetries on summing over partial waves. In order to compare with experimental data for rotational excitation rates of N2 in the n=1 excited vibrational level colliding with ground vibrational level (n=0) bath N2 molecules, it is assumed that exchange scattering between molecules in different vibrational levels is negligible and direct scattering is independent of n so that distinguishable molecule rigid rotor rates may be used. With these assumptions good agreement is obtained. Although

  15. A Calculation of Spatial Range of Colloidal Silicic Acid Deposited Downstream from the Alkali Front

    NASA Astrophysics Data System (ADS)

    Niibori, Yuichi; Iijima, Kazuki; Tamura, Naoyuki; Mimura, Hitoshi

    A high alkali domain spreads out due to the use of cement materials for the construction of the repository of radioactive wastes. Sudden change of pH at this alkali front produces colloidal silicic acid (polymeric silicic acid) in addition to the deposition of supersaturated monomeric silicic acid onto the fracture surface of flow-pathway. The colloidal silicic acid also deposits with relatively small rate-constant in the co-presence of solid phase. Once the flow-path surface is covered with the amorphous silica, the surface seriously degrades the sorption behavior of radionuclides (RNs). Therefore, so far, the authors have examined the deposition rates of supersaturated silicic acid. This study summarized the deposition rate-constants defined by the first-order reaction equation under various conditions of co-presence of amorphous silica powder. Then, using the smallest rate-constant (1.0×10-12 m/s in the co-presence of calcium ions of 1 mM) and a simulation code, COLFRAC-MRL, the spatial range of colloidal silicic acid deposited downstream from the alkali front was estimated. The results suggested the clogging caused by the deposition of colloidal silicic acid in flow-path. The altered spatial range in the flow-path was limited to around 30 m in fracture and to several centimeters in rock matrix.

  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.

    2016-09-01

    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. Dayside pickup oxygen ion precipitation at Venus and Mars - Spatial distributions, energy deposition and consequences

    NASA Astrophysics Data System (ADS)

    Luhmann, J. G.; Kozyra, J. U.

    1991-04-01

    The fluxes and energy spectra of picked-up planetary O(+) ions incident on the dayside atmospheres of Venus and Mars are calculated. Maps of precipitating ion number flux and energy flux are presented which show the asymmetrical distribution of dayside energy deposition expected from this source. Although the associated heating of the atmosphere and ionosphere is found to be negligible compared to that from the usual sources, backscattered or sputtered neutral oxygen atoms are produced at energies which exceed that needed for escape from the gravitational fields of both planets. These neutral 'winds', driven by pickup ion precipitation, represent a possibly significant loss of atmospheric constituents over the age of the solar system.

  18. Atomic Layer Deposition of Bismuth Vanadates for Solar Energy Materials.

    PubMed

    Stefik, Morgan

    2016-07-01

    The fabrication of porous nanocomposites is key to the advancement of energy conversion and storage devices that interface with electrolytes. Bismuth vanadate, BiVO4 , is a promising oxide for solar water splitting where the controlled fabrication of BiVO4 layers within porous, conducting scaffolds has remained a challenge. Here, the atomic layer deposition of bismuth vanadates is reported from BiPh3 , vanadium(V) oxytriisopropoxide, and water. The resulting films have tunable stoichiometry and may be crystallized to form the photoactive scheelite structure of BiVO4 . A selective etching process was used with vanadium-rich depositions to enable the synthesis of phase-pure BiVO4 after spinodal decomposition. BiVO4 thin films were measured for photoelectrochemical performance under AM 1.5 illumination. The average photocurrents were 1.17 mA cm(-2) at 1.23 V versus the reversible hydrogen electrode using a hole-scavenging sulfite electrolyte. The capability to deposit conformal bismuth vanadates will enable a new generation of nanocomposite architectures for solar water splitting.

  19. 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

  20. Exploiting the Properties of Aquaporin to Calculate Free Energy

    NASA Astrophysics Data System (ADS)

    Espejel, Hugo; Chen, Liao

    2010-03-01

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

  1. High-energy photoelectron diffraction: model calculations and future possibilities

    NASA Astrophysics Data System (ADS)

    Winkelmann, Aimo; Fadley, Charles S.; Garcia de Abajo, F. Javier

    2008-11-01

    We discuss the theoretical modeling of x-ray photoelectron diffraction (XPD) with hard x-ray excitation at up to 20 keV, using the dynamical theory of electron diffraction to illustrate the characteristic aspects of the diffraction patterns resulting from such localized emission sources in a multilayer crystal. We show via dynamical calculations for diamond, Si and Fe that the dynamical theory predicts well the available current data for lower energies around 1 keV, and that the patterns for energies above about 1 keV are dominated by Kikuchi bands, which are created by the dynamical scattering of electrons from lattice planes. The origin of the fine structure in such bands is discussed from the point of view of atomic positions in the unit cell. The profiles and positions of the element-specific photoelectron Kikuchi bands are found to be sensitive to lattice distortions (e.g. a 1% tetragonal distortion) and the position of impurities or dopants with respect to lattice sites. We also compare the dynamical calculations with results from a cluster model that is more often used to describe lower energy XPD. We conclude that hard XPD (HXPD) should be capable of providing unique bulk-sensitive structural information for a wide variety of complex materials in future experiments.

  2. Characteristic properties of the Casimir free energy for metal films deposited on metallic plates

    NASA Astrophysics Data System (ADS)

    Klimchitskaya, G. L.; Mostepanenko, V. M.

    2016-04-01

    The Casimir free energy and pressure of thin metal films deposited on metallic plates are considered using the Lifshitz theory and the Drude and plasma model approaches to the role of conduction electrons. The bound electrons are taken into account by using the complete optical data of film and plate metals. It is shown that for films of several tens of nanometers thickness the Casimir free energy and pressure calculated using these approaches differ by hundreds and thousands percent and can be easily discriminated experimentally. According to our results, the free energy of a metal film does not vanish in the limiting case of ideal metal if the Drude model approach is used in contradiction with the fact that the fluctuating field cannot penetrate in its interior. Numerical computations of the Casimir free energy and pressure of Ag and Au films deposited on Cu and Al plates have been performed using both theoretical approaches. It is shown that the free energy of a film can be both negative and positive depending on the metals used. For a Au film on a Ag plate and vice versa the Casimir energy of a film changes its sign with increasing film thickness. Applications of the obtained results for resolving the Casimir puzzle and the problem of stability of thin films are discussed.

  3. Comparisons of Solar Wind Coupling Parameters with Auroral Energy Deposition Rates

    NASA Technical Reports Server (NTRS)

    Elsen, R.; Brittnacher, M. J.; Fillingim, M. O.; Parks, G. K.; Germany G. A.; Spann, J. F., Jr.

    1997-01-01

    Measurement of the global rate of energy deposition in the ionosphere via auroral particle precipitation is one of the primary goals of the Polar UVI program and is an important component of the ISTP program. The instantaneous rate of energy deposition for the entire month of January 1997 has been calculated by applying models to the UVI images and is presented by Fillingim et al. In this session. A number of parameters that predict the rate of coupling of solar wind energy into the magnetosphere have been proposed in the last few decades. Some of these parameters, such as the epsilon parameter of Perrault and Akasofu, depend on the instantaneous values in the solar wind. Other parameters depend on the integrated values of solar wind parameters, especially IMF Bz, e.g. applied flux which predicts the net transfer of magnetic flux to the tail. While these parameters have often been used successfully with substorm studies, their validity in terms of global energy input has not yet been ascertained, largely because data such as that supplied by the ISTP program was lacking. We have calculated these and other energy coupling parameters for January 1997 using solar wind data provided by WIND and other solar wind monitors. The rates of energy input predicted by these parameters are compared to those measured through UVI data and correlations are sought. Whether these parameters are better at providing an instantaneous rate of energy input or an average input over some time period is addressed. We also study if either type of parameter may provide better correlations if a time delay is introduced; if so, this time delay may provide a characteristic time for energy transport in the coupled solar wind-magnetosphere-ionosphere system.

  4. Validation of back-calculated body lengths and timing of growth mark deposition in Hawaiian green sea turtles.

    PubMed

    Goshe, Lisa R; Snover, Melissa L; Hohn, Aleta A; Balazs, George H

    2016-05-01

    Somatic growth rate data for wild sea turtles can provide insight into life-stage durations, time to maturation, and total lifespan. When appropriately validated, the technique of skeletochronology allows prior growth rates of sea turtles to be calculated with considerably less time and labor than required by mark--recapture studies. We applied skeletochronology to 10 dead, stranded green turtles Chelonia mydas that had previously been measured, tagged, and injected with OTC (oxytetracycline) during mark-recapture studies in Hawaii for validating skeletochronological analysis. We tested the validity of back-calculating carapace lengths (CLs) from diameters of LAGs (lines of arrested growth), which mark the outer boundaries of individual skeletal growth increments. This validation was achieved by comparing CLs estimated from measurements of the LAG proposed to have been deposited closest to the time of tagging to actual CLs measured at the time of tagging. Measureable OTC-mark diameters in five turtles also allowed us to investigate the time of year when LAGs are deposited. We found no significant difference between CLs measured at tagging and those estimated through skeletochronology, which supports calculation of somatic growth rates by taking the difference between CLs estimated from successive LAG diameters in humerus bones for this species. Back-calculated CLs associated with the OTC mark and growth mark deposited closest to tagging indicated that annual LAGs are deposited in the spring. The results of this validation study increase confidence in utilization of skeletochronology to rapidly obtain accurate age and growth data for green turtles. PMID:27096079

  5. 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.

  6. 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.

  7. Calculations of the response of shielded detectors to gamma rays at MeV-range energies

    SciTech Connect

    R. C. Byrd

    2000-03-01

    Nuclear instruments designed to detect gamma rays at energies from 0.1 to 10 MeV respond primarily to the electrons produced by gamma-ray scattering and absorption in either the instrument itself or in the surrounding materials. Although tabulated attenuation coefficients are very useful for estimating macroscopic quantities such as bulk energy depositions, such quantities are averages over several different phenomena at the microscopic level. For detectors with active elements that are thin compared with an electron range, the competing effects of inscattering and outscattering result in complicated responses, as evidenced by the strong energy dependence of the resulting pulse-height spectra. Thus, for some applications the macroscopic averages are entirely sufficient, but for others a full microscopic analysis is needed. The author first reviews the literature on the responses of several types of detectors to gamma rays at energies below 10 MeV, and then they use a series of simple Monte Carlo calculations to illustrate the important physics issues. These simple calculations are followed by thorough studies of the energy and angle responses of two proposed instruments, including their responses to instantaneous pulses of large numbers of simultaneous incident photons.

  8. Fossil fuel energy resources of Ethiopia: Oil shale deposits

    NASA Astrophysics Data System (ADS)

    Wolela, Ahmed

    2006-10-01

    The energy crisis affects all countries in the world. Considering the price scenarios, many countries in Africa have begun to explore various energy resources. Ethiopia is one of the countries that depend upon imported petroleum products. To overcome this problem, geological studies suggest a significant occurrence of oil shale deposits in Ethiopia. The Inter-Trappean oil shale-bearing sediments are widely distributed on the South-Western Plateau of Ethiopia in the Delbi-Moye, Lalo-Sapo, Sola, Gojeb-Chida and Yayu Basins. The oil shale-bearing sediments were deposited in fluviatile and lacustrine environments. The oil shales contain mixtures of algal, herbaceous and higher plant taxa. They are dominated by algal-derived liptinite with minor amounts of vitrinite and inertinite. The algal remains belong to Botryococcus and Pediastrum. Laboratory results confirm that the Ethiopian oil shales are dominated by long-chain aliphatic hydrocarbons and have a low sulphur content. Type-II and Type-I kerogen dominated the studied oil shales. Type-II and Type-I are good source rocks for oil and gas generation. Hydrogen index versus Tmax value plots indicated that most of the oil shale samples fall within the immature-early mature stage for hydrocarbon generation, consistent with the Ro values that range from 0.3% to 0.64%. Pyrolysis data of the oil shales sensu stricto indicate excellent source rocks with up to 61.2% TOC values. Calorific value ranges from 400 to 6165 cal/g. Palynological studies confirmed that the oil shale-bearing sediments of Ethiopia range from Eocene to Miocene in age. A total of about 253,000,000 ton of oil shale is registered in the country. Oil shale deposits in Ethiopia can be used for production of oil and gas.

  9. Ab initio calculations of free-energy reaction barriers.

    PubMed

    Bucko, T

    2008-02-13

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

  10. Ab initio calculations of free-energy reaction barriers

    NASA Astrophysics Data System (ADS)

    Bucko, T.

    2008-02-01

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

  11. Effect of Energy Input on the Characteristic of AISI H13 and D2 Tool Steels Deposited by a Directed Energy Deposition Process

    NASA Astrophysics Data System (ADS)

    Park, Jun Seok; Park, Joo Hyun; Lee, Min-Gyu; Sung, Ji Hyun; Cha, Kyoung Je; Kim, Da Hye

    2016-05-01

    Among the many additive manufacturing technologies, the directed energy deposition (DED) process has attracted significant attention because of the application of metal products. Metal deposited by the DED process has different properties than wrought metal because of the rapid solidification rate, the high thermal gradient between the deposited metal and substrate, etc. Additionally, many operating parameters, such as laser power, beam diameter, traverse speed, and powder mass flow rate, must be considered since the characteristics of the deposited metal are affected by the operating parameters. In the present study, the effect of energy input on the characteristics of H13 and D2 steels deposited by a direct metal tooling process based on the DED process was investigated. In particular, we report that the hardness of the deposited H13 and D2 steels decreased with increasing energy input, which we discuss by considering microstructural observations and thermodynamics.

  12. Athermal Energy Loss from X-rays Deposited in Thin Superconducting Films on Solid Substrates

    NASA Technical Reports Server (NTRS)

    Kozorezov, Alexander G.; Lambert, Colin J.; Bandler, Simon R.; Balvin, Manuel A.; Busch, Sarah E.; Sagler, Peter N.; Porst, Jan-Patrick; Smith, Stephen J.; Stevenson, Thomas R.; Sadleir, John E.

    2013-01-01

    When energy is deposited in a thin-film cryogenic detector, such as from the absorption of an X-ray, an important feature that determines the energy resolution is the amount of athermal energy that can be lost to the heat bath prior to the elementary excitation systems coming into thermal equilibrium. This form of energy loss will be position-dependent and therefore can limit the detector energy resolution. An understanding of the physical processes that occur when elementary excitations are generated in metal films on dielectric substrates is important for the design and optimization of a number of different types of low temperature detector. We have measured the total energy loss in one relatively simple geometry that allows us to study these processes and compare measurements with calculation based upon a model for the various di.erent processes. We have modeled the athermal phonon energy loss in this device by finding an evolving phonon distribution function that solves the system of kinetic equations for the interacting system of electrons and phonons. Using measurements of device parameters such as the Debye energy and the thermal di.usivity we have calculated the expected energy loss from this detector geometry, and also the position-dependent variation of this loss. We have also calculated the predicted impact on measured spectral line-shapes, and shown that they agree well with measurements. In addition, we have tested this model by using it to predict the performance of a number of other types of detector with di.erent geometries, where good agreement is also found.

  13. Scaling of energy deposition in fast ignition targets.

    SciTech Connect

    Welch, Dale R.; Slutz, Stephen A.; Mehlhorn, Thomas Alan; Campbell, Robert B.

    2005-07-01

    We examine the scaling to ignition of the energy deposition of laser generated electrons in compressed fast ignition cores. Relevant cores have densities of several hundred g/cm{sup 3}, with a few keV initial temperature. As the laser intensities increase approaching ignition systems, on the order of a few 10{sup 21}W/cm{sup 2}, the hot electron energies expected to approach 100MeV. Most certainly anomalous processes must play a role in the energy transfer, but the exact nature of these processes, as well as a practical way to model them, remain open issues. Traditional PIC explicit methods are limited to low densities on current and anticipated computing platforms, so the study of relevant parameter ranges has received so far little attention. We use LSP to examine a relativistic electron beam (presumed generated from a laser plasma interaction) of legislated energy and angular distribution is injected into a 3D block of compressed DT. Collective effects will determine the stopping, most likely driven by magnetic field filamentation. The scaling of the stopping as a function of block density and temperature, as well as hot electron current and laser intensity is presented. Sub-grid models may be profitably used and degenerate effects included in the solution of this problem.

  14. An analysis of energy deposition in a tissue equivalent proportional counter onboard the space shuttle.

    PubMed

    Shinn, J L; Badhwar, G D; Xapsos, M A; Cucinotta, F A; Wilson, J W

    1999-02-01

    An improved prediction for space radiations in the lower earth orbits measured by the shuttle TEPC is obtained when energy loss straggling and chord length distribution of the detector are considered. A generalized analytic model is used to describe the energy deposition of direct ion interaction events in a micron-size detector. The transport calculation accounting for the shuttle configuration is accomplished by using a new version of HZETRN that has been extensively verified with laboratory and flight data. The agreement of predicted and measured lineal energy spectra is within 70% for the region above 2 keV/micrometer but within a factor of 2.3 underpredicted for the region below this value. The inclusion of indirect delta ray events in the model is needed before possible causes for the underprediction below 2 keV/micrometer can be assessed.

  15. Modeling Planetary Atmospheric Energy Deposition By Energetic Ions

    NASA Astrophysics Data System (ADS)

    Parkinson, Christopher; Bougher, Stephen; Gronoff, Guillaume; Barthelemy, Mathieu

    2016-07-01

    The structure, dynamics, chemistry, and evolution of planetary upper atmospheres are in large part determined by the available sources of energy. In addition to the solar EUV flux, the solar wind and solar energetic particle (SEP) events are also important sources. Both of these particle populations can significantly affect an atmosphere, causing atmospheric loss and driving chemical reactions. Attention has been paid to these sources from the standpoint of the radiation environment for humans and electronics, but little work has been done to evaluate their impact on planetary atmospheres. At unmagnetized planets or those with crustal field anomalies, in particular, the solar wind and SEPs of all energies have direct access to the atmosphere and so provide a more substantial energy source than at planets having protective global magnetic fields. Additionally, solar wind and energetic particle fluxes should be more significant for planets orbiting more active stars, such as is the case in the early history of the solar system for paleo-Venus and Mars. Therefore quantification of the atmospheric energy input from the solar wind and SEP events is an important component of our understanding of the processes that control their state and evolution. We have applied a full Lorentz motion particle transport model to study the effects of particle precipitation in the upper atmospheres of Mars and Venus. Such modeling has been previously done for Earth and Mars using a guiding center precipitation model. Currently, this code is only valid for particles with small gyroradii in strong uniform magnetic fields. There is a clear necessity for a Lorentz formulation, hence, a systematic study of the ionization, excitation, and energy deposition has been conducted, including a comparison of the influence relative to other energy sources (namely EUV photons). The result is a robust examination of the influence of energetic ion transport on the Venus and Mars upper atmosphere which

  16. Evaluation of energy deposition and secondary particle production in proton therapy of brain using a slab head phantom

    PubMed Central

    Jia, Sayyed Bijan; Hadizadeh, Mohammad Hadi; Mowlavi, Ali Asghar; Loushab, Mahdy Ebrahimi

    2014-01-01

    Aim Evaluation of energy deposition of protons in human brain and calculation of the secondary neutrons and photons produced by protons in proton therapy. Background Radiation therapy is one of the main methods of treating localized cancer tumors. The use of high energy proton beam in radiotherapy was proposed almost 60 years ago. In recent years, there has been a revival of interest in this subject in the context of radiation therapy. High energy protons suffer little angular deflection and have a well-defined penetration range, with a sharp increase in the energy loss at the end of their trajectories, namely the Bragg peak. Materials and methods A slab head phantom was used for the purpose of simulating proton therapy in brain tissue. In this study simulation was carried out using the Monte Carlo MCNPX code. Results By using mono energetic proton pencil beams, energy depositions in tissues, especially inside the brain, as well as estimating the neutron and photon production as a result of proton interactions in the body, together with their energy spectra, were calculated or obtained. The amount of energy escaped from the head by secondary neutrons and photons was determined. Conclusions It was found that for high energy proton beams the amount of escaped energy by neutrons is almost 10 times larger than that by photons. We estimated that at 110 MeV beam energy, the overall proton energy “leaked” from the head by secondary photons and neutrons to be around 1%. PMID:25337410

  17. Magnetic field effects on the energy deposition spectra of MV photon radiation.

    PubMed

    Kirkby, C; Stanescu, T; Fallone, B G

    2009-01-21

    Several groups worldwide have proposed various concepts for improving megavoltage (MV) radiotherapy that involve irradiating patients in the presence of a magnetic field-either for image guidance in the case of hybrid radiotherapy-MRI machines or for purposes of introducing tighter control over dose distributions. The presence of a magnetic field alters the trajectory of charged particles between interactions with the medium and thus has the potential to alter energy deposition patterns within a sub-cellular target volume. In this work, we use the MC radiation transport code PENELOPE with appropriate algorithms invoked to incorporate magnetic field deflections to investigate electron energy fluence in the presence of a uniform magnetic field and the energy deposition spectra within a 10 microm water sphere as a function of magnetic field strength. The simulations suggest only very minor changes to the electron fluence even for extremely strong magnetic fields. Further, calculations of the dose-averaged lineal energy indicate that a magnetic field strength of at least 70 T is required before beam quality will change by more than 2%.

  18. Absorbed dose calculations to blood and blood vessels for internally deposited radionuclides

    SciTech Connect

    Akabani, G. ); Poston, J.W. . Dept. of Nuclear Engineering)

    1991-05-01

    At present, absorbed dose calculations for radionuclides in the human circulatory system used relatively simple models and are restricted in their applications. To determine absorbed doses to the blood and to the surface of the blood vessel wall, EGS4 Monte Carlo calculations were performed. Absorbed doses were calculated for the blood and the blood vessel wall (lumen) for different blood vessels sizes. The radionuclides chosen for this study were those commonly used in nuclear medicine. No diffusion of the radionuclide into the blood vessel was assumed nor cross fire between vessel was assumed. Results are useful in assessing the dose in blood and blood vessel walls for different nuclear medicine procedures. 6 refs., 6 figs., 5 tabs.

  19. Absorbed dose calculations to blood and blood vessels for internally deposited radionuclides

    SciTech Connect

    Akabani, G.; Poston, J.W. Sr. )

    1991-05-01

    At present, absorbed dose calculations for radionuclides in the human circulatory system used relatively simple models and are restricted in their applications. To determine absorbed doses to the blood and to the surface of the blood vessel wall, EGS4 Monte Carlo calculations were performed. Absorbed doses were calculated for the blood and the blood vessel wall (lumen) for different blood vessels sizes. The radionuclides chosen for this study were those commonly used in nuclear medicine. No penetration of the radionuclide into the blood vessel was assumed nor was cross fire between the vessel assumed. The results are useful in assessing the dose to blood and blood vessel walls for different nuclear medicine procedures.

  20. Energy deposition rates by charged particles measured during the energy budget campaign

    NASA Technical Reports Server (NTRS)

    Urban, A.; Torkar, K. M.; Bjordal, J.; Lundblad, J. A.; Soraas, F.; Grandal, B.; Smith, L. G.; Ulwick, J. C.; Vancour, R. P.

    1982-01-01

    Measurements of the precipitation of electrons and positive ions (in the keV to MeV range) detected aboard eight rockets launched from Northern Scandinavia are reported together with corresponding satellite data. The downgoing integral fluxes indicate the temporal fluctuations during each flight. Height profiles of the energy deposition into the atmosphere at different levels of geomagnetic disturbance are given.

  1. Energy deposition and non-equilibrium infared radiation of energetic auroral electrons

    NASA Astrophysics Data System (ADS)

    Wu, Yadong; Gao, Bo; Zhu, Guangsheng; Li, Ziguang

    2016-07-01

    Infrared radiation caused by energetic auroral electrons plays an important role in the thermospheric hear budget, and may be seen as background by infrared surveillance sensors. The auroral electron deposition leads to the ionization, excitation, and dissociation of neutral species(N2,O2,and O), and initiates a series of chemical reaction in the upper atmosphere, finally causes the optical emission of infared excited emitters. In this study, the whole progress from the initial auroral electrons energy deposition to the final infrared emissions has been modeled, which including space plasma, atmospheric physical chemistry, and radiative transfer. The initial atmosphere parameters before auroral disturbing are given by MSIS00 model. The primary electron flux at the top of atmosphere is given by a statistical fitting with the sum of three distribution terms, a power law, a Maxwellian and a Guassian. A semi-emprical model is used in the calculation of energy depositon of single primary electron. The total integral ion pairs production rate is obtained after combining with the initial primary electron flux. The production rate and flux of secondary electrons are modeled with a continuous slow down approximation, using different excitation, ionization, dissociation cross sections of N2, O2, and O to electrons. The photochemical reactions with auroral disturbance is analysed, and its calculation model is established. A "three-step" calculation method is created to obtain number densities of eleven species in the hight between 90-160 km, which containing N2+, O2+, O+, O2+(a4Π), O+(2D), O+(2P), N2(A3Σ), N(2D), N(4S), NO+, and N+. Number densities of different vibraional levels of NO and NO+ are got with steady state assumption, considering 1-12 vibrational levels of NO and 1-14 vibrational levels of NO+. The infared emissions and the spectral lines of the two radiating bodies are calculated with a fuzzy model of spectral band.

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

    PubMed

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

    2016-06-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2016-02-01

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

  5. Local Measurement of Fuel Energy Deposition and Heat Transfer Environment During Fuel Lifetime Using Controlled Calorimetry

    SciTech Connect

    Don W. Miller; Andrew Kauffmann; Eric Kreidler; Dongxu Li; Hanying Liu; Daniel Mills; Thomas D. Radcliff; Joseph Talnagi

    2001-12-31

    A comprehensive description of the accomplishments of the DOE grant titled, ''Local Measurement of Fuel Energy Deposition and Heat Transfer Environment During Fuel Lifetime using Controlled Calorimetry''.

  6. Energy deposition and radiation quality of radon and radon daughters. Final report

    SciTech Connect

    Karam, L.R.; Caswell, R.S.

    1996-09-09

    This program was aimed at creating a quantitative physical description, at the micrometer and nanometer levels, of the physical interactions of the alpha particles from radon and its daughters with cells at risk in the bronchial epithelium. The authors calculated alpha-particle energy spectra incident upon the cells and also energy deposition spectra in micrometer- and nanometer-sized sites as a function of cell depth, site size, airway diameter, activities of {sup 218}Po and {sup 214}Po, and other parameters. These data are now being applied, using biophysical models of radiation effects, to predict cell killing, mutations, and cell transformation. The model predictions are then compared to experimental biophysical, biochemical, and biological information. These studies contribute to a detailed understanding of the mechanisms of the biological effectiveness of the radiations emitted by radon and its progeny.

  7. RF energy deposition in a heterogeneous model of man: near-field exposures

    SciTech Connect

    Stuchly, M.A.; Kraszewski, A.; Stuchly, S.S.; Hartsgrove, G.W.; Spiegel, R.J.

    1987-12-01

    The electric field strength was measured in a full-scale heterogeneous model of man exposed in the near field of resonant dipoles. The model was comprised of skull, spinal cord, rib cage, all other major bones, brain, lung, and muscle tissue. Electrical properties of these simulated tissues were the same as respective live tissue properties at test frequencies of 160, 350, and 915 MHz. The rates of energy absorption were calculated on the basis of the measured field strengths and tissue conductivities. Patterns of the energy deposition are compared for two orientations of the antennas with respect to the body. Also the results for the heterogeneous model are compared to data for homogeneous model having average tissue electrical properties.

  8. Vapor-deposited porous films for energy conversion

    DOEpatents

    Jankowski, Alan F.; Hayes, Jeffrey P.; Morse, Jeffrey D.

    2005-07-05

    Metallic films are grown with a "spongelike" morphology in the as-deposited condition using planar magnetron sputtering. The morphology of the deposit is characterized by metallic continuity in three dimensions with continuous and open porosity on the submicron scale. The stabilization of the spongelike morphology is found over a limited range of the sputter deposition parameters, that is, of working gas pressure and substrate temperature. This spongelike morphology is an extension of the features as generally represented in the classic zone models of growth for physical vapor deposits. Nickel coatings were deposited with working gas pressures up 4 Pa and for substrate temperatures up to 1000 K. The morphology of the deposits is examined in plan and in cross section views with scanning electron microscopy (SEM). The parametric range of gas pressure and substrate temperature (relative to absolute melt point) under which the spongelike metal deposits are produced appear universal for other metals including gold, silver, and aluminum.

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

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  11. 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.

  12. Halite depositional facies in a solar salt pond: A key to interpreting physical energy and water depth in ancient deposits?

