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

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

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

    PubMed

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

    2011-01-01

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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

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

    SciTech Connect

    Loewe, W.E.

    1980-04-03

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

  9. 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.

  10. 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

  11. The COOLER Code: A Novel Analytical Approach to Calculate Subcellular Energy Deposition by Internal Electron Emitters.

    PubMed

    Siragusa, Mattia; Baiocco, Giorgio; Fredericia, Pil M; Friedland, Werner; Groesser, Torsten; Ottolenghi, Andrea; Jensen, Mikael

    2017-08-01

    COmputation Of Local Electron Release (COOLER), a software program has been designed for dosimetry assessment at the cellular/subcellular scale, with a given distribution of administered low-energy electron-emitting radionuclides in cellular compartments, which remains a critical step in risk/benefit analysis for advancements in internal radiotherapy. The software is intended to overcome the main limitations of the medical internal radiation dose (MIRD) formalism for calculations of cellular S-values (i.e., dose to a target region in the cell per decay in a given source region), namely, the use of the continuous slowing down approximation (CSDA) and the assumption of a spherical cell geometry. To this aim, we developed an analytical approach, entrusted to a MATLAB-based program, using as input simulated data for electron spatial energy deposition directly derived from full Monte Carlo track structure calculations with PARTRAC. Results from PARTRAC calculations on electron range, stopping power and residual energy versus traveled distance curves are presented and, when useful for implementation in COOLER, analytical fit functions are given. Example configurations for cells in different culture conditions (V79 cells in suspension or adherent culture) with realistic geometrical parameters are implemented for use in the tool. Finally, cellular S-value predictions by the newly developed code are presented for different cellular geometries and activity distributions (uniform activity in the nucleus, in the entire cell or on the cell surface), validated against full Monte Carlo calculations with PARTRAC, and compared to MIRD standards, as well as results based on different track structure calculations (Geant4-DNA). The largest discrepancies between COOLER and MIRD predictions were generally found for electrons between 25 and 30 keV, where the magnitude of disagreement in S-values can vary from 50 to 100%, depending on the activity distribution. In calculations for

  12. 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.

  13. The calculation of proportional counter energy-deposition spectra from experimental data.

    NASA Technical Reports Server (NTRS)

    Steigerwalt, J. E.; Baily, N. A.

    1973-01-01

    The experimental approach considered requires the measurement of energy-absorption distributions for a set of pathlengths which define a biological volume. A suitable folding procedure is necessary to produce composite energy-absorption distributions. The investigation is concerned with the quality of the prediction of energy-deposition distributions, taking into account distributions measured with a proportional counter.

  14. Monte Carlo calculations of the energy deposited in biological samples and shielding materials

    NASA Astrophysics Data System (ADS)

    Akar Tarim, U.; Gurler, O.; Ozmutlu, E. N.; Yalcin, S.

    2014-03-01

    The energy deposited by gamma radiation from the Cs-137 isotope into body tissues (bone and muscle), tissue-like medium (water), and radiation shielding materials (concrete, lead, and water), which is of interest for radiation dosimetry, was obtained using a simple Monte Carlo algorithm. The algorithm also provides a realistic picture of the distribution of backscattered photons from the target and the distribution of photons scattered forward after several scatterings in the scatterer, which is useful in studying radiation shielding. The presented method in this work constitutes an attempt to evaluate the amount of energy absorbed by body tissues and shielding materials.

  15. 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.

  16. Calculated Energy Deposits from the Decay of Tritium and Other Radioisotopes Incorporated into Bacteria

    PubMed Central

    Bockrath, Richard; Person, Stanley; Funk, Fred

    1968-01-01

    Transmutation of the radioisotope tritium occurs with the production of a low energy electron, having a range in biological material similar to the dimensions of a bacterium. A computer program was written to determine the radiation dose distributions which may be expected within a bacterium as a result of tritium decay, when the isotope has been incorporated into specific regions of the bacterium. A nonspherical model bacterium was used, represented by a cylinder with hemispherical ends. The energy distributions resulting from a wide variety of simulated labeled regions were determined; the results suggested that the nuclear region of a bacterium receives on the average significantly different per decay doses, if the labeled regions were those conceivably produced by the incorporation of thymidine-3H, uracil-3H, or 3H-amino acids. Energy distributions in the model bacterium were also calculated for the decay of incorporated 14carbon, 35sulfur, and 32phosphorous. PMID:5678319

  17. 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.

  18. 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

  19. Laser surgery of port wine stains using local vacuum [corrected] pressure: changes in calculated energy deposition (Part II).

    PubMed

    Franco, Walfre; Childers, Michael; Nelson, J Stuart; Aguilar, Guillermo

    2007-02-01

    Application of local vacuum pressure to human skin during laser irradiation results in less absorption in the epidermis and more light delivered to targeted vessels with an increased blood volume. The objective of the present numerical study is to assess the effect of applying local vacuum pressure on the temperatures of the epidermis and small vessels during port wine stain (PWS) laser treatment. STUDY DESIGN/ MATERIALS AND METHODS: Mathematical models of light deposition and heat diffusion are used to compute absorbed energy and temperature distributions of skin and blood vessels with different diameters (10-60 microm) at various depths (200-800 microm) exposed to laser irradiation under atmospheric and vacuum pressures. Under 50 kPa (15 in Hg) vacuum pressure, peak temperatures at the inner walls of small diameter vessels (10-30 microm) located 200-300 microm below the skin surface are approximately 10 degrees C higher than those under atmospheric pressure, and peak temperatures in the epidermis of patients with skin phototype II are approximately 5 degrees C lower. In patients with darker skin phototype (IV), the peak temperature at the inner wall of a 10 microm diameter vessel located 200 microm below the skin surface is approximately 5 degrees C higher than that under atmospheric pressure, and the peak temperature in the epidermis is approximately 10 degrees C lower. Additional energy deposition in a larger blood volume permits higher temperatures to be achieved at vessel walls in response to laser irradiation. While more energy is deposited in every vessel, temperature gains in small diameter vessels (10-30 microm) are greater, increasing the likelihood of irreversible thermal damage to such vessels. In addition, temperatures in the epidermis decrease because less energy is absorbed therein due to reduced epidermal thickness and concentration of melanin per unit area. (c) 2007 Wiley-Liss, Inc.

  20. 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).

  1. Calculation of the energy deposition in nanovolumes by protons and HZE particles: geometric patterns of initial distributions of DNA repair foci.

    PubMed

    Plante, Ianik; Ponomarev, Artem L; Cucinotta, Francis A

    2013-09-21

    The biological effects of high-linear energy transfer (LET) radiation are different from those caused by low-LET radiation due to the difference in the patterns of energy deposition in cells. In this work, we studied the role of the track structure in the spatial distribution of radiation-induced double-strand breaks (DSBs). In the first part, the irradiation of a cubic volume of 12 µm of side by 300 MeV protons (LET ∼0.3 keV µm(-1)) and by 1 GeV/amu iron ion particles (LET∼150 keV µm(-1)) was simulated with the Monte Carlo code RITRACKS (relativistic ion tracks) and the dose was calculated in voxels of different sizes. In the second part, dose calculations were combined with chromosomes simulated by a random walk (RW) model to assess the formation of DSBs. The number of DSBs was calculated as a function of the dose and particle fluence for 1 GeV protons, 293 MeV/u carbon, and 1 GeV/u iron particles. Finally, the DSB yield was obtained as a function of the LET for protons, helium, and carbon. In general, the number and distribution of calculated DSBs were similar to experimental DNA repair foci data. From this study, we concluded that a stochastic model combining nanoscopic dose calculations and chromosomes simulated by RWs is a useful approach to study radiation-induced DSBs.

  2. Calculation of the energy deposition in nanovolumes by protons and HZE particles: geometric patterns of initial distributions of DNA repair foci

    NASA Astrophysics Data System (ADS)

    Plante, Ianik; Ponomarev, Artem L.; Cucinotta, Francis A.

    2013-09-01

    The biological effects of high-linear energy transfer (LET) radiation are different from those caused by low-LET radiation due to the difference in the patterns of energy deposition in cells. In this work, we studied the role of the track structure in the spatial distribution of radiation-induced double-strand breaks (DSBs). In the first part, the irradiation of a cubic volume of 12 µm of side by 300 MeV protons (LET ˜0.3 keV µm-1) and by 1 GeV/amu iron ion particles (LET˜150 keV µm-1) was simulated with the Monte Carlo code RITRACKS (relativistic ion tracks) and the dose was calculated in voxels of different sizes. In the second part, dose calculations were combined with chromosomes simulated by a random walk (RW) model to assess the formation of DSBs. The number of DSBs was calculated as a function of the dose and particle fluence for 1 GeV protons, 293 MeV/u carbon, and 1 GeV/u iron particles. Finally, the DSB yield was obtained as a function of the LET for protons, helium, and carbon. In general, the number and distribution of calculated DSBs were similar to experimental DNA repair foci data. From this study, we concluded that a stochastic model combining nanoscopic dose calculations and chromosomes simulated by RWs is a useful approach to study radiation-induced DSBs.

  3. 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.

  4. SU-E-T-329: Dosimetric Impact of Implementing Metal Artifact Reduction Methods and Metal Energy Deposition Kernels for Photon Dose Calculations

    SciTech Connect

    Huang, J; Followill, D; Howell, R; Liu, X; Mirkovic, D; Stingo, F; Kry, S

    2015-06-15

    Purpose: To investigate two strategies for reducing dose calculation errors near metal implants: use of CT metal artifact reduction methods and implementation of metal-based energy deposition kernels in the convolution/superposition (C/S) method. Methods: Radiochromic film was used to measure the dose upstream and downstream of titanium and Cerrobend implants. To assess the dosimetric impact of metal artifact reduction methods, dose calculations were performed using baseline, uncorrected images and metal artifact reduction Methods: Philips O-MAR, GE’s monochromatic gemstone spectral imaging (GSI) using dual-energy CT, and GSI imaging with metal artifact reduction software applied (MARs).To assess the impact of metal kernels, titanium and silver kernels were implemented into a commercial collapsed cone C/S algorithm. Results: The CT artifact reduction methods were more successful for titanium than Cerrobend. Interestingly, for beams traversing the metal implant, we found that errors in the dimensions of the metal in the CT images were more important for dose calculation accuracy than reduction of imaging artifacts. The MARs algorithm caused a distortion in the shape of the titanium implant that substantially worsened the calculation accuracy. In comparison to water kernel dose calculations, metal kernels resulted in better modeling of the increased backscatter dose at the upstream interface but decreased accuracy directly downstream of the metal. We also found that the success of metal kernels was dependent on dose grid size, with smaller calculation voxels giving better accuracy. Conclusion: Our study yielded mixed results, with neither the metal artifact reduction methods nor the metal kernels being globally effective at improving dose calculation accuracy. However, some successes were observed. The MARs algorithm decreased errors downstream of Cerrobend by a factor of two, and metal kernels resulted in more accurate backscatter dose upstream of metals. Thus

  5. Landfill Gas Energy Benefits Calculator

    EPA Pesticide Factsheets

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

  6. 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

  7. Calculating The Resistivity Of A Deposited Film

    NASA Technical Reports Server (NTRS)

    Oberle, Lawrence G.; Fralick, Gustave C.