    NASA Astrophysics Data System (ADS)

    Robertson Handford, C.

    1990-08-01

    Subaqueous deposits of aragonite, gypsum, and halite are accumulating in shallow solar salt ponds constructed in the Pekelmeer, a sea-level sauna on Bonaire, Netherlands Antilles. Several halite facies are deposited in the crystallizer ponds in response to differences in water depth and wave energy. Cumulate halite, which originates as floating rafts, is present only along the protected, upwind margins of ponds where low-energy conditions foster their formation and preservation. Cornet crystals with peculiar mushroom- and mortarboard-shaped caps precipitate in centimetre-deep brine sheets within a couple of metres of the upwind or low-energy margins. Downwind from these margins, cornet and chevron halite precipitate on the pond floors in water depths ranging from a few centimetres to ˜60 cm. Halite pisoids with radial-concentric structure are precipitated in the swash zone along downwind high-energy shorelines where they form pebbly beaches. This study suggests that primary halite facies are energy and/or depth dependent and that some primary features, if preserved in ancient halite deposits, can be used to infer physical energy conditions, subenvironments such as low- to high-energy shorelines, and extremely shallow water depths in ancient evaporite basins.

  13. Calculated concentrations of any radionuclide deposited on the ground by release from underground nuclear detonations, tests of nuclear rockets, and tests of nuclear ramjet engines

    SciTech Connect

    Hicks, H.G.

    1981-11-01

    This report presents calculated gamma radiation exposure rates and ground deposition of related radionuclides resulting from three types of event that deposited detectable radioactivity outside the Nevada Test Site complex, namely, underground nuclear detonations, tests of nuclear rocket engines and tests of nuclear ramjet engines.

  14. Calculation Of A Micro Discharge Energy Balance With PIC-MCC Method

    SciTech Connect

    Benstaali, W.; Belasri, A.; Hagelaar, G. J. M.; Boeuf, J. P.

    2008-09-23

    In this paper, we present a 1D Particle in Cell with Monte Carlo Collisions model, developed in order to calculate the energy balance in a micro-discharge, under conditions similar to those of a Plasma Display Panel (PDP) cell. The discharge takes place in a xenon-neon (10%-;90%) mixture at 560 torr and for a gap length of 100 {mu}m. The model is used to analyze in details the energy deposition during the discharge pulse. The results show the amount of energy dissipated by ions (collisions in the gas and on the cathode), by electrons (excitation of the different electronic states, ionization), and their variations with the applied voltage. This model will be used in the future to test the approximations of the fluid models which are generally used to optimize PDP operating conditions, and to check whether or not fluid models can correctly predict the trends in the variations of the energy balance with parameters such as voltage, pressure, gas mixture.

  15. Gold deposited on a Ge(0 0 1) surface: DFT calculations.

    PubMed

    Tsay, Shiow-Fon

    2016-11-01

    The atomic geometry, stability and electronic properties of self-organized Au induced nanowires on a Ge(0 0 1) surface are investigated based on the density-functional theory in the generalized gradient approximation and the stoichiometry of Au. According to the formation energy and the simulated STM image, the Ge atoms substituted by the Au atoms have been confirmed as occurring at a Au coverage lower than 0.25 Ml. The STM image with single and double dimer vacancies looks like the Au atoms have penetrated the subsurface. The energetically favorable dimer-row arrayed structures at 0.50 Ml and 0.75 Ml Au coverages have a 4  ×  1, 4  ×  2 or c(8  ×  2) transition symmetry, which comprise a flat Au-Au homodimer row and an alternating various buckling phase Ge-Ge or Au-Ge dimer row. The c(8  ×  2) zigzag-shaped protruding chains of shallow-groove STM images are highly consistent with the observations, but a long-range order dimer-row arrayed structure formation requires sufficient mobile energy to complete mass transport of the substituted Ge atoms in order to avoid the re-adsorption of these atoms; otherwise a deep-groove structure reconstruction is sequentially formed. A quasi-1D electron-like energy trough aligns in the direction perpendicular to the nanowire of the dimer-row arrayed structure in the c(8  ×  2) phase on a 0.75 Ml Au/Ge(0 0 1) surface, which is contributed by the Au-Ge dimer rows and the subsurface Ge atoms below them. The bottom energy of the energy trough is consistent with angle-resolved photo-emission spectroscopy studies (Schäfer et al 2008 Phys. Rev. Lett. 101 236802, Meyer et al 2011 Phys. Rev. B 83 121411(R)). PMID:27603175

  16. Gold deposited on a Ge(0 0 1) surface: DFT calculations

    NASA Astrophysics Data System (ADS)

    Tsay, Shiow-Fon

    2016-11-01

    The atomic geometry, stability and electronic properties of self-organized Au induced nanowires on a Ge(0 0 1) surface are investigated based on the density-functional theory in the generalized gradient approximation and the stoichiometry of Au. According to the formation energy and the simulated STM image, the Ge atoms substituted by the Au atoms have been confirmed as occurring at a Au coverage lower than 0.25 Ml. The STM image with single and double dimer vacancies looks like the Au atoms have penetrated the subsurface. The energetically favorable dimer-row arrayed structures at 0.50 Ml and 0.75 Ml Au coverages have a 4  ×  1, 4  ×  2 or c(8  ×  2) transition symmetry, which comprise a flat Au-Au homodimer row and an alternating various buckling phase Ge-Ge or Au-Ge dimer row. The c(8  ×  2) zigzag-shaped protruding chains of shallow-groove STM images are highly consistent with the observations, but a long-range order dimer-row arrayed structure formation requires sufficient mobile energy to complete mass transport of the substituted Ge atoms in order to avoid the re-adsorption of these atoms; otherwise a deep-groove structure reconstruction is sequentially formed. A quasi-1D electron-like energy trough aligns in the direction perpendicular to the nanowire of the dimer-row arrayed structure in the c(8  ×  2) phase on a 0.75 Ml Au/Ge(0 0 1) surface, which is contributed by the Au-Ge dimer rows and the subsurface Ge atoms below them. The bottom energy of the energy trough is consistent with angle-resolved photo-emission spectroscopy studies (Schäfer et al 2008 Phys. Rev. Lett. 101 236802, Meyer et al 2011 Phys. Rev. B 83 121411(R)).

  17. Deposition of dopant impurities and pulsed energy drive-in

    DOEpatents

    Wickboldt, P.; Carey, P.G.; Smith, P.M.; Ellingboe, A.R.

    1999-06-29

    A semiconductor doping process which enhances the dopant incorporation achievable using the Gas Immersion Laser Doping (GILD) technique is disclosed. The enhanced doping is achieved by first depositing a thin layer of dopant atoms on a semiconductor surface followed by exposure to one or more pulses from either a laser or an ion-beam which melt a portion of the semiconductor to a desired depth, thus causing the dopant atoms to be incorporated into the molten region. After the molten region recrystallizes the dopant atoms are electrically active. The dopant atoms are deposited by plasma enhanced chemical vapor deposition (PECVD) or other known deposition techniques. 2 figs.

  18. Deposition of dopant impurities and pulsed energy drive-in

    DOEpatents

    Wickboldt, Paul; Carey, Paul G.; Smith, Patrick M.; Ellingboe, Albert R.

    2008-01-01

    A semiconductor doping process which enhances the dopant incorporation achievable using the Gas Immersion Laser Doping (GILD) technique. The enhanced doping is achieved by first depositing a thin layer of dopant atoms on a semiconductor surface followed by exposure to one or more pulses from either a laser or an ion-beam which melt a portion of the semiconductor to a desired depth, thus causing the dopant atoms to be incorporated into the molten region. After the molten region recrystallizes the dopant atoms are electrically active. The dopant atoms are deposited by plasma enhanced chemical vapor deposition (PECVD) or other known deposition techniques.

  19. Deposition of dopant impurities and pulsed energy drive-in

    DOEpatents

    Wickboldt, Paul; Carey, Paul G.; Smith, Patrick M.; Ellingboe, Albert R.

    1999-01-01

    A semiconductor doping process which enhances the dopant incorporation achievable using the Gas Immersion Laser Doping (GILD) technique. The enhanced doping is achieved by first depositing a thin layer of dopant atoms on a semiconductor surface followed by exposure to one or more pulses from either a laser or an ion-beam which melt a portion of the semiconductor to a desired depth, thus causing the dopant atoms to be incorporated into the molten region. After the molten region recrystallizes the dopant atoms are electrically active. The dopant atoms are deposited by plasma enhanced chemical vapor deposition (PECVD) or other known deposition techniques.

  20. 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…

  1. Investigation of various energy deposition kernel refinements for the convolution/superposition method

    SciTech Connect

    Huang, Jessie Y.; Howell, Rebecca M.; Mirkovic, Dragan; Followill, David S.; Kry, Stephen F.; Eklund, David; Childress, Nathan L.

    2013-12-15

    Purpose: Several simplifications used in clinical implementations of the convolution/superposition (C/S) method, specifically, density scaling of water kernels for heterogeneous media and use of a single polyenergetic kernel, lead to dose calculation inaccuracies. Although these weaknesses of the C/S method are known, it is not well known which of these simplifications has the largest effect on dose calculation accuracy in clinical situations. The purpose of this study was to generate and characterize high-resolution, polyenergetic, and material-specific energy deposition kernels (EDKs), as well as to investigate the dosimetric impact of implementing spatially variant polyenergetic and material-specific kernels in a collapsed cone C/S algorithm.Methods: High-resolution, monoenergetic water EDKs and various material-specific EDKs were simulated using the EGSnrc Monte Carlo code. Polyenergetic kernels, reflecting the primary spectrum of a clinical 6 MV photon beam at different locations in a water phantom, were calculated for different depths, field sizes, and off-axis distances. To investigate the dosimetric impact of implementing spatially variant polyenergetic kernels, depth dose curves in water were calculated using two different implementations of the collapsed cone C/S method. The first method uses a single polyenergetic kernel, while the second method fully takes into account spectral changes in the convolution calculation. To investigate the dosimetric impact of implementing material-specific kernels, depth dose curves were calculated for a simplified titanium implant geometry using both a traditional C/S implementation that performs density scaling of water kernels and a novel implementation using material-specific kernels.Results: For our high-resolution kernels, we found good agreement with the Mackie et al. kernels, with some differences near the interaction site for low photon energies (<500 keV). For our spatially variant polyenergetic kernels, we found

  2. Ab initio atomistic thermodynamics calculations of the initial deposition of epitaxial MgO film on GaAs(001)-{beta}2(2 Multiplication-Sign 4)

    SciTech Connect

    Tamarany, Rizcky; Lee, Seung-Cheol; Kim, Hyung-Jun; Choi, Jung-Hae

    2013-02-07

    Ab initio calculations were performed to investigate the initial deposition of epitaxial MgO on GaAs(001)-{beta}2(2 Multiplication-Sign 4). The differences between the chemical bonding of Mg-As and O-As were characterized by the adsorption energies of atomic O and Mg at several symmetrically distinct sites, and O bonding was substantially stronger than that of Mg. Thermodynamics were analyzed through the introduction of environmental chemical potentials simulating in situ growth conditions by the sputtering of a stoichiometric MgO target. A surface phase diagram was generated under Mg and O environments with constrained equilibrium, and the results explained the initial formation of an epitaxial MgO phase on GaAs(001)-{beta}2(2 Multiplication-Sign 4).

  3. Evaluation of the mean energy deposit during the impact of charged particles on liquid water

    NASA Astrophysics Data System (ADS)

    Bernal, M. A.

    2012-04-01

    The DNA strand break yield due to the impact of ionizing particles on living beings is closely related to the number of inelastic events per unit absorbed dose produced by these particles. The higher this number, the higher the probability of causing DNA strand breaks per unit absorbed dose. In a previous work, it was found that the total number of events produced by primary particles and the secondary electrons is almost independent of the type and energy of the incident particle (or LET). This finding could be supported by a quasi-constant mean energy deposit by inelastic event (\\bar{\\varepsilon }). In this work, \\bar{\\varepsilon } was defined and determined for electrons and the non-negative charge states of hydrogen (H0, +) and helium (He0, +, 2 +) species impacting on liquid water. Ionization, excitation and charge transfer (up to two-electron transfers) processes have been included in present calculations. We found that, for liquid water, \\bar{\\varepsilon } is within 13.7 ± 4.1 eV, 14.2 ± 1.7 eV and 13.8 ± 1.4 eV for electrons, hydrogen and helium species, respectively, with impact energies changing over three orders of magnitude. Unlike the mean excitation energy, the mean energy deposit per inelastic event depends not only on the target molecule but also on the projectile features. However, this dependence is relatively weak. This fact supports the quasi-independent number of inelastic events per unit absorbed dose found previously when charged particles impact on matter.

  4. Use of energy deposition spectrometer Liulin for individual monitoring of aircrew.

    PubMed

    Ploc, O; Pachnerová Brabcová, K; Spurny, F; Malušek, A; Dachev, T

    2011-03-01

    Silicon energy deposition spectrometer Liulin was primarily developed for cosmic radiation monitoring onboard spacecrafts. Nowadays, Liulin type detectors are also used to characterise radiation field on board aircraft, at alpine observatories and behind the shielding of heavy ion accelerators. In this work, experiments and calibrations performed in these radiation fields are presented and the method developed for calculation of ambient dose equivalent H*(10) on board aircraft is described. Since 2001, a simple method employing the energy deposition spectra had been used to determine H*(10) on board aircraft but, in 2004, it became clear that the resulting values were strongly biased at locations close to Earth's equator. An improved method for the determination of H*(10) on board aircraft using the Liulin detector was developed. It took into account the composition of the radiation field via the ratio of absorbed doses D(low) and D(neut) reflecting the contributions from low-LET particles and neutrons, respectively. It resulted in much better agreement with the EPCARD computer code for all aircraft locations; relative differences were within 11 % for low-LET and 20 % for neutron components of H*(10).

  5. Benchmark study for charge deposition by high energy electrons in thick slabs

    NASA Technical Reports Server (NTRS)

    Jun, I.

    2002-01-01

    The charge deposition profiles created when highenergy (1, 10, and 100 MeV) electrons impinge ona thick slab of elemental aluminum, copper, andtungsten are presented in this paper. The chargedeposition profiles were computed using existing representative Monte Carlo codes: TIGER3.0 (1D module of ITS3.0) and MCNP version 4B. The results showed that TIGER3.0 and MCNP4B agree very well (within 20% of each other) in the majority of the problem geometry. The TIGER results were considered to be accurate based on previous studies. Thus, it was demonstrated that MCNP, with its powerful geometry capability and flexible source and tally options, could be used in calculations of electron charging in high energy electron-rich space radiation environments.

  6. Track structure simulations at relativistic energies: an update on cross section calculations

    NASA Astrophysics Data System (ADS)

    Dingfelder, Michael

    Charged particle track structure simulations follow the primary, as well as all (produced) sec-ondary particles in an event-by-event matter, from starting or ejection energies down to total stopping. They provide detailed information on the spacial distributions of energy depositions, interaction types, and radical species produced. These quantities provide a starting point to describe the interaction of the radiation with matter of biological interest and to explore and estimate the effects of radiation quality on various biological responses of these systems. Of special interest is liquid water which serves as surrogate for soft tissue. Ionization and excitation cross sections for bare charged particles can be calculated within the framework of the (relativistic) plane-wave Born approximation or the (relativistic) Bethe approximation. Both theories rely on a realistic model of the dielectric response function of the material under consideration and need to address relativistic medium polarization effects like the Fermi-density effect in a consistent way. In this talk we will review and present new and updated aspects of charged particle cross section calculations for relativistic heavy ions with liquid water and other materials of biological interest. This includes an updated model for the dielectric response function of liquid water to better reflect new data from inelastic X-ray scattering (IXS) experiments using synchrotron radiation and a model for the dielectric response function of calcium, which serves as a bone surrogate. We will also discuss the implementation of relativistic effect, especially of the Fermi-density effect into the cross section calculations. This work is supported by the National Aeronautics and Space Administration (NASA), grant no. NNJ04HF39G.

  7. CALCULATION OF GAMMA SPECTRA IN A PLASTIC SCINTILLATOR FOR ENERGY CALIBRATIONAND DOSE COMPUTATION.

    PubMed

    Kim, Chankyu; Yoo, Hyunjun; Kim, Yewon; Moon, Myungkook; Kim, Jong Yul; Kang, Dong Uk; Lee, Daehee; Kim, Myung Soo; Cho, Minsik; Lee, Eunjoong; Cho, Gyuseong

    2016-09-01

    Plastic scintillation detectors have practical advantages in the field of dosimetry. Energy calibration of measured gamma spectra is important for dose computation, but it is not simple in the plastic scintillators because of their different characteristics and a finite resolution. In this study, the gamma spectra in a polystyrene scintillator were calculated for the energy calibration and dose computation. Based on the relationship between the energy resolution and estimated energy broadening effect in the calculated spectra, the gamma spectra were simply calculated without many iterations. The calculated spectra were in agreement with the calculation by an existing method and measurements. PMID:27127208

  8. Energy Deposition onto an Asteroid or Comet Nucleus from a Nuclear Burst

    NASA Astrophysics Data System (ADS)

    Plesko, C. S.; Weaver, R.; Huebner, W. F.

    2010-12-01

    There is substantial controversy about the potential use and efficacy of a nuclear burst for the prevention of an impact of an asteroid or cometary nucleus on the Earth. Previous papers (e.g. Holsapple 2004) have called for a more careful analysis of the physics of this process, specifically energy deposition and internal shock processes. We begin to explore this question quantitatively by modeling the deposition of energy onto materials relevant to cosmic objects from a simulated nuclear burst. We use Los Alamos National Laboratory (LANL) particle transport codes and cross-section libraries to explore the deposition of neutrons and gamma rays onto various targets. We also use LANL radiation hydrocodes, tabular equations of state and opacities to study the deposition of x-ray energy within the material. We will report the amount and spatial distribution of energy deposition and the effects of burst height, target material variation, and mesh resolution on the simulation results.

  9. Dayside pickup oxygen ion precipitation at Venus and Mars: Spatial distributions, energy deposition and consequences

    SciTech Connect

    Luhmann, J.G. ); Kozyra, J.U. )

    1991-04-01

    The fluxes and energy spectra of picked-up planetary O{sup +} ions incident on the dayside atmospheres of Venus and Mars are calculated using the neutral exposure models of Nagy and Cravens (1988) and the Spreiter and Stahara (1980) gasdynamic model of the magnetosheath electric and magnetic field. Cold ({approximately}10 eV) O{sup +} ions are launched from hemispherical grids of starting points covering the daysides of the planets and their trajectories are followed until they either impact the dayside obstacle or cross the terminator plane. The impacting, or precipitating, ion fluxes are weighted according to the altitude of the hemispherical starting point grid in a manner consistent with the exosphere density models and the local photoion production rate. Maps of precipitating ion number flux and energy flux show the asymmetrical distribution of dayside energy deposition expected from this source which is unique to the weakly magnetized planets. Although the associated heating of the atmosphere and ionsphere is found to be negligible compared to that from the usual sources, backscattered or sputtered neutral oxygen atoms are produced at energies exceeding that needed for escape from the gravitational fields of both planets. These neutral winds, driven by pickup ion precipitation, represent a possibly significant loss of atmospheric constituents over the age of the solar system.

  10. Monte Carlo approach to the spatial deposition of energy by electrons in molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Heaps, M. G.; Green, A. E. S.

    1974-01-01

    The Monte Carlo (MC) and continuous slowdown approximation (CSDA) approaches to the spatial deposition of energy by electrons are compared using the same detailed atomic cross section (DACS). It is found that the CSDA method overestimates the amount of energy that is deposited near the end of the path for electrons above a few hundred electron volts. The MC results are in approximate agreement with experimental data in such a way as to be relatively independent of the actual gas used. Our MC results are extended to obtain the three-dimensional deposition of energy by sub-keV electrons in molecular hydrogen.

  11. Is it Possible that the Solar Corona Temperature Profile Does Not Require Mechanical Deposition of Energy?

    NASA Astrophysics Data System (ADS)

    Scudder, J. D.; Roytershteyn, V.; Karimabadi, H.; Daughton, W. S.

    2012-12-01

    The solar corona, like other main sequence stars, has a non-monotonic temperature inversion. Prevailing ideas have suggested that the inversion is the result of deposition of mechanical energy near the temperature maximum, possibly afforded by the damping of wave trains. The adequacy of ones quantitative description of heat flow in the corona plays a central role in the association of non-monotonic profile and a heating requirement. Using first principles calculations we demonstrate that neither the size nor the direction of the heat flow in the corona is implied by knowing the temperature profile. The usually used Spitzer-Braginskii transport is not appropriate for the solar corona, but has until now been used to infer the sign of the heat flow divergence at the temperature maximum. By vacating the certainty of heat flow diverging from the coronal temperature maximum there is no immediate connection between the non-monotonic temperature profile and the need for energy or momentum addition to the corona at the temperature maximum. Thus the coronal problem is to explain the temperature profile, not necessarily produce an energy deposition, predicted by a broken transport description. The same argument that shows that Spitzer-Braginskii transport is inadequate also implies that the underlying kinetic state of the plasma is non-local and will be permeated by non-thermal distributions. Such non-thermal distributions are a necessary prerequisite for the alternate velocity filtration model that explains the non-monotonic temperature profile of the solar corona as well as all stars on the zero age main sequence.

  12. Multiscale modeling approach for calculating grain-boundary energies from first principles

    SciTech Connect

    Shenderova, O.A.; Brenner, D.W.; Nazarov, A.A.; Romanov, A.E.; Yang, L.H.

    1998-02-01

    A multiscale modeling approach is proposed for calculating energies of tilt-grain boundaries in covalent materials from first principles over an entire misorientation range for given tilt axes. The method uses energies from density-functional calculations for a few key structures as input into a disclination structural-units model. This approach is demonstrated by calculating energies of {l_angle}001{r_angle}-symmetrical tilt-grain boundaries in diamond. {copyright} {ital 1998} {ital The American Physical Society}

  13. A Simplified Confinement Method (SCM) for Calculating Absolute Free Energies and Free Energy and Entropy Differences

    PubMed Central

    Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin

    2013-01-01

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

  14. SU-E-T-78: Comparison of Dose-Averaged Linear Energy Transfer Calculation Methods Used in Monte Carlo Simulations of Clinical Proton Beams

    SciTech Connect

    Cortes-Giraldo, M A; Carabe-Fernandez, A

    2014-06-01

    Purpose: To evaluate the differences in dose-averaged linear energy transfer (LETd) maps calculated in water by means of different strategies found in the literature in proton therapy Monte Carlo simulations and to compare their values with dose-mean lineal energy microdosimetry calculations. Methods: The Geant4 toolkit (version 9.6.2) was used. Dose and LETd maps in water were scored for primary protons with cylindrical voxels defined around the beam axis. Three LETd calculation methods were implemented. First, the LETd values were computed by calculating the unrestricted linear energy transfer (LET) associated to each single step weighted by the energy deposition (including delta-rays) along the step. Second, the LETd was obtained for each voxel by computing the LET along all the steps simulated for each proton track within the voxel, weighted by the energy deposition of those steps. Third, the LETd was scored as the quotient between the second momentum of the LET distribution, calculated per proton track, over the first momentum. These calculations were made with various voxel thicknesses (0.2 – 2.0 mm) for a 160 MeV proton beamlet and spread-out Bragg Peaks (SOBP). The dose-mean lineal energy was calculated in a uniformly-irradiated water sphere, 0.005 mm radius. Results: The value of the LETd changed systematically with the voxel thickness due to delta-ray emission and the enlargement of the LET distribution spread, especially at shallow depths. Differences of up to a factor 1.8 were found at the depth of maximum dose, leading to similar differences at the central and distal depths of the SOBPs. The third LETd calculation method gave better agreement with microdosimetry calculations around the Bragg Peak. Conclusion: Significant differences were found between LETd map Monte Carlo calculations due to both the calculation strategy and the voxel thickness used. This could have a significant impact in radiobiologically-optimized proton therapy treatments.

  15. 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.

  16. Sensitivity of methods for calculating energy expenditure by use of doubly labeled water

    SciTech Connect

    Seale, J.; Miles, C.; Bodwell, C.E.

    1989-02-01

    Attempts to estimate human energy expenditure by use of doubly labeled water have produced three methods currently used for calculating carbon dioxide production from isotope disappearance data: (1) the two-point method, (2) the regression method, and (3) the integration method. An ideal data set was used to determine the error produced in the calculated energy expenditure for each method when specific variables were perturbed. The analysis indicates that some of the calculation methods are more susceptible to perturbations in certain variables than others. Results from an experiment on one adult human subject are used to illustrate the potential for error in actual data. Samples of second void urine, 24-h urine, and breath collected every other day for 21 days are used to calculate the average daily energy expenditure by three calculation methods. The difference between calculated energy expenditure and metabolizable energy on a weight-maintenance diet is used to estimate the error associated with the doubly labeled water method.

  17. Comparisons of calculated respiratory tract deposition of particles based on the NCRP/ITRI model and the new ICRP66 model

    SciTech Connect

    Yeh, Hsu-Chi; Phalen, R.F.; Chang, I.

    1995-12-01

    The National Council on Radiation Protection and Measurements (NCRP) in the United States and the International Commission on Radiological Protection (ICRP) have been independently reviewing and revising respiratory tract dosimetry models for inhaled radioactive aerosols. The newly proposed NCRP respiratory tract dosimetry model represents a significant change in philosophy from the old ICRP Task Group model. The proposed NCRP model describes respiratory tract deposition, clearance, and dosimetry for radioactive substances inhaled by workers and the general public and is expected to be published soon. In support of the NCRP proposed model, ITRI staff members have been developing computer software. Although this software is still incomplete, the deposition portion has been completed and can be used to calculate inhaled particle deposition within the respiratory tract for particle sizes as small as radon and radon progeny ({approximately} 1 nm) to particles larger than 100 {mu}m. Recently, ICRP published their new dosimetric model for the respiratory tract, ICRP66. Based on ICRP66, the National Radiological Protection Board of the UK developed PC-based software, LUDEP, for calculating particle deposition and internal doses. The purpose of this report is to compare the calculated respiratory tract deposition of particles using the NCRP/ITRI model and the ICRP66 model, under the same particle size distribution and breathing conditions. In summary, the general trends of the deposition curves for the two models were similar.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Horn, Paul R.; Head-Gordon, Martin

    2016-02-01

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

  20. The role of Energy Deposition in the Epitaxial Layer in Triggering SEGR in Power MOSFETs

    NASA Technical Reports Server (NTRS)

    Selva, L.; Swift, G.; Taylor, W.; Edmonds, L.

    1999-01-01

    In these SEGR experiments, three identical-oxide MOSFET types were irradiated with six ions of significantly different ranges. Results show the prime importance of the total energy deposited in the epitaxial layer.

  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. Suprathermal electron energy deposition in plasmas with the Fokker-Planck method

    SciTech Connect

    Wienke, B.R.

    1983-08-01

    A one-dimensional, multigroup, discrete-ordinates technique for computing electron energy deposition in plasmas is detailed. The Fokker-Planck collision operator is employed in the continuous approximation and electric fields (considered external) are included in the equation. Bremsstrahlung processes are not treated. Comparisons with analytic and Monte Carlo results are given. Fits to deposition and energy scaling are proposed and discussed for monoenergetic and Maxwellian sources in the rnge 0--150 keV, with and without uniform fields.

  3. Cell to Cell Variability of Radiation-Induced Foci: Relation between Observed Damage and Energy Deposition.

    PubMed

    Gruel, Gaëtan; Villagrasa, Carmen; Voisin, Pascale; Clairand, Isabelle; Benderitter, Marc; Bottollier-Depois, Jean-François; Barquinero, Joan Francesc

    2016-01-01

    Most studies that aim to understand the interactions between different types of photon radiation and cellular DNA assume homogeneous cell irradiation, with all cells receiving the same amount of energy. The level of DNA damage is therefore generally determined by averaging it over the entire population of exposed cells. However, evaluating the molecular consequences of a stochastic phenomenon such as energy deposition of ionizing radiation by measuring only an average effect may not be sufficient for understanding some aspects of the cellular response to this radiation. The variance among the cells associated with this average effect may also be important for the behaviour of irradiated tissue. In this study, we accurately estimated the distribution of the number of radiation-induced γH2AX foci (RIF) per cell nucleus in a large population of endothelial cells exposed to 3 macroscopic doses of gamma rays from 60Co. The number of RIF varied significantly and reproducibly from cell to cell, with its relative standard deviation ranging from 36% to 18% depending on the macroscopic dose delivered. Interestingly, this relative cell-to-cell variability increased as the dose decreased, contrary to the mean RIF count per cell. This result shows that the dose effect, in terms of the number of DNA lesions indicated by RIF is not as simple as a purely proportional relation in which relative SD is constant with dose. To analyse the origins of this observed variability, we calculated the spread of the specific energy distribution for the different target volumes and subvolumes in which RIF can be generated. Variances, standard deviations and relative standard deviations all changed similarly from dose to dose for biological and calculated microdosimetric values. This similarity is an important argument that supports the hypothesis of the conservation of the association between the number of RIF per nucleus and the specific energy per DNA molecule. This comparison allowed us to

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

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    2015-03-01

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

  5. Variational Approach to Enhanced Sampling and Free Energy Calculations

    NASA Astrophysics Data System (ADS)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

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

  6. Monte Carlo investigations of distance-dependent effects on energy deposition in K-shell x-ray fluorescence bone lead measurement.

    PubMed

    Ahmed, Naseer; Fleming, David E B; O'Meara, Joanne M

    2004-09-01

    Radiation energy deposition results are presented from a Monte Carlo code simulating the lower part of a leg during an in vivo 109Cd K-shell x-ray fluorescence (KXRF) bone lead measurement. The simulations were run for a leg phantom model representing an adult subject, assuming concentrations of 10 microg Pb per gram bone mineral and tracing 500 million photons in each simulation. Trials were performed over a range (0.5-6.0 cm) of source-to-sample (S-S) distances. Energies deposited due to Compton and photoelectric processes occurring in the bone and the soft tissue were obtained. The data show an increase in the amount of energy deposited in the bone as the sample is moved closer to the source (from 2.0 cm to 0.5 cm). However, there is a decrease in the amount of energy deposited in the soft tissue as the sample is moved closer to the source over the same distance interval. In decreasing the S-S distance from 2.0 cm to 0.5 cm, the amount of energy deposited in the sample as a whole was found to increase by 11%. By calculating the energy deposition in the bone and in the soft tissue as a fraction of the total energy deposited in the sample, the corresponding changes are quantified as a function of S-S distance. Similarly, the proportions of energy deposited via the photoelectric effect and Compton scattering are presented as a function of S-S distance.

  7. Energy deposition studies for the high-luminosity Large Hadron Collider inner triplet magnets

    NASA Astrophysics Data System (ADS)

    Mokhov, N. V.; Rakhno, I. L.; Tropin, I. S.; Cerutti, F.; Esposito, L. S.; Lechner, A.

    2015-05-01

    A detailed model of the high-luminosity LHC inner triplet region with new large-aperture Nb3Sn magnets, field maps, corrector packages, and segmented tungsten inner absorbers was built and implemented into the fluka and mars15 codes. Detailed simulations have been performed coherently with the codes on the impact of particle debris from the 14-TeV center-of-mass pp-collisions on the short- and long-term stability of the inner triplet magnets. After optimizing the absorber configuration, the peak power density averaged over the magnet inner cable width is found to be safely below the quench limit at the luminosity of 5 ×1034 cm-2 s-1 . For the anticipated lifetime integrated luminosity of 3000 fb-1 , the peak dose calculated for the innermost magnet insulator ranges from 20 to 35 MGy, a figure close to the commonly accepted limit. Dynamic heat loads to the triplet magnet cold mass are calculated to evaluate the cryogenic capability. fluka and mars results on energy deposition are in very good agreement.

  8. Laser energy deposition and its dynamic uniformity for direct-drive capsules

    SciTech Connect

    Xu, Yan; Wu, SiZhong; Zheng, WuDi

    2015-04-15

    The total laser energy deposition of multi-laser-beam irradiation is not only associated with the dynamic behavior of capsule but also the time-dependent angular distribution of the energy deposition of each beam around its axis. The dynamic behavior of laser energy deposition does not linearly respond to the dynamic behavior of laser irradiation. The laser energy deposition uniformity determines the symmetry of implosion. The dynamic behavior of laser energy deposition non-uniformity in OMEGA for laser with square beam shape intensity profile is investigated. In the case of smaller laser spot, the initial non-uniformity caused by laser beam overlap is very high. The shell asymmetry caused by the high initial laser irradiation non-uniformity is estimated by the extent of distortion of shock front which is not as severe as expected before the shock driven by main pulse arrives. This suggests that the large initial non-uniformity due to smaller laser spot is one of the elements that seed disturbance before the main pulse. The rms of laser energy deposition during the main pulse remains above 2%. Since the intensity of main driving pulse usually is several times higher than that of picket pulses, the non-uniformity in main pulse period may jeopardize the symmetrical implosion. When dynamic behavior of capsule is considered, the influence of beam pointing error, the target positioning error, and beam-to-beam power unbalance is quite different for the case of static capsule.

  9. Energy deposition characteristics of nanosecond dielectric barrier discharge plasma actuators: Influence of dielectric material

    NASA Astrophysics Data System (ADS)

    Correale, G.; Winkel, R.; Kotsonis, M.

    2015-08-01

    An experimental study aimed at the characterization of energy deposition of nanosecond Dielectric Barrier Discharge (ns-DBD) plasma actuators was carried out. Special attention was given on the effect of the thickness and material used for dielectric barrier. The selected materials for this study were polyimide film (Kapton), polyamide based nylon (PA2200), and silicone rubber. Schlieren measurements were carried out in quiescent air conditions in order to observe density gradients induced by energy deposited. Size of heated area was used to qualify the energy deposition coupled with electrical power measurements performed using the back-current shunt technique. Additionally, light intensity measurements showed a different nature of discharge based upon the material used for barrier, for a fixed thickness and frequency of discharge. Finally, a characterisation study was performed for the three tested materials. Dielectric constant, volume resistivity, and thermal conductivity were measured. Strong trends between the control parameters and the energy deposited into the fluid during the discharge were observed. Results indicate that efficiency of energy deposition mechanism relative to the thickness of the barrier strongly depends upon the material used for the dielectric barrier itself. In general, a high dielectric strength and a low volumetric resistivity are preferred for a barrier, together with a high heat capacitance and a low thermal conductivity coefficient in order to maximize the efficiency of the thermal energy deposition induced by an ns-DBD plasma actuator.

  10. Stabilizing laser energy density on a target during pulsed laser deposition of thin films

    DOEpatents

    Dowden, Paul C.; Jia, Quanxi

    2016-05-31

    A process for stabilizing laser energy density on a target surface during pulsed laser deposition of thin films controls the focused laser spot on the target. The process involves imaging an image-aperture positioned in the beamline. This eliminates changes in the beam dimensions of the laser. A continuously variable attenuator located in between the output of the laser and the imaged image-aperture adjusts the energy to a desired level by running the laser in a "constant voltage" mode. The process provides reproducibility and controllability for deposition of electronic thin films by pulsed laser deposition.

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

    SciTech Connect

    Candy, J.

    2013-08-15

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

  12. Advancing QCD-based calculations of energy loss

    NASA Astrophysics Data System (ADS)

    Tywoniuk, Konrad

    2013-08-01

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

  13. 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.

  14. Biological characterization of low-energy ions with high-energy deposition on human cells.

    PubMed

    Saha, Janapriya; Wilson, Paul; Thieberger, Peter; Lowenstein, Derek; Wang, Minli; Cucinotta, Francis A

    2014-09-01

    During space travel, astronauts are exposed to cosmic radiation that is comprised of high-energy nuclear particles. Cancer patients are also exposed to high-energy nuclear particles when treated with proton and carbon beams. Nuclear interactions from high-energy particles traversing shielding materials and tissue produce low-energy (<10 MeV/n) secondary particles of high-LET that contribute significantly to overall radiation exposures. Track structure theories suggest that high charge and energy (HZE) particles and low-energy secondary ions of similar LET will have distinct biological effects for cellular and tissue damage endpoints. We investigated the biological effects of low-energy ions of high LET utilizing the Tandem Van de Graaff accelerator at the Brookhaven National Laboratory (BNL), and compared these to experiments with HZE particles, that mimic the space environment produced at NASA Space Radiation Laboratory (NSRL) at BNL. Immunostaining for DNA damage response proteins was carried out after irradiation with 5.6 MeV/n boron (LET 205 keV/μm), 5.3 MeV/n silicon (LET 1241 keV/μm), 600 MeV/n Fe (LET 180 keV/μm) and 77 MeV/n oxygen (LET 58 keV/μm) particles. Low-energy ions caused more persistent DNA damage response (DDR) protein foci in irradiated human fibroblasts and esophageal epithelial cells compared to HZE particles. More detailed studies comparing boron ions to Fe particles, showed that boron-ion radiation resulted in a stronger G2 delay compared to Fe-particle exposure, and boron ions also showed an early recruitment of Rad51 at double-strand break (DSB) sites, which suggests a preference of homologous recombination for DSB repair in low-energy albeit high-LET particles. Our experiments suggest that the very high-energy radiation deposition by low-energy ions, representative of galactic cosmic radiation and solar particle event secondary radiation, generates massive but localized DNA damage leading to delayed DSB repair, and distinct cellular

  15. Biological characterization of low-energy ions with high-energy deposition on human cells.

    PubMed

    Saha, Janapriya; Wilson, Paul; Thieberger, Peter; Lowenstein, Derek; Wang, Minli; Cucinotta, Francis A

    2014-09-01

    During space travel, astronauts are exposed to cosmic radiation that is comprised of high-energy nuclear particles. Cancer patients are also exposed to high-energy nuclear particles when treated with proton and carbon beams. Nuclear interactions from high-energy particles traversing shielding materials and tissue produce low-energy (<10 MeV/n) secondary particles of high-LET that contribute significantly to overall radiation exposures. Track structure theories suggest that high charge and energy (HZE) particles and low-energy secondary ions of similar LET will have distinct biological effects for cellular and tissue damage endpoints. We investigated the biological effects of low-energy ions of high LET utilizing the Tandem Van de Graaff accelerator at the Brookhaven National Laboratory (BNL), and compared these to experiments with HZE particles, that mimic the space environment produced at NASA Space Radiation Laboratory (NSRL) at BNL. Immunostaining for DNA damage response proteins was carried out after irradiation with 5.6 MeV/n boron (LET 205 keV/μm), 5.3 MeV/n silicon (LET 1241 keV/μm), 600 MeV/n Fe (LET 180 keV/μm) and 77 MeV/n oxygen (LET 58 keV/μm) particles. Low-energy ions caused more persistent DNA damage response (DDR) protein foci in irradiated human fibroblasts and esophageal epithelial cells compared to HZE particles. More detailed studies comparing boron ions to Fe particles, showed that boron-ion radiation resulted in a stronger G2 delay compared to Fe-particle exposure, and boron ions also showed an early recruitment of Rad51 at double-strand break (DSB) sites, which suggests a preference of homologous recombination for DSB repair in low-energy albeit high-LET particles. Our experiments suggest that the very high-energy radiation deposition by low-energy ions, representative of galactic cosmic radiation and solar particle event secondary radiation, generates massive but localized DNA damage leading to delayed DSB repair, and distinct cellular

  16. 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.

  17. 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.

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

    SciTech Connect

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

    2009-05-28

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

  19. 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.

  20. Quantitation of absorbed or deposited materials on a substrate that measures energy deposition

    DOEpatents

    Grant, Patrick G.; Bakajin, Olgica; Vogel, John S.; Bench, Graham

    2005-01-18

    This invention provides a system and method for measuring an energy differential that correlates to quantitative measurement of an amount mass of an applied localized material. Such a system and method remains compatible with other methods of analysis, such as, for example, quantitating the elemental or isotopic content, identifying the material, or using the material in biochemical analysis.

  1. Energy deposition issues at 8 GeV H- beam collimation and injection to the Fermilab Main Injector

    SciTech Connect

    Drozhdin, A.I.; Kostin, M.A.; Mokhov, N.V.; /Fermilab

    2005-05-01

    The energy deposition and radiation issues at 8 GeV h{sup -} beam collimation in the beam transfer line and at stripping injection to the Fermilab Main Injector (MI) are analyzed. Detailed calculations with the STRUCT [1] and MARS15 [2] codes are performed on heating of collimators and stripping foils, as well as on accelerator elements radioactivation at normal operation. Extraction of the unstripped part of the beam to the external beam dump and loss of the excited-state H{sup 0} atoms in MI are also studied.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

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

    2008-05-21

    ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort. PMID:18500853

  4. Calculation of resonance energy transfer in crowded biological membranes.

    PubMed

    Zimet, D B; Thevenin, B J; Verkman, A S; Shohet, S B; Abney, J R

    1995-04-01

    Analytical and numerical models were developed to describe fluorescence resonance energy transfer (RET) in crowded biological membranes. It was assumed that fluorescent donors were linked to membrane proteins and that acceptors were linked to membrane lipids. No restrictions were placed on the location of the donor within the protein or the partitioning of acceptors between the two leaflets of the bilayer; however, acceptors were excluded from the area occupied by proteins. Analytical equations were derived that give the average quantum yield of a donor at low protein concentrations. Monte Carlo simulations were used to generate protein and lipid distributions that were linked numerically with RET equations to determine the average quantum yield and the distribution of donor fluorescence lifetimes at high protein concentrations, up to 50% area fraction. The Monte Carlo results show such crowding always reduces the quantum yield, probably because crowding increases acceptor concentrations near donor-bearing proteins; the magnitude of the reduction increases monotonically with protein concentration. The Monte Carlo results also show that the distribution of fluorescence lifetimes can differ markedly, even for systems possessing the same average lifetime. The dependence of energy transfer on acceptor concentration, protein radius, donor position within the protein, and the fraction of acceptors in each leaflet was also examined. The model and results are directly applicable to the analysis of RET data obtained from biological membranes; their application should result in a more complete and accurate determination of the structures of membrane components. PMID:7787045

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

  6. Influence of the Presence of Tissue Expanders on Energy Deposition for Post-Mastectomy Radiotherapy

    PubMed Central

    Trombetta, Débora M.; Cardoso, Simone C.; Facure, Alessandro; da Silva, Ademir X.; da Rosa, Luiz Antonio R.

    2013-01-01

    An increasing number of studies have shown that post-mastectomy radiotherapy presents benefits associated with the patients survival and a significant fraction of the treated patients makes use of tissue expanders for breast reconstruction. Some models of tissue expanders have a magnetic disk on their surface that constitutes heterogeneity in the radiation field, which can affect the dose distribution during the radiotherapy treatment. In this study, the influence of a metallic heterogeneity positioned in a breast tissue expander was evaluated by means of Monte Carlo simulations using the MCNPX code and using Eclipse treatment planning system. Deposited energy values were calculated in structures which have clinical importance for the treatment. Additionally, the effect in the absorbed energy due to backscattering and attenuation of the incident beam caused by the heterogeneity, as well as due to the expansion of the prosthesis, was evaluated in target structures for a 6 MV photon beam by simulations. The dose distributions for a breast treatment were calculated using a convolution/superposition algorithm from the Eclipse treatment planning system. When compared with the smallest breast expander volume, underdosage of 7% was found for the largest volume of breast implant, in the case of frontal irradiation of the chest wall, by Monte Carlo simulations. No significant changes were found in dose distributions for the presence of the heterogeneity during the treatment planning of irradiation with an opposed pair of beams. Even considering the limitation of the treatment planning system, the results obtained with its use confirm those ones found by Monte Carlo simulations for a tangent beam irradiation. The presence of a heterogeneity didńt alters the dose distributions on treatment structures. The underdosage of 7% observed with Monte Carlo simulations were found for irradiation at 0°, not used frequently in a clinical routine. PMID:23405149

  7. ECOSYS-87: model calculations of the activity in cattle meat related to deposition time and feeding regimes after a nuclear fallout.

    PubMed

    Riesen, T K; Gottofrey, J; Heiz, H J; Schenker-Wicki, A

    1996-12-01

    The radioecological model ECOSYS-87 was used to evaluate the effect of countermeasures for reducing the ingestion dose by eating cattle meat after an accidental release of radioactive material. Calculations were performed using a database adapted to Swiss conditions for the case that (1) contaminated grass or hay is replaced by clean fodder; (2) the last 100 days before slaughter, taking place one year after an accident, only uncontaminated fodder is given; and (3) alternative feeding regimes are chosen. Seasonal effects were considered by doing all calculations for a deposition at each month of the year. Feeding uncontaminated forage 100 d before slaughter (case 2) proved to be the most effective countermeasure and reduced the integrated activity in meat by 90% to 99%. The effect of replacing contaminated grass (case 1) was less uniform and depended strongly on the time a deposition occurred. In this case the reduction was between 50% and 100% one year after deposition. The substitution of contaminated hay (case 1) was less effective compared to the substitution of grass. The choice of alternative feeding regimes (case 3) led to a reduction of the integrated activity of up to 40% one year after deposition. The present model calculations clearly reveal the importance of the seasonality and demonstrate the usefulness of such calculations as a basis for generating countermeasures in decision support systems. PMID:8919069

  8. ECOSYS-87: Model calculations of the activity in cattle meat related to deposition time and feeding regimes after a nuclear fallout

    SciTech Connect

    Riesen, T.K.; Gottofrey, J.; Heiz, H.J.; Schenker-Wicki, A.

    1996-12-01

    The radioecological model ECOSYS087 was used to evaluate the effect of countermeasures for reducing the ingestion dose by eating cattle meat after an accidental release of radioactive material. Calculations were performed using a database adapted to Swiss conditions for the case that (1) contaminated grass or hay is replaced by clean fodder; (2) the last 100 days before slaughter, taking place one year after an accident, only uncontaminated fodder is given; and (3) alternative feeding regimes are chosen. Seasonal effects were considered by doing all calculations for a deposition at each month of the year. Feeding uncontaminated forage 100 d before slaughter (case 2) proved to be the most effective countermeasure and reduced the integrated activity in meat by 90% to 99%. The effect of replacing contaminated grass (case 1) was less uniform and depended strongly on the time a deposition occurred. In this case the reduction was between 50% and 100% one year after deposition. The substitution of contaminated hay (case 1) was less effective compared to the substitution of grass. The choice of alternative feeding regimes (case 1) was less effective compared to the substitution of grass. The choice of alternative feeding regimes (case 3) led to a reduction of the integrated activity of up to 40% one year after deposition. The present model calculations clearly reveal the importance of the seasonality and demonstrate the usefulness of such calculations as a basis for generating countermeasures in decision support systems. 8 refs., 1 fig., 5 tabs.

  9. Energy deposition in the breast during CT scanning: quantification and implications for dose reduction

    NASA Astrophysics Data System (ADS)

    Rupcich, Franco; Kyprianou, Iacovos; Badal, Andreu; Schmidt, Taly G.

    2011-03-01

    Studies suggest that dose to the breast leads to a higher lifetime attributable cancer incidence risk from a chest CT scan for women compared to men. Numerous methods have been proposed for reducing dose to the breast during CT scanning, including bismuth shielding, tube current modulation, partial-angular scanning, and reduced kVp. These methods differ in how they alter the spectrum and fluence across projection angle. This study used Monte Carlo CT simulations of a voxelized female phantom to investigate the energy (dose) deposition in the breast as a function of both photon energy and projection angle. The resulting dose deposition matrix was then used to investigate several questions regarding dose reduction to the breast: (1) Which photon energies deposit the most dose in the breast, (2) How does increased filtration compare to tube current reduction in reducing breast dose, and (3) Do reduced kVp scans reduce dose to breast, and if so, by what mechanism? The results demonstrate that while high-energy photons deposit more dose per emitted photon, the low-energy photons deposit more dose to the breast for a 120 kVp acquisition. The results also demonstrate that decreasing the tube current for the AP views to match the fluence exiting a shield deposits nearly the same dose to the breast as when using a shield (within ~1%). Finally, results suggest that the dose reduction observed during lower kVp scans is caused by reduced photon fluence rather than the elimination of high-energy photons from the beam. Overall, understanding the mechanisms of dose deposition in the breast as a function of photon energy and projection angle enables comparisons of dose reduction methods and facilitates further development of optimized dose reduction schemes.

  10. 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.

  11. On the Total Energy Deposition Between Periodically Occurring Activations of the Aurora

    NASA Technical Reports Server (NTRS)

    Spann, James F., Jr.; Germany, G. A.; Parks, G. K.; Brittnacher, M. J.; Winglee, R. W.

    1998-01-01

    Total energy deposition in the northern latitudes is used in models to determine the state of the magnetosphere. It is known that on occasion, a series of intensifications of the aurora occur that are regularly spaced. The energy profile of the total energy deposited reflects this occurance. What can be said of the state of the magnetosphere based on these profiles. We present the result of a study which looks at several of these periods when a series of intensifications occur. Conclusions as to what the magnetosphere may be doing are presented.

  12. Large Storm Energy Deposition and Solar Wind Drivers: A Study of Geoeffectiveness

    NASA Astrophysics Data System (ADS)

    Turner, N. E.; Lopez, R. E.

    2004-12-01

    We examine the role of solar wind driving conditions in the deposition of large amounts of energy in the magnetosphere-ionosphere system. Our database consists of eight storms ranging in size, including especially the October and November 2003 superstorms. We estimate energy deposition into the ring current, ionospheric Joule heating, and auroral precipitation for each event and compare with relevant solar wind data. Results suggest that the magnetosonic Mach number of the solar wind may be a useful parameter in identifying the potential for large amounts of energy deposition, possibly because of the role of the bow shock in modulating the magnetosheath field, and therefore its influence of reconnection rates. We use Dst, ionospheric indices, and MHD simulation results where available to investigate the magnetospheric response to different types of solar wind energy input. Our results are examined with a focus on superstorms and the driving conditions observed in connection with them.

  13. Global Auroral Energy Deposition during Substorm Onset Compared with Local Time and Solar Wind IMF Conditions

    NASA Technical Reports Server (NTRS)

    Spann, J. F.; Brittnacher, M.; Fillingim, M. O.; Germany, G. A.; Parks, G. K.

    1998-01-01

    The global images made by the Ultraviolet Imager (UVI) aboard the IASTP/Polar Satellite are used to derive the global auroral energy deposited in the ionosphere resulting from electron precipitation. During a substorm onset, the energy deposited and its location in local time are compared to the solar wind IMF conditions. Previously, insitu measurements of low orbiting satellites have made precipitating particle measurements along the spacecraft track and global images of the auroral zone, without the ability to quantify energy parameters, have been available. However, usage of the high temporal, spatial, and spectral resolution of consecutive UVI images enables quantitative measurement of the energy deposited in the ionosphere not previously available on a global scale. Data over an extended period beginning in January 1997 will be presented.

  14. Numerical Laser Energy Deposition on Supersonic Cavity Flow and Sensor Placement Strategies to Control the Flow

    PubMed Central

    Aradag, Selin

    2013-01-01

    In this study, the impact of laser energy deposition on pressure oscillations and relative sound pressure levels (SPL) in an open supersonic cavity flow is investigated. Laser energy with a magnitude of 100 mJ is deposited on the flow just above the cavity leading edge and up to 7 dB of reduction is obtained in the SPL values along the cavity back wall. Additionally, proper orthogonal decomposition (POD) method is applied to the x-velocity data obtained as a result of computational fluid dynamics simulations of the flow with laser energy deposition. Laser is numerically modeled using a spherically symmetric temperature distribution. By using the POD results, the effects of laser energy on the flow mechanism are presented. A one-dimensional POD methodology is applied to the surface pressure data to obtain critical locations for the placement of sensors for real time flow control applications. PMID:24363612

  15. Numerical laser energy deposition on supersonic cavity flow and sensor placement strategies to control the flow.

    PubMed

    Yilmaz, Ibrahim; Aradag, Selin

    2013-01-01

    In this study, the impact of laser energy deposition on pressure oscillations and relative sound pressure levels (SPL) in an open supersonic cavity flow is investigated. Laser energy with a magnitude of 100 mJ is deposited on the flow just above the cavity leading edge and up to 7 dB of reduction is obtained in the SPL values along the cavity back wall. Additionally, proper orthogonal decomposition (POD) method is applied to the x-velocity data obtained as a result of computational fluid dynamics simulations of the flow with laser energy deposition. Laser is numerically modeled using a spherically symmetric temperature distribution. By using the POD results, the effects of laser energy on the flow mechanism are presented. A one-dimensional POD methodology is applied to the surface pressure data to obtain critical locations for the placement of sensors for real time flow control applications. PMID:24363612

  16. Experiment of Flow Control Using Laser Energy Deposition Around High Speed Propulsion System

    NASA Astrophysics Data System (ADS)

    Lee, HyoungJin; Jeung, InSeuck; Lee, SangHun; Kim, Seihwan

    2011-11-01

    An experimental investigation was conducted to examine the effect of a pulsed Nd:YAG laser energy deposition on the shock structures in supersonic/hypersonic flow and quiescent air. The effect of the laser energy and pressure in the blast wave generation were also investigated. As a result, the strength of plasma and blast wave becomes stronger as pressure or laser energy increase. And the breakdown threshold of air by laser energy deposition is 0.015 bar at 508 mJ laser energy, the blast wave threshold generation in air by laser energy deposition is 0.100 bar at same laser energy. As qualitative analysis, schlieren images are also obtained. After the series of experiments, the effect of laser energy deposition (LED) on high speed flow around the shock—shock interaction created by a wedge and blunt body. By LED, the structure of shock—shock interaction was collapsed momentary and the pressure of the stagnation point was fluctuated while interference of wave.

  17. 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.

  18. Solid-liquid phase equilibria from free-energy perturbation calculations

    NASA Astrophysics Data System (ADS)

    Angioletti-Uberti, Stefano; Asta, Mark; Finnis, Mike W.; Lee, P. D.

    2008-10-01

    A method for calculating free-energy differences based on a free-energy perturbation (FEP) formalism in an alloy system described by two different Hamiltonians is reported. The intended application is the calculation of solid-liquid phase equilibria in alloys with the accuracy of first-principles electronic density-functional theory (DFT). For this purpose free energies are derived with a classical interatomic potential, and FEP calculations are used to compute corrections to these reference values. For practical applications of this approach, due to the relatively high computational cost of DFT calculations, it is critical that the FEP calculations converge rapidly in terms of the number of samples used to estimate relevant ensemble averages. This issue is investigated in the current study employing two classical interatomic-potential models for Ni-Cu. These models yield differences in predicted phase-boundary temperatures of approximately 100 K, comparable to those that might be expected between a DFT Hamiltonian and a well-fit classical potential. We show that for pure elements the FEP calculations converge rapidly with the number of samples, yielding free-energy differences converged to within a fraction of a meV/atom in a few dozen energy calculations. For a concentrated equiatomic alloy similar precision requires roughly a hundred samples. The results suggest that the proposed methodology could provide a computationally tractable framework for calculating solid-liquid phase equilibria in concentrated alloys with DFT accuracy.

  19. Effect of Low-Energy Ions on Plasma-Enhanced Deposition of Cubic Boron Nitride

    NASA Astrophysics Data System (ADS)

    Torigoe, M.; Fukui, S.; Teii, K.; Matsumoto, S.

    2015-09-01

    The effect of low-energy ions on deposition of cubic boron nitride (cBN) films in an inductively coupled plasma with the chemistry of fluorine is studied in terms of ion energy, ion flux, and ion to boron flux ratio onto the substrate. The ion energy and the ion to boron flux ratio are determined from the sheath potential and the ratio of incident ion flux to net deposited boron flux, respectively. For negative substrate biases where sp2-bonded BN phase only or no deposit is formed, both the ion energy and the ion to boron flux ratio are high. For positive substrate biases where cBN phase is formed, the ion energy and the ion to boron flux ratio are estimated in the range of a few eV to 35 eV and 100 to 130, respectively. The impact of negative ions is presumed to be negligible due to their low kinetic energy relative to the sheath potential over the substrate surface. The impact of positive ions with high ion to boron flux ratios is primarily responsible for reduction of the ion energy for cBN film deposition. Work supported in part by a Grant-in-Aid for Scientific Research (B), a Funding Program for Next Generation World-Leading Researchers, and an Industrial Technology Research Grant Program 2008.

  20. Energy dependence of island nucleation density during ion beam deposition

    NASA Astrophysics Data System (ADS)

    Pomeroy, Joshua M.; Brock, Joel D.

    2002-03-01

    Thin copper films were grown on single crystal copper substrates using highly collimated copper ion beams with precisely controlled incidence energies. The energetic collisions between the copper ions and the surface can form adatom-vacancy pairs or sputter eject atoms into the vaccuum. Island nucleation densities are affected by these atomistic mechanisms, which increase surface adatom densities and surface defect densities. This paper reports STM measurements of the island nucleation density for films grown both thermally and at energies between 10-150 eV. The measured island nucleation density systematically deviates with increasing energy from the density predicted by mean field nucleation theory (J.A. Venables, et.al., Rep. Prog. Phys. 47 (1984) p. 399-459). This deviation can be understood using a phenomenological extension of mean field nucleation theory that includes the effects of adatom-vacancy pair production and sputter ejection on the effective flux.