    1990-01-01

    Iterative procedure computes resistivity from measurements by four-probe method. Computer program and technique developed to aid in solution of class of problems in which measurements of electrical resistivity needed for substance deposited on substrate of higher resistivity than deposited layer.

  8. Calculating The Resistivity Of A Deposited Film

    NASA Technical Reports Server (NTRS)

    Oberle, Lawrence G.; Fralick, Gustave C.

    1990-01-01

    Iterative procedure computes resistivity from measurements by four-probe method. Computer program and technique developed to aid in solution of class of problems in which measurements of electrical resistivity needed for substance deposited on substrate of higher resistivity than deposited layer.

  9. 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.

  10. Photon dose calculation based on electron multiple-scattering theory: primary dose deposition kernels.

    PubMed

    Wang, L; Jette, D

    1999-08-01

    The transport of the secondary electrons resulting from high-energy photon interactions is essential to energy redistribution and deposition. In order to develop an accurate dose-calculation algorithm for high-energy photons, which can predict the dose distribution in inhomogeneous media and at the beam edges, we have investigated the feasibility of applying electron transport theory [Jette, Med. Phys. 15, 123 (1988)] to photon dose calculation. In particular, the transport of and energy deposition by Compton electron and electrons and positrons resulting from pair production were studied. The primary photons are treated as the source of the secondary electrons and positrons, which are transported through the irradiated medium using Gaussian multiple-scattering theory [Jette, Med. Phys. 15, 123 (1988)]. The initial angular and kinetic energy distribution(s) of the secondary electrons (and positrons) emanating from the photon interactions are incorporated into the transport. Due to different mechanisms of creation and cross-section functions, the transport of and the energy deposition by the electrons released in these two processes are studied and modeled separately based on first principles. In this article, we focus on determining the dose distribution for an individual interaction site. We define the Compton dose deposition kernel (CDK) or the pair-production dose deposition kernel (PDK) as the dose distribution relative to the point of interaction, per unit interaction density, for a monoenergetic photon beam in an infinite homogeneous medium of unit density. The validity of this analytic modeling of dose deposition was evaluated through EGS4 Monte Carlo simulation. Quantitative agreement between these two calculations of the dose distribution and the average energy deposited per interaction was achieved. Our results demonstrate the applicability of the electron dose-calculation method to photon dose calculation.

  11. Note: the influence of exploding foil shape on energy deposition.

    PubMed

    Zeng, Qingxuan; Lv, Junjun; Li, Mingyu

    2013-06-01

    The main influence factors of exploding bridge foil were studied in order to improve energy utilization of the explosion foil initiator. "Square" and "curving" shaped bridge foils were fabricated using magnetron sputtering and chemical etching techniques, and the key dimension of the bridge foil was measured using surface profiler. Commercial software MATLAB was employed to calculate the burst current, burst voltage, and energy deposition. Simulation results were in good agreement with experiment data. In this study, the energy deposition ratio of "square" shaped bridge is between 45%-50%, while the value of "curving" shaped bridge is between 55%-75%.

  12. 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.

  13. 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.

  14. Theoretical study of energy deposition in ionization chambers for tritium measurements

    SciTech Connect

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

    2013-10-15

    Energy deposition in ionization chambers has been theoretically studied for tritium measurements in gaseous form. A one-dimension model is introduced to establish the quantitative relationship between energy deposition rate and many factors, including carrier gas, gas pressure, wall material, chamber size, and gas temperature. Energy deposition rate has been calculated at pressure varying from 5 kPa to 500 kPa based on some approximations. It is found that energy deposition rate varies greatly for different parameters, especially at low gas pressure. For the same chamber, energy deposition rate in argon is much higher than in deuterium, as much as 70.7% higher at 5 kPa. Gold plated chamber gives highest energy deposition rate in the calculations while aluminum chamber results in the lowest. As chamber size gets smaller, β ray emitted by tritium will deposit less energy in the sensitive region of the chamber. For chambers flowing through with the same gas, energy deposition rate in a 10 L chamber is 23.9% higher than in a 0.05 L chamber at 5 kPa. Gas temperature also places slight influence on energy deposition rate, and 373 K will lead to 6.7% lower deposition rate than 233 K at 5 kPa. In addition, experiments have been performed to obtain energy deposition rate in a gold plated chamber, which show good accordance with theoretical calculations.

  15. Theoretical study of energy deposition in ionization chambers for tritium measurements

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    Energy deposition in ionization chambers has been theoretically studied for tritium measurements in gaseous form. A one-dimension model is introduced to establish the quantitative relationship between energy deposition rate and many factors, including carrier gas, gas pressure, wall material, chamber size, and gas temperature. Energy deposition rate has been calculated at pressure varying from 5 kPa to 500 kPa based on some approximations. It is found that energy deposition rate varies greatly for different parameters, especially at low gas pressure. For the same chamber, energy deposition rate in argon is much higher than in deuterium, as much as 70.7% higher at 5 kPa. Gold plated chamber gives highest energy deposition rate in the calculations while aluminum chamber results in the lowest. As chamber size gets smaller, β ray emitted by tritium will deposit less energy in the sensitive region of the chamber. For chambers flowing through with the same gas, energy deposition rate in a 10 L chamber is 23.9% higher than in a 0.05 L chamber at 5 kPa. Gas temperature also places slight influence on energy deposition rate, and 373 K will lead to 6.7% lower deposition rate than 233 K at 5 kPa. In addition, experiments have been performed to obtain energy deposition rate in a gold plated chamber, which show good accordance with theoretical calculations.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Beam-induced energy deposition in muon storage rings

    SciTech Connect

    Nikolai V. Mokhov; Carol J. Johnstone; Brett Parker

    2001-06-22

    Beam-induced radiation effects have been simulated for 20 and 50 GeV muon storage rings designed for a Neutrino Factory. It is shown that by appropriately shielding the superconducting magnets, quench stability, acceptable dynamic heat loads, and low residual dose rates can be achieved. Alternatively, if a specially-designed skew focusing magnet without superconducting coils on the magnet's mid-plane is used, then the energy is deposited preferentially in the warm iron yoke or outer cryostat layers and internal shielding may not be required. In addition to the component irradiation analysis, shielding studies have been performed. Calculations of the external radiation were done for both designs but the internal energy deposition calculations for the 20 GeV Study-2 lattice are still in progress.

  3. BEAM INDUCED ENERGY DEPOSITION IN MUON STORAGE RINGS.

    SciTech Connect

    MOKHOV,N.V.; JOHNSTONE,C.J.; PARKER,B.L.

    2001-06-18

    Beam-induced radiation effects have been simulated for 20 and 50 GeV muon storage rings designed for a Neutrino Factory. It is shown that by appropriately shielding the superconducting magnets, quench stability, acceptable dynamic heat loads, and low residual dose rates can be achieved. Alternatively, if a specially-designed skew focusing magnet without superconducting coils on the magnet's mid-plane is used, then the energy is deposited preferentially in the warm iron yoke or outer cryostat layers and internal shielding may not be required. In addition to the component irradiation analysis, shielding studies have been performed. Calculations of the external radiation were done for both designs but the internal energy deposition calculations for the 20 GeV Study-2 lattice are still in progress.

  4. Calculations of specific cellular doses for low-energy electrons

    NASA Astrophysics Data System (ADS)

    Liu, C. S.; Tung, C.-J.; Hu, Y. H.; Chou, C. M.; Chao, T. C.; Lee, C. C.

    2009-05-01

    The objectives of this work were to calculate the cellular doses and the lineal energies of low-energy electrons in liquid water for different source-target geometry in a cell. Calculated specific cellular doses and their variations were analyzed for the dependences on electron energy, source-target geometry, elastic interaction, and type of energy depositions, i.e. starter, stopper, insider and crosser. Two approaches, i.e. the probabilistic method and the mixed method, were applied. In the probabilistic method, the Monte Carlo Penelope code was used. In the mixed method, the range-energy relation and the sampling of electron paths were applied. It was found that for N ← Cy elastic interactions led to a change of the specific cellular dose by about 30% for electron energies below 10 keV. Here N ← Cy denotes electrons emitted from the source region, Cy (cytoplasm), to deposit energy in the target region, N (cell nucleus). The variation of specific cellular dose was found greater (more than 10%) for N ← Cy than N ← N, C ← C and C ← CS, where C and CS denote the cell and cell surface, respectively. The lineal energy distribution varied substantially with electron energy, source-target geometry, and target size. The maximum values of the relative dose-mean lineal energy for 1, 5 and 10 keV electrons, relative to 36 keV reference electrons used to define the relative biological effectiveness, occurred at target radii of several tens, hundreds and thousands nanometers, respectively.

  5. Predicting proteinase specificities from free energy calculations.

    PubMed

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

    2006-10-01

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

  6. 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…

  7. 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…

  8. Using Bayes' theorem for free energy calculations

    NASA Astrophysics Data System (ADS)

    Rogers, David M.

    Statistical mechanics is fundamentally based on calculating the probabilities of molecular-scale events. Although Bayes' theorem has generally been recognized as providing key guiding principals for setup and analysis of statistical experiments [83], classical frequentist models still predominate in the world of computational experimentation. As a starting point for widespread application of Bayesian methods in statistical mechanics, we investigate the central quantity of free energies from this perspective. This dissertation thus reviews the basics of Bayes' view of probability theory, and the maximum entropy formulation of statistical mechanics before providing examples of its application to several advanced research areas. We first apply Bayes' theorem to a multinomial counting problem in order to determine inner shell and hard sphere solvation free energy components of Quasi-Chemical Theory [140]. We proceed to consider the general problem of free energy calculations from samples of interaction energy distributions. From there, we turn to spline-based estimation of the potential of mean force [142], and empirical modeling of observed dynamics using integrator matching. The results of this research are expected to advance the state of the art in coarse-graining methods, as they allow a systematic connection from high-resolution (atomic) to low-resolution (coarse) structure and dynamics. In total, our work on these problems constitutes a critical starting point for further application of Bayes' theorem in all areas of statistical mechanics. It is hoped that the understanding so gained will allow for improvements in comparisons between theory and experiment.

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

    SciTech Connect

    Kusuda, T

    1980-10-31

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

  10. 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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  13. Zero energy scattering calculation in Euclidean space

    NASA Astrophysics Data System (ADS)

    Carbonell, J.; Karmanov, V. A.

    2016-03-01

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

  14. Interaction region design driven by energy deposition

    NASA Astrophysics Data System (ADS)

    Martin, Roman; Besana, Maria Ilaria; Cerutti, Francesco; Langner, Andy; Tomás, Rogelio; Cruz-Alaniz, Emilia; Dalena, Barbara

    2017-08-01

    The European Strategy Group for High Energy Physics recommends to study collider designs for the post-LHC era. Among the suggested projects there is the circular 100 TeV proton-proton collider FCC-hh. Starting from LHC and its proposed upgrade HL-LHC, this paper outlines the development of the interaction region design for FCC-hh. We identify energy deposition from debris of the collision events as a driving factor for the layout and draft the guiding principles to unify protection of the superconducting final focus magnets from radiation with a high luminosity performance. Furthermore, we offer a novel strategy to mitigate the lifetime limitation of the first final focus magnet due to radiation load, the Q1 split.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. Laser energy deposition in crossing shock interaction

    NASA Astrophysics Data System (ADS)

    Yan, H.; Knight, D.; Elliott, G.