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

    PubMed

    Klimovich, Pavel V; Mobley, David L

    2015-11-01

    Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations. PMID:26487189

  2. 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.

  3. 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.

  4. Energy deposition dynamics of femtosecond pulses in water

    SciTech Connect

    Minardi, Stefano Pertsch, Thomas; Milián, Carles; Couairon, Arnaud; Majus, Donatas; Tamošauskas, Gintaras; Dubietis, Audrius; Gopal, Amrutha

    2014-12-01

    We exploit inverse Raman scattering and solvated electron absorption to perform a quantitative characterization of the energy loss and ionization dynamics in water with tightly focused near-infrared femtosecond pulses. A comparison between experimental data and numerical simulations suggests that the ionization energy of water is 8 eV, rather than the commonly used value of 6.5 eV. We also introduce an equation for the Raman gain valid for ultra-short pulses that validates our experimental procedure.

  5. Photon Energy Deposition in Strong-Field Single Ionization of Multielectron Molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Wenbin; Li, Zhichao; Lu, Peifen; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Lin, Kang; Ma, Junyang; He, Feng; Zeng, Heping; Wu, Jian

    2016-09-01

    Molecules exposed to strong laser fields may coherently absorb multiple photons and deposit the energy into electrons and nuclei, triggering the succeeding dynamics as the primary stage of the light-molecule interaction. We experimentally explore the electron-nuclear sharing of the absorbed photon energy in above-threshold multiphoton single ionization of multielectron molecules. Using CO as a prototype, vibrational and orbital resolved electron-nuclear sharing of the photon energy is observed. Different from the simplest one- or two-electron systems, the participation of the multiple orbitals and the coupling of various electronic states in the strong-field ionization and dissociation processes alter the photon energy deposition dynamics of the multielectron molecule. The population of numerous vibrational states of the molecular cation as the energy reservoir in the ionization process plays an important role in photon energy sharing between the emitted electron and the nuclear fragments.

  6. Photon Energy Deposition in Strong-Field Single Ionization of Multielectron Molecules.

    PubMed

    Zhang, Wenbin; Li, Zhichao; Lu, Peifen; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Lin, Kang; Ma, Junyang; He, Feng; Zeng, Heping; Wu, Jian

    2016-09-01

    Molecules exposed to strong laser fields may coherently absorb multiple photons and deposit the energy into electrons and nuclei, triggering the succeeding dynamics as the primary stage of the light-molecule interaction. We experimentally explore the electron-nuclear sharing of the absorbed photon energy in above-threshold multiphoton single ionization of multielectron molecules. Using CO as a prototype, vibrational and orbital resolved electron-nuclear sharing of the photon energy is observed. Different from the simplest one- or two-electron systems, the participation of the multiple orbitals and the coupling of various electronic states in the strong-field ionization and dissociation processes alter the photon energy deposition dynamics of the multielectron molecule. The population of numerous vibrational states of the molecular cation as the energy reservoir in the ionization process plays an important role in photon energy sharing between the emitted electron and the nuclear fragments. PMID:27636472

  7. Photon Energy Deposition in Strong-Field Single Ionization of Multielectron Molecules.

    PubMed

    Zhang, Wenbin; Li, Zhichao; Lu, Peifen; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Lin, Kang; Ma, Junyang; He, Feng; Zeng, Heping; Wu, Jian

    2016-09-01

    Molecules exposed to strong laser fields may coherently absorb multiple photons and deposit the energy into electrons and nuclei, triggering the succeeding dynamics as the primary stage of the light-molecule interaction. We experimentally explore the electron-nuclear sharing of the absorbed photon energy in above-threshold multiphoton single ionization of multielectron molecules. Using CO as a prototype, vibrational and orbital resolved electron-nuclear sharing of the photon energy is observed. Different from the simplest one- or two-electron systems, the participation of the multiple orbitals and the coupling of various electronic states in the strong-field ionization and dissociation processes alter the photon energy deposition dynamics of the multielectron molecule. The population of numerous vibrational states of the molecular cation as the energy reservoir in the ionization process plays an important role in photon energy sharing between the emitted electron and the nuclear fragments.

  8. Calculations of the C2 fragmentation energies of higher fullerenes C80 and C82.

    PubMed

    Dolgonos, Grygoriy A; Peslherbe, Gilles H

    2007-09-01

    The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C2 corrections were included in the calculation of fragmentation energies for comparison with experimental C2 fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C2 fragmentation of C80, the calculated [Formula: see text] agree well with experimental data, whereas in the case of C(82) fragmentation, the calculated [Formula: see text] exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C2 fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.

  9. Particle production and energy deposition studies for the neutrino factory target station

    NASA Astrophysics Data System (ADS)

    Back, John J.; Densham, Chris; Edgecock, Rob; Prior, Gersende

    2013-02-01

    We present FLUKA and MARS simulation studies of the pion production and energy deposition in the Neutrino Factory baseline target station, which consists of a 4 MW proton beam interacting with a liquid mercury jet target within a 20 T solenoidal magnetic field. We show that a substantial increase in the shielding is needed to protect the superconducting coils from too much energy deposition. Investigations reveal that it is possible to reduce the magnetic field in the solenoid capture system without adversely affecting the pion production efficiency. We show estimates of the amount of concrete shielding that will be required to protect the environment from the high radiation doses generated by the target station facility. We also present yield and energy deposition results for alternative targets: gallium liquid jet, tungsten powder jet, and solid tungsten bars.

  10. Collisional energy deposition threshold for extended damage depths in ion-implanted silicates

    SciTech Connect

    Arnold, G.W.; Battaglin, G.; Boscolo-Boscoletto, A.; Caccavalle, F.; De Marchi, G.; Mazzoldi, P.; Miotello, A.

    1991-12-31

    Many properties of implanted fused silica (e.g., surface stress, hardness) exhibit maximum implantation-induced changes for collisional energy deposition values of {approximately}10{sup 20} keV/cm{sup 3}. We have observed a second critical energy deposition threshold value of about 10{sup 22} keV/cm{sup 3} in stress and hardness measurements as well as in many other experiments on silicate glasses (leaching, alkali depletion, etching rate, gaseous implant redistribution). The latter show evidence for damage depths exceeding TRIM ranges by about a factor of 2. For crystalline quartz, a similar threshold value has been found for extended damage depths (greater than TRIM) for 250 kev ions (H-Au) as measured by RBS and interference fringes. This phenomenon at high damage deposition energy may involve the large stress gradients between damaged and undamaged regions and the much increased diffusion coefficient for defect transport. 13 refs., 6 figs.

  11. Collisional energy deposition threshold for extended damage depths in ion-implanted silicates

    SciTech Connect

    Arnold, G.W. ); Battaglin, G. ); Boscolo-Boscoletto, A. ); Caccavalle, F.; De Marchi, G.; Mazzoldi, P. ); Miotello, A. (Consorzio INFM, Dipartiment

    1991-01-01

    Many properties of implanted fused silica (e.g., surface stress, hardness) exhibit maximum implantation-induced changes for collisional energy deposition values of {approximately}10{sup 20} keV/cm{sup 3}. We have observed a second critical energy deposition threshold value of about 10{sup 22} keV/cm{sup 3} in stress and hardness measurements as well as in many other experiments on silicate glasses (leaching, alkali depletion, etching rate, gaseous implant redistribution). The latter show evidence for damage depths exceeding TRIM ranges by about a factor of 2. For crystalline quartz, a similar threshold value has been found for extended damage depths (greater than TRIM) for 250 kev ions (H-Au) as measured by RBS and interference fringes. This phenomenon at high damage deposition energy may involve the large stress gradients between damaged and undamaged regions and the much increased diffusion coefficient for defect transport. 13 refs., 6 figs.

  12. Energy deposition at the bone-tissue interface from nuclear fragments produced by high-energy nucleons

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Hajnal, Ferenc; Wilson, John W.

    1990-01-01

    The transport of nuclear fragmentation recoils produced by high-energy nucleons in the region of the bone-tissue interface is considered. Results for the different flux and absorbed dose for recoils produced by 1 GeV protons are presented in a bidirectional transport model. The energy deposition in marrow cavities is seen to be enhanced by recoils produced in bone. Approximate analytic formulae for absorbed dose near the interface region are also presented for a simplified range-energy model.

  13. Separated topologies—A method for relative binding free energy calculations using orientational restraints

    NASA Astrophysics Data System (ADS)

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.

    2013-02-01

    Orientational restraints can improve the efficiency of alchemical free energy calculations, but they are not typically applied in relative binding calculations, which compute the affinity difference been two ligands. Here, we describe a new "separated topologies" method, which computes relative binding free energies using orientational restraints and which has several advantages over existing methods. While standard approaches maintain the initial and final ligand in a shared orientation, the separated topologies approach allows the initial and final ligands to have distinct orientations. This avoids a slowly converging reorientation step in the calculation. The separated topologies approach can also be applied to determine the relative free energies of multiple orientations of the same ligand. We illustrate the approach by calculating the relative binding free energies of two compounds to an engineered site in Cytochrome C Peroxidase.

  14. Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-.

    PubMed

    Muller, R P; Warshel, A

    1996-01-01

    This paper describes a hybrid ab initio quantum mechanical/molecular mechanics (QM/MM) method for calculating activation free energies of chemical reactions in solution, using molecular mechanics force fields for the solvent and an ab initio technique that incorporates the potential from the solvent in its Hamiltonian for the solute. The empirical valence bond (EVB) method is used as a reference potential for the ab initio free energy calculation, and drives the reaction along the proper coordinate, thus overcoming problems encountered by direct attempts to use molecular orbital methods in calculations of activation free energies. The utility of our method is illustrated by calculating the activation free energy for proton transfer between fluoride ions in the [FHF]-system, in both polar and nonpolar solution.

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

    PubMed

    Ghosh, Soumya; Hammes-Schiffer, Sharon

    2015-01-01

    Electrochemical electron transfer reactions play an important role in energy conversion processes with many technological applications. Electrodes modified by self-assembled monolayers (SAMs) exhibit reduced double layer effects and are used in molecular electronics. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in the solute geometry and the environment. In this Letter, an approach for calculating the electrochemical reorganization energy for a redox molecule attached to or near a SAM modified electrode is presented. This integral equations formalism polarizable continuum model (IEF-PCM) approach accounts for the detailed electronic structure of the molecule, as well as the contributions from the electrode, SAM, and electronic and inertial solvent responses. The calculated total reorganization energies are in good agreement with experimental data for a series of metal complexes in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts. PMID:26263083

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

    SciTech Connect

    Not Available

    2004-02-01

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

  17. Flux and energy analysis of species in hollow cathode magnetron ionized physical vapor deposition of copper

    NASA Astrophysics Data System (ADS)

    Wu, L.; Ko, E.; Dulkin, A.; Park, K. J.; Fields, S.; Leeser, K.; Meng, L.; Ruzic, D. N.

    2010-12-01

    To meet the stringent requirements of interconnect metallization for sub-32 nm technologies, an unprecedented level of flux and energy control of film forming species has become necessary to further advance ionized physical vapor deposition technology. Such technology development mandates improvements in methods to quantify the metal ion fraction, the gas/metal ion ratio, and the associated ion energies in the total ion flux to the substrate. In this work, a novel method combining planar Langmuir probes, quartz crystal microbalance (QCM), and gridded energy analyzer (GEA) custom instrumentation is developed to estimate the plasma density and temperature as well as to measure the metal ion fraction and ion energy. The measurements were conducted in a Novellus Systems, Inc. Hollow Cathode Magnetron (HCMTM) physical vapor deposition source used for deposition of Cu seed layer for 65-130 nm technology nodes. The gridded energy analyzer was employed to measure ion flux and ion energy, which was compared to the collocated planar Langmuir probe data. The total ion-to-metal neutral ratio was determined by the QCM combined with GEA. The data collection technique and the corresponding analysis are discussed. The effect of concurrent resputtering during the deposition process on film thickness profile is also discussed.

  18. Flux and energy analysis of species in hollow cathode magnetron ionized physical vapor deposition of copper

    SciTech Connect

    Wu, L.; Ko, E.; Dulkin, A.; Park, K. J.; Fields, S.; Leeser, K.; Meng, L.; Ruzic, D. N.

    2010-12-15

    To meet the stringent requirements of interconnect metallization for sub-32 nm technologies, an unprecedented level of flux and energy control of film forming species has become necessary to further advance ionized physical vapor deposition technology. Such technology development mandates improvements in methods to quantify the metal ion fraction, the gas/metal ion ratio, and the associated ion energies in the total ion flux to the substrate. In this work, a novel method combining planar Langmuir probes, quartz crystal microbalance (QCM), and gridded energy analyzer (GEA) custom instrumentation is developed to estimate the plasma density and temperature as well as to measure the metal ion fraction and ion energy. The measurements were conducted in a Novellus Systems, Inc. Hollow Cathode Magnetron (HCM{sup TM}) physical vapor deposition source used for deposition of Cu seed layer for 65-130 nm technology nodes. The gridded energy analyzer was employed to measure ion flux and ion energy, which was compared to the collocated planar Langmuir probe data. The total ion-to-metal neutral ratio was determined by the QCM combined with GEA. The data collection technique and the corresponding analysis are discussed. The effect of concurrent resputtering during the deposition process on film thickness profile is also discussed.

  19. Void formation in amorphous germanium due to high electronic energy deposition

    SciTech Connect

    Gaertner, K.; Joehrens, J.; Steinbach, T.; Schnohr, C. S.; Wesch, W.; Ridgway, M. C.

    2011-06-01

    The effect of high electronic energy deposition in amorphous germanium has been studied experimentally by Au irradiation with ion energies of up to 185 MeV and different angles of incidence and by molecular dynamics computer simulations. In both cases, the energy deposition leads to void formation accompanied by strong swelling of the amorphous germanium. The simulation results prove that the formation of the voids is mainly based on a shock wave mechanism and the swelling is determined by the competing processes of the formation and growth of voids on the one hand and the shrinking and annihilation of voids on the other hand. In full agreement between experiment and simulation, the amount of the swelling is a linear function of the total energy deposited into electronic processes and there exists a threshold value of the electronic energy loss per ion and depth for swelling. A comparison of the threshold values obtained by the experiment and the simulation suggests that approximately 20% of the energy deposited into electronic processes is converted into atomic motion.

  20. Mitigation of effects of beam-induced energy deposition in the LHC high-luminosity interaction regions

    SciTech Connect

    Nikolai V. Mokhov et al.

    2003-05-28

    Beam-induced energy deposition in the LHC high luminosity interaction region components is one of the serious limits for the machine performance. The results of further optimization and comprehensive MARS14 calculations in the IP1 and IP5 inner and outer triplets are summarized for the updated lattice, calculation model, baseline pp-collision source term, and for realistic engineering constraints on the hardware design. It is shown that the optimized layout and absorbers would provide a sufficient reduction of peak power density and dynamic heat load in the superconducting components with an adequate safety margin. Accumulated dose and residual dose rates in and around the region components are also kept below the tolerable limits in the proposed design.

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  4. Measuring internal energy deposition in collisional activation using hydrated ion nanocalorimetry to obtain peptide dissociation energies and entropies.

    PubMed

    Demireva, Maria; Williams, Evan R

    2010-07-01

    The internal energy deposited in both on- and off-resonance collisional activation in Fourier transform ion cyclotron resonance mass spectrometry is measured with ion nanocalorimetry and is used to obtain information about the dissociation energy and entropy of a protonated peptide. Activation of Na(+)(H(2)O)(30) results in sequential loss of water molecules, and the internal energy of the activated ion can be obtained from the abundances of the product ions. Information about internal energy deposition in on-resonance collisional activation of protonated peptides is inferred from dissociation data obtained under identical conditions for hydrated ions that have similar m/z and degrees-of-freedom. From experimental internal energy deposition curves and Rice-Ramsperger-Kassel-Marcus (RRKM) theory, dissociation data as a function of collision energy for protonated leucine enkephalin, which has a comparable m/z and degrees-of-freedom as Na(+)(H(2)O)(30), are modeled. The threshold dissociation energies and entropies are correlated for data acquired at a single time point, resulting in a relatively wide range of threshold dissociation energies (1.1 to 1.7 eV) that can fit these data. However, this range of values could be significantly reduced by fitting data acquired at different dissociation times. By measuring the internal energy of an activated ion, the number of fitting parameters necessary to obtain information about the dissociation parameters by modeling these data is reduced and could result in improved accuracy for such methods.

  5. 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.

  6. Accuracy assessment and automation of free energy calculations for drug design.

    PubMed

    Christ, Clara D; Fox, Thomas

    2014-01-27

    As the free energy of binding of a ligand to its target is one of the crucial optimization parameters in drug design, its accurate prediction is highly desirable. In the present study we have assessed the average accuracy of free energy calculations for a total of 92 ligands binding to five different targets. To make this study and future larger scale applications possible we automated the setup procedure. Starting from user defined binding modes, the procedure decides which ligands to connect via a perturbation based on maximum common substructure criteria and produces all necessary parameter files for free energy calculations in AMBER 11. For the systems investigated, errors due to insufficient sampling were found to be substantial in some cases whereas differences in estimators (thermodynamic integration (TI) versus multistate Bennett acceptance ratio (MBAR)) were found to be negligible. Analytical uncertainty estimates calculated from a single free energy calculation were found to be much smaller than the sample standard deviation obtained from two independent free energy calculations. Agreement with experiment was found to be system dependent ranging from excellent to mediocre (RMSE = [0.9, 8.2, 4.7, 5.7, 8.7] kJ/mol). When restricting analyses to free energy calculations with sample standard deviations below 1 kJ/mol agreement with experiment improved (RMSE = [0.8, 6.9, 1.8, 3.9, 5.6] kJ/mol).

  7. 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.

  8. A Template-Matching Method For Measuring Energy Depositions In TES Films

    NASA Astrophysics Data System (ADS)

    Shank, Benjamin; Yen, Jeffrey; Cabrera, Blas; Kreikebaum, John Mark; Moffatt, Robert; Redl, Peter; Young, Betty; Brink, Paul; Cherry, Matthew; Tomada, Astrid

    2014-03-01

    Transition edge sensors (TES) have a wide variety of applications in particle ∖astrophysics for detecting incoming particles with high energy resolution. In TES design, the need for sufficient heat capacity to avoid saturation limits the ultimate energy resolution. Building on the TES model developed for SuperCDMS by Yen et al. for tungsten TESs deposited next to aluminum collection fins, we outline a time-domain non-linear optimal filter method for reconstructing energy depositions in TES films. This allows us to operate devices into their saturation region while taking into account changing noise performance and loss of energy collection. We show how this method has improved our understanding of quasiparticle diffusion and energy collection in our superconducting sensors.

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

    PubMed

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

    2009-09-01

    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.

  10. Modeling dose deposition and DNA damage due to low-energy β(-) emitters.

    PubMed

    Alloni, D; Cutaia, C; Mariotti, L; Friedland, W; Ottolenghi, A

    2014-09-01

    One of the main issues of low-energy internal emitters concerns the very short ranges of the beta particles, versus the dimensions of the biological targets. Depending on the chemical form, the radionuclide may be more concentrated either in the cytoplasm or in the nucleus of the target cell. Consequently, since in most cases conventional dosimetry neglects this issue it may overestimate or underestimate the dose to the nucleus and hence the biological effects. To assess the magnitude of these deviations and to provide a realistic evaluation of the localized energy deposition by low-energy internal emitters, the biophysical track-structure code PARTRAC was used to calculate nuclear doses, DNA damage yields and fragmentation patterns for different localizations of radionuclides in human interphase fibroblasts. The nuclides considered in the simulations were tritium and nickel-63, which emit electrons with average energies of 5.7 (range in water of 0.42 μm) and 17 keV (range of 5 μm), respectively, covering both very short and medium ranges of beta-decay products. The simulation results showed that the largest deviations from the conventional dosimetry occur for inhomogeneously distributed short-range emitters. For uniformly distributed radionuclides selectively in the cytoplasm but excluded from the cell nucleus, the dose in the nucleus is 15% of the average dose in the cell in the case of tritium but 64% for nickel-63. Also, the numbers of double-strand breaks (DSBs) and the distributions of DNA fragments depend on subcellular localization of the radionuclides. In the low- and medium-dose regions investigated here, DSB numbers are proportional to the nuclear dose, with about 50 DSB/Gy for both studied nuclides. In addition, DSB numbers on specific chromosomes depend on the radionuclide localization in the cell as well, with chromosomes located more peripherally in the cell nucleus being more damaged by short-ranged emitters in cytoplasm compared with chromosomes

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

    NASA Astrophysics Data System (ADS)

    Perfetti, Christopher M.; Rearden, Bradley T.

    2014-06-01

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

  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. Experimental investigation on the energy deposition and expansion rate under the electrical explosion of aluminum wire in vacuum

    SciTech Connect

    Shi, Zongqian; Wang, Kun; Shi, Yuanjie; Wu, Jian; Han, Ruoyu

    2015-12-28

    Experimental investigations on the electrical explosion of aluminum wire using negative polarity current in vacuum are presented. Current pulses with rise rates of 40 A/ns, 80 A/ns, and 120 A/ns are generated for investigating the influence of current rise rate on energy deposition. Experimental results show a significant increase of energy deposition into the wire before the voltage breakdown with the increase of current rise rate. The influence of wire dimension on energy deposition is investigated as well. Decreasing the wire length allows more energy to be deposited into the wire. The energy deposition of a 0.5 cm-long wire explosion is ∼2.5 times higher than the energy deposition of a 2 cm-long wire explosion. The dependence of the energy deposition on wire diameter demonstrates a maximum energy deposition of 2.7 eV/atom with a diameter of ∼18 μm. Substantial increase in energy deposition is observed in the electrical explosion of aluminum wire with polyimide coating. A laser probe is applied to construct the shadowgraphy, schlieren, and interferometry diagnostics. The morphology and expansion trajectory of exploding products are analyzed based on the shadowgram. The interference phase shift is reconstructed from the interferogram. Parallel dual wires are exploded to estimate the expansion velocity of the plasma shell.

  15. Gamma-point lattice free energy estimates from O1 force calculations.

    PubMed

    Voss, Johannes; Vegge, Tejs

    2008-05-14

    We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum of the phonon eigenvectors obtained from a fast-relative to, e.g., density-functional theory (DFT)-Hessian calculation using interatomic potentials. These potentials are based here on effective charges obtained from a DFT calculation of the ground state electronic charge density but could also be based on other, e.g., empiric approaches.

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

    NASA Astrophysics Data System (ADS)

    Montgomery, Jason

    2007-12-01

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

  17. Sensitivity of methods for calculating energy expenditure by use of doubly labeled water.

    PubMed

    Seale, J; Miles, C; Bodwell, C E

    1989-02-01

    Attempts to estimate human energy expenditure by use of doubly labeled water have produced three methods currently used for calculating carbon dioxide production from isotope disappearance data: 1) the two-point method, 2) the regression method, and 3) the integration method. An ideal data set was used to determine the error produced in the calculated energy expenditure for each method when specific variables were perturbed. The analysis indicates that some of the calculation methods are more susceptible to perturbations in certain variables than others. Results from an experiment on one adult human subject are used to illustrate the potential for error in actual data. Samples of second void urine, 24-h urine, and breath collected every other day for 21 days are used to calculate the average daily energy expenditure by three calculation methods. The difference between calculated energy expenditure and metabolizable energy on a weight-maintenance diet is used to estimate the error associated with the doubly labeled water method. PMID:2496076

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

    SciTech Connect

    Gee, R.

    1983-01-01

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

  19. Application of adjusted data in calculating fission-product decay energies and spectra

    NASA Astrophysics Data System (ADS)

    George, D. C.; Labauve, R. J.; England, T. R.

    1982-06-01

    The code ADENA, which approximately calculates fussion-product beta and gamma decay energies and spectra in 19 or fewer energy groups from a mixture of U235 and Pu239 fuels, is described. The calculation uses aggregate, adjusted data derived from a combination of several experiments and summation results based on the ENDF/B-V fission product file. The method used to obtain these adjusted data and the method used by ADENA to calculate fission-product decay energy with an absorption correction are described, and an estimate of the uncertainty of the ADENA results is given. Comparisons of this approximate method are made to experimental measurements, to the ANSI/ANS 5.1-1979 standard, and to other calculational methods. A listing of the complete computer code (ADENA) is contained in an appendix. Included in the listing are data statements containing the adjusted data in the form of parameters to be used in simple analytic functions.

  20. QED calculation of the ground-state energy of berylliumlike ions

    NASA Astrophysics Data System (ADS)

    Malyshev, A. V.; Volotka, A. V.; Glazov, D. A.; Tupitsyn, I. I.; Shabaev, V. M.; Plunien, G.

    2014-12-01

    Ab initio QED calculations of the ground-state binding energies of berylliumlike ions are performed for the wide range of the nuclear charge number: Z =18 -96 . The calculations are carried out in the framework of the extended Furry picture starting with three different types of the screening potential. The rigorous QED calculations up to the second order of the perturbation theory are combined with the third- and higher-order electron-correlation contributions obtained within the Breit approximation by the use of the large-scale configuration-interaction Dirac-Fock-Sturm method. The effects of nuclear recoil and nuclear polarization are taken into account. The ionization potentials are obtained by subtracting the binding energies of the corresponding lithiumlike ions. In comparison with the previous calculations the accuracy of the binding energies and the ionization potentials is significantly improved.

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

    SciTech Connect

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

    1992-11-01

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

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

    SciTech Connect

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

    1992-01-01

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

  3. 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…

  4. 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...

  5. 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}

  6. Chemical vapour deposition of thermochromic vanadium dioxide thin films for energy efficient glazing

    SciTech Connect

    Warwick, Michael E.A.; Binions, Russell

    2014-06-01

    Vanadium dioxide is a thermochromic material that undergoes a semiconductor to metal transitions at a critical temperature of 68 °C. This phase change from a low temperature monoclinic structure to a higher temperature rutile structure is accompanied by a marked change in infrared reflectivity and change in resistivity. This ability to have a temperature-modulated film that can limit solar heat gain makes vanadium dioxide an ideal candidate for thermochromic energy efficient glazing. In this review we detail the current challenges to such glazing becoming a commercial reality and describe the key chemical vapour deposition technologies being employed in the latest research. - Graphical abstract: Schematic demonstration of the effect of thermochromic glazing on solar radiation (red arrow represents IR radiation, black arrow represents all other solar radiation). - Highlights: • Vanadium dioxide thin films for energy efficient glazing. • Reviews chemical vapour deposition techniques. • Latest results for thin film deposition for vanadium dioxide.

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

    NASA Astrophysics Data System (ADS)

    Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav

    2016-02-01

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

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

    PubMed

    Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav

    2016-02-14

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

  9. Energy deposition by heavy ions: additivity of kinetic and potential energy contributions in hillock formation on CaF2.

    PubMed

    Wang, Y Y; Grygiel, C; Dufour, C; Sun, J R; Wang, Z G; Zhao, Y T; Xiao, G Q; Cheng, R; Zhou, X M; Ren, J R; Liu, S D; Lei, Y; Sun, Y B; Ritter, R; Gruber, E; Cassimi, A; Monnet, I; Bouffard, S; Aumayr, F; Toulemonde, M

    2014-07-18

    Modification of surface and bulk properties of solids by irradiation with ion beams is a widely used technique with many applications in material science. In this study, we show that nano-hillocks on CaF2 crystal surfaces can be formed by individual impact of medium energy (3 and 5 MeV) highly charged ions (Xe(22+) to Xe(30+)) as well as swift (kinetic energies between 12 and 58 MeV) heavy xenon ions. For very slow highly charged ions the appearance of hillocks is known to be linked to a threshold in potential energy (Ep) while for swift heavy ions a minimum electronic energy loss per unit length (Se) is necessary. With our results we bridge the gap between these two extreme cases and demonstrate, that with increasing energy deposition via Se the Ep-threshold for hillock production can be lowered substantially. Surprisingly, both mechanisms of energy deposition in the target surface seem to contribute in an additive way, which can be visualized in a phase diagram. We show that the inelastic thermal spike model, originally developed to describe such material modifications for swift heavy ions, can be extended to the case where both kinetic and potential energies are deposited into the surface.

  10. Energy deposition by heavy ions: additivity of kinetic and potential energy contributions in hillock formation on CaF2.