    A combined computational and experimental study was performed to investigate the effect of a single laser energy pulse on the transition from a Mach Reflection (MR) to a Regular Reflection (RR) in the Dual Solution Domain (DSD). The freestream Mach number is 3.45 and two oblique shock waves are formed by two symmetric 22° wedges. These conditions correspond to a point midway within the DSD wherein either an MR or an RR is possible. A steady MR was first obtained experimentally and numerically, then a single laser pulse was deposited above the horizontal center plane. The experiment showed that the Mach stem height decreased to 30% of its original height due to the interaction with the thermal spot generated by the laser pulse and then returned to its original height by 300μs. That the Mach stem returned to its original height was most likely due to freestream turbulence in the wind tunnel. The numerical simulation successfully predicted the reverse transition from a stable MR to a stable RR and the stable RR persisted across the span. This study showed the capability of a laser energy pulse to control the reverse transition of MR → RR within the Dual Solution Domain.

  1. 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

  2. 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

  3. Influence of deposited energy on shock wave induced by underwater pulsed current discharge

    NASA Astrophysics Data System (ADS)

    Li, Xian-Dong; Liu, Yi; Liu, Si-Wei; Li, Zhi-Yuan; Zhou, Gu-Yue; Li, Hua; Lin, Fu-Chang; Pan, Yuan

    2016-10-01

    In this paper, an integrated experimental system is established to study the influence of deposited energy on the intensity of the shock wave induced by underwater pulse discharge. Considering the time varying behavior of the arc, the calculation methods of the deposited energy into the plasma channel and the average arc resistance are proposed and presented. The effect of the breakdown process on the deposited energy and the shock wave is analyzed. It can be concluded that the shock wave intensity can be improved by depositing more energy in the first half oscillation period and increasing the arc resistance. It is also found that the energy deposition and the shock wave intensity are significantly influenced by the breakdown time delay and the shape of the initial plasma channel.

  4. CHP Energy and Emissions Savings Calculator

    EPA Pesticide Factsheets

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

  5. Energy and momentum deposited into a QCD medium by a jet shower.

    PubMed

    Qin, G-Y; Majumder, A; Song, H; Heinz, U

    2009-10-09

    For a hard parton moving through a dense QCD medium, we compute self-consistently the energy loss and the fraction deposited into the medium due to showering and rescattering of the shower, assuming weak coupling between probe and medium. The same transport coefficients thus determine both the energy loss and its deposition into the medium. This allows a parameter free calculation of the latter once the former are computed or measured. We compute them for a weakly interacting medium. Assuming a short thermalization time for the deposited energy, we determine the medium's hydrodynamical response and obtain a conical pattern that is strongly enhanced by showering.

  6. Optimization of energetic electron energy degradation calculations

    NASA Astrophysics Data System (ADS)

    Swartz, W. E.

    1985-07-01

    It is pointed out that, in the past two decades, much progress has been made in the theoretical computation of energetic electron transport and thermalization in the ionosphere. The present investigation is concerned with an optimized scheme which uses the same discrete formalism at all energies, and guarantees numerical energy conservation independently of the energy grid size or configuration. The considered method was employed by Kelley et al. (1977) and by Swartz et al. (1979). Attention is given to energy degradation and reapportionment with energy conservation following inelastic collisions, energy reapportionment with energy conservation of emergent primaries following ionizing collisions, the establishment of consistent sources for numerical comparisons, and an example of an energy grid with the minimum number of cells.

  7. 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

  8. 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.

  9. KDEP: A Resource for Calculating Particle Deposition in the Respiratory Tract.

    PubMed

    Klumpp, John; Bertelli, Luiz

    2017-08-01

    This paper presents KDEP, an open-source implementation of the ICRP lung deposition model developed by the authors. KDEP, which is freely available to the public, can be used to calculate lung deposition values under a variety of different conditions using the ICRP methodology. The paper describes how KDEP implements this model and discusses some key points of the implementation. The published lung deposition values for intakes by workers were reproduced, and new deposition values were calculated for intakes by members of the public. KDEP can be obtained for free at github.com or by emailing the authors directly.

  10. KDEP: A resource for calculating particle deposition in the respiratory tract

    DOE PAGES

    Klumpp, John A.; Bertelli, Luiz

    2017-08-01

    This study presents KDEP, an open-source implementation of the ICRP lung deposition model developed by the authors. KDEP, which is freely available to the public, can be used to calculate lung deposition values under a variety of different conditions using the ICRP methodology. The paper describes how KDEP implements this model and discusses some key points of the implementation. The published lung deposition values for intakes by workers were reproduced, and new deposition values were calculated for intakes by members of the public. KDEP can be obtained for free at github.com or by emailing the authors directly.

  11. Energy Band Calculations for Maximally Even Superlattices

    NASA Astrophysics Data System (ADS)

    Krantz, Richard; Byrd, Jason

    2007-03-01

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

  12. 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.

  13. 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)

  14. Ionizing Energy Depositions After Fast Neutron Interactions in Silicon

    DOE PAGES

    Bergmann, Benedikt; Pospisil, Stanislav; Caicedo, Ivan; ...

    2016-06-01

    In our study we present the ionizing energy depositions in a 300 μm thick silicon layer after fast neutron impact. With the Time-of-Flight (ToF) technique, the ionizing energy deposition spectra of recoil silicons and secondary charged particles were assigned to (quasi-)monoenergetic neutron energies in the range from 180 keV to hundreds of MeV. We also show and interpret representative measured energy spectra. By separating the ionizing energy losses of the recoil silicon from energy depositions by products of nuclear reactions, the competition of ionizing (IEL) and non-ionizing energy losses (NIEL) of a recoil silicon within the silicon lattice was investigated.more » Furthermore, the data give supplementary information to the results of a previous measurement and are compared with different theoretical predictions.« less

  15. Ionizing Energy Depositions After Fast Neutron Interactions in Silicon

    SciTech Connect

    Bergmann, Benedikt; Pospisil, Stanislav; Caicedo, Ivan; Kierstead, James; Takai, Helio; Frojdh, Erik

    2016-06-01

    In our study we present the ionizing energy depositions in a 300 μm thick silicon layer after fast neutron impact. With the Time-of-Flight (ToF) technique, the ionizing energy deposition spectra of recoil silicons and secondary charged particles were assigned to (quasi-)monoenergetic neutron energies in the range from 180 keV to hundreds of MeV. We also show and interpret representative measured energy spectra. By separating the ionizing energy losses of the recoil silicon from energy depositions by products of nuclear reactions, the competition of ionizing (IEL) and non-ionizing energy losses (NIEL) of a recoil silicon within the silicon lattice was investigated. Furthermore, the data give supplementary information to the results of a previous measurement and are compared with different theoretical predictions.

  16. Ionizing Energy Depositions After Fast Neutron Interactions in Silicon

    SciTech Connect

    Bergmann, Benedikt; Pospisil, Stanislav; Caicedo, Ivan; Kierstead, James; Takai, Helio; Frojdh, Erik

    2016-06-01

    In our study we present the ionizing energy depositions in a 300 μm thick silicon layer after fast neutron impact. With the Time-of-Flight (ToF) technique, the ionizing energy deposition spectra of recoil silicons and secondary charged particles were assigned to (quasi-)monoenergetic neutron energies in the range from 180 keV to hundreds of MeV. We also show and interpret representative measured energy spectra. By separating the ionizing energy losses of the recoil silicon from energy depositions by products of nuclear reactions, the competition of ionizing (IEL) and non-ionizing energy losses (NIEL) of a recoil silicon within the silicon lattice was investigated. Furthermore, the data give supplementary information to the results of a previous measurement and are compared with different theoretical predictions.

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

    SciTech Connect

    Hamilton, John C.

    2005-06-01

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

  18. Calculation of total deposition fraction of ultrafine aerosols in human extrathoracic and intrathoracic regions

    SciTech Connect

    Cheng, K.H.; Swift, D.L. )

    1995-02-01

    Total deposition fraction during inspiration and expiration can be considered as an index of cumulative doses of inhaled particles. We have calculated the total deposition fraction of ultrafine aerosols for the 5-200-nm-diameter range in the extrathoracic and intrathoracic airways for two breathing rates, 7.5 and 15 L min[sup [minus]1], based on the total respiratory deposition measurements of Schiller et al. (1988) and the empirical extrathoracic aerosol deposition equations of Cheng et al. (1993) and Swift et al. (1993). Our results indicate that extrathoracic particle deposition during expiration is an important component of total extrathoracic deposition fraction for particle diameters less than 20 nm. The intrathoracic deposition fraction increases as particle diameter increases from 5 to 20 nm, and decreases with increasing particle diameter from 20 to 200 nm. These trends were observed for both oral and nasal breathing for both respiratory flow rates. 7 refs., 2 figs., 4 tabs.

  19. Calculation of molecular free energies in classical potentials

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2016-02-01

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

  20. Energy deposition in ultrathin extreme ultraviolet resist films: extreme ultraviolet photons and keV electrons

    NASA Astrophysics Data System (ADS)

    Kyser, David F.; Eib, Nicholas K.; Ritchie, Nicholas W. M.

    2016-07-01

    The absorbed energy density (eV/cm3) deposited by extreme ultraviolet (EUV) photons and electron beam (EB) high-keV electrons is proposed as a metric for characterizing the sensitivity of EUV resist films. Simulations of energy deposition are used to calculate the energy density as a function of the incident aerial flux (EUV: mJ/cm2, EB: μC/cm2). Monte Carlo calculations for electron exposure are utilized, and a Lambert-Beer model for EUV absorption. The ratio of electron flux to photon flux which results in equivalent energy density is calculated for a typical organic chemically amplified resist film and a typical inorganic metal-oxide film. This ratio can be used to screen EUV resist materials with EB measurements and accelerate advances in EUV resist systems.

  1. Comparison of measured electron density rise and calculated neutral beam particle deposition in the TFTR tokamak

    SciTech Connect

    Park, H.; Budny, R.; McCune, D.; Taylor, G.; Zarnstorff, M.C. . Plasma Physics Lab.); Barnes, C.W. )

    1991-12-01

    The initial rate of rise of the central electron density during {approximately}100 keV deuterium neutral beam injection is found to agree well with calculations of the beam deposition rate. The best agreement is with beam deposition calculations using older tabulations of the atomic cross-sections; the effects of using new tabulations or including multi-step ionization processes appear to approximately cancel. The neutral-beam deposition profile is a strong function of both the magnitude and the shape of the target plasma density. Peaked heating profiles can be achieved at high target densities only from peaked target density profiles. 15 refs., 4 figs.

  2. Tests of MULTIMODE calculations of rovibrational energies of CH 4

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

  3. Asteroid fragmentation approaches for modeling atmospheric energy deposition

    NASA Astrophysics Data System (ADS)

    Register, Paul J.; Mathias, Donovan L.; Wheeler, Lorien F.

    2017-03-01

    During asteroid entry, energy is deposited in the atmosphere through thermal ablation and momentum-loss due to aerodynamic drag. Analytic models of asteroid entry and breakup physics are used to compute the energy deposition, which can then be compared against measured light curves and used to estimate ground damage due to airburst events. This work assesses and compares energy deposition results from four existing approaches to asteroid breakup modeling, and presents a new model that combines key elements of those approaches. The existing approaches considered include a liquid drop or "pancake" model where the object is treated as a single deforming body, and a set of discrete fragment models where the object breaks progressively into individual fragments. The new model incorporates both independent fragments and aggregate debris clouds to represent a broader range of fragmentation behaviors and reproduce more detailed light curve features. All five models are used to estimate the energy deposition rate versus altitude for the Chelyabinsk meteor impact, and results are compared with an observationally derived energy deposition curve. Comparisons show that four of the five approaches are able to match the overall observed energy deposition profile, but the features of the combined model are needed to better replicate both the primary and secondary peaks of the Chelyabinsk curve.

  4. 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.

  5. Density functional theory for comprehensive orbital energy calculations

    NASA Astrophysics Data System (ADS)

    Nakata, Ayako; Tsuneda, Takao

    2013-08-01

    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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Nadykto, B. A.

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

  8. 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.

  9. 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

  10. Effect of layer thickness setting on deposition characteristics in direct energy deposition (DED) process

    NASA Astrophysics Data System (ADS)

    Shim, Do-Sik; Baek, Gyeong-Yun; Seo, Jin-Seon; Shin, Gwang-Yong; Kim, Kee-Poong; Lee, Ki-Yong

    2016-12-01

    Direct energy deposition is an additive manufacturing technique that involves the melting of metal powder with a high-powered laser beam and is used to build a variety of components. In laser-assisted metal deposition, the mechanical and metallurgical properties achieved are influenced by many factors. This paper addresses methods for selecting an appropriate layer thickness setting, which is an important parameter in layer-by-layer deposition manufacturing. A new procedure is proposed for determining the layer thickness setting for use in slicing of a part based on the single-layer height for a given depositing condition. This procedure was compared with a conventional method that uses an empirically determined layer thickness and with a feedback control method. The micro-hardness distribution, location of the melting pool, and microstructures of the deposited layers after deposition of a simple target shape were investigated for each procedure. The experimental results show that even though the feedback control method is the most effective method for obtaining the desired geometry, the deposited region was characterized by inhomogeneity of micro-hardness due to the time-variable depositing conditions involved. The largest dimensional error was associated with the conventional deposition procedure, which produced a rise in the melting zone due to over-deposition with respect to the slicing thickness, especially at the high laser power level considered. In contrast, the proposed procedure produced a stable melting zone position during deposition, which resulted in the deposited part having reasonable dimensional accuracy and uniform micro-hardness throughout the deposited region.

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  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. Stochastic spatial energy deposition profiles for MeV protons and keV electrons

    NASA Astrophysics Data System (ADS)

    Udalagama, C.; Bettiol, A. A.; Watt, F.

    2009-12-01

    With the rapid advances being made in novel high-energy ion-beam techniques such as proton beam writing, single-ion-event effects, ion-beam-radiation therapy, ion-induced fluorescence imaging, proton/ion microscopy, and ion-induced electron imaging, it is becoming increasingly important to understand the spatial energy-deposition profiles of energetic ions as they penetrate matter. In this work we present the results of comprehensive yet straightforward event-by-event Monte Carlo calculations that simulate ion/electron propagation and secondary electron ( δ ray) generation to yield spatial energy-deposition data. These calculations combine SRIM/TRIM features, EEDL97 data and volume-plasmon-localization models with a modified version of one of the newer δ ray generation models, namely, the Hansen-Kocbach-Stolterfoht. The development of the computer code DEEP (deposition of energy due to electrons and protons) offers a unique means of studying the energy-deposition/redistribution problem while still retaining the important stochastic nature inherent in these processes which cannot be achieved with analytical modeling. As an example of an application of DEEP we present results that compare the energy-deposition profiles of primary MeV protons and primary keV electrons in polymethymethacrylate. Such data are important when comparing proximity effects in the direct write lithography processes of proton-beam writing and electron-beam writing. Our calculations demonstrate that protons are able to maintain highly compact spatial energy-deposition profiles compared with electrons.

  17. Guidelines for the analysis of free energy calculations

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  18. 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.

  19. 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

  20. Energy deposition model for I-125 photon radiation in water

    NASA Astrophysics Data System (ADS)

    Fuss, M. C.; Muñoz, A.; Oller, J. C.; Blanco, F.; Limão-Vieira, P.; Williart, A.; Huerga, C.; Téllez, M.; García, G.

    2010-10-01

    In this study, an electron-tracking Monte Carlo algorithm developed by us is combined with established photon transport models in order to simulate all primary and secondary particle interactions in water for incident photon radiation. As input parameters for secondary electron interactions, electron scattering cross sections by water molecules and experimental energy loss spectra are used. With this simulation, the resulting energy deposition can be modelled at the molecular level, yielding detailed information about localization and type of single collision events. The experimental emission spectrum of I-125 seeds, as used for radiotherapy of different tumours, was used for studying the energy deposition in water when irradiating with this radionuclide.

  1. Calculation of electron binding energies of {Na}_{55}^- clusters

    NASA Astrophysics Data System (ADS)

    Melikyan, Armen; Minassian, Hayk; Grigoryan, Valeri G.; Springborg, Michael

    2016-07-01

    Within the frame of the one-electron approximation, we calculate the electron binding energies of the {Na}_{55}^- cluster which allows for the identification of the icosahedral structure of the cluster through comparison with experimental photoelectron spectroscopy data. The surface of the icosahedral cluster is represented as a slightly deformed spherical surface, and the corresponding splitting of the energy levels caused by this symmetry reduction is calculated. Subsequently, we demonstrate that the calculated energies of photoelectrons agree very well with the experimental values. This gives an unambiguous demonstration of the role of the cluster structure in photoelectron spectra, whereas electronic shell filling effects are less important.

  2. Monte Carlo simulation and analysis of proton energy-deposition patterns in the Bragg peak

    NASA Astrophysics Data System (ADS)

    González-Muñoz, Gloria; Tilly, Nina; Fernández-Varea, José M.; Ahnesjö, Anders

    2008-06-01

    The spatial pattern of energy depositions is crucial for understanding the mechanisms that modify the relative biological effectiveness of different radiation qualities. In this paper, we present data on energy-deposition properties of mono-energetic protons (1-20 MeV) and their secondary electrons in liquid water. Proton-impact ionization was described by means of the Hansen-Kocbach-Stolterfoht doubly differential cross section (DDCS), thus modelling both the initial energy and angle of the emitted electron. Excitation by proton impact was included to account for the contribution of this interaction channel to the electronic stopping power of the projectile. Proton transport was implemented assuming track-segment conditions, whereas electrons were followed down to 50 eV by the Monte Carlo code PENELOPE. Electron intra-track energy-deposition properties, such as slowing-down and energy-imparted spectra of electrons, were calculated. Furthermore, the use of DDCSs enabled the scoring of electron inter-track properties. We present novel results for 1, 5 and 20 MeV single-proton-track frequencies of distances between the nearest inter- (e--e-, e--H+) and intra-track (e--e-, e--H+, H+-H+) energy-deposition events. By setting a threshold energy of 17.5 eV, commonly employed as a surrogate to discriminate for elementary damage in the DNA, the variation in these frequencies was studied as well. The energy deposited directly by the proton represents a large amount of the total energy deposited along the track, but when an energy threshold is adopted the relative contribution of the secondary electrons becomes larger for increasing energy of the projectile. We found that the frequencies of closest energy-deposition events per nanometre decrease with proton energy, i.e. for lower proton energies a denser ionization occurs, following the trend of the characteristic LET curves. In conclusion, considering the energy depositions due to the delta electrons and at the core of the

  3. Monte Carlo simulation and analysis of proton energy-deposition patterns in the Bragg peak.

    PubMed

    González-Muñoz, Gloria; Tilly, Nina; Fernández-Varea, José M; Ahnesjö, Anders

    2008-06-07

    The spatial pattern of energy depositions is crucial for understanding the mechanisms that modify the relative biological effectiveness of different radiation qualities. In this paper, we present data on energy-deposition properties of mono-energetic protons (1-20 MeV) and their secondary electrons in liquid water. Proton-impact ionization was described by means of the Hansen-Kocbach-Stolterfoht doubly differential cross section (DDCS), thus modelling both the initial energy and angle of the emitted electron. Excitation by proton impact was included to account for the contribution of this interaction channel to the electronic stopping power of the projectile. Proton transport was implemented assuming track-segment conditions, whereas electrons were followed down to 50 eV by the Monte Carlo code PENELOPE. Electron intra-track energy-deposition properties, such as slowing-down and energy-imparted spectra of electrons, were calculated. Furthermore, the use of DDCSs enabled the scoring of electron inter-track properties. We present novel results for 1, 5 and 20 MeV single-proton-track frequencies of distances between the nearest inter- (e(-)-e(-), e(-)-H+) and intra-track (e(-)-e(-), e(-)-H+, H+-H+) energy-deposition events. By setting a threshold energy of 17.5 eV, commonly employed as a surrogate to discriminate for elementary damage in the DNA, the variation in these frequencies was studied as well. The energy deposited directly by the proton represents a large amount of the total energy deposited along the track, but when an energy threshold is adopted the relative contribution of the secondary electrons becomes larger for increasing energy of the projectile. We found that the frequencies of closest energy-deposition events per nanometre decrease with proton energy, i.e. for lower proton energies a denser ionization occurs, following the trend of the characteristic LET curves. In conclusion, considering the energy depositions due to the delta electrons and at the

  4. Calculation of astrophysical S factor at low energy levels

    NASA Astrophysics Data System (ADS)

    Andic, Halil Ibrahim; Ozer, Okan

    2017-02-01

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

  5. EXCEDE Energy Deposition. Theory and Experiment Compared.

    DTIC Science & Technology

    1980-11-30

    1 -2 -1 -1 15 ergs cm sec ster (or 10 ergs CID sec ster at 391 1 A) . The calculated initensity (Figure 3-()), under the same viewingo Condi tions...t kli a s fo r 1 himn i fig filltfire IK\\CElE exper iment s ,itI i s v\\O I.. i mIo rt ant to0 bc able t1 dC 1 ISt i1 i,11i sli bet iSo.OlJI theSe rel

  6. 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.

  7. Formation mechanism of overlapping grain boundaries in graphene chemical vapor deposition growth† †Electronic supplementary information (ESI) available: Fig. S1, Table S1, calculation of formation energies of different graphene edges, calculation of the Gibbs free energy variation during the overlapping of two H terminated graphene edges, calculations on the chemical potential of H2 and thermodynamic diagrams. See DOI: 10.1039/c6sc04535a Click here for additional data file.

    PubMed Central

    Dong, Jichen; Wang, Huan; Peng, Hailin; Liu, Zhongfan

    2017-01-01

    The formation of grain boundaries (GBs) in graphene films is both fundamentally interesting and practically important for many applications. A GB in graphene is known as a linear defect and is formed during the coalescence of two single crystalline graphene domains. The covalent binding between domains is broadly known as the mechanism of GB formation during graphene chemical vapor deposition (CVD) growth. Here, we demonstrate another GB formation mechanism, where two graphene domains are connected by weak van der Waals interactions between overlapping graphene layers. The formation mechanism of the overlapping GBs (OLGBs) is systematically explored theoretically and the proposed conditions for forming OLGBs are validated by experimental observations. This discovery leads to a deep understanding of the mechanism of graphene CVD growth and reveals potential means for graphene quality control in CVD synthesis. PMID:28507676

  8. 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.