    PubMed

    Wang, Y Y; Grygiel, C; Dufour, C; Sun, J R; Wang, Z G; Zhao, Y T; Xiao, G Q; Cheng, R; Zhou, X M; Ren, J R; Liu, S D; Lei, Y; Sun, Y B; Ritter, R; Gruber, E; Cassimi, A; Monnet, I; Bouffard, S; Aumayr, F; Toulemonde, M

    2014-01-01

    Modification of surface and bulk properties of solids by irradiation with ion beams is a widely used technique with many applications in material science. In this study, we show that nano-hillocks on CaF2 crystal surfaces can be formed by individual impact of medium energy (3 and 5 MeV) highly charged ions (Xe(22+) to Xe(30+)) as well as swift (kinetic energies between 12 and 58 MeV) heavy xenon ions. For very slow highly charged ions the appearance of hillocks is known to be linked to a threshold in potential energy (Ep) while for swift heavy ions a minimum electronic energy loss per unit length (Se) is necessary. With our results we bridge the gap between these two extreme cases and demonstrate, that with increasing energy deposition via Se the Ep-threshold for hillock production can be lowered substantially. Surprisingly, both mechanisms of energy deposition in the target surface seem to contribute in an additive way, which can be visualized in a phase diagram. We show that the inelastic thermal spike model, originally developed to describe such material modifications for swift heavy ions, can be extended to the case where both kinetic and potential energies are deposited into the surface. PMID:25034006

  11. 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)

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

    SciTech Connect

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

    2015-05-21

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

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

    PubMed

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

    2015-05-21

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

  14. Evaluation of eruptive energy of a pyroclastic deposit applying fractal geometry to fragment size distributions

    NASA Astrophysics Data System (ADS)

    Paredes Marino, Joali; Morgavi, Daniele; Di Vito, Mauro; de Vita, Sandro; Sansivero, Fabio; Perugini, Diego

    2016-04-01

    Fractal fragmentation theory has been applied to characterize the particle size distribution of pyroclastic deposits generated by volcanic explosions. Recent works have demonstrated that fractal dimension on grain size distributions can be used as a proxy for estimating the energy associated with volcanic eruptions. In this work we seek to establish a preliminary analytical protocol that can be applied to better characterize volcanic fall deposits and derive the potential energy for fragmentation that was stored in the magma prior/during an explosive eruption. The methodology is based on two different techniques for determining the grain-size distribution of the pyroclastic samples: 1) dry manual sieving (particles larger than 297μm), and 2) automatic grain size analysis via a CamSizer-P4®device, the latter measure the distribution of projected area, obtaining a cumulative distribution based on volume fraction for particles up to 30mm. Size distribution data have been analyzed by applying the fractal fragmentation theory estimating the value of Df, i.e. the fractal dimension of fragmentation. In order to test our protocol we studied the Cretaio eruption, Ischia island, Italy. Results indicate that size distributions of pyroclastic fall deposits follow a fractal law, indicating that the fragmentation process of these deposits reflects a scale-invariant fragmentation mechanism. Matching the results from manual and automated techniques allows us to obtain a value of the "fragmentation energy" from the explosive eruptive events that generate the Cretaio deposits. We highlight the importance of these results, based on fractal statistics, as an additional volcanological tool for addressing volcanic risk based on the analyses of grain size distributions of natural pyroclastic deposits. Keywords: eruptive energy, fractal dimension of fragmentation, pyroclastic fallout.

  15. Analysis of CRRES PHA Data for Low-Energy-Deposition Events

    NASA Technical Reports Server (NTRS)

    McNulty, P. J.; Hardage, Donna

    2004-01-01

    This effort analyzed the low-energy deposition Pulse Height Analyzer (PHA) data from the Combined Release and Radiation Effects Satellite (CRRES). The high-energy deposition data had been previously analyzed and shown to be in agreement with spallation reactions predicted by the Clemson University Proton Interactions in Devices (CUPID) simulation model and existing environmental and orbit positioning models (AP-8 with USAF B-L coordinates). The scope of this project was to develop and improve the CUPID model by increasing its range to lower incident particle energies, and to expand the modeling to include contributions from elastic interactions. Before making changes, it was necessary to identify experimental data suitable for benchmarking the codes; then, the models to the CRRES PHA data could be applied. It was also planned to test the model against available low-energy proton or neutron SEU data obtained with mono-energetic beams.

  16. Energy Deposition and Shielding Study of the Front End for the Neutrino Factory

    SciTech Connect

    Snopok, Pavel; Neuffer, David; Rogers, Chris

    2013-06-01

    In the Neutrino Factory and Muon Collider muons are produced by firing high energy protons onto a target to produce pions. The pions decay to muons which are then accelerated. This method of pion production results in significant background from protons and electrons, which may result in heat deposition on superconducting materials and activation of the machine preventing manual handling. In this paper we discuss the design of a secondary particle handling system. The system comprises a solenoidal chicane that filters high momentum particles, followed by a proton absorber that reduces the energy of all particles, resulting in the rejection of low energy protons that pass through the solenoid chicane. We detail the design and optimization of the system and energy deposition and shielding analysis in MARS15.

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

    PubMed

    Podeszwa, Rafał; Cencek, Wojciech; Szalewicz, Krzysztof

    2012-06-12

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

  18. 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.

  19. Effect of forage energy intake and supplementation on marbling deposition in growing beef cattle.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Glucose is the primary carbon source for fatty acid synthesis in intramuscular fat, whereas, acetate is primarily utilized by subcutaneous fat. Our objective was to examine the effect of forage energy intake and type of fermentation on marbling deposition by stocker cattle grazing dormant native ra...

  20. Low energy, low latitude wave-dominated shallow marine depositional systems: examples from northern Borneo

    NASA Astrophysics Data System (ADS)

    Lambiase, Joseph J.; Suraya Tulot

    2013-12-01

    The depositional environments of the wave-dominant successions in the middle to late Miocene Belait and Sandakan Formations in northwestern and northern Borneo, respectively, were determined based on grain size distributions, sedimentary structures and facies successions, as well as trace and microfossil assemblages. Generally, progradational shoreface successions in the Belait Formation were deposited in very low wave energy environments where longshore currents were too weak to generate trough cross-bedding. Shoreface sands are laterally continuous for several km and follow the basin contours, suggesting attached beaches similar to the modern Brunei coastline. In contrast, trough cross-bedding is common in the coarser Sandakan Formation and back-barrier mangrove swamp deposits cap the progradational succession as on the modern northern Dent Peninsula coastline, indicating barrier development and higher wave energy conditions than in the Belait Formation. The Borneo examples indicate that barrier systems that include significant tidal facies form under higher wave energy conditions than attached beaches with virtually no tidal facies. Also, Borneo's low latitude climate promotes back-barrier mangrove which reduces tidal exchange and reduces tidal influence relative to comparable temperate climate systems. The results of the study indicate that depositional systems on low energy, wave-dominated coasts are highly variable, as are the sand bodies and facies associations they generate.

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

    NASA Astrophysics Data System (ADS)

    Li, Ming; Kapusta, Joseph I.

    2016-08-01

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

  2. Effects of acidic deposition and other energy emissions on wildlife: a compendium

    SciTech Connect

    Newman, J.R.; Schreiber, R.K.

    1985-10-01

    Energy emissions, including acidic depositions, pose potential problems for wildlife populations. Historical and recent events show both direct, acute effects and indirect, chronic effects from a variety of airborne pollutants. Information on effects of selected gaseous and particulate energy emissions on domestic animals and livestock and on wildlife is compared. Our understanding of wildlife effects can be improved by the evaluation of veterinary toxicological information and research on the ecological equivalents of domestic and laboratory animals. 42 references.

  3. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.

    PubMed

    Jia, Xiangyu; Wang, Xianwei; Liu, Jinfeng; Zhang, John Z H; Mei, Ye; He, Xiao

    2013-12-01

    An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. 125, 094906 (2006)], quantum mechanical (QM) calculation is applied to deal with short-range non-neighboring interactions replacing the classical treatment. Numerical studies are carried out for proteins up to 3837 atoms at the HF/6-31G* level. As compared to standard full system CPCM calculations, EE-GMFCC-CPCM shows clear improvement over the MFCC-CPCM method for both the total electrostatic solvation energy and its components (the polarized solute-solvent reaction field energy and wavefunction distortion energy of the solute). For large proteins with 1000-4000 atoms, where the standard full system ab initio CPCM calculations are not affordable, the EE-GMFCC-CPCM gives larger relative wavefunction distortion energies and weaker relative electrostatic solvation energies for proteins, as compared to the corresponding energies calculated by the Divide-and-Conquer Poisson-Boltzmann (D&C-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and D&C-PB is observed. This study demonstrates that the linear-scaling EE-GMFCC-CPCM approach is an accurate and also efficient method for the calculation of electrostatic solvation energy of proteins.

  4. 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.

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

    PubMed

    Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

    2016-06-27

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

  6. Diffusion enhancement due to low-energy ion bombardment during sputter etching and deposition

    SciTech Connect

    Eltoukhy, A.H.; Greene, J.E.

    1980-08-01

    The effects of low-energy ion bombardment on enhancing elemental diffusion rates at both heterojunction interfaces during film deposition and over the compositionally altered layer created during sputter etching alloy targets have been considered. Depth dependent enhanced interdiffusion coefficients, expressed as D*(x)=D*(0) exp(-x/L/sub d/), where D*(0) is more than five orders of magnitude greater than thermal diffusion values, were measured in InSb/GaSb multilayer structures deposited by multitarget bias sputering. D*(0) was determined from the amplitude u of the compositional modulation in the multilayered films (layer thicknesses between 20 and 45 A) as measured by superlattice x-ray diffraction techniques. The value of D*(0) was found to increase from 3 x 10/sup -17/ to 1 x 10/sup -16/ cm/sup 2//sec as the applied substrate bias was increased from 0 to -75 V. However even at V/sub a/=0, the diffusion coefficient was enhanced owing to an induced substrate potential with respect to the positive space-charge region in the Ar discharge. The diffusion length of L/sub d/ of the ion bombardment created defects was approx.1000 A. Enhanced diffusion also has a significiant effect on the altered layer thickness x/sub e/ and the total sputtering time t/sub e/ (or ion dose) required to reach steady state during ion etching of multielement targets. The effects of using an exponentially depth dependent versus a constant value of the enhanced diffusion coefficient on calculated values of x/sub e/ and t/sub e/ in single-phase binary alloys were considered. The results show that both x/sub e/ and t/sub e/ are considerably larger using a depth dependent D*(x), when L/sub d/D*(0)/v, the usual case for most sputtering applications, the two solutions approach each other.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  8. Measurements and Monte Carlo calculations of photon energy distributions in MAYAK PA workplaces.

    PubMed

    Smetanin, M; Vasilenko, E; Semenov, M; Xanthos, S; Takoudis, G; Clouvas, A; Silva, J; Potiriadis, C

    2008-01-01

    Photon energy distributions were measured in different workplaces of the Mayak Production Association (MPA), which was the first plutonium production plant in the former Soviet Union. In situ gamma spectrometry measurements were performed with a portable germanium detector. The spectral stripping method is used for the conversion of the in situ gamma-ray spectra to photon fluence rate energy distribution. This method requires the simulation of the portable germanium detector, which has been performed based on the MCNP code of Los Alamos. Measured photon fluence rate energy distributions were compared with calculated photon energy distributions (with the MCNP code) in two different workplaces: in the first workplace the geometry exposure was known. On the contrary, in the second workplace, as in most workplaces of MPA, the exposure geometry was unknown. The results obtained from the comparison between the experimental and calculated photon fluence rate energy distributions are presented and discussed. PMID:18682405

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

    We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. PMID:26958888

  11. 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.

  12. Lime-mud layers in high-energy tidal channels: a record of hurricane deposition

    USGS Publications Warehouse

    Shinn, E.A.; Steinen, R.P.; Dill, R.F.; Major, R.

    1993-01-01

    During or immediately following the transit of Hurricane Andrew (August 23-24, 1992) across the northern part of the Great Bahama Bank, thin laminated beds of carbonate mud were deposited in high-energy subtidal channels (4 m depth) through the ooid shoals of south Cat Cay and Joulters Cays. Thicker, more cohesive (and therefore older) mud beds and angular mud fragments associated with ooids from Joulters Cays have similar characteristics but lack fresh plant fragments. We infer that these older beds were similarly deposited and thus record the passage of previous hurricanes or tropical storms. -from Authors

  13. The frozen orbital approximation for calculating ionization energies with application to propane

    NASA Astrophysics Data System (ADS)

    Müller, Wolfgang; Nager, Christoph; Rosmus, Pavel

    1980-09-01

    In the frozen orbital approximation (FOA), the influence of reorganization on correlation contributions to ionization energies is neglected. It is particularly useful in calculations for large molecules because of the advantage that only one integral transformation is required for the calculation of all ionic states. In connection with the concept of independent orbital correlation contributions, the dimensions of the CI matrices can be drastically reduced. The method is applied to the calculation of the valence ionization energies of propane, and compared to more rigorous ab initio results and a recent calculation in which inner valence shell contributions to electron correlation are neglected. The ordering of the first three ionizations in the photoelectron spectrum of propane, which has not been definitively assigned, is shown to be 2B1(2b1),2A1(6a1) and 2B2(4b2), in agreement with Koopmans' theorem.

  14. Fast electron energy deposition in a magnetized plasma: Kinetic theory and particle-in-cell simulation

    SciTech Connect

    Robiche, J.; Rax, J.-M.; Bonnaud, G.; Gremillet, L.

    2010-03-15

    The collisional dynamics of a relativistic electron jet in a magnetized plasma are investigated within the framework of kinetic theory. The relativistic Fokker-Planck equation describing slowing down, pitch angle scattering, and cyclotron rotation is derived and solved. Based on the solution of this Fokker-Planck equation, an analytical formula for the root mean square spot size transverse to the magnetic field is derived and this result predicts a reduction in radial transport. Some comparisons with particle-in-cell simulation are made and confirm striking agreement between the theory and the simulation. For fast electron with 1 MeV typical kinetic energy interacting with a solid density hydrogen plasma, the energy deposition density in the transverse direction increases by a factor 2 for magnetic field of the order of 1 T. Along the magnetic field, the energy deposition profile is unaltered compared with the field-free case.

  15. Method for controlling energy density for reliable pulsed laser deposition of thin films

    SciTech Connect

    Dowden, P. C. E-mail: qxjia@lanl.gov; Bi, Z.; Jia, Q. X. E-mail: qxjia@lanl.gov

    2014-02-15

    We have established a methodology to stabilize the laser energy density on a target surface in pulsed laser deposition of thin films. To control the focused laser spot on a target, we have imaged a defined aperture in the beamline (so called image-focus) instead of focusing the beam on a target based on a simple “lens-focus.” To control the laser energy density on a target, we have introduced a continuously variable attenuator between the output of the laser and the imaged aperture to manipulate the energy to a desired level by running the laser in a “constant voltage” mode to eliminate changes in the lasers’ beam dimensions. This methodology leads to much better controllability/reproducibility for reliable pulsed laser deposition of high performance electronic thin films.

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

    NASA Technical Reports Server (NTRS)

    Vavilov, Y. N.; Dedenko, L. G.

    1985-01-01

    The intensity of narrow muon groups observed in Kolar Gold Field (KGF) at the depth of 3375 m.w.e. was calculated in terms of quark-gluon strings model for high energy hadron - air nuclei interactions by the method of direct modeling of nuclear cascade in the air and muon propagation in the ground for normal primary cosmic ray composition. The calculated intensity has been found to be approx. 10 to the 4 times less than one observed experimentally.

  17. 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.

  18. New method for calculating binding energies in quantum mechanics and quantum field theories

    SciTech Connect

    Gat, G.; Rosenstein, B. Institute of Physics, Academia Sinica, Taipei, 11529 )

    1993-01-04

    We propose a systematic perturbative method for calculating the binding energy of threshold bound states---states which exist for arbitrary small coupling. The starting point is a (regularized) free theory. Explicit calculations are performed for quantum mechanics with arbitrary short-range potential in 1D and various (1+1)-dimensional quantum field theories. We check the method by comparing the results with exact formulas available in solvable models.

  19. Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.

    PubMed

    Lettieri, Steven; Mamonov, Artem B; Zuckerman, Daniel M

    2011-04-30

    Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via library-based Monte Carlo) and for obtaining absolute free energies using a polymer-growth formalism. Here, we combine the two approaches to extend the size of systems for which free energies can be calculated. We study a series of all-atom poly-alanine systems in a simple dielectric solvent and find that precise free energies can be obtained rapidly. For instance, for 12 residues, less than an hour of single-processor time is required. The combined approach is formally equivalent to the annealed importance sampling algorithm; instead of annealing by decreasing temperature, however, interactions among fragments are gradually added as the molecule is grown. We discuss implications for future binding affinity calculations in which a ligand is grown into a binding site.

  20. Calculation of neutron and gamma ray energy spectra for fusion reactor shield design: comparison with experiment

    SciTech Connect

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

    1980-08-01

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

  1. 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.

  2. Measuring the energy flux at the substrate position during magnetron sputter deposition processes

    SciTech Connect

    Cormier, P.-A.; Thomann, A.-L.; Dussart, R.; Semmar, N.; Mathias, J.; Balhamri, A.; Snyders, R.; Konstantinidis, S.

    2013-01-07

    In this work, the energetic conditions at the substrate were investigated in dc magnetron sputtering (DCMS), pulsed dc magnetron sputtering (pDCMS), and high power impulse magnetron sputtering (HiPIMS) discharges by means of an energy flux diagnostic based on a thermopile sensor, the probe being set at the substrate position. Measurements were performed in front of a titanium target for a highly unbalanced magnetic field configuration. The average power was always kept to 400 W and the probe was at the floating potential. Variation of the energy flux against the pulse peak power in HiPIMS was first investigated. It was demonstrated that the energy per deposited titanium atom is the highest for short pulses (5 {mu}s) high pulse peak power (39 kW), as in this case, the ion production is efficient and the deposition rate is reduced by self-sputtering. As the argon pressure is increased, the energy deposition is reduced as the probability of scattering in the gas phase is increased. In the case of the HiPIMS discharge run at moderate peak power density (10 kW), the energy per deposited atom was found to be lower than the one measured for DCMS and pDCMS discharges. In these conditions, the HiPIMS discharge could be characterized as soft and close to a pulsed DCMS discharge run at very low duty cycle. For the sake of comparison, measurements were also carried out in DCMS mode with a balanced magnetron cathode, in the same working conditions of pressure and power. The energy flux at the substrate is significantly increased as the discharge is generated in an unbalanced field.

  3. 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.

  4. Experimental investigation on the energy deposition and morphology of the electrical explosion of copper wire in vacuum

    NASA Astrophysics Data System (ADS)

    Shi, Zongqian; Shi, Yuanjie; Wang, Kun; Jia, Shenli

    2016-03-01

    This paper presents the experimental results of the electrical explosion of copper wires in vacuum using negative nanosecond-pulsed current with magnitude of 1-2 kA. The 20 μm-diameter copper wires with different lengths are exploded with three different current rates. A laser probe is applied to construct the shadowgraphy and interferometry diagnostics to investigate the distribution and morphology of the exploding product. The interference phase shift is reconstructed from the interferogram, by which the atomic density distribution is calculated. Experimental results show that there exist two voltage breakdown modes depending on the amount of the specific energy deposition. For the strong-shunting mode, shunting breakdown occurs, leading to the short-circuit-like current waveform. For the weak-shunting mode with less specific energy deposition, the plasma generated during the voltage breakdown is not enough to form a conductive plasma channel, resulting in overdamped declining current waveform. The influence of the wire length and current rate on the characteristics of the exploding wires is also analyzed.

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

    SciTech Connect

    Rescigno, T.N.

    1991-08-01

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

  6. Charge deposition dependence and energy loss of electrons transmitted through insulating PET nanocapillaries

    NASA Astrophysics Data System (ADS)

    Keerthisinghe, D.; Dassanayake, B. S.; Wickramarachchi, S. J.; Stolterfoht, N.; Tanis, J. A.

    2013-12-01

    The charge deposition dependence and energy loss in the transmission of electrons through insulating polyethylene terephthalate (PET) were studied for incident energies of 500 and 800 eV. Charge evolution at the sample tilt angles ψ = 0.0° and -1.7° was investigated. After an initial quiescent period transmission was observed and found to reach equilibrium rather quickly. Inelastic behavior of the transmitted electrons was observed during the initial transmission as well as after reaching equilibrium for ψ = -1.7° for both incident energies.

  7. 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.

  8. Hot-electron-mediated desorption rates calculated from excited-state potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Olsen, Thomas; Gavnholt, Jeppe; Schiøtz, Jakob

    2009-01-01

    We present a model for desorption induced by (multiple) electronic transitions [DIET (DIMET)] based on potential energy surfaces calculated with the delta self-consistent field extension of density-functional theory. We calculate potential energy surfaces of CO and NO molecules adsorbed on various transition-metal surfaces and show that classical nuclear dynamics does not suffice for propagation in the excited state. We present a simple Hamiltonian describing the system with parameters obtained from the excited-state potential energy surface and show that this model can describe desorption dynamics in both the DIET and DIMET regimes and reproduce the power-law behavior observed experimentally. We observe that the internal stretch degree of freedom in the molecules is crucial for the energy transfer between the hot electrons and the molecule when the coupling to the surface is strong.

  9. Deposition of carbonate mud beds within high-energy subtidal sand Dunes, Bahamas

    SciTech Connect

    Dill, R.F.; Steinen, R.P.

    1988-01-01

    Laminated, carbonate mud beds are being deposited in the interisland channels of the Exuma Cays in the Bahamas. They are associated with stromatolites and interbedded with ooid sands that form large migrating subtidal dunes on flood tidal deltas and bars. Currents up to 3 knots sweep in and out of the 4-8 m deep channels 3 hours out of every 6 hours, creating a high-energy bank margin environment not usually considered to be the site of mud-sized particle deposition. Mud deposits reach thicknesses of 1 m and have individual beds 2-5 cm thick. When exposed to flowing seawater, bed surfaces become encrusted with carbonate cement and algal mats. The white interior of mud beds between the crusts appears homogeneous, is soft, and has the consistency of ''tooth paste.'' Loose uncemented ooid sand is found above and below the mud beds, showing that both are occupying the same depositional environment. Rip-up clasts of the crusted mud beds, formed by scour of underlying sands, are carried throughout the channels and accumulate as a lag deposit within the troughs of migrating dunes. Some clasts are colonized by algal mats that trap ooid and skeletal sands forming stromatolite structures that can grow up to 2 m high.

  10. 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.

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

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

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

  12. Methods of Calculating Ionization Energies of Multielectron (Five or More) Isoelectronic Atomic Ions

    PubMed Central

    Lang, Peter F.; Smith, Barry C.

    2013-01-01

    We have previously used simple empirical equations to reproduce the literature values of the ionization energies of isoelectronic sequences of up to four electrons which gave very good agreement. We reproduce here a kinetic energy expression with corrections for relativity and Lamb shift effects which give excellent agreement with the literature values. These equations become more complex as the number of electrons in the system increases. Alternative simple quadratic expressions for calculating ionization energies of multielectron ions are discussed. A set of coefficients when substituted into a simple expression produces very good agreement with the literature values. Our work shows that Slater's rules are not appropriate for predicting trends or screening constants. This work provides very strong evidence that ionization energies are not functions of complete squares, and when calculating ionization energies electron transition/relaxation has to be taken into account. We demonstrate clearly that for particular isoelectronic sequences, the ionizing electrons may occupy different orbitals and in such cases more than one set of constants are needed to calculate the ionization energies. PMID:23766674

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

    This paper presents a combined Monte Carlo and analytic approach to the calculation of the pixel-to-pixel distribution of proton-induced damage in a HgCdTe sensor array and compares the results to measured dark current distributions after damage by 63 MeV protons. The moments of the Coulombic, nuclear elastic and nuclear inelastic damage distributions were extracted from Monte Carlo simulations and combined to form a damage distribution using the analytic techniques first described in [1]. The calculations show that the high energy recoils from the nuclear inelastic reactions (calculated using the Monte Carlo code MCNPX [2]) produce a pronounced skewing of the damage energy distribution. While the nuclear elastic component (also calculated using the MCNPX) contributes only a small fraction of the total nonionizing damage energy, its inclusion in the shape of the damage across the array is significant. The Coulombic contribution was calculated using MRED [3-5], a Geant4 [4,6] application. The comparison with the dark current distribution strongly suggests that mechanisms which are not linearly correlated with nonionizing damage produced according to collision kinematics are responsible for the observed dark current increases. This has important implications for the process of predicting the on-orbit dark current response of the HgCdTe sensor array.

  14. Efficient calculation of relative binding free energies by umbrella sampling perturbation.

    PubMed

    Zeller, Fabian; Zacharias, Martin

    2014-12-01

    An important task of biomolecular simulation is the calculation of relative binding free energies upon chemical modification of partner molecules in a biomolecular complex. The potential of mean force (PMF) along a reaction coordinate for association or dissociation of the complex can be used to estimate binding affinities. A free energy perturbation approach, termed umbrella sampling (US) perturbation, has been designed that allows an efficient calculation of the change of the PMF upon modification of a binding partner based on the trajectories obtained for the wild type reference complex. The approach was tested on the interaction of modified water molecules in aqueous solution and applied to in silico alanine scanning of a peptide-protein complex. For the water interaction test case, excellent agreement with an explicit PMF calculation for each modification was obtained as long as no long range electrostatic perturbations were considered. For the alanine scanning, the experimentally determined ranking and binding affinity changes upon alanine substitutions could be reproduced within 0.1-2.0 kcal/mol. In addition, good agreement with explicitly calculated PMFs was obtained mostly within the sampling uncertainty. The combined US and perturbation approach yields, under the condition of sufficiently small system modifications, rigorously derived changes in free energy and is applicable to any PMF calculation.

  15. 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

  16. X-ray Attenuation and Absorption Calculations.

    1988-02-25

    This point-source, polychromatic, discrete energy X-ray transport and energy deposition code system calculates first-order spectral estimates of X-ray energy transmission through slab materials and the associated spectrum of energy absorbed by the material.

  17. 1-D Van der Waals Foams Heated by Ion Beam Energy Deposition

    SciTech Connect

    Zylstra, A. B.; Barnard, J. J.; More, R. M.

    2009-12-23

    One dimensional simulations of various initial average density aluminum foams (modeled as slabs of solid metal separated by low density regions) heated by volumetric energy deposition are conducted with a Lagrangian hydrodynamics code using a van der Waals equation of tate (EOS). The resulting behavior is studied to facilitate the design of future warm dense matter (WDM) experiments at LBNL. In the simulations the energy deposition ranges from 10 to 30 kJ/g and from 0.075 to 4.0 ns total pulse length, resulting in temperatures from approximately 1 o 4 eV. We study peak pressures and temperatures in the foams, expansion velocity, and the phase evolution. Five relevant time scales in the problem are identified. Additionally, we present a method for characterizing the level of inhomogeneity in a foam target as it is heated and the time it takes for a foam to homogenize.

  18. 1-D Van der Waals Foams Heated by Ion Beam Energy Deposition

    SciTech Connect

    Zylstra, A; Barnard, J J; More, R M

    2010-03-19

    One dimensional simulations of various initial average density aluminum foams (modeled as slabs of solid metal separated by low density regions) heated by volumetric energy deposition are conducted with a Lagrangian hydrodynamics code using a van der Waals equation of state (EOS). The resulting behavior is studied to facilitate the design of future warm dense matter (WDM) experiments at LBNL. In the simulations the energy deposition ranges from 10 to 30 kJ/g and from 0.075 to 4.0 ns total pulse length, resulting in temperatures from approximately 1 to 4 eV. We study peak pressures and temperatures in the foams, expansion velocity, and the phase evolution. Five relevant time scales in the problem are identified. Additionally, we present a method for characterizing the level of inhomogeneity in a foam target as it is heated and the time it takes for a foam to homogenize.

  19. 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

  20. 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.

  1. 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.

  2. On the calculation of the gauge volume size for energy-dispersive X-ray diffraction.

    PubMed

    Rowles, Matthew R

    2011-11-01

    Equations for the calculation of the dimensions of a gauge volume, also known as the active volume or diffraction lozenge, in an energy-dispersive diffraction experiment where the detector is collimated by two ideal slits have been developed. Equations are given for equatorially divergent and parallel incident X-ray beams, assuming negligible axial divergence. PMID:21997921

  3. 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)

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

    ERIC Educational Resources Information Center

    Vargas, Francisco M.

    2014-01-01

    The temperature dependence of the Gibbs energy and important quantities such as Henry's law constants, activity coefficients, and chemical equilibrium constants is usually calculated by using the Gibbs-Helmholtz equation. Although, this is a well-known approach and traditionally covered as part of any physical chemistry course, the required…

  5. 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.