  9. Protein Thermostability Calculations Using Alchemical Free Energy Simulations

    PubMed Central

    Seeliger, Daniel; de Groot, Bert L.

    2010-01-01

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

  10. Spectrum of energy depositions in the Auger Water Cherenkov Detector

    NASA Astrophysics Data System (ADS)

    Salazar, Humberto

    1999-08-01

    The measured spectrum of energy depositions in a Water Cherenkov Detector (WCD) prototype for the Pierre Auger Observatory is presented. A WCD (area 10 m2 )is located in the Puebla University campus at a depth of 800 g/cm2 (2200 m above sea level). Differential and integral spectra in a wide energy deposition range (0.5 - 150 of vertical equivalent muons) are presented. The problem of the WCD "self calibration" procedure (by rate of the muon events) is discussed. The characteristic change of the slopes of the differential spectrum at the transition from single muon signals to EAS signals is also discussed. The measured energy deposition spectrum at extreme signals is used to estimate the linearity of the response of the WCD PMTs. Key words: Auger array, water Cherenkov detector, extensive air showers

  11. 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.

  12. Exposure assessment and associated lung deposition calculations for vehicular exhaust in four metropolitan cities of Pakistan.

    PubMed

    Majid, Hussain; Alam, Khan; Madl, Pierre; Hofmann, Werner

    2013-06-01

    Ambient aerosol concentrations along the roadside of metropolitan cities of Pakistan were measured using a Grimm 1.109 dust monitor. Considering the high ambient aerosol concentrations, regional lung deposition of aerosol particles in the human respiratory tract was calculated to assess extent of exposure. Lung deposition was computed in terms of mass concentration and the associated surface area for 12 male traffic wardens using the latest version of the stochastic lung deposition code Inhalation, Deposition, and Exhalation of Aerosols in the Lung. The results have revealed 4 to 10 times higher concentrations than recommended by WHO guidelines. The deposition results derived from the model disclose that extrathoracic deposition is in the range of 22 to 28 % with total lung deposition ranging from 40 to 44 % for the scanned particle window of 0.25-10 μm. Considering an average 8-h shift per day and an average breathing rate of 1.3 m(3) h(-1), it is approximated that in a worker, up to 1.6 mg of inhalable particle mass can deposit per day.

  13. Energy deposition in discharge chamber of lightning protection multichamber system

    NASA Astrophysics Data System (ADS)

    Pinchuk, M. E.; Budin, A. V.; Kumkova, I. I.; Bogomaz, A. A.; Sivaev, A. D.; Chusov, A. N.; Zaynalov, R. I.

    2016-11-01

    The experimental data of energy deposition distribution along discharge chamber of lightning protection multichamber system in initial stage of discharge process aimed to model lightning current impulse up to 10 kA is presented. A multichamber system is a series connection of discharge chambers. According to our experiments the shock wave formation occurs during the breakdown phase between electrodes located at the bottom of discharge chamber. The consequent energy deposition during discharge development goes in the whole volume bounded by shock wave front.

  14. 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.

  15. Biological consequences of nanoscale energy deposition near irradiated heavy atom nanoparticles

    PubMed Central

    McMahon, Stephen J.; Hyland, Wendy B.; Muir, Mark F.; Coulter, Jonathan A.; Jain, Suneil; Butterworth, Karl T.; Schettino, Giuseppe; Dickson, Glenn R.; Hounsell, Alan R.; O'Sullivan, Joe M.; Prise, Kevin M.; Hirst, David G.; Currell, Fred J.

    2011-01-01

    Gold nanoparticles (GNPs) are being proposed as contrast agents to enhance X-ray imaging and radiotherapy, seeking to take advantage of the increased X-ray absorption of gold compared to soft tissue. However, there is a great discrepancy between physically predicted increases in X-ray energy deposition and experimentally observed increases in cell killing. In this work, we present the first calculations which take into account the structure of energy deposition in the nanoscale vicinity of GNPs and relate this to biological outcomes, and show for the first time good agreement with experimentally observed cell killing by the combination of X-rays and GNPs. These results are not only relevant to radiotherapy, but also have implications for applications of heavy atom nanoparticles in biological settings or where human exposure is possible because the localised energy deposition high-lighted by these results may cause complex DNA damage, leading to mutation and carcinogenesis. PMID:22355537

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Kaya, Cemal; Kaya, Savaş; Banerjee, Priyabrata

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kürpick, P.; Thumm, U.

    1996-03-01

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

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

    PubMed

    Andersen, Torben B

    2015-09-01

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

  1. Mechanical characteristics of a tool steel layer deposited by using direct energy deposition

    NASA Astrophysics Data System (ADS)

    Baek, Gyeong Yun; Shin, Gwang Yong; Lee, Eun Mi; Shim, Do Sik; Lee, Ki Yong; Yoon, Hi-Seak; Kim, Myoung Ho

    2017-07-01

    This study focuses on the mechanical characteristics of layered tool steel deposited using direct energy deposition (DED) technology. In the DED technique, a laser beam bonds injected metal powder and a thin layer of substrate via melting. In this study, AISI D2 substrate was hardfaced with AISI H13 and M2 metal powders for mechanical testing. The mechanical and metallurgical characteristics of each specimen were investigated via microstructure observation and hardness, wear, and impact tests. The obtained characteristics were compared with those of heat-treated tool steel. The microstructures of the H13- and M2-deposited specimens show fine cellular-dendrite solidification structures due to melting and subsequent rapid cooling. Moreover, the cellular grains of the deposited M2 layer were smaller than those of the H13 structure. The hardness and wear resistance were most improved in the M2-deposited specimen, yet the H13-deposited specimen had higher fracture toughness than the M2-deposited specimen and heat-treated D2.

  2. GIS supported calculations of (137)Cs deposition in Sweden based on precipitation data.

    PubMed

    Almgren, Sara; Nilsson, Elisabeth; Erlandsson, Bengt; Isaksson, Mats

    2006-09-15

    It is of interest to know the spatial variation and the amount of (137)Cs e.g. in case of an accident with a radioactive discharge. In this study, the spatial distribution of the quarterly (137)Cs deposition over Sweden due to nuclear weapons fallout (NWF) during the period 1962-1966 was determined by relating the measured deposition density at a reference site to the amount of precipitation. Measured quarterly values of (137)Cs deposition density per unit precipitation at three reference sites and quarterly precipitation at 62 weather stations distributed over Sweden were used in the calculations. The reference sites were assumed to represent areas with different quarterly mean precipitation. The extent of these areas was determined from the distribution of the mean measured precipitation between 1961 and 1990 and varied according to seasonal variations in the mean precipitation pattern. Deposition maps were created by interpolation within a geographical information system (GIS). Both integrated (total) and cumulative (decay corrected) deposition densities were calculated. The lowest levels of NWF (137)Cs deposition density were noted in north-eastern and eastern parts of Sweden and the highest levels in the western parts of Sweden. Furthermore the deposition density of (137)Cs, resulting from the Chernobyl accident was determined for an area in western Sweden based on precipitation data. The highest levels of Chernobyl (137)Cs in western Sweden were found in the western parts of the area along the coast and the lowest in the east. The sum of the deposition densities from NWF and Chernobyl in western Sweden was then compared to the total activity measured in soil samples at 27 locations. Comparisons between the predicted values of this study show a good agreement with measured values and other studies.

  3. 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.

  4. 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.

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

    DTIC Science & Technology

    2016-12-01

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

  6. Towards a standardized setup for surface energy calculations

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    High-throughput design of new materials with desired electronic properties, based on screening of large collections of crystal structures organized in the from of libraries or databases require fast, widely applicable, consistent and unsupervised methods to calculate the property of interest. In this work we present an approach for the calculation of surface energies of two-dimensional periodic crystal lattices which meets all these requirements. For materials slabs which are terminated with two identical surfaces, the task of calculating the surface energy is trivial. More problematic are the cases where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed approach addresses this problem. It relies on appropriately chosen capping atoms, whose bonding energy contributions are used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surface energies with errors that are below 10%, and that are as low as 2% in many cases. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations.

  7. Calculating fusion neutron energy spectra from arbitrary reactant distributions

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  8. 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

  9. Lead optimization mapper: automating free energy calculations for lead optimization

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

    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.

  10. Lead optimization mapper: automating free energy calculations for lead optimization.

    PubMed

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

    2013-09-01

    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.

  11. 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.

  12. 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.

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

    PubMed

    Ahnesjö, A

    1989-01-01

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

  14. Removing the barrier to the calculation of activation energies

    SciTech Connect

    Mesele, Oluwaseun O.; Thompson, Ward H.

    2016-10-06

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

  15. Removing the barrier to the calculation of activation energies

    SciTech Connect

    Mesele, Oluwaseun O.; Thompson, Ward H.

    2016-10-06

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

  16. 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.

  17. Perspective: Alchemical free energy calculations for drug discovery

    PubMed Central

    Mobley, David L.; Klimovich, Pavel V.

    2012-01-01

    Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery. PMID:23267463

  18. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

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

    2017-02-16

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

  19. Atomistic calculations of dislocation core energy in aluminium

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  20. Perspective: Alchemical free energy calculations for drug discovery

    NASA Astrophysics Data System (ADS)

    Mobley, David L.; Klimovich, Pavel V.

    2012-12-01

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

  1. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

    Zhou, Xiaowang W.; Sills, Ryan B.; Ward, Donald K.; ...

    2017-02-16

    A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy:more » Ec = Asin2β + Bcos2β, and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. As a result, with our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.« less

  2. A database of frequency distributions of energy depositions in small-size targets by electrons and ions.

    PubMed

    Nikjoo, H; Uehara, S; Emfietzoglou, D; Pinsky, L

    2011-02-01

    Linear energy transfer (LET) is an average quantity, which cannot display the stochastics of the interactions of radiation tracks in the target volume. For this reason, microdosimetry distributions have been defined to overcome the LET shortcomings. In this paper, model calculations of frequency distributions for energy depositions in nanometre size targets, diameters 1-100 nm, and for a 1 μm diameter wall-less TEPC, for electrons, protons, alpha particles and carbon ions are reported. Frequency distributions for energy depositions in small-size targets with dimensions similar to those of biological molecules are useful for modelling and calculations of DNA damage. Monte Carlo track structure codes KURBUC and PITS99 were used to generate tracks of primary electrons 10 eV to 1 MeV, and ions 1 keV µm(-1) to 300 MeV µm(-1) energies. Distribution of absolute frequencies of energy depositions in volumes with diameters of 1-100 nm randomly positioned in unit density water irradiated with 1 Gy of the given radiation was obtained. Data are presented for frequency of energy depositions and microdosimetry quantities including mean lineal energy, dose mean lineal energy, frequency mean specific energy and dose mean specific energy. The modelling and calculations presented in this work are useful for characterisation of the quality of radiation beam in biophysical studies and in radiation therapy.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Effects of internal gain assumptions in building energy calculations

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Perkins, R.

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

  8. 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.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2014-04-21

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

  11. Improvements to the FLASH Laser Energy Deposition Package

    NASA Astrophysics Data System (ADS)

    Flocke, Norbert; Bachan, J.; Couch, S.; Daley, C.; Dubey, A.; Fatenejad, M.; Graziani, C.; Lamb, Don; Lee, Dongwook; Scopatz, A.; Tzeferacos, P.; Weide, K.

    2012-10-01

    FLASH is an open source, compressible, spatially-adaptive, radiation magnetohydrodynamics code that is currently used at a number of institutions for simulating laser-driven HEDP experiments. FLASH uses ray-tracing to model laser energy deposition via the inverse-Bremsstrahlung process on an Eulerian block-structured mesh. We describe recent improvements to the laser ray-tracing package in FLASH which have led to increased accuracy and performance. A ``3D-in-2D'' ray-trace model has been developed which transports rays in three-dimensions when FLASH is configured to run in 2D cylindrical geometry. Several options have been added which allow users greater flexibility in choosing the initial ray placement. These options can be used to reduce the number of rays needed to accurately represent the energy deposition. Several models have been added to FLASH for smoothing the deposited laser energy to reduce numerical noise. The laser package has also been modified to use threading and mesh-replication for parallelization to improve computational performance. Finally, we will present the results of FLASH simulations that use these improvements and compare results using different laser options.

  12. Latest Developments to the FLASH Laser Energy Deposition Package

    NASA Astrophysics Data System (ADS)

    Flocke, Norbert; Daley, Chris; Fatenejad, Milad; Tzeferacos, Petros; Lamb, Don Q.

    2013-10-01

    We describe recent improvements to the FLASH laser energy deposition package. FLASH is an open source, compressible, spatially-adaptive, radiation hydro/MHD code based on an Eulerian AMR grid. Laser energy deposition is modeled using geometric optics ray-tracing algorithms and the inverse-Bremsstrahlung process. A large variety of options exist for users, which allows for a flexible setup of the laser. Several domain geometries are possible (1D, 2D cartesian and cylindrical, 3D in 2D ray-tracing, 3D cartesian) and several beam cross-sections are available (ray placements on square, radial or statistical grids). The original treatment is based on the Kaiser algorithm, which represents the electron number density as a cell-by-cell, piece-wise linear continuous function. We have added a second option that uses cubic interpolation of the electron number density, resulting in a smoother distribution of the energy deposition. We have also improved the computational performance of the package through threading and asynchronous communication when rays cross a block boundary. We present the results of performance and verification tests of the improved package. This work was supported by DOE NNSA ASC.

  13. Computer Program for the Calculation of Multicomponent Convective Diffusion Deposition Rates from Chemically Frozen Boundary Layer Theory

    NASA Technical Reports Server (NTRS)

    Gokoglu, S. A.; Chen, B. K.; Rosner, D. E.

    1984-01-01

    The computer program based on multicomponent chemically frozen boundary layer (CFBL) theory for calculating vapor and/or small particle deposition rates is documented. A specific application to perimter-averaged Na2SO4 deposition rate calculations on a cylindrical collector is demonstrated. The manual includes a typical program input and output for users.

  14. Mathematical modelling of energy expenditure during tissue deposition.

    PubMed

    Hall, Kevin D

    2010-07-01

    Predicting the magnitude and rate of weight gain for a given increase of energy intake requires a model of whole-body energy expenditure that includes the energy cost of tissue deposition. Here, I introduce a mathematical framework for modelling energy expenditure that elucidates conceptual problems with the classical Kielanowski method for estimating the efficiencies of body fat and protein deposition. An alternative approach uses the theoretical biochemical efficiencies for protein and fat synthesis in combination with models of energy expenditure that include body fat and protein turnover costs. I illustrate this alternative approach using a simple mathematical model applied to previously published data from growing rats and human infants and compare the simple model results with the classical Kielanowski model. While both models fit the data reasonably well (R2>0.87 in rats and R2>0.67 in infants), the Kielanowski method resulted in parameter estimates that varied widely across experiments, had poor precision, and occasionally produced efficiency estimates greater than 1. In contrast, the new method provided precise parameter values and revealed consistencies across different experiments. The proposed mathematical framework has implications for interpreting studies of animal nutrition as well as providing a roadmap for future modelling efforts.

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  16. Calculated stacking-fault energies of elemental metals

    NASA Astrophysics Data System (ADS)

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

    1993-05-01

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

  17. Surface energy balance calculations for small northern lakes

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  18. 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.

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

    NASA Technical Reports Server (NTRS)

    Liu, Yen; Shakib, Farzin; Vinokur, Marcel

    1990-01-01

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

  20. 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

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

    NASA Technical Reports Server (NTRS)

    Liu, Yen; Shakib, Farzin; Vinokur, Marcel

    1990-01-01

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

  2. Low energy dipole strength from large scale shell model calculations

    NASA Astrophysics Data System (ADS)

    Sieja, Kamila

    2017-09-01

    Low energy enhancement of radiative strength functions has been deduced from experiments in several mass regions of nuclei. Such an enhancement is believed to impact the calculated neutron capture rates which are crucial input for reaction rates of astrophysical interest. Recently, shell model calculations have been performed to explain the upbend of the γ-strength as due to the M1 transitions between close-lying states in the quasi-continuum in Fe and Mo nuclei. Beyond mean-↓eld calculations in Mo suggested, however, a non-negligible role of electric dipole in the low energy enhancement. So far, no calculations of both dipole components within the same theoretical framework have been presented in this context. In this work we present newly developed large scale shell model appraoch that allows to treat on the same footing natural and non-natural parity states. The calculations are performed in a large sd - pf - gds model space, allowing for 1p{1h excitations on the top of the full pf-shell con↓guration mixing. We restrict the discussion to the magnetic part of the dipole strength, however, we calculate for the ↓rst time the magnetic dipole strength between states built of excitations going beyond the classical shell model spaces. Our results corroborate previous ↓ndings for the M1 enhancement for the natural parity states while we observe no enhancement for the 1p{1h contributions. We also discuss in more detail the e↑ects of con↓guration mixing limitations on the enhancement coming out from shell model calculations.

  3. Energy deposition in the ionosphere derived from LEO satellite observations

    NASA Astrophysics Data System (ADS)

    Stolle, Claudia; Park, Jaeheung; Buchert, Stephan; Trulik, Vladimir; Bilitza, Dieter

    2014-05-01

    Ten years of successful operation of the multi-instrument CHAMP satellite mission at a unique orbit altitude of about 400 km revealed many interesting features of the coupling between the thermosphere and ionosphere. Different processes contribute to the deposition of solar and magnetospheric energy into the thermosphere. One important venue is heating through thermal electrons transferring energy by collisions with ions and neutrals. In the ionospheric F region thermal electrons are heated primarily through photoelectrons by local or non-local processes. At high latitudes soft precipitation and electromagnetic heating play a major role. The energy deposition can be quantified by a family of chemo-physical equations (Schunk and Nagy, 2009) that depend on plasma and neutral densities and temperatures. One important indicator for the energy transfer is the difference between electron and ion- and neutral- temperatures. Electron cooling leads to thermospheric heating and and we expect that this process leads to a local enhancement of mass density (air drag). Sizable electron cooling rates in the F region have been published from EISCAT radar observations in the ionospheric cusp. Based on CHAMP observation of electron density and temperature we estimate the energy deposit in the F-region through cooling of the thermal electron gas caused by elastic and inelastic processes. We find that a significant deposition is present during day at mid latitudes. At low latitudes the energy flux remains important until midnight. Observed heating rates depend on the satellite altitudes, but they are globally available from the CHAMP data. Missing observations in the CHAMP dataset, e.g., ion temperature, are derived from empirical models as IRI or MSIS. We investigate the global distribution of the electron cooling rate, we quantify the contributions of the different processes (equations) to the total energy transfer, e.g., depending on height, and we intend to compare our results

  4. 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

  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. 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.

  7. 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).

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

    DTIC Science & Technology

    1984-02-02

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

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

    PubMed

    Evenhuis, Christian R; Manthe, Uwe

    2008-07-14

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

  10. Calculated thermochemistry of aminonitroacetylene: a new high-energy material?

    PubMed

    Mathews, Kelly Y; Ball, David W

    2009-04-30

    As part of an increased interest in amino- and nitro-substituted high-energy-density materials (as exemplified by FOX-7, 1,1-diamino-2,2-dinitroethylene), here we present calculated properties of aminonitroacetylene, NH(2)-CC-NO(2). Our results indicate that while the specific enthalpy of combustion is less than that of acetylene, its specific enthalpy of decomposition is greater than that of TNT, and its predicted density is large enough to predict substantial high-energy-density properties for this substance.

  11. Effects of internal gain assumptions in building energy calculations

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Perkins, R.

    1981-01-01

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

  12. Effects of internal gain assumptions in building energy calculations

    SciTech Connect

    Christensen, C.; Perkins, R.

    1981-01-01

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

  13. Complex energy approaches for calculating isobaric analogue states

    SciTech Connect

    Betan, R. Id; Kruppa, A. T.; Vertse, T.

    2008-10-15

    Parameters of isobaric analog resonance (IAR) are calculated in the framework of the Lane model using different methods. In the standard method, the direct numerical solution of the coupled channel (CC) Lane equations served as a reference for checking two complex energy methods, namely the complex energy shell model (CXSM) and the complex scaling (CS) approaches. The IAR parameters calculated by the CXSM and the CS methods agree with that of the CC results within 1 keV for all partial waves considered. Although the CXSM and the CS methods have similarities, an important difference is that only the CXSM method offers a direct way for studying the configurations of the IAR wave function.

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

    PubMed

    Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele

    2011-09-07

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

  15. 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.

  16. Calculating Free Energy Changes in Continuum Solvation Models

    DOE PAGES

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

    We recently showed for a large dataset of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations,more » as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol-1 and 25 kJ mol-1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less

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

    PubMed Central

    2016-01-01

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

  18. Calculating Free Energy Changes in Continuum Solvation Models

    SciTech Connect

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

    We recently showed for a large dataset of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations, as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol-1 and 25 kJ mol-1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.

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

    PubMed

    Min, Donghong; Yang, Wei

    2008-05-21

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

  20. 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.

  1. Calculating free energies of organic molecules on insulating substrates.

    PubMed

    Gaberle, Julian; Gao, David Z; Shluger, Alexander L

    2017-01-01

    The challenges and limitations in calculating free energies and entropies of adsorption and interaction of organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free energy profiles and entropy changes were calculated for step adhesion and dimer formation of these molecules. However, converging these calculations is nontrivial and comes at large computational cost. We illustrate the difficulties as well as the possibilities of applying these methods towards understanding dynamic processes of organic molecules on insulating substrates.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Charge state dependent energy deposition by ion impact.

    PubMed

    Lake, R E; Pomeroy, J M; Grube, H; Sosolik, C E

    2011-08-05

    We report on a measurement of craters in thin dielectric films formed by Xe(Q+) (26 ≤ Q ≤ 44) projectiles. Tunnel junction devices with ion-irradiated barriers were used to amplify the effect of charge-dependent cratering through the exponential dependence of tunneling conductance on barrier thickness. Electrical conductance of a crater σ(c)(Q) increased by 4 orders of magnitude (7.9 × 10(-4) μS to 6.1 μS) as Q increased, corresponding to crater depths ranging from 2 to 11 Å. By employing a heated spike model, we determine that the energy required to produce the craters spans from 8 to 25 keV over the investigated charge states. Considering energy from preequilibrium nuclear and electronic stopping as well as neutralization, we find that at least (27 ± 2)% of available projectile neutralization energy is deposited into the thin film during impact.