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

    SciTech Connect

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

    2007-01-01

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

  7. 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.

  8. Use of convolution/superposition-based treatment planning system for dose calculations in the kilovoltage energy range

    NASA Astrophysics Data System (ADS)

    Alaei, Parham

    2000-11-01

    A number of procedures in diagnostic radiology and cardiology make use of long exposures to x rays from fluoroscopy units. Adverse effects of these long exposure times on the patients' skin have been documented in recent years. These include epilation, erythema, and, in severe cases, moist desquamation and tissue necrosis. Potential biological effects from these exposures to other organs include radiation-induced cataracts and pneumonitis. Although there have been numerous studies to measure or calculate the dose to skin from these procedures, there have only been a handful of studies to determine the dose to other organs. Therefore, there is a need for accurate methods to measure the dose in tissues and organs other than the skin. This research was concentrated in devising a method to determine accurately the radiation dose to these tissues and organs. The work was performed in several stages: First, a three dimensional (3D) treatment planning system used in radiation oncology was modified and complemented to make it usable with the low energies of x rays used in diagnostic radiology. Using the system for low energies required generation of energy deposition kernels using Monte Carlo methods. These kernels were generated using the EGS4 Monte Carlo system of codes and added to the treatment planning system. Following modification, the treatment planning system was evaluated for its accuracy of calculations in low energies within homogeneous and heterogeneous media. A study of the effects of lungs and bones on the dose distribution was also performed. The next step was the calculation of dose distributions in humanoid phantoms using this modified system. The system was used to calculate organ doses in these phantoms and the results were compared to those obtained from other methods. These dose distributions can subsequently be used to create dose-volume histograms (DVHs) for internal organs irradiated by these beams. Using this data and the concept of normal tissue

  9. 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

  10. Energy Deposition in Magnetic Cloud and High Speed Stream Driven Storms

    NASA Astrophysics Data System (ADS)

    Mitchell, E. J.; Turner, N. E.

    2004-12-01

    The solar wind couples a large amount of energy into the magnetosphere-ionosphere system; this energy is released in the form of geomagnetic storms. While the precise mechanism for this coupling and release is yet unclear, it is well established that different solar wind conditions create different responses within the magnetosphere-ionosphere system. We are examining the impact of high speed stream-driven and magnetic cloud-driven storms on the global redistribution of energy throughout the magnetosphere-ionosphere system. Data are used from ACE, WIND, and ground magnetometers. We estimate the energy input and output for multiple geomagnetic storms spanning from1995 to 1998. The comparison of storms reveals high speed stream-driven storms deposit less energy per second, but over longer durations. The comparison further reveals magnetic cloud-driven storms have deeper Dst* depressions but with shorter durations. Our results suggest magnetic cloud-driven storms with similar input parameters as high speed stream-driven storms produce an overall lower energy deposition.

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

    SciTech Connect

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

    2015-03-07

    A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB{sub 4} molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q){sup −2} type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH{sub 4} molecule is demonstrated.

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

    SciTech Connect

    Mezhenin, A V; Azyazov, V N

    2012-12-31

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

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  14. Improved method for calculating strain energy release rate based on beam theory

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  15. Energy deposition of H and He ion beams in hydroxyapatite films: A study with implications for ion-beam cancer therapy

    NASA Astrophysics Data System (ADS)

    Limandri, Silvina; de Vera, Pablo; Fadanelli, Raul C.; Nagamine, Luiz C. C. M.; Mello, Alexandre; Garcia-Molina, Rafael; Behar, Moni; Abril, Isabel

    2014-02-01

    Ion-beam cancer therapy is a promising technique to treat deep-seated tumors; however, for an accurate treatment planning, the energy deposition by the ions must be well known both in soft and hard human tissues. Although the energy loss of ions in water and other organic and biological materials is fairly well known, scarce information is available for the hard tissues (i.e., bone), for which the current stopping power information relies on the application of simple additivity rules to atomic data. Especially, more knowledge is needed for the main constituent of human bone, calcium hydroxyapatite (HAp), which constitutes 58% of its mass composition. In this work the energy loss of H and He ion beams in HAp films has been obtained experimentally. The experiments have been performed using the Rutherford backscattering technique in an energy range of 450-2000 keV for H and 400-5000 keV for He ions. These measurements are used as a benchmark for theoretical calculations (stopping power and mean excitation energy) based on the dielectric formalism together with the MELF-GOS (Mermin energy loss function-generalized oscillator strength) method to describe the electronic excitation spectrum of HAp. The stopping power calculations are in good agreement with the experiments. Even though these experimental data are obtained for low projectile energies compared with the ones used in hadron therapy, they validate the mean excitation energy obtained theoretically, which is the fundamental quantity to accurately assess energy deposition and depth-dose curves of ion beams at clinically relevant high energies. The effect of the mean excitation energy choice on the depth-dose profile is discussed on the basis of detailed simulations. Finally, implications of the present work on the energy loss of charged particles in human cortical bone are remarked.

  16. Constrained LDA ab-initio calculation of screening of charging energy in C60

    NASA Astrophysics Data System (ADS)

    Sau, Jay; Neaton, Jeffrey; Khoo, K. H.; Choi, Hyoung; Louie, Steven; Cohen, Marvin

    2006-03-01

    Recent measurements and theoretical calculations of the electronic properties of C60 on metal substrates have shown that the electron-electron repulsion parameter U, which determines the coulomb blockade transport properties, is strongly screened in the presence of a metal susbtrate. Since standard Density Functional Theory calculations treat this charging energy in a mean field sense, it ignores the discreteness of the charge on the C60 that is critical to coulomb blockade. To account for the effect of the screened U in transport experiments we calculate the charging energy of C60 in a few environments using a constrained LDA approach and explore the implications for coulomb blockade transport phenomena. This work was supported by National Science Foundation Grant No. DMR04-39768 and by the Director, Office of Science, Office of Basic Energy Sciences, Division of Material Sciences and Engineering, U. S Department of Energy under Contract No. DE-AC03-76SF00098. Computational resources have been provided by DOE at the National Energy Research Scientific Computing Center(NERSC)

  17. Determination of Electron and Ion Energy Distribution Functions in a Plasma Ion Assisted Deposition (PIAD) Process

    NASA Astrophysics Data System (ADS)

    Harhausen, J.; Foest, R.; Ohl, A.

    2011-10-01

    High performance optical coatings are commonly produced by PIAD in order to achieve comparably high deposition rates. Here, the plasma source is a hot cathode direct current discharge with an auxiliary magnetic field (APS). Its design is such to generate a population of fast ions to be released into the deposition chamber. A detailed understanding of the plasma properties in the chamber is mandatory to increase the level of uniformity and reproducibility of the deposition process. In order to determine the electron and ion energy distribution functions (EEDF, IEDF) the concepts of the Langmuir probe, the retarding field energy analyzer and optical emission spectroscopy are employed. Fundamental findings are that the EEDF can be described in the framework of the non-local approximation and that the degree of ionization inside the APS is close to unity. The shape of the IEDF and its evolution along the beam path can be described consistently by considering charge exchange reactions with the background neutral gas and the profile of the plasma potential. High performance optical coatings are commonly produced by PIAD in order to achieve comparably high deposition rates. Here, the plasma source is a hot cathode direct current discharge with an auxiliary magnetic field (APS). Its design is such to generate a population of fast ions to be released into the deposition chamber. A detailed understanding of the plasma properties in the chamber is mandatory to increase the level of uniformity and reproducibility of the deposition process. In order to determine the electron and ion energy distribution functions (EEDF, IEDF) the concepts of the Langmuir probe, the retarding field energy analyzer and optical emission spectroscopy are employed. Fundamental findings are that the EEDF can be described in the framework of the non-local approximation and that the degree of ionization inside the APS is close to unity. The shape of the IEDF and its evolution along the beam path can be

  18. Simulation of submarine gas hydrate deposits as a sustainable energy source and CO2 storage

    NASA Astrophysics Data System (ADS)

    Janicki, G.; Hennig, T.; Schlüter, S.; Deerberg, G.

    2012-04-01

    Being aware that conventionally exploitable natural gas resources are limited, research concentrates on the development of new technologies for the extraction of methane from gas hydrate deposits in subsea sediments. The quantity of methane stored in hydrate form is considered to be a promising means to overcome future shortages in energy resources. In combination with storing carbon dioxide (CO2) as hydrates in the deposits chances for sustainable energy supply systems are given. The combustion of hydrate-based natural gas can contribute to the energy supply, but the coupled CO2 emissions cause climate change effects. At present, the possible options to capture and subsequently store CO2 (CCS-Technology) become of particular interest. To develop a sustainable hydrate-based energy supply system, the production of natural gas from hydrate deposits has to be coupled with the storage of CO2. Hence, the simultaneous storage of CO2 in hydrate deposits has to be developed. Decomposition of methane hydrate in combination with CO2 sequestration appears to be promising because CO2 hydrate is stable within a wider range of pressure and temperature than methane hydrate. As methane hydrate provides structural integrity and stability in its natural formation, incorporating CO2 hydrate as substitute for methane hydrate will help to preserve the natural sediments' stability. Regarding the technological implementation, many problems have to be overcome. Especially heat and mass transfer in the deposits are limiting factors causing very long process times. Within the scope of the German research project »SUGAR«, different technological approaches are evaluated and compared by means of dynamic system simulations and analysis. Detailed mathematical models for the most relevant chemical and physical effects are developed. The basic mechanisms of gas hydrate formation/dissociation and heat and mass transport in porous media are considered and implemented into simulation programs like

  19. Unloading Versus Driven Processes Derived from Auroral Energy Deposition and Polar Cap Size

    NASA Technical Reports Server (NTRS)

    Brittnacher, M. J.; Parks, G. K.; Fillingim, M. O.; Elsen, R.; Chua, D.; Germany, G. A.; Spann, J. F., Jr.

    1998-01-01

    The intensity of far ultraviolet auroral emissions at all local times during the three substorm phases has been monitored by the Ultraviolet Imager (UVI) on the Polar spacecraft for many substorms. Changes in the energy flux and characteristic energy of the precipitating electrons can be derived from these observations by modeling of the spectral emission processes. The global and local energy deposition is a new parameter that can be used in substorm studies since it provides a measure of energy transfer from the tail to the ionosphere due to precipitating electrons at a time resolution of three minutes. The polar cap area and area of auroral emissions can also be determined at high time resolution during substorms from the UVI images. An example of a substorm that appears to be driven by solar wind dynamic pressure alone will be presented. The polar cap area and other parameters do not indicate a growth phase prior to substorm onset. In another example, the slow growth phase followed by a very rapid increase in energy deposition during the expansion phase will be shown. This substorm was preceded by a southward IMF orientation. In these two examples, the role the solar wind in determining polar cap area is discussed. The time development of the area of auroral emissions is also discussed in relation to substorm phase and energy deposition. If the auroral emissions occur on closed field lines then the area of auroral emissions may provide an indication of changes in the thickness of the plasma sheet during each substorm phase.

  20. 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

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Shah, Syed Naseem Hussain

    2010-07-01

    This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function. The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.

  4. 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.

  5. Parametric study of the energy deposition inside the calorimeter measuring the nuclear heating in Material Testing Reactors

    NASA Astrophysics Data System (ADS)

    Amharrak, H.; Reynard-Carette, C.; Lyoussi, A.; Carette, M.; Brun, J.; De Vita, C.; Fourmentel, D.; Villard, J.-F.

    2015-11-01

    The nuclear heating measurements in Material Testing Reactors (MTRs) are crucial for the study of nuclear materials and fuels under irradiation. The reference measurements of this nuclear heating are especially performed by a differential calorimeter including a graphite sample material and two calorimetric cells. Then these measurements are used for other experimental conditions in order to predict the nuclear heating and thermal conditions induced in the irradiation devices. This paper will present simulations with MCNP5 Monte-Carlo transport code (using ENDF/B-VI nuclear data library) to evaluate the nuclear heating inside the calorimeter during irradiation campaigns of the CARMEN-1P mock-up inside OSIRIS reactor periphery (MTR based on Saclay, France). The whole complete geometry of the sensor has been considered. The calculation method corresponds to a calculation in two steps. Consequently, we used as an input source in the model, the neutron and photon spectra calculated in various experimental locations tested during the irradiation campaign (H9, H10, H11, D9). After a description of the differential calorimeter sensor, the MCNP5 model used for the calculations of nuclear heating inside the calorimeter elements is introduced by two quantities: KERMA and energy deposition rate per mass unit. The Charged Particle Equilibrium (CPE) inside the calorimeter elements is studied. The contribution of prompt gamma and neutron is determined. A comparison between this total nuclear heating calculation and the experimental results in a graphite sample will be made. Then parametric studies performed on the influence of the various calorimeter components on the nuclear heating are presented and discussed. The studies of the influence of the nature of materials, the sensor jacket, the source type and the comparison of the results obtained for the two calorimetric cells leads to some proposals for the sensor improvement.

  6. Energy deposition of heavy ions in the regime of strong beam-plasma correlations.

    PubMed

    Gericke, D O; Schlanges, M

    2003-03-01

    The energy loss of highly charged ions in dense plasmas is investigated. The applied model includes strong beam-plasma correlation via a quantum T-matrix treatment of the cross sections. Dynamic screening effects are modeled by using a Debye-like potential with a velocity dependent screening length that guarantees the known low and high beam velocity limits. It is shown that this phenomenological model is in good agreement with simulation data up to very high beam-plasma coupling. An analysis of the stopping process shows considerably longer ranges and a less localized energy deposition if strong coupling is treated properly.

  7. Front end energy deposition and collimation studies for IDS-NF

    SciTech Connect

    Rogers, C.; Neuffer, D.; Snopok, P.; /IIT, Chicago /Fermilab

    2011-03-01

    The function of the Neutrino Factory front end is to reduce the energy spread and size of the muon beam to a manageable level that will allow reasonable throughput to subsequent system components. Since the Neutrino Factory is a tertiary machine (protons to pions to muons), there is an issue of large background from the pion-producing target. The implications of energy deposition in the front end lattice for the Neutrino Factory are addressed. Several approaches to mitigating the effect are proposed and discussed, including proton absorbers, chicanes, beam collimation, and shielding.

  8. Energy deposition of heavy ions in the regime of strong beam-plasma correlations.

    PubMed

    Gericke, D O; Schlanges, M

    2003-03-01

    The energy loss of highly charged ions in dense plasmas is investigated. The applied model includes strong beam-plasma correlation via a quantum T-matrix treatment of the cross sections. Dynamic screening effects are modeled by using a Debye-like potential with a velocity dependent screening length that guarantees the known low and high beam velocity limits. It is shown that this phenomenological model is in good agreement with simulation data up to very high beam-plasma coupling. An analysis of the stopping process shows considerably longer ranges and a less localized energy deposition if strong coupling is treated properly. PMID:12689203

  9. 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.

  10. 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.

  11. Effect of energy deposition rate on plasma expansion characteristics and nanoparticle generation by electrical explosion of conductors

    NASA Astrophysics Data System (ADS)

    Sahoo, Somanand; Saxena, Alok K.; Kaushik, Trilok C.; Gupta, Satish C.

    2015-12-01

    The process of electrical explosion of metal conductors has been used to produce nano particles under normal atmospheric conditions. The impact of average rate of energy deposition, overheat factor on size distribution of particles and expansion characteristics of plasma generated from exploding conductors have been experimentally investigated. The particle size was characterized by TEM and XRD while expansion rate was measured using streak photography.The geometric mean diameter of size distribution was found to be influenced by rate of energy deposition in the conductors. It is observed that higher the rate of energy deposition, higher will be the expansion velocity, and smaller will be the size of particles formed.

  12. Low-Energy Plasma Spray (LEPS) Deposition of Hydroxyapatite/Poly-ɛ-Caprolactone Biocomposite Coatings

    NASA Astrophysics Data System (ADS)

    Garcia-Alonso, Diana; Parco, Maria; Stokes, Joseph; Looney, Lisa

    2012-01-01

    Thermal spraying is widely employed to deposit hydroxyapatite (HA) and HA-based biocomposites on hip and dental implants. For thick HA coatings (>150 μm), problems are generally associated with the build-up of residual stresses and lack of control of coating crystallinity. HA/polymer composite coatings are especially interesting to improve the pure HA coatings' mechanical properties. For instance, the polymer may help in releasing the residual stresses in the thick HA coatings. In addition, the selection of a bioresorbable polymer may enhance the coatings' biological behavior. However, there are major challenges associated with spraying ceramic and polymeric materials together because of their very different thermal properties. In this study, pure HA and HA/poly-ɛ-caprolactone (PCL) thick coatings were deposited without significant thermal degradation by low-energy plasma spraying (LEPS). PCL has never been processed by thermal spraying, and its processing is a major achievement of this study. The influence of selected process parameters on microstructure, composition, and mechanical properties of HA and HA/PCL coatings was studied using statistical design of experiments (DOE). The HA deposition rate was significantly increased by the addition of PCL. The average porosity of biocomposite coatings was slightly increased, while retaining or even improving in some cases their fracture toughness and microhardness. Surface roughness of biocomposites was enhanced compared with HA pure coatings. Cell culture experiments showed that murine osteoblast-like cells attach and proliferate well on HA/PCL biocomposite deposits.

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

    NASA Astrophysics Data System (ADS)

    Komatsu, Y.; Umemura, M.; Shoji, M.; Shiraishi, K.; Kayanuma, M.; Yabana, K.

    2014-03-01

    Among several proposed biosignatures, red edge is a direct evidence of photosynthetic life if it is detected (Kiang et al 2007). Red edge is a sharp change in reflectance spectra of vegetation in NIR region (about 700-750 nm). The sign of red edge is observed by Earthshine or remote sensing (Wolstencroft & Raven 2002, Woolf et al 2002). But, why around 700-750 nm? The photosynthetic organisms on Earth have evolved to optimize the sunlight condition. However, if we consider about photosynthetic organism on extrasolar planets, they should have developed to utilize the spectra of its principal star. Thus, it is not strange even if it shows different vegetation spectra. In this study, we focused on the light absorption mechanism of photosynthetic organisms on Earth and investigated the fundamental properties of the light harvesting mechanisms, which is the first stage for the light absorption. Light harvesting complexes contain photosynthetic pigments like chlorophylls. Effective light absorption and the energy transfer are accomplished by the electronic excitations of collective photosynthetic pigments. In order to investigate this mechanism, we constructed an energy transfer model by using a dipole-dipole approximation for the interactions between electronic excitations. Transition moments and transition energies of each pigment are calculated at the time-dependent density functional theory (TDDFT) level (Marques & Gross 2004). Quantum dynamics simulation for the excitation energy transfer was calculated by the Liouvelle's equation. We adopted the model to purple bacteria, which has been studied experimentally and known to absorb lower energy. It is meaningful to focus on the mechanism of this bacteria, since in the future mission, M planets will become a important target. We calculated the oscillator strengths in one light harvesting complex and confirmed the validity by comparing to the experimental data. This complex is made of an inner and an outer ring. The

  14. Plutonium-aerosol emission rates and human pulmonary deposition calculations for Nuclear Site 201, Nevada Test Site

    SciTech Connect

    Shinn, J.H.; Homan, D.N.

    1982-06-21

    This study determined the plutonium-aerosol fluxes from the soil to quantify (1) the extent of potential human exposure by deep-lung retention of alpha-emitting particles; (2) the source term should there be any significant, long-term, transport of plutonium aerosols; and (3) the resuspension factor and rate so that, for the first time at any nuclear site, one may calculate how long it will take for wind erosion to carry away a significant amount of the contaminated soil. High-volume air samplers and cascade impactors were used to characterize the plutonium aerosols. Meteorological flux-profile methods were used to calculate dust and plutonium aerosol emission rates. A floorless wind tunnel (10-m long) was used to examine resuspension under steady-state, high wind speed. The resuspension factor was two orders of magnitude lower than the other comparable sites at NTS and elsewhere, and the average resuspension rate of 5.3 x 10/sup -8//d was also very low, so that the half-time for resuspension by wind erosion was about 36,000 y.

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

    SciTech Connect

    Singleton, Robert L

    2012-09-10

    In this brief report, I summarize the rather involved recent work of Brown, Preston, and Singleton (BPS). In Refs. [2] and [3], BPS calculate the energy partition into ions and electrons as a charged particle traverses a non-equilibrium two-temperature plasma. These results are exact to leading and next-to-leading order in the plasma coupling g, and are therefore extremely accurate in a weakly coupled plasma. The new BPS calculations are compared with the more standard work of Fraley et al. [12]. The results differ substantially at higher temperature when T{sub I} {ne} T{sub e}.

  16. 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.

  17. Transformation of potential energy surfaces for estimating isotopic shifts in anharmonic vibrational frequency calculations

    SciTech Connect

    Meier, Patrick; Oschetzki, Dominik; Rauhut, Guntram; Berger, Robert

    2014-05-14

    A transformation of potential energy surfaces (PES) being represented by multi-mode expansions is introduced, which allows for the calculation of anharmonic vibrational spectra of any isotopologue from a single PES. This simplifies the analysis of infrared spectra due to significant CPU-time savings. An investigation of remaining deviations due to truncations and the so-called multi-level approximation is provided. The importance of vibrational-rotational couplings for small molecules is discussed in detail. In addition, an analysis is proposed, which provides information about the quality of the transformation prior to its execution. Benchmark calculations are provided for a set of small molecules.

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

    PubMed

    Rashev, Svetoslav; Moule, David C

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1999-06-01

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

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

    SciTech Connect

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

    2012-07-01

    Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the Shift Monte Carlo code within the SCALE code package. The methods were used for two small-scale test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods. (authors)

  1. Mayer sampling: calculation of cluster integrals using free-energy perturbation methods.

    PubMed

    Singh, Jayant K; Kofke, David A

    2004-06-01

    Free-energy simulation methods are applied toward the calculation of cluster integrals that appear in diagrammatic methods of statistical mechanics. In this approach, Monte Carlo sampling is performed on a number of molecules equal to the order of the integral, and configurations are weighted according to the absolute value of the integrand. An umbrella-sampling average yields the value of the cluster integral in reference to a known integral. Virial coefficients, up to the sixth for the Lennard-Jones model and the fifth for the SPCE model of water, are calculated as a demonstration.

  2. 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.

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

    PubMed

    Poehlsgaard, Jacob; Harpsøe, Kasper; Jørgensen, Flemming Steen; Olsen, Lars

    2012-02-27

    The binding affinity of a drug-like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, then the molecule is unlikely to bind to its target. Determination of the global minimum energy conformation and calculation of conformational penalties of binding is a prerequisite for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic compounds generated by conformational analysis with modified electrostatics are good approximations of the conformational distributions predicted by experimental data and with molecular dynamics performed in explicit solvent. Finally the method is used to calculate conformational penalties for zwitterionic GluA2 agonists and to filter false positives from a docking study. PMID:21985436

  4. 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.

  5. Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5–18 eV) electron interactions with DNA

    SciTech Connect

    Rezaee, Mohammad Hunting, Darel J.; Sanche, Léon

    2014-07-15

    be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.

  6. A Comparison of the ab Initio Calculated and Experimental Conformational Energies of Alkylcyclohexanes

    NASA Astrophysics Data System (ADS)

    Freeman, Fillmore; Tsegai, Zufan M.; Kasner, Marc L.; Hehre, Warren J.

    2000-05-01

    Ab initio 6-31G(d) and MP2/6-31G(d)//6-31G(d) methods were used to calculate the energies of the rotamers of the chair conformers of alkylcyclohexanes and trimethylsilylcyclohexane. The MP2/6-31G(d)//6-31G(d) calculated conformational energies ( ? or A values, in kcal/mol) of the alkylcyclohexanes (Me = 1.96; Et = 1.80; Pr = 1.73 iso-Pr = 1.60; t-Bu = 5.45; neo-pent = 1.32) and trimethylsilylcyclohexane (SiMe3 = 2.69) are similar to the experimental values. Plots of the calculated conformational energies for the alkylcyclohexanes and trimethylsilylcyclohexane versus their experimental values are linear (slope = 1.253 and r = .993 for 6-31G(d) and slope = 1.114 and r = .982 for MP2/6-31G(d)//6-31G(d)). The conformational energies are determined primarily by steric effects which include gauche (synclinal) interactions and repulsive nonbonded interactions in both the axial and equatorial conformers.

  7. A review on minimum energy calculations for ideal and nonideal distillations

    SciTech Connect

    Koehler, J.; Poellmann, P.; Blass, E.

    1995-04-01

    The minimum energy requirement of a distillation sets a lower, thermodynamically defined operating limit, which is increasingly important in practice due to growing interest in saving energy. During the conceptual design phase this energy information can also be used to quickly compare distillation configurations. This paper gives a summary of the most important methods published to date for the calculation of the minimum energy requirement. Firstly, the occurrence of so-called pinch zones will be systematically described. These are sections of the column in which at minimum reflux an infinite number of separation stages would be necessary. Then exact and approximating solutions of the problems both for ideal and for nonideal mixtures will be discussed. For ideal mixtures a rapid calculation is possible using the well-known Underwood equations, which can also be applied to complex columns (e.g., several feeds and side products, side stream strippers and enrichers). However, strongly nonideal multicomponent mixtures still require time-consuming simulations of columns having large numbers of plates. In such cases serious convergence problems must often be reckoned with. Recent developments aim at avoiding column simulations and at calculating pinch points directly.

  8. 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.

  9. Glasses and Liquids Low on the Energy Landscape Prepared by Physical Vapor Deposition

    NASA Astrophysics Data System (ADS)

    Dalal, Shakeel; Fakhraai, Zahra; Ediger, Mark

    2014-03-01

    The lower portions of the potential energy landscape for glass-forming materials such as polymers and small molecules were historically inaccessible by experiments. Physical vapor deposition is uniquely able to prepare materials in this portion of the energy landscape, with the properties of the deposited material primarily modulated by the substrate temperature. Here we report on high-throughput experiments which utilize a temperature gradient stage to enable rapid screening of vapor-deposited organic glasses. Using ellipsometry, we characterize a 100 K range of substrate temperatures in a single experiment, allowing us to rapidly determine the density, kinetic stability, fictive temperature and molecular orientation of these glasses. Their properties fall into three temperature regimes. At substrate temperatures as low as 0.97Tg, we prepare materials which are equivalent to the supercooled liquid produced by cooling the melt. Below 0.9Tg (1.16TK) the properties of materials are kinetically controlled and highly tunable. At intermediate substrate temperatures we are able to produce materials whose bulk properties match those expected for the equilibrium supercooled liquid, down to 1.16TK, but are structurally anisotropic.

  10. 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.

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

    PubMed Central

    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. PMID:24432201

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  13. 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.

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

    PubMed

    Ceriotti, Michele; Manolopoulos, David E

    2012-09-01

    Light nuclei at room temperature and below exhibit a kinetic energy which significantly deviates from the predictions of classical statistical mechanics. This quantum kinetic energy is responsible for a wide variety of isotope effects of interest in fields ranging from chemistry to climatology. It also furnishes the second moment of the nuclear momentum distribution, which contains subtle information about the chemical environment and has recently become accessible to deep inelastic neutron scattering experiments. Here, we show how, by combining imaginary time path integral dynamics with a carefully designed generalized Langevin equation, it is possible to dramatically reduce the expense of computing the quantum kinetic energy. We also introduce a transient anisotropic Gaussian approximation to the nuclear momentum distribution which can be calculated with negligible additional effort. As an example, we evaluate the structural properties, the quantum kinetic energy, and the nuclear momentum distribution for a first-principles simulation of liquid water.

  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

    2012-09-01

    Light nuclei at room temperature and below exhibit a kinetic energy which significantly deviates from the predictions of classical statistical mechanics. This quantum kinetic energy is responsible for a wide variety of isotope effects of interest in fields ranging from chemistry to climatology. It also furnishes the second moment of the nuclear momentum distribution, which contains subtle information about the chemical environment and has recently become accessible to deep inelastic neutron scattering experiments. Here, we show how, by combining imaginary time path integral dynamics with a carefully designed generalized Langevin equation, it is possible to dramatically reduce the expense of computing the quantum kinetic energy. We also introduce a transient anisotropic Gaussian approximation to the nuclear momentum distribution which can be calculated with negligible additional effort. As an example, we evaluate the structural properties, the quantum kinetic energy, and the nuclear momentum distribution for a first-principles simulation of liquid water. PMID:23005275

  17. Ablation of atheroma by laser energy: a comparative study of the efficacy of different temporal rates of energy deposition

    NASA Astrophysics Data System (ADS)

    Ramsay, Donald J.; Walker, Philip J.; Dadswell, Nicola G.; May, James; Piper, James A.; Wacher, Christine

    1990-06-01

    Laser angioplasty continues to attract interest as a potential method for treating atherosclerotic arterial disease. Current efforts are aimed at finding the most effective combination of laser and delivery system. High energy pulsed ultraviolet or infrared lasers demonstrate good photoablative properties but there remain practical difficulties with the optical fibre delivery. Continuous wave lasers are widely used in conjunction with "hot-tip" fibres for thermal ablation but their direct (optical) ablation efficiency is low, causing significant surrounding thermal damage in soft tissue. While considerable attention has been directed previously at the ablative effects for different laser wavelengths, little systematic study has been made of the efficacy for different temporal rates of energy deposition. We have compared the efficacy for tissue ablation in cadaveric human aorta of three different laser systems with similar wavelengths in the visible (green) but different temporal rates of energy deposition. The laser sources were the continuous wave argon ion laser (514.5 nm), the high pulse energy, frequency doubled Nd:YAG laser (532 nm) and the copper vapour laser. The copper vapour laser is a high repetition rate, high average power, pulsed laser emitting in the green (511 nm) and yellow (578 nm) which has temporal characteristics intermediate between those of the Nd:YAG laser and the argon ion laser, and has the potential to be effective both for direct optical ablation and hot-tip thermal ablation.

  18. 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.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-01

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

  2. 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.

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

    SciTech Connect

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

    2014-09-21

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

  4. 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.

  5. 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.

  6. Calculating interaction energies in transition metal complexes with local electron correlation methods

    NASA Astrophysics Data System (ADS)

    Hill, J. Grant; Platts, James A.

    2008-10-01

    The results of density fitting and local approximations applied to the calculation of transition metal-ligand binding energies using second order Møller-Plesset perturbation theory are reported. This procedure accurately reproduces counterpoise corrected binding energies from the canonical method for a range of test complexes. While counterpoise corrections for basis set superposition error are generally small, this procedure can be time consuming, and in some cases gives rise to unphysical dissociation of complexes. In circumventing this correction, a local treatment of electron correlation offers major efficiency savings with little loss of accuracy. The use of density fitting for the underlying Hartree-Fock calculations is also tested for sample Ru complexes, leading to further efficiency gains but essentially no loss in accuracy.

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

    SciTech Connect

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

    2012-09-04

    The {alpha} eigenvalue has implications for time-dependent problems where the system is sub- or supercritical. We present methods and results from calculating the {alpha}-eigenvalue spectrum for a continuous-energy infinite medium with a simplified Monte Carlo transport code. We formulate the {alpha}-eigenvalue problem, detail the Monte Carlo code physics, and provide verification and results. We have a method for calculating the {alpha}-eigenvalue spectrum in a continuous-energy infinite-medium. The continuous-time Markov process described by the transition rate matrix provides a way of obtaining the {alpha}-eigenvalue spectrum and kinetic modes. These are useful for the approximation of the time dependence of the system.

  8. 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.

  9. 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.

  10. S-matrix calculations of energy levels of the lithium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Sapirstein, J.; Cheng, K. T.

    2012-06-01

    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, 2p1/2 and 2p3/2 energy levels as well as the 2s-2p1/2 and 2s-2p3/2 transition energies for Z=10-100 is presented.

  11. S-matrix calculations of energy levels of the lithium isoelectronic sequence

    NASA Astrophysics Data System (ADS)

    Sapirstein, J.; Cheng, K. T.

    2011-01-01

    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, 2p1/2, and 2p3/2 energy levels as well as the 2s-2p1/2 and 2s-2p3/2 transition energies for Z=10-100 is presented.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  14. 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.

  15. 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

  16. 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

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

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

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

  18. DFT calculations on nitrodiborane compounds as new potential high energy materials.

    PubMed

    Abdelmalik, John; Ball, David W

    2010-05-01

    We have used DFT methods to determine the structures and thermochemistry of several nitro-substituted diborane molecules in an attempt to rate their potential as high energy materials. The properties of nitrodiborane, three isomers of dinitrodiborane, trinitrodiborane, and tetranitrodiborane were calculated using the B3LYP density functional method. Our results indicate that the absolute enthalpy of combustion decreases with increasing nitro content, in contrast with other nitro-substituted systems that have been studied previously.

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

    SciTech Connect

    Chibani, O. |

    1998-10-01

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

  20. Spectroscopic and electrical calculation of band alignment between atomic layer deposited SiO{sub 2} and β-Ga{sub 2}O{sub 3} (2{sup ¯}01)

    SciTech Connect

    Jia, Ye; Zeng, Ke; Singisetti, Uttam; Wallace, Joshua S.; Gardella, Joseph A

    2015-03-09

    The energy band alignment between atomic layer deposited (ALD) SiO{sub 2} and β-Ga{sub 2}O{sub 3} (2{sup ¯}01) is calculated using x-ray photoelectron spectroscopy and electrical measurement of metal-oxide semiconductor capacitor structures. The valence band offset between SiO{sub 2} and Ga{sub 2}O{sub 3} is found to be 0.43 eV. The bandgap of ALD SiO{sub 2} was determined to be 8.6 eV, which gives a large conduction band offset of 3.63 eV between SiO{sub 2} and Ga{sub 2}O{sub 3}. The large conduction band offset makes SiO{sub 2} an attractive gate dielectric for power devices.

  1. 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.

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

    PubMed

    Lundborg, Magnus; Lindahl, Erik

    2015-01-22

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

  3. 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.

  4. Transmission of electrons through insulating PET foils: Dependence on charge deposition, tilt angle and incident energy

    NASA Astrophysics Data System (ADS)

    Keerthisinghe, D.; Dassanayake, B. S.; Wickramarachchi, S. J.; Stolterfoht, N.; Tanis, J. A.

    2016-09-01

    Transmission of electrons through insulating polyethylene terephthalate (PET) nanocapillaries was observed as a function of charge deposition, angular and energy dependence. Two samples with capillary diameters 100 and 200 nm and pore densities 5 × 108/cm2 and 5 × 107/cm2, respectively, were studied for incident electron energies of 300, 500 and 800 eV. Transmission and steady state of the electrons were attained after a time delay during which only a few electron counts were observed. The transmission through the capillaries depended on the tilt angle with both elastic and inelastic electrons going through. The guiding ability of electrons was found to increase with the incident energy in contrast to previous measurements in our laboratory for a similar PET foil.

  5. On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations.

    PubMed

    Garate, Jose Antonio; Perez-Acle, Tomas; Oostenbrink, Chris

    2014-03-21

    Single-file water chains confined in carbon nanotubes have been extensively studied using molecular dynamics simulations. Specifically, the pore loading process of periodic (6,6) and (5,5) single-walled carbon nanotubes was thermodynamically characterized by means of free-energy calculations at every loading state and compared to bulk water employing thermodynamic cycles. Long simulations of each end-state allowed for the partitioning of the free energy into its energetic and entropic components. The calculations revealed that the initial loading states are dominated by entropic (both translational and rotational) components, whereas the latter stages are energetically driven by strong dipolar interactions among the water molecules in the file.

  6. 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.

  7. 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.

  8. Biasing Potential Replica Exchange Multi-Site λ-Dynamics for Efficient Free Energy Calculations

    PubMed Central

    Armacost, Kira A.; Goh, Garrett B.; Brooks, Charles L.

    2016-01-01

    Traditional free energy calculation methods are well known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. In the present work, we report on the development of biasing potential replica exchange multi-site λ-dynamics (BP-REX MSλD), which is a free energy method that is capable of performing simultaneous alchemical free energy transformations, including perturbations between flexible moieties. BP-REX MSλD and the original MSλD are applied to a series of symmetrical 2,5-benzoquinone derivatives covering a diverse chemical space and range of conformational flexibility. Improved λ-space sampling is observed for the BP-REX MSλD simulations, yielding a 2–5-fold increase in the number of transitions between substituents compared to traditional MSλD. We also demonstrate the efficacy of varying the value of c, the parameter that controls the ruggedness of the landscape mediating the sampling of λ-states, based on the flexibility of the fragment. Finally, we developed a protocol for maximizing the transition frequency between fragments. This protocol reduces the “kinetic barrier” for alchemically transforming fragments by grouping and ordering based on volume. These findings are applied to a challenging test set involving a series of geldanamycin-based inhibitors of heat shock protein 90 (Hsp90). Even though the perturbations span volume changes by as large as 60 Å3, the values for the free energy change achieve an average unsigned error (AUE) of 1.5 kcal/mol relative to experimental Kd measurements with a reasonable correlation (R = 0.56). Our results suggest that the BP-REX MSλD algorithm is a highly efficient and scalable free energy method, which when utilized will enable routine calculations on the order of hundreds of compounds using only a few simulations. PMID:26579773

  9. 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).

  10. Hydrodynamic planetary thermosphere model: 2. Coupling of an electron transport/energy deposition model

    NASA Astrophysics Data System (ADS)

    Tian, Feng; Solomon, Stanley C.; Qian, Liying; Lei, Jiuhou; Roble, Raymond G.

    2008-07-01

    An electron transport/energy deposition model is expanded to include atomic nitrogen and is coupled with a 1-D hydrodynamic thermosphere model. The coupled model is used to investigate the response of the Earth's thermosphere under extreme solar EUV conditions and is compared with previous studies. It is found that (1) the parameterization of Swartz and Nisbet (1972) underestimates the ambient electron heating by photoelectrons significantly in the upper thermosphere of the Earth under conditions with greater than 3 times the present solar EUV irradiance; (2) the transition of the Earth's thermosphere from a hydrostatic equilibrium regime to a hydrodynamic regime occurs at a smaller solar EUV flux condition when enhanced, more realistic, and self-consistent, ambient electron heating by photoelectrons is accounted for; (3) atomic nitrogen becomes the dominant neutral species in the upper thermosphere (competing against atomic oxygen) under extreme solar EUV conditions, and the electron impact processes of atomic nitrogen are important for both the chemistry and energetics in the corresponding thermosphere/ionosphere; (4) N+ remains a minor ion compared to O+, even when atomic nitrogen dominates the exobase; and (5) adiabatic cooling does not play an important role in electron gas energy budget. These findings highlight the importance of an electron transport/energy deposition model when investigating the thermosphere and ionosphere of terrestrial planets in their early evolutionary stages.

  11. 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

  12. 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.

  13. Calculations of many-particle--many-hole deformed state energies: Near degeneracies, deformation condensates

    SciTech Connect

    Zheng, D.C.; Berdichevsky, D.; Zamick, L.

    1988-07-01

    In deformed Hartree-Fock calculations with Skyrme interactions we observe a near degeneracy of the mean energies of many-particle--many-hole deformed intrinsic states. For example, in /sup 40/Ca the np-nh states with n = 2, 3, 4, 5, 6, 7, and 8 are nearly degenerate. The deformation parameter ..beta.. increases steadily from n = 2 to 8. The intrinsic state energy of the 8p-8h state is lower than that of the 4p-4h state for the interactions used here: SK III, SK IV, and SK VI. The calculations are also performed with the Skyrme III interaction for the even-even calcium and titanium isotopes. For /sup 44/Ti there is a near degeneracy of 6p-2h and 8p-4h. For the N>Z isotopes above, the two protons excitation lies lowest. Whereas the intrinsic state energies are much higher than the observed energies of the lowest-lying deformed states, the results when projection of J = 0/sup +/ states is carried out and pairing effects are taken into account, are encouraging.

  14. Calculations of many-particle-many-hole deformed state energies: Near degeneracies, deformation condensates

    NASA Astrophysics Data System (ADS)

    Zheng, D. C.; Berdichevsky, D.; Zamick, L.

    1988-07-01

    In deformed Hartree-Fock calculations with Skyrme interactions we observe a near degeneracy of the mean energies of many-particle-many-hole deformed intrinsic states. For example, in 40Ca the np-nh states with n=2, 3, 4, 5, 6, 7, and 8 are nearly degenerate. The deformation parameter β increases steadily from n=2 to 8. The intrinsic state energy of the 8p-8h state is lower than that of the 4p-4h state for the interactions used here-SK III, SK IV, and SK VI. The calculations are also performed with the Skyrme III interaction for the even-even calcium and titanium isotopes. For 44Ti there is a near degeneracy of 6p-2h and 8p-4h. For the N>Z isotopes above, the two protons excitation lies lowest. Whereas the intrinsic state energies are much higher than the observed energies of the lowest-lying deformed states, the results when projection of J=0+ states is carried out and pairing effects are taken into account, are encouraging.

  15. Role of suprathermal electrons during nanosecond laser energy deposit in fused silica

    SciTech Connect

    Grua, P.; Hébert, D.; Lamaignère, L.; Rullier, J.-L.

    2014-08-25

    An accurate description of interaction between a nanosecond laser pulse and a wide band gap dielectric, such as fused silica, requires the understanding of energy deposit induced by temperature changes occurring in the material. In order to identify the fundamental processes involved in laser-matter interaction, we have used a 1D computational model that allows us to describe a wide set of physical mechanisms and intended for comparison with specially designed “1D experiments.” We have pointed out that suprathermal electrons are very likely implicated in heat conduction, and this assumption has allowed the model to reproduce the experiments.

  16. PIV analysis of the homogeneity of energy deposition during development of a plasma actuator channel

    NASA Astrophysics Data System (ADS)

    Glazyrin, F. N.; Znamenskaya, I. A.; Mursenkova, I. V.; Naumov, D. S.; Sysoev, N. N.

    2016-01-01

    Nonstationary velocity fields that arise during the development of flows behind shock (blast) waves initiated by pulsed surface sliding discharge in air at a pressure of (2-4) × 104 Pa have been experimentally studied by the particle image velocimetry (PIV) technique. Plasma sheets (nanosecond discharges slipping over a dielectric surface) were initiated on walls of a rectangular chamber. Spatial analysis of the shape of shock-wave fronts and the distribution of flow velocities behind these waves showed that the pulsed energy deposition is homogeneous along discharge channels of a plasma sheet, while the integral visible plasma glow intensity decreases in the direction of channel propagation.

  17. Direct evidence of strongly inhomogeneous energy deposition in target heating with laser-produced ion beams.

    PubMed

    Brambrink, E; Schlegel, T; Malka, G; Amthor, K U; Aléonard, M M; Claverie, G; Gerbaux, M; Gobet, F; Hannachi, F; Méot, V; Morel, P; Nicolai, P; Scheurer, J N; Tarisien, M; Tikhonchuk, V; Audebert, P

    2007-06-01

    We report on strong nonuniformities in target heating with intense, laser-produced proton beams. The observed inhomogeneity in energy deposition can strongly perturb equation of state (EOS) measurements with laser-accelerated ions which are planned in several laboratories. Interferometric measurements of the target expansion show different expansion velocities on the front and rear surfaces, indicating a strong difference in local temperature. The nonuniformity indicates at an additional heating mechanism, which seems to originate from electrons in the keV range. PMID:17677318

  18. Energy deposition in parallel-plate plasma accelerators. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Dicapua, M. S.

    1971-01-01

    To appraise the ratio of energy deposition into kinetic and thermal modes in plasma accelerators, a parallel-plate plasma accelerator has been operated in the quasi-steady mode with current pulses in the range of 10 to 100 kilo-amperes (kA), durations of the order of one millisecond, and argon mass flows up to 100 grams/sec. From photographic observations, spectroscopic measurements of velocity and electron density, and pressure measurements with a fast-rise piezoelectric transducer it is found that, for currents between 50 and 90 kA, the accelerated argon plasma is supersonic with ion velocities of 5 to 6 kilometers/sec.

  19. 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.

  20. 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.

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

    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. PMID:25637967

  2. Molecular dynamics and free energy perturbation calculations on fluorocarbons and aspartyl protease inhibitors

    SciTech Connect

    Gough, C.A.

    1992-01-01

    Molecular dynamics (MD) simulations of pure tetrafluoromethane and trifluoromethane were performed to determine the van der Waals parameters R[sup *] and [epsilon] for fluorine and for the hydrogen of trifluoromethane. The best values of R[sup *] and [epsilon] for fluorine were determined to be 1.75 [angstrom] and 0.061 kcal/mole. For the hydrogen, the optimal R[sup *] and [epsilon] were determined to be 1.21 [angstrom] and 0.015 kcal/mole. The relative free energies of aqueous solvation of several fluorinated derivatives of methane were calculated using the FEP method. The calculations duplicated the experimental free energies relatively well, but the calculation of the bond-potential of mean force (bond-PMF) contribution was necessary in order to get the most satisfactory agreement with experiment. In addition, results of an ethanol-to-ethane perturbation in aqueous solution show that the bond-PMF contribution is important even for FEP calculations not involving large changes in size if the length of a bond is changed during the perturbation. MD simulations were run to determine the structure of the waters solvating fluoromethane, trifluoromethane, and tetrafluoromethane. The calculated radical distribution functions and water orientations suggest that, on average, there is one water-fluorine hydrogen bond in the case of fluoromethane. In contrast, there is no evidence of water-flourine hydrogen-bonding in the cases of trifluoromethane or tetrafluoromethane. These results suggest that the greater aqueous solubility of fluromethane relative to trifluoromethane is largely due to the poorer quality of the water-fluorine electrostatic interactions in trifluoromethane.

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

    PubMed Central

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

    2015-01-01

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

  4. Low energy cluster beam deposited BN films as the cascade for field emission

    NASA Astrophysics Data System (ADS)

    Song, F.; Zhang, L.; Zhu, L.; Ge, J.; Wang, G.

    2005-07-01

    The atomic deposited BN films with the thickness of nanometers (ABN) were prepared by radio frequency magnetron sputtering method and the nanostructured BN films (CBN) were prepared by Low Energy Cluster Beam Deposition. UV-Vis Absorption measurement proves the band gap of 4.27 eV and field emission of the BN films were carried out. F-N plots of all the samples give a good fitting and demonstrate the F-N tunneling of the emission process. The emission of ABN begins at the electric field of 14.6 V/μ m while that of CBN starts at 5.10 V/μ m. Emission current density of 1 mA/cm2 for ABN needs the field of 20 V/μ m while that of CBN needs only 12.1 V/μ m. The cluster-deposited BN on n-type Silicon substrate proves a good performance in terms of the lower gauge voltage, more emission sites and higher electron intensity and seems a promising substitute for the cascade of field emission.

  5. Sensing for directed energy deposition and powder bed fusion additive manufacturing at Penn State University

    NASA Astrophysics Data System (ADS)

    Nassar, Abdalla R.; Reutzel, Edward W.; Brown, Stephen W.; Morgan, John P.; Morgan, Jacob P.; Natale, Donald J.; Tutwiler, Rick L.; Feck, David P.; Banks, Jeffery C.

    2016-04-01

    Additive manufacturing of metal components through directed energy deposition or powder bed fusion is a complex undertaking, often involving hundreds or thousands of individual laser deposits. During processing, conditions may fluctuate, e.g. material feed rate, beam power, surrounding gas composition, local and global temperature, build geometry, etc., leading to unintended variations in final part geometry, microstructure and properties. To assess or control as-deposited quality, researchers have used a variety of methods, including those based on sensing of melt pool and plume emission characteristics, characteristics of powder application, and layer-wise imaging. Here, a summary of ongoing process monitoring activities at Penn State is provided, along with a discussion of recent advancements in the area of layer-wise image acquisition and analysis during powder bed fusion processing. Specifically, methods that enable direct comparisons of CAD model, build images, and 3D micro-tomographic scan data will be covered, along with thoughts on how such analyses can be related to overall process quality.

  6. 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

  7. 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.

  8. Free Energies of Redox Half-Reactions from First-Principles Calculations.

    PubMed

    Tazhigulov, Ruslan N; Bravaya, Ksenia B

    2016-07-01

    Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    SciTech Connect

    Hansen, L.F.

    1985-05-01

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

  11. 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.

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

    PubMed

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

    2015-09-28

    In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The protocol, coined LIE-D, builds on the linear relationship between the empirical coefficient γ in the standard LIE scheme and the D parameter, introduced in our work. The D-parameter encompasses the balance (difference) between electrostatic (polar) and van der Waals (nonpolar) energies in protein–ligand complexes. Leave-one-out cross-validation showed that LIE-D reproduced accurately the absolute binding free energies for our training set of protein–ligand complexes (<|error|> = 0.92 kcal/mol, SDerror = 0.66 kcal/mol, R(2) = 0.90, QLOO(2) = 0.89, and sPRESS(LOO) = 1.28 kcal/mol). We also demonstrated LIE-D robustness by predicting accurately the binding free energies for three different protein–ligand systems outside the training data set, where the electrostatic and van der Waals interaction energies were calculated with different force fields. PMID:26180998

  13. 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.

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

    PubMed

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

    2015-09-28

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

  15. Quantum chemical calculations of the reorganization energy of blue-copper proteins.

    PubMed Central

    Olsson, M. H.; Ryde, U.; Roos, B. O.

    1998-01-01

    The inner-sphere reorganization energy for several copper complexes related to the active site in blue-copper protein has been calculated with the density functional B3LYP method. The best model of the blue-copper proteins, Cu(Im)2(SCH3)(S(CH3)2)(0/+), has a self-exchange inner-sphere reorganization energy of 62 kJ/mol, which is at least 120 kJ/mol lower than for Cu(H2O)4(+/2+). This lowering of the reorganization energy is caused by the soft ligands in the blue-copper site, especially the cysteine thiolate and the methionine thioether groups. Soft ligands both make the potential surfaces of the complexes flatter and give rise to oxidized structures that are quite close to a tetrahedron (rather than tetragonal). Approximately half of the reorganization energy originates from changes in the copper-ligand bond lengths and half of this contribution comes from the Cu-S(Cys) bond. A tetragonal site, which is present in the rhombic type 1 blue-copper proteins, has a slightly higher (16 kJ/mol) inner-sphere reorganization energy than a trigonal site, present in the axial type 1 copper proteins. A site with the methionine ligand replaced by an amide group, as in stellacyanin, has an even higher reorganization energy, about 90 kJ/mol. PMID:9865961

  16. 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.

  17. High voltage electrophoretic deposition for electrochemical energy storage and other applications

    NASA Astrophysics Data System (ADS)

    Santhanagopalan, Sunand

    High voltage electrophoretic deposition (HVEPD) has been developed as a novel technique to obtain vertically aligned forests of one-dimensional nanomaterials for efficient energy storage. The ability to control and manipulate nanomaterials is critical for their effective usage in a variety of applications. Oriented structures of one-dimensional nanomaterials provide a unique opportunity to take full advantage of their excellent mechanical and electrochemical properties. However, it is still a significant challenge to obtain such oriented structures with great process flexibility, ease of processing under mild conditions and the capability to scale up, especially in context of efficient device fabrication and system packaging. This work presents HVEPD as a simple, versatile and generic technique to obtain vertically aligned forests of different one-dimensional nanomaterials on flexible, transparent and scalable substrates. Improvements on material chemistry and reduction of contact resistance have enabled the fabrication of high power supercapacitor electrodes using the HVEPD method. The investigations have also paved the way for further enhancements of performance by employing hybrid material systems and AC/DC pulsed deposition. Multi-walled carbon nanotubes (MWCNTs) were used as the starting material to demonstrate the HVEPD technique. A comprehensive study of the key parameters was conducted to better understand the working mechanism of the HVEPD process. It has been confirmed that HVEPD was enabled by three key factors: high deposition voltage for alignment, low dispersion concentration to avoid aggregation and simultaneous formation of holding layer by electrodeposition for reinforcement of nanoforests. A set of suitable parameters were found to obtain vertically aligned forests of MWCNTs. Compared with their randomly oriented counterparts, the aligned MWCNT forests showed better electrochemical performance, lower electrical resistance and a capability to

  18. Reactive ballistic deposition of nanostructured model materials for electrochemical energy conversion and storage.

    PubMed

    Flaherty, David W; Hahn, Nathan T; May, R Alan; Berglund, Sean P; Lin, Yong-Mao; Stevenson, Keith J; Dohnalek, Zdenek; Kay, Bruce D; Mullins, C Buddie

    2012-03-20

    Porous, high surface area materials have critical roles in applications including catalysis, photochemistry, and energy storage. In these fields, researchers have demonstrated that the nanometer-scale structure modifies mechanical, optical, and electrical properties of the material, greatly influencing its behavior and performance. Such complex chemical systems can involve several distinct processes occurring in series or parallel. Understanding the influence of size and structure on the properties of these materials requires techniques for producing clean, simple model systems. In the fields of photoelectrochemistry and lithium storage, for example, researchers need to evaluate the effects of changing the electrode structure of a single material or producing electrodes of many different candidate materials while maintaining a distinctly favorable morphology. In this Account, we introduce our studies of the formation and characterization of high surface area, porous thin films synthesized by a process called reactive ballistic deposition (RBD). RBD is a simple method that provides control of the morphology, porosity, and surface area of thin films by manipulating the angle at which a metal-vapor flux impinges on the substrate during deposition. This approach is largely independent of the identity of the deposited material and relies upon limited surface diffusion during synthesis, which enables the formation of kinetically trapped structures. Here, we review our results for the deposition of films from a number of semiconductive materials that are important for applications such as photoelectrochemical water oxidation and lithium ion storage. The use of RBD has enabled us to systematically control individual aspects of both the structure and composition of thin film electrodes in order to probe the effects of each on the performance of the material. We have evaluated the performance of several materials for potential use in these applications and have identified

  19. Reactive ballistic deposition of nanostructured model materials for electrochemical energy conversion and storage.

    PubMed

    Flaherty, David W; Hahn, Nathan T; May, R Alan; Berglund, Sean P; Lin, Yong-Mao; Stevenson, Keith J; Dohnalek, Zdenek; Kay, Bruce D; Mullins, C Buddie

    2012-03-20

    Porous, high surface area materials have critical roles in applications including catalysis, photochemistry, and energy storage. In these fields, researchers have demonstrated that the nanometer-scale structure modifies mechanical, optical, and electrical properties of the material, greatly influencing its behavior and performance. Such complex chemical systems can involve several distinct processes occurring in series or parallel. Understanding the influence of size and structure on the properties of these materials requires techniques for producing clean, simple model systems. In the fields of photoelectrochemistry and lithium storage, for example, researchers need to evaluate the effects of changing the electrode structure of a single material or producing electrodes of many different candidate materials while maintaining a distinctly favorable morphology. In this Account, we introduce our studies of the formation and characterization of high surface area, porous thin films synthesized by a process called reactive ballistic deposition (RBD). RBD is a simple method that provides control of the morphology, porosity, and surface area of thin films by manipulating the angle at which a metal-vapor flux impinges on the substrate during deposition. This approach is largely independent of the identity of the deposited material and relies upon limited surface diffusion during synthesis, which enables the formation of kinetically trapped structures. Here, we review our results for the deposition of films from a number of semiconductive materials that are important for applications such as photoelectrochemical water oxidation and lithium ion storage. The use of RBD has enabled us to systematically control individual aspects of both the structure and composition of thin film electrodes in order to probe the effects of each on the performance of the material. We have evaluated the performance of several materials for potential use in these applications and have identified

  20. Theoretical investigation into the feasibility to deposit RF energy centrally in the head-and-neck region

    SciTech Connect

    Paulides, Margarethus M. . E-mail: M.Paulides@ErasmusMC.nl; Vossen, Stefan H.J.A.; Zwamborn, Adrianus P.M.; Rhoon, Gerard C. van

    2005-10-01

    Purpose: To investigate the ability to deposit radiofrequency energy centrally in the neck as a function of antenna positions, number of antennas, and operating frequency. Methods and Materials: Power absorption (PA) distributions in a realistic model of the head-and-neck anatomy are calculated in which the head model is irradiated by an array of dipole antennas. The relative PA distributions corresponding to different setups are visualized and analyzed using the ratio of the average PA (aPA) in the target and neck region. Results: Both the PA distributions and aPA ratios indicate an optimal focusing ability of the setups (i.e., the ability to direct energy efficiently into the target region), between 400 and 600 MHz. In this frequency band, the focusing ability depends only moderately on the size of the neck. Finally, it is found that the focusing ability at 433 MHz is increased significantly by increasing the number of antenna elements. Conclusions: The optimal frequency is found to be highly dependent on the size of the target volume; thus, a single optimum is hard to define. However, future clinical research will focus on 433 MHz based on the optimal range of frequencies, as found in this study.

  1. On the importance of full-dimensionality in low-energy molecular scattering calculations.

    PubMed

    Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof

    2016-01-01

    Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm(-1) in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870

  2. Refractive index, band gap energy, dielectric constant and polarizability calculations of ferroelectric Ethylenediaminium Tetrachlorozincate crystal

    NASA Astrophysics Data System (ADS)

    Kalyanaraman, S.; Shajinshinu, P. M.; . Vijayalakshmi, S.