  7. The calculation of the optical gap energy of ZnXO (X = Bi, Sn and Fe)

    NASA Astrophysics Data System (ADS)

    Benramache, Said; Benhaoua, Boubaker

    2016-01-01

    In this paper, a new mathematical model has been developed to calculate the optical properties of nano materials a function of their size and structure. ZnO has good characterizatics in optical, electrical, and structural crystallisation; We will demonstrate that the direct optical gap energy of ZnO films grown by US and SP spray deposition can be calculated by investigating the correlation between solution molarity, doping levels of doped films and their Urbache energy. A simulation model has been developed to calculate the optical band gap energy of undoped and Bi, Sn and Fe doped ZnO thin films. The measurements by thus proposed models are in agreement with experimental data, with high correlation coefficients in the range 0.94-0.99. The maximum calculated enhancement of the optical gap energy of Sn doped ZnO thin films is always higher than the enhancement attainable with an Fe doped film, where the minimum error was found for Bi and Sn doped ZnO thin films to be 2,345 and 3,072%, respectively. The decrease in the relative errors from undoped to doped films can be explained by the good optical properties which can be observed in the fewer number of defects as well as less disorder.

  8. Energy deposition model based on electron scattering cross section data from water molecules

    NASA Astrophysics Data System (ADS)

    Muñoz, A.; Oiler, J. C.; Blanco, F.; Gorfinkiel, J. D.; Limão-Vieira, P.; Maira-Vidal, A.; Borge, M. J. G.; Tengblad, O.; Huerga, C.; Téllez, M.; García, G.

    2008-10-01

    A complete set of electrons scattering cross sections by water molecules over a broad energy range, from the me V to the Me V ranges, is presented in this study. These data have been obtained by combining experiments and calculations and cover most relevant processes, both elastic and inelastic, which can take place in the considered energy range. A new Monte Carlo simulation programme has been developed using as input parameter these cross sectional data as well as experimental energy loss spectra. The simulation procedure has been applied to obtain electron tracks and energy deposition plots in water when irradiated by a Ru-106 plaque as those used for brachyteraphy of ocular tumours. Finally, the low energy electron tracks provided by the present model have been compared with those obtained with other codes available in the literature

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

    PubMed

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

    2010-05-06

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

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

    PubMed

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

    2013-08-15

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

  11. Distinctive features of kinetics of plasma at high specific energy deposition

    NASA Astrophysics Data System (ADS)

    Lepikhin, Nikita; Popov, Nikolay; Starikovskaia, Svetlana

    2016-09-01

    A nanosecond capillary discharge in pure nitrogen at moderate pressures is used as an experimental tool for plasma kinetics studies at conditions of high specific deposited energy up to 1 eV/molecule. Experimental observations based on electrical (back current shunts, capacitive probe) and spectroscopic measurements (quenching rates; translational, rotational and vibrational temperature measurements) demonstrate that high specific deposited energy, at electric fields of 200-300 Td, can significantly change gas kinetics in the discharge and in the afterglow. The numerical calculations in 1D axially symmetric geometry using experimental data as input parameters show that changes in the plasma kinetics are caused by extremely high excitation degree: up to 10% of molecular nitrogen is electronically excited at present conditions. Distinctive features of kinetics of plasma at high specific energy deposition as well as details of the experimental technique and numerical calculations will be present. The work was partially supported by French National Agency, ANR (PLASMAFLAME Project, 2011 BS09 025 01), AOARD AFOSR, FA2386-13-1-4064 grant (Program Officer Prof. Chiping Li), LabEx Plas@Par and Linked International Laboratory LIA KaPPA (France-Russia).

  12. 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.

  13. Dirac Calculations for Proton Inelastic Scattering at Intermediate Energies

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  14. Kinetic treatment of alpha-particle loss and energy deposition in ELMO Bumpy Torus

    SciTech Connect

    Fenstermacher, M.E.; Uckan, N.A.

    1982-12-01

    A formalism has been developed in terms of a drift kinetic equation with a Fokker-Planck collision operator to calculate alpha particle loss and energy deposition rate coefficients for one position in space and for steady-state operating conditions. A bounce-averaged drift kinetic equation for an ELMO Bumpy Torus (EBT) is expressed in invariant variables E = v/sup 2//2 and lambda = v/sub perpendicular//sup 2/B/sub MID//v/sup 2/B(l) and is used with energy scattering and pitch angle scattering terms in the collision operator. The alpha particle distribution function is expanded in terms of energy coefficients and pitch angle eigenfunctions. For the case of a square well magnetic field shape, the pitch angle eigenfunctions are the Legendre polynominals. With an expression for the distribution function the particle loss and energy deposition rates are calculated by taking the zeroth and first-order energy moments, respectively, of the kinetic equation.

  15. 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.

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

    PubMed

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

    2013-11-07

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

  17. 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.

  18. SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

    SciTech Connect

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

    2016-02-25

    Sensitivity coefficients describe the fractional change in a system response that is induced by changes to system parameters and nuclear data. The Tools for Sensitivity and UNcertainty Analysis Methodology Implementation (TSUNAMI) code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, including quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.

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

    PubMed

    Stefik, Morgan

    2016-07-07

    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.

  1. Transported Geothermal Energy Technoeconomic Screening Tool - Calculation Engine

    DOE Data Explorer

    Liu, Xiaobing

    2016-09-21

    This calculation engine estimates technoeconomic feasibility for transported geothermal energy projects. The TGE screening tool (geotool.exe) takes input from input file (input.txt), and list results into output file (output.txt). Both the input and ouput files are in the same folder as the geotool.exe. To use the tool, the input file containing adequate information of the case should be prepared in the format explained below, and the input file should be put into the same folder as geotool.exe. Then the geotool.exe can be executed, which will generate a output.txt file in the same folder containing all key calculation results. The format and content of the output file is explained below as well.

  2. 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.

  3. Correlation between energy deposition and AlN crystal growth induced by ion bombardment

    NASA Astrophysics Data System (ADS)

    Kenzo, Kobayashi; Masaya, Iwaki; Takanobu, Fujihana

    1991-07-01

    A study has been made of the effects of ion (He, O, N and Ne) bombardment on the crystallization of AlN. AlN 0.8 thin films 100 nm thick were deposited on Si (111) wafers by an activated reactive evaporation method in a nitrogen atmosphere. He, O, N and Ne ions were bombarded onto films at room temperature to a dose of 5 × 10 17 ions/cm 2, using an energy of 150 keV. This energy was chosen to place the average projected range of the ions in the substrate interior. XRD measurements were carried out using CuK α radiation (40 keV, 30 mA). The quantities of energy deposited in the films, through ionization and by recoil atoms, were calculated using TRIM-88. It is concluded that ion bombardment of AlN 0.8 thin films causes crystal growth of AlN, with the c-axis oriented perpendicular to the substrate plane, near to room temperature without any thermal annealing. Energy deposition through the ionization plays an essential role in the crystallization of AlN in AlN x thin films.

  4. 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.

  5. Investigation of Multipole Electrostatics in Hydration Free Energy Calculations

    PubMed Central

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

    2010-01-01

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

  6. Advancing Drug Discovery through Enhanced Free Energy Calculations.

    PubMed

    Abel, Robert; Wang, Lingle; Harder, Edward D; Berne, B J; Friesner, Richard A

    2017-07-18

    A principal goal of drug discovery project is to design molecules that can tightly and selectively bind to the target protein receptor. Accurate prediction of protein-ligand binding free energies is therefore of central importance in computational chemistry and computer aided drug design. Multiple recent improvements in computing power, classical force field accuracy, enhanced sampling methods, and simulation setup have enabled accurate and reliable calculations of protein-ligands binding free energies, and position free energy calculations to play a guiding role in small molecule drug discovery. In this Account, we outline the relevant methodological advances, including the REST2 (Replica Exchange with Solute Temperting) enhanced sampling, the incorporation of REST2 sampling with convential FEP (Free Energy Perturbation) through FEP/REST, the OPLS3 force field, and the advanced simulation setup that constitute our FEP+ approach, followed by the presentation of extensive comparisons with experiment, demonstrating sufficient accuracy in potency prediction (better than 1 kcal/mol) to substantially impact lead optimization campaigns. The limitations of the current FEP+ implementation and best practices in drug discovery applications are also discussed followed by the future methodology development plans to address those limitations. We then report results from a recent drug discovery project, in which several thousand FEP+ calculations were successfully deployed to simultaneously optimize potency, selectivity, and solubility, illustrating the power of the approach to solve challenging drug design problems. The capabilities of free energy calculations to accurately predict potency and selectivity have led to the advance of ongoing drug discovery projects, in challenging situations where alternative approaches would have great difficulties. The ability to effectively carry out projects evaluating tens of thousands, or hundreds of thousands, of proposed drug candidates

  7. Calculation of Modulated Transport Coefficients for Recovery of ECH Deposition Profiles

    NASA Astrophysics Data System (ADS)

    Brookman, M. W.; Austin, M. E.; Horton, C. W.; Petty, C. C.

    2015-11-01

    Ray tracing of ECRF power through fixed plasma profiles may significantly underestimate the ECH and ECCD deposition profile width. Density fluctuations present in tokamak plasmas modify the path of radiation on a fluctuation timescale, spreading the heating power over a wide area. Deposition is hard to measure as transport quickly spreads power, and transport effects are difficult to separate from a truly broadened profile. While the total power deposited should be unchanged in an ITER-like scenario, tearing mode suppression is sensitive to the alignment and width of the ECCD profile. A novel integral method for calculating thermal transport coefficients based on ECE measurements of Te is presented and applied to DIII-D data. These are compared with computational predictions of broadening from the ray tracing code C3PO and distribution code LUKE. This work will provide the analytical framework for measuring fluctuation broadening in a future DIII-D experiment. Supported by the US DOE under DE-FG03-97ER54415 & DE-FG02-04ER54761.

  8. 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.

  9. Multiple scattering calculations of relativistic electron energy loss spectra

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  10. 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.

  11. Hydrothermal transport, deposition, and fractionation of the REE: Experimental data and thermodynamic calculations

    SciTech Connect

    Migdisov, Artaches; Williams-Jones, A. E.; Brugger, J.; Caporuscio, Florie Andre

    2016-06-11

    For many years, our understanding of the behavior of the REE in hydrothermal systems was based on semi-empirical estimates involving extrapolation of thermodynamic data obtained at 25 °C. Since then, a substantial body of experimental data has accumulated on the stability of aqueous complexes of the REE. These data have shown that some of the predictions of Haas et al. (1995) are accurate, but others may be in error by several orders of magnitude. However, application of the data in modeling hydrothermal transport and deposition of the REE has been severely hampered by the lack of data on the thermodynamic properties of even the most common REE minerals. The discrepancies between the predictions and experimental determinations of the thermodynamic properties of aqueous REE species, together with the paucity of data on the stability of REE minerals, raise serious questions about the reliability of some models that have been proposed for the hydrothermal mobility of these critical metals. In this contribution, we review a body of high-temperature experimental data collected over the past 15 years on the stability of REE aqueous species and minerals. Using this new thermodynamic dataset, we re-evaluate the mechanisms responsible for hydrothermal transport and deposition of the REE. We also discuss the mechanisms that can result in REE fractionation during their hydrothermal transport and deposition. Here, our calculations suggest that in hydrothermal solutions, the main REE transporting ligands are chloride and sulfate, whereas fluoride, carbonate, and phosphate likely play an important role as depositional ligands. In addition to crystallographic fractionation, which is based on the differing affinity of mineral structures for the REE, our models suggest that the REE can be fractionated hydrothermally due to the differences in the stability of the LREE and HREE as aqueous chloride complexes.