    2015-11-01

    Single crystal of Ethylenediaminium Tetrachlorozincate has been grown by slow evaporation method. The single crystal XRD study confirms the orthorhombic structure of the crystal. The presence of functional group vibrations are ascertained through FTIR and Raman studies. In optical studies, the insulating behaviour of the material is established by Tauc plot. The refractive index and the real dielectric constant of the crystal are calculated. The electronic polarizability in the high frequency optical region is also calculated from the dielectric constant values by using the Clausius-Mossotti equation. The large value of dielectric constant is identified through dielectric studies and it points to the ferroelectric behaviour of the material. Further an experimental study confirms the ferroelectric behaviour of the material. The total polarizability of the crystal owing to the space charge, dipole, ionic and electronic polarizability contributions is obtained experimentally, and it matches well with the theoretically obtained value from Penn analysis. Further, Plasmon energy and Fermi energy of the material are also calculated using Penn analysis.

  3. 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.

  4. 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

  5. Al(fcc):Al{sub 3}Sc(L1{sub 2}) interphase boundary energy calculations

    SciTech Connect

    Hyland, R.W. Jr.; Rohrer, C.L.; Asta, M.; Foiles, S.M.

    1998-06-12

    These calculations assess the applicability of classical nucleation theory to the reaction f.c.c. {r_arrow} L1{sub 2} occurring in dilute Al-Sc alloys. The orientation and temperature dependence of the energies of coherent Al(f.c.c.):Al{sub 3}Sc(L1{sub 2}) interphase boundaries were studied using atomistic simulation and a low temperature expansion (LTE) of the grand potential. Embedded atom method potentials were developed for both sets of calculations. Atomistic 0 K results for the anisotropy of the interphase boundary enthalpy gave {gamma}{sub (100)} < {gamma}{sub (110)} < {gamma}{sub (111)} with values of 32.5, 51.3, and 66.3 mJ/m{sup 2}, respectively. LTE calculations of the excess grand potential of the (100) interface predicted a nearly temperature independent interfacial energy below 400 K that decreased modestly above 400 K. Monte Carlo (MC) simulations produced a compositional diffuseness of about 4 atomic layers separating the two bulk phases. Because the spatial extent of this region is very similar to the classically determined critical nucleus dimensions extracted from nucleation rate data, it is concluded that critical nuclei of Al{sub 3}Sc are most likely of nonclassical design at high undercooling.

  6. Monte Carlo simulation of energy-deposit clustering for ions of the same LET in liquid water.

    PubMed

    Francis, Z; Incerti, S; Ivanchenko, V; Champion, C; Karamitros, M; Bernal, M A; El Bitar, Z

    2012-01-01

    This work presents a Monte Carlo study of energy depositions due to protons, alpha particles and carbon ions of the same linear-energy-transfer (LET) in liquid water. The corresponding track structures were generated using the Geant4-DNA toolkit, and the energy deposition spatial distributions were analyzed using an adapted version of the DBSCAN clustering algorithm. Combining the Geant4 simulations and the clustering algorithm it was possible to compare the quality of the different radiation types. The ratios of clustered and single energy depositions are shown versus particle LET and frequency-mean lineal energies. The estimated effect of these types of radiation on biological tissues is then discussed by comparing the results obtained for different particles with the same LET.

  7. Alternative Approaches to Calculate Benefits of an Energy Imbalance Market With Wind and Solar Energy: Preprint

    SciTech Connect

    Kirby, B.; King, J.; Milligan, M.

    2012-06-01

    The anticipated increase in variable generation in the Western Interconnection over the next several years has raised concerns about how to maintain system balance, especially in smaller Balancing Authority Areas (BAAs). Given renewable portfolio standards in the West, it is possible that more than 50 gigawatts of wind capacity will be installed by 2020. Significant quantities of solar generation are likely to be added as well. The consequent increase in variability and uncertainty that must be managed by the conventional generation fleet and responsive loads has resulted in a proposal for an Energy Imbalance Market (EIM). This paper extends prior work to estimate the reserve requirements for regulation, spinning, and non-spinning reserves with and without the EIM. We also discuss alternative approaches to allocating reserve requirements and show that some apparently attractive allocation methods have undesired consequences.

  8. 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

  9. SU-E-T-491: Importance of Energy Dependent Protons Per MU Calibration Factors in IMPT Dose Calculations Using Monte Carlo Technique

    SciTech Connect

    Randeniya, S; Mirkovic, D; Titt, U; Guan, F; Mohan, R

    2014-06-01

    Purpose: In intensity modulated proton therapy (IMPT), energy dependent, protons per monitor unit (MU) calibration factors are important parameters that determine absolute dose values from energy deposition data obtained from Monte Carlo (MC) simulations. Purpose of this study was to assess the sensitivity of MC-computed absolute dose distributions to the protons/MU calibration factors in IMPT. Methods: A “verification plan” (i.e., treatment beams applied individually to water phantom) of a head and neck patient plan was calculated using MC technique. The patient plan had three beams; one posterior-anterior (PA); two anterior oblique. Dose prescription was 66 Gy in 30 fractions. Of the total MUs, 58% was delivered in PA beam, 25% and 17% in other two. Energy deposition data obtained from the MC simulation were converted to Gy using energy dependent protons/MU calibrations factors obtained from two methods. First method is based on experimental measurements and MC simulations. Second is based on hand calculations, based on how many ion pairs were produced per proton in the dose monitor and how many ion pairs is equal to 1 MU (vendor recommended method). Dose distributions obtained from method one was compared with those from method two. Results: Average difference of 8% in protons/MU calibration factors between method one and two converted into 27 % difference in absolute dose values for PA beam; although dose distributions preserved the shape of 3D dose distribution qualitatively, they were different quantitatively. For two oblique beams, significant difference in absolute dose was not observed. Conclusion: Results demonstrate that protons/MU calibration factors can have a significant impact on absolute dose values in IMPT depending on the fraction of MUs delivered. When number of MUs increases the effect due to the calibration factors amplify. In determining protons/MU calibration factors, experimental method should be preferred in MC dose calculations

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

    PubMed

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

    2015-11-10

    Evaluation of solvation (binding) free energies with implicit solvent models in different dielectric environments for biological simulations as well as high throughput ligand screening remain challenging endeavors. In order to address how well implicit solvent models approximate explicit ones we examined four generalized Born models (GB(Still), GB(HCT), GB(OBC)I, and GB(OBC)II) for determining the dimerization free energy (ΔG(0)) of β-cyclodextrin monomers in 17 implicit solvents with dielectric constants (D) ranging from 5 to 80 and compared the results to previous free energy calculations with explicit solvents ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 12684 - 12693 ). The comparison indicates that neglecting the environmental dependence of Born radii appears acceptable for such calculations involving cyclodextrin and that the GB(Still) and GB(OBC)I models yield a reasonable estimation of ΔG(0), although the details of binding are quite different from explicit solvents. Large discrepancies between implicit and explicit solvent models occur in high-dielectric media with strong hydrogen bond (HB) interruption properties. ΔG(0) with the GB models is shown to correlate strongly to 2(D-1)/(2D+1) (R(2) ∼ 0.90) in line with the Onsager reaction field ( Onsager J. Am. Chem. Soc. 1936 , 58 , 1486 - 1493 ) but to be very sensitive to D (D < 10) as well. Both high-dielectric environments where hydrogen bonds are of interest and low-dielectric media such as protein binding pockets and membrane interiors therefore need to be considered with caution in GB-based calculations. Finally, a literature analysis of Gibbs energy of solvation of small molecules in organic liquids shows that the Onsager relation does not hold for real molecules since the correlation between ΔG(0) and 2(D-1)/(2D+1) is low for most solutes. Interestingly, explicit solvent calculations of the solvation free energy ( Zhang et al. J. Chem. Inf. Model . 2015 , 55 , 1192 - 1201 ) reproduce the weak

  11. 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.

  12. The impact of covariance information on criticality safety calculations in the resolved resonance energy range.

    SciTech Connect

    Naberejnev, D. G.; Palmiotti, G.; Yang, W. S.

    2004-06-11

    Resonance data play a significant role in the calculations of systems considered for criticality safety applications. K{sub eff}, the major parameter of interest in such a type of calculations, can be heavily dependent both on the quality of the resonance data as well as on the accuracy achieved in the processing of these data. If reasonable uncertainty values are available, in conjunction with their correlation in energy and among type of resonance parameters, one can exploit existing methodologies, based on perturbation theory, in order to evaluate their impact on the integral parameter of interest, i.e., K{sub eff} in our case, in practical applications. In this way, one could be able to judge if the uncertainty on specific quantities, e.g., covariances on resonance data, have a significant impact and, therefore, deserve a careful evaluation. This report, first, will recall the basic principles that lie behind an uncertainty evaluation and review the current situation in the field of covariance data. Then an attempt is made for defining a methodology that allows calculating covariances values for resolved resonance parameters. Finally, practical applications, of interest for criticality safety calculations, illustrate the impact of different assumptions on correlations among resolved resonance parameters.

  13. Formation energies of intrinsic point defects in monoclinic VO2 studied by first-principles calculations

    NASA Astrophysics Data System (ADS)

    Cui, Yuanyuan; Liu, Bin; Chen, Lanli; Luo, Hongjie; Gao, Yanfeng

    2016-10-01

    VO2 is an attractive candidate for intelligent windows and thermal sensors. There are challenges for developing VO2-based devices, since the properties of monoclinic VO2 are very sensitive to its intrinsic point defects. In this work, the formation energies of the intrinsic point defects in monoclinic VO2 were studied through the first-principles calculations. Vacancies, interstitials, as well as antisites at various charge states were taken into consideration, and the finite-size supercell correction scheme was adopted as the charge correction scheme. Our calculation results show that the oxygen interstitial and oxygen vacancy are the most abundant intrinsic defects in the oxygen rich and oxygen deficient condition, respectively, indicating a consistency with the experimental results. The calculation results suggest that the oxygen interstitial or oxygen vacancy is correlated with the charge localization, which can introduce holes or electrons as free carriers and subsequently narrow the band gap of monoclinic VO2. These calculations and interpretations concerning the intrinsic point defects would be helpful for developing VO2-based devices through defect modifications.

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

    NASA Astrophysics Data System (ADS)

    Srivastava, Amit; Granek, Rony

    2015-02-01

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

  15. Heat deposition in thick targets due to interaction of high energy protons and thermal hydraulics analysis

    NASA Astrophysics Data System (ADS)

    Kumawat, H.; Dutta, D.; Mantha, V.; Mohanty, A. K.; Satyamurthy, P.; Choudhury, R. K.; Kailas, S.

    2008-02-01

    Heat deposition inside thick targets due to interaction of high energy protons (Ep ∼ GeV) has been estimated using an improved version of the Monte Carlo simulation code CASCADE.04.h. The results are compared with the available experimental data for thick targets of Be, Al, Fe, Cu, Pb and Bi at proton energies of 0.8 GeV, 1.0 GeV and 1.2 GeV. A more continuous heat deposition approach which has been adopted in CASCADE.04.h yields results which are in better agreement with the experimental data as compared to the ones from the earlier version of CASCADE.04. The results are also compared with the predictions of the FLUKA Monte Carlo code. Both CASCADE.04.h and FLUKA predictions are nearly similar for heavy targets and both agree with the experimental measurements. However, they do have differences in predictions for lighter targets where measurements also differ from the predictions. It is observed that the maximum heat loss in thick targets occurs at the beginning of the target due to increasing nuclear reaction contributions. This aspect is crucial in designing the window of a spallation neutron target employed in an accelerator driven sub-critical system (ADS) as this is the first material to be traversed by the proton beam and is subjected to the maximum temperature gradient. Optimization of the target-window parameters requires a careful estimation of heat deposition in the window region and this has been demonstrated through thermal hydraulic studies related to the design of a realistic lead bismuth eutectic (LBE) spallation neutron target for an ADS system.

  16. Ultrafast triggered transient energy storage by atomic layer deposition into porous silicon for integrated transient electronics.

    PubMed

    Douglas, Anna; Muralidharan, Nitin; Carter, Rachel; Share, Keith; Pint, Cary L

    2016-04-14

    Here we demonstrate the first on-chip silicon-integrated rechargeable transient power source based on atomic layer deposition (ALD) coating of vanadium oxide (VOx) into porous silicon. A stable specific capacitance above 20 F g(-1) is achieved until the device is triggered with alkaline solutions. Due to the rational design of the active VOx coating enabled by ALD, transience occurs through a rapid disabling step that occurs within seconds, followed by full dissolution of all active materials within 30 minutes of the initial trigger. This work demonstrates how engineered materials for energy storage can provide a basis for next-generation transient systems and highlights porous silicon as a versatile scaffold to integrate transient energy storage into transient electronics. PMID:26984120

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

    NASA Astrophysics Data System (ADS)

    Pham, Tri T.; Shirts, Michael R.

    2011-07-01

    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).

  18. 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

  19. Surface free energy of non-stick coatings deposited using closed field unbalanced magnetron sputter ion plating

    NASA Astrophysics Data System (ADS)

    Sun, Chen-Cheng; Lee, Shih-Chin; Dai, Shyue-Bin; Tien, Shein-Long; Chang, Chung-Chih; Fu, Yaw-Shyan

    2007-02-01

    Semiconductor IC packaging molding dies require wear resistance, corrosion resistance and non-sticking (with a low surface free energy). The molding releasing capability and performance are directly associated with the surface free energy between the coating and product material. The serious sticking problem reduces productivity and reliability. Depositing TiN, TiMoS, ZrN, CrC, CrN, NiCr, NiCrN, CrTiAlN and CrNiTiAlN coatings using closed field unbalanced magnetron sputter ion plating, and characterizing their surface free energy are the main object in developing a non-stick coating system for semiconductor IC molding tools. The contact angle of water, diiodomethane and ethylene glycol on the coated surfaces were measured at temperature in 20 °C using a Dataphysics OCA-20 contact angle analyzer. The surface free energy of the coatings and their components (dispersion and polar) were calculated using the Owens-Wendt geometric mean approach. The surface roughness was investigated by atomic force microscopy (AFM). The adhesion force of these coatings was measured using direct tensile pull-off test apparatus. The experimental results showed that NiCrN, CrN and NiCrTiAlN coatings outperformed TiN, ZrN, NiCr, CiTiAlN, CrC and TiMoS coatings in terms of non-sticking, and thus have the potential as working layers for injection molding industrial equipment, especially in semiconductor IC packaging molding applications.

  20. Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

    2016-02-01

    We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Long, Shiyang; Tian, Pu

    2016-03-01

    We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy.

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

    PubMed

    Wang, Kai; Long, Shiyang; Tian, Pu

    2016-01-01

    We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy. PMID:26974524

  4. 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

  5. Studies on high electronic energy deposition in transparent conducting indium tin oxide thin films

    NASA Astrophysics Data System (ADS)

    Deshpande, N. G.; Gudage, Y. G.; Ghosh, A.; Vyas, J. C.; Singh, F.; Tripathi, A.; Sharma, Ramphal

    2008-02-01

    We have examined the effect of swift heavy ions using 100 MeV Au8+ ions on the electrical properties of transparent, conducting indium tin oxide polycrystalline films with resistivity of 0.58 × 10-4 Ω cm and optical transmission greater than 78% (pristine). We report on the modifications occurring after high electronic energy deposition. With the increase in fluency, x-ray line intensity of the peaks corresponding to the planes (1 1 0), (4 0 0), (4 4 1) increased, while (3 3 1) remained constant. Surface morphological studies showed a pomegranate structure of pristine samples, which was highly disturbed with a high dose of irradiation. For the high dose, there was a formation of small spherical domes uniformly distributed over the entire surface. The transmittance was seen to be decreasing with the increase in ion fluency. At higher doses, the resistivity and photoluminescence intensity was seen to be decreased. In addition, the carrier concentration was seen to be increased, which was in accordance with the decrease in resistivity. The observed modifications after high electronic energy deposition in these films may lead to fruitful device applications.

  6. Initial studies of Bremsstrahlung energy deposition in small-bore superconducting undulator structures in linac environments

    SciTech Connect

    Cremer, T.; Tatchyn, R.

    1995-12-31

    One of the more promising technologies for developing minimal-length insertion devices for linac-driven, single-pass Free Electron Lasers (FELs) operating in the x-ray range is based on the use of superconducting (SC) materials. In recent FEL simulations, for example, a bifilar helical SC device with a 2 cm period and 1.8 T field was found to require a 30 m saturation length for operation at 1.5{Angstrom} on a 15 GeV linac, more than 40% shorter than an alternative hybrid/permanent magnet (hybrid/PM) undulator. AT the same time, however, SC technology is known to present characteristic difficulties for insertion device design, both in engineering detail and in operation. Perhaps the most critical problem, as observed, e.g., by Madey and co-workers in their initial FEL experiments, was the frequent quenching induced by scattered electrons upstream of their (bifilar) device. Postulating that this quenching was precipitated by directly-scattered or bremsstrahlung-induced particle energy deposited into the SC material or into material contiguous with it, the importance of numerical and experimental characterizations of this phenomenon for linac-based, user-facility SC undulator design becomes evident. In this paper we discuss selected prior experimental results and report on initial EGS4 code studies of scattered and bremsstrahlung induced particle energy deposition into SC structures with geometries comparable to a small-bore bifilar helical undulator.

  7. Atomic-layer-deposition-assisted formation of carbon nanoflakes on metal oxides and energy storage application.

    PubMed

    Guan, Cao; Zeng, Zhiyuan; Li, Xianglin; Cao, Xiehong; Fan, Yu; Xia, Xinhui; Pan, Guoxiang; Zhang, Hua; Fan, Hong Jin

    2014-01-29

    Nanostructured carbon is widely used in energy storage devices (e.g., Li-ion and Li-air batteries and supercapacitors). A new method is developed for the generation of carbon nanoflakes on various metal oxide nanostructures by combining atomic layer deposition (ALD) and glucose carbonization. Various metal oxide@nanoflake carbon (MO@f-C) core-branch nanostructures are obtained. For the mechanism, it is proposed that the ALD Al2 O3 and glucose form a composite layer. Upon thermal annealing, the composite layer becomes fragmented and moves outward, accompanied by carbon deposition on the alumina skeleton. When tested as electrochemical supercapacitor electrode, the hierarchical MO@f-C nanostructures exhibit better properties compared with the pristine metal oxides or the carbon coating without ALD. The enhancement can be ascribed to increased specific surface areas and electric conductivity due to the carbon flake coating. This peculiar carbon coating method with the unique hierarchical nanostructure may provide a new insight into the preparation of 'oxides + carbon' hybrid electrode materials for energy storage applications.

  8. Improvement of Energy Deposition in Absorber-free Laser Welding through Quasi-simultaneous Irradiation

    NASA Astrophysics Data System (ADS)

    Mamuschkin, Viktor; Engelmann, Christoph; Olowinsky, Alexander

    Laser transmission welding is usually known to put little thermal stress on the joining partners, indicated by a small heat affected zone (HAZ). However, this only applies when the joining partners have adapted optical properties. When it comes to welding of optically equal thermoplastics without absorbers, the main issue is the HAZ extending far from the interface. To enable welding without absorbers, lasers emitting within the polymer's intrinsic absorption bands are used. So far, different beam shaping approaches have already been investigated to achieve a selective energy deposition at the interface but, with little success to date. The approach presented in this paper is irradiating the welding path quasi-simultaneously to exploit the poor heat conductivity of polymers. Therefore, the influence of the irradiation regime on the seam formation is considered in detail. Another aspect investigated is the length of the irradiated contour which is a crucial factor in quasi-simultaneous welding. The results show that the energy deposition can be significantly improved when the welding contour length does not exceed a critical length determined by the capability of the welding system. However, by welding in segments the approach can also be applied to longer contours without any noticeable loss in welding time. The ideal irradiation regime obtained in the trials corresponds to an effective welding speed of 37mm/s and reduces the vertical extent of the HAZ by 30%.

  9. Optimization of the LHC interaction region with respect to beam-induced energy deposition

    SciTech Connect

    Mokhov, N.V.; Strait, J.B.

    1996-06-01

    Energy deposition in the superconducting magnets by particles from p- p collisions is a significant challenge for the design of the LHC high luminosity insertions. We have studies the dependence of the energy deposition on the apertures and strengths of insertion magnets and on the placement of absorbers in front of and within the quadrupoles. Monte Carlo simulations were made using the code DTUJET to generate 7{times}7 TeV p-p events and the code MARS to follow hadronic and electromagnetic cascades induced in the insertion components. The 3D geometry and magnetic field descriptions of the LHC-4.1 lattice were used. With a quadrupole coil aperture {ge}70 mm, absorbers can be placed within the magnet bore which reduce the peak power density, at full luminosity, below 0.5 mW/g, a level that should allow the magnets to operate at their design field. The total heat load can be removed by a cooling system similar to that used in the main magnets.

  10. Free Energy Calculations for DNA Near Surfaces Using an Ellipsoidal Geometry

    PubMed Central

    Ambia-Garrido, J.; Pettitt, B. Montgomery

    2009-01-01

    The change in some thermodynamic quantities such as Gibbs' free energy, entropy and enthalpy of the binding of two DNA strands (forming a double helix), while one is tethered to a surface and are analytically calculated. These particles are submerged in an electrolytic solution; the ionic strength of the media allows the linearized version of the Poisson-Boltzmann equation (from the theory of the double layer interaction) to properly describe the interactions [13]. There is experimental and computational evidence that an ion penetrable ellipsoid is an adequate model for the single strand and the double helix [22–25]. The analytic solution provides simple calculations useful for DNA chip design. The predicted electrostatic effects suggest the feasibility of electronic control and detection of DNA hybridization in the fast growing area of DNA recognition. PMID:20011625

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

    DOE PAGES

    Daene, Markus; Kim, Soo Kyung; Surh, Michael P.; Aberg, Daniel; Benedict, Lorin X.

    2015-06-15

    We present and discuss density functional theory calculations of magnetic properties of the family of ferromagnetic compounds, (Fe1-xCox)2B, focusing specifically on the magnetocrystalline anisotropy energy (MAE). Using periodic supercells of various sizes (up to 96 atoms), it is shown that the general qualitative features of the composition dependence of the MAE is in agreement with experimental findings, while our predicted magnitudes are larger than those of experiment. We find that the use of small supercells (6 and 12-atom) favors larger MAE values relative to a statistical sample of configurations constructed with 96-atom supercells. As a result, the effect of latticemore » relaxations is shown to be small. Calculations of the Curie temperature for this alloy are also presented.« less

  12. Development and deposition of resilin in energy stores for locust jumping.

    PubMed

    Burrows, Malcolm

    2016-08-15

    Locusts jump by using a catapult mechanism in which energy produced by slow contractions of the extensor tibiae muscles of the hind legs is stored in distortions of the exoskeleton, most notably (1) the two semi-lunar processes at each knee joint and (2) the tendons of the extensor muscles themselves. The energy is then suddenly released from these stores to power the rapid, propulsive movements of the hind legs. The reliance on the mechanical storage of energy is likely to impact on jumping because growth occurs by a series of five moults, at each of which the exoskeleton is replaced by a new one. All developmental stages (instars) nevertheless jump as a means of forward locomotion, or as an escape movement. Here, I show that in each instar, resilin is added to the semi-lunar processes and to the core of the extensor tendons so that their thickness increases. As the next moult approaches, a new exoskeleton forms within the old one, with resilin already present in the new semi-lunar processes. The old exoskeleton, the tendons and their resilin are discarded at moulting. The resilin of the semi-lunar processes and tendons of the new instar is initially thin, but a similar pattern of deposition results in an increase of their thickness. In adults, resilin continues to be deposited so that at 4 weeks old the thickness in the semi-lunar processes has increased fourfold. These changes in the energy stores accompany changes in jumping ability and performance during each moulting cycle. PMID:27259374

  13. Development and deposition of resilin in energy stores for locust jumping.

    PubMed

    Burrows, Malcolm

    2016-08-15

    Locusts jump by using a catapult mechanism in which energy produced by slow contractions of the extensor tibiae muscles of the hind legs is stored in distortions of the exoskeleton, most notably (1) the two semi-lunar processes at each knee joint and (2) the tendons of the extensor muscles themselves. The energy is then suddenly released from these stores to power the rapid, propulsive movements of the hind legs. The reliance on the mechanical storage of energy is likely to impact on jumping because growth occurs by a series of five moults, at each of which the exoskeleton is replaced by a new one. All developmental stages (instars) nevertheless jump as a means of forward locomotion, or as an escape movement. Here, I show that in each instar, resilin is added to the semi-lunar processes and to the core of the extensor tendons so that their thickness increases. As the next moult approaches, a new exoskeleton forms within the old one, with resilin already present in the new semi-lunar processes. The old exoskeleton, the tendons and their resilin are discarded at moulting. The resilin of the semi-lunar processes and tendons of the new instar is initially thin, but a similar pattern of deposition results in an increase of their thickness. In adults, resilin continues to be deposited so that at 4 weeks old the thickness in the semi-lunar processes has increased fourfold. These changes in the energy stores accompany changes in jumping ability and performance during each moulting cycle.

  14. Pulsed nanosecond discharge in air at high specific deposited energy: fast gas heating and active particle production

    NASA Astrophysics Data System (ADS)

    Popov, N. A.

    2016-08-01

    The results of a numerical study on kinetic processes initiated by a pulsed nanosecond discharge in air at high specific deposited energy, when the dissociation degree of oxygen molecules is high, are presented. The calculations of the temporal dynamics of the electron concentration, density of atomic oxygen, vibrational distribution function of nitrogen molecules, and gas temperature agree with the experimental data. It is shown that quenching of electronically excited states of nitrogen N2(B3Πg), N2(C3Πu), N2(a‧1 Σ \\text{u}- ) by oxygen molecules leads to the dissociation of O2. This conclusion is based on the comparison of calculated dynamics of atomic oxygen in air, excited by a pulsed nanosecond discharge, with experimental data. In air plasma at a high dissociation degree of oxygen molecules ([O]/[O2] > 10%), relaxation of the electronic energy of atoms and molecules in reactions with O atoms becomes extremely important. Active production of NO molecules and fast gas heating in the discharge plasma due to the quenching of electronically excited N2(B3Πg, C3Πu, a‧1 Σ \\text{u}- ) molecules by oxygen atoms is notable. Owing to the high O atom density, electrons are effectively detached from negative ions in the discharge afterglow. As a result, the decay of plasma in the afterglow is determined by electron-ion recombination, and the electron density remains relatively high between the pulses. An increase in the vibrational temperature of nitrogen molecules at the periphery of the plasma channel at time delay t = 1-30 μs after the discharge is obtained. This is due to intense gas heating and, as a result, gas-dynamic expansion of a hot gas channel. Vibrationally excited N2(v) molecules produced near the discharge axis move from the axial region to the periphery. Consequently, at the periphery the vibrational temperature of nitrogen molecules is increased.

  15. Calculation of Zeeman splitting and Zeeman transition energies of spherical quantum dot in uniform magnetic field

    NASA Astrophysics Data System (ADS)

    Çakır, Bekir; Atav, Ülfet; Yakar, Yusuf; Özmen, Ayhan

    2016-08-01

    In this study we report a detailed theoretical investigation of the effect of an external magnetic field on the 1s-, 2p-, 3d- and 4f-energy states of a spherical quantum dot. We treat the contribution of the diamagnetic term as a perturbation and discuss the effect of the diamagnetic term on the 1s-, 2p-, 3d- and 4f-energy states. We also have calculated the Zeeman transition energies between 2p → 1s and 3d → 2p states with m = 0, ±1 and 0, ±1, ±2 as a function of dot radius and the magnetic field strength. The results show that the magnetic field, impurity charge and dot radius have a strong influence on the energy states and the Zeeman transitions. It is found that the energies of the electronic states with m < 0 addition of the diamagnetic term firstly decrease toward a minimum, and then increase with the increasing magnetic field strength. We have seen that as magnetic field intensity is adjusted, frequency of the emitted light can be changed for Zeeman transitions.

  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

    DOE Data Explorer

    Kyle Gluesenkamp

    2016-02-01

    This spreadsheet allows the user to calculate parameters relevant to techno-economic performance of a two-step absorption process to transport low temperature geothermal heat some distance (1-20 miles) for use in building air conditioning. The parameters included are (1) energy density of aqueous LiBr and LiCl solutions, (2) transportation cost of trucking solution, and (3) equipment cost for the required chillers and cooling towers in the two-step absorption approach. More information is available in the included public report: "A Technical and Economic Analysis of an Innovative Two-Step Absorption System for Utilizing Low-Temperature Geothermal Resources to Condition Commercial Buildings"

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

    NASA Technical Reports Server (NTRS)

    Chaney, William S.

    1961-01-01

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

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

    PubMed

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

    2016-02-21

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