  12. Hydrothermal transport, deposition, and fractionation of the REE: Experimental data and thermodynamic calculations

    DOE PAGES

    Migdisov, Artaches; Williams-Jones, A. E.; Brugger, J.; ...

    2016-06-11

    For many years, our understanding of the behavior of the REE in hydrothermal systems was based on semi-empirical estimates involving extrapolation of thermodynamic data obtained at 25 °C. Since then, a substantial body of experimental data has accumulated on the stability of aqueous complexes of the REE. These data have shown that some of the predictions of Haas et al. (1995) are accurate, but others may be in error by several orders of magnitude. However, application of the data in modeling hydrothermal transport and deposition of the REE has been severely hampered by the lack of data on the thermodynamicmore » properties of even the most common REE minerals. The discrepancies between the predictions and experimental determinations of the thermodynamic properties of aqueous REE species, together with the paucity of data on the stability of REE minerals, raise serious questions about the reliability of some models that have been proposed for the hydrothermal mobility of these critical metals. In this contribution, we review a body of high-temperature experimental data collected over the past 15 years on the stability of REE aqueous species and minerals. Using this new thermodynamic dataset, we re-evaluate the mechanisms responsible for hydrothermal transport and deposition of the REE. We also discuss the mechanisms that can result in REE fractionation during their hydrothermal transport and deposition. Here, our calculations suggest that in hydrothermal solutions, the main REE transporting ligands are chloride and sulfate, whereas fluoride, carbonate, and phosphate likely play an important role as depositional ligands. In addition to crystallographic fractionation, which is based on the differing affinity of mineral structures for the REE, our models suggest that the REE can be fractionated hydrothermally due to the differences in the stability of the LREE and HREE as aqueous chloride complexes.« less

  13. 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.

  14. 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.

  15. 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.

  16. Isotope Separation and Decay Energy Calculation for LISA Commissioning Experiment

    NASA Astrophysics Data System (ADS)

    Taylor, Nathaniel; Barker, Alyson; Garrett, Sierra; Rogers, Warren F.; MoNA Collaboration

    2013-10-01

    The commissioning experiment for the Large multi-Institutional Scintillator Array (LISA) was designed to investigate properties of neutron-unstable excited states of the 24O. The array is located at the NSCL, MSU and is used in conjunction with the Modular Neutron Array (MoNA) and the Sweeper Magnet. Oxygen fragments produced by the 26F secondary beam incident on a Be target are directed through the Sweeper Chamber which includes two tracking CRDC detectors, an ion chamber, and a thin and thick scintillator. Plotting the fragment's trajectory position vs. angle vs. time of flight allows for separation of the individual 22 , 23 , and 24 O isotopes, necessary for the calculation of the decay properties of individual states. Anomalous features in the fragments' emittance distribution, believed to result from little understood issues with the tracking detectors, required that we adopt a slightly different approach than that developed recently by the collaboration. Once the isotopes are successfully separated, decay energies are calculated by applying mass-invariant decay spectroscopy by associating the fragment's precise trajectory (determined by inverse-tracking through the Sweeper Magnet) and energy with those of the emitted neutron. Work supported by NSF grant PHY-1101745.

  17. Valence calculations of binding energies of mid-row lanthanides

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

    Binding energies of mid-row lanthanides have been calculated by taking advantage of the >90% LS purity of the 4f^n subgroups of their neutral ground states ootnotetextAtomic Energy Levels -- The Rare-Earth Elements, edited by W. C. Martin, R. Zalubas, and L. Hagan, Natl. Bur. Stand. Ref. Data Ser. Natl. Bur. Stand. (U.S.) Circ. No. 60 (U.S. GPO, Washington, D.C., 1978).. As described in our recent work on Nd^- ootnotetextS. M. O'Malley and D. R. Beck, Phy. Rev. A 77, 012505 (2008)., the 4f^n electrons were treated as core-like and restricted to a single LS term throughout all Dirac-Fock and correlation configurations, resulting in manageable relativistic configuration-interaction calculations for these computationally complex systems. Several weakly bound 6p attachments (<200 meV) were found for each negative ion, and these were carefully analyzed with respect to approximate LS total configuration as well as the j's of the the 4f^n subgroup and 6p electron.

  18. Microscopic calculations of {lambda} single-particle energies.

    SciTech Connect

    Usmani, Q. N.

    1998-02-12

    {Lambda} binding energy data for total baryon number A {le} 208 and for {Lambda} angular momenta {ell}{sub {Lambda}} {le} 3 are analyzed in terms of phenomenological (but generally consistent with meson-exchange) {Lambda}N and {Lambda}NN potentials. The Fermi-Hypernetted-Chain technique is used to calculate the expectation values for the {Lambda} binding to nuclear matter. Accurate effective {Lambda}N and {Lambda}NN potentials are obtained which are folded with the core nucleus nucleon densities to calculate the {Lambda} single particle potential U{sub {Lambda}}(r). We use a dispersive {Lambda}NN potential but also include an explicit {rho} dependence to allow for reduced repulsion in the surface, and the best fits have a large {rho} dependence giving consistency with the variational Monte Carlo calculations for {sub {Lambda}}{sup 5}He. The exchange fraction of the {Lambda}N space-exchange potential is found to be 0.2-0.3 corresponding to m{sub {Lambda}}* {approx_equal} (0.74-0.82)m{sub {Lambda}}. Charge symmetry breaking is found to be significant for heavy hypernuclei with a large neutron excess, with a strength consistent with that obtained from the A = 4 hypernuclei.

  19. 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.

  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. 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

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

    PubMed

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

    2016-02-09

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

  3. 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.

  4. 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.

  5. Energy deposition of multi-MeV protons in compressed targets of fast-ignition inertial confinement fusion.

    PubMed

    Mahdavi, M; Koohrokhi, T

    2012-01-01

    The energy loss and penetration of multi-megelectronvolt protons into a uniform deuterium-tritium (DT) plasma has been calculated. The effects of nuclear elastic scattering and Coulomb interactions are treated from a unified point of view. In general, multiple scattering enhances the proton linear-energy transfer along the initial proton direction, thus the energy deposition increases near the end of its range. The net effect of multiple scattering is to reduce the penetration from 1.20 to 1.02 g cm-2 for 12 MeV protons in a ρ=500 g cm-3 plasma at T=5 keV. These results should have relevance to proton fast ignition, specifically to energy deposition calculations that critically assess quantitative ignition requirements.

  6. Energy deposition in low-power coaxial plasma thrusters

    NASA Technical Reports Server (NTRS)

    Myers, R. M.; Kelly, A. J.; Jahn, R. G.

    1991-01-01

    An experimental examination of energy deposition in self-field, coaxial plasma thrusters revealed that the thrust efficiency ranged from 2-9 percent and that the dominant losses resulted from electrode heating and propellant ionization. Sensible enthalpy and radiative losses were negligible. Thruster specific impulse increased with current, ranging from 550-1750 seconds. Spectroscopic studies of the plume plasma showed that the electron temperature ranged from 0.5-2.5 eV and that the dominant species were singly and doubly ionized argon. Attempts to raise thruster efficiency by increasing the chamber pressure resulted in reduced electrode losses and lowered I(sp), but the thrust efficiency decreased because of a current redistribution that lowered the thrust beyond expectations.

  7. Enhancement of fast electron energy deposition by external magnetic fields

    NASA Astrophysics Data System (ADS)

    Honrubia, J. J.; Murakami, M.; Mima, K.; Johzaki, T.; Sunahara, A.; Nagatomo, H.; Fujioka, S.; Shiraga, H.; Azechi, H.

    2016-03-01

    Recently, generation of external magnetic fields of a few kT has been reported [Fujioka et al. Scientific Reports 2013 3 1170]. These fields can be used in fast ignition to mitigate the large fast electron divergence. In this summary, two fast ignition applications are briefly outlined. The first one deals with electron guiding by external B-fields applied at the end of the shell implosion of a re-entrant cone target. Preliminary results show that the B-field strength at the time of peak ρR may be sufficiently high for fast electron guiding. The second application deals with guiding of fast electrons in magnetized wires surrounded by plasma. Results show a significant enhancement of electron energy deposition at the end of the wire, which is particularly important for low-Z wires.

  8. Energy deposition in low-power coaxial plasma thrusters

    NASA Technical Reports Server (NTRS)

    Myers, R. M.; Kelly, A. J.; Jahn, R. G.

    1991-01-01

    An experimental examination of energy deposition in self-field, coaxial plasma thrusters revealed that the thrust efficiency ranged from 2-9 percent and that the dominant losses resulted from electrode heating and propellant ionization. Sensible enthalpy and radiative losses were negligible. Thruster specific impulse increased with current, ranging from 550-1750 seconds. Spectroscopic studies of the plume plasma showed that the electron temperature ranged from 0.5-2.5 eV and that the dominant species were singly and doubly ionized argon. Attempts to raise thruster efficiency by increasing the chamber pressure resulted in reduced electrode losses and lowered I(sp), but the thrust efficiency decreased because of a current redistribution that lowered the thrust beyond expectations.

  9. Free-energy calculation of structure-H hydrates

    NASA Astrophysics Data System (ADS)

    Okano, Yamato; Yasuoka, Kenji

    2006-01-01

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

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

    PubMed

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

    2010-08-10

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

  11. Energy-dependent deposition processes of size-selected Ag nanoclusters on highly-oriented pyrolytic graphite

    NASA Astrophysics Data System (ADS)

    Yamaguchi, W.; Yoshimura, K.; Tai, Y.; Maruyama, Y.; Igarashi, K.; Tanemura, S.; Murakami, J.

    2000-06-01

    Singly charged cations of silver atoms and clusters (Agn+, n=1,3,5,7,9) were deposited on highly oriented pyrolytic graphite substrates at well-controlled, various collision energies. The total amount of Ag atoms remaining on the substrates after collision was quantified by measuring the Ag3d5/2 photoelectron intensities. The collision energy dependence of the amount of deposited Ag atoms revealed that, for all the species, there are three distinct energy regions, for which soft landing, rebounding, or implantation is a dominant process, and that the energy ranges for the processes strongly depend on the cluster size. The deposition efficiency vs collision energy curve for each cluster is well fitted to that for Ag1, by considering the difference between the contact area of Ag1 with the surface and that of the cluster, reflecting the compactness of the clusters. Boundaries between the different deposition regimes for the clusters were less distinct than those for Ag1. Considering anisotropy in shape of a cluster, deposition efficiency around the implantation threshold was calculated, which well explains the indistinctness of the threshold observed in the experimental data. This supports the picture that the energy given to a unit surface area determines the collision process.

  12. Energy deposition, heat flow, and rapid solidification during laser and electron beam irradiation of materials

    SciTech Connect

    White, C.W.; Aziz, M.J.

    1985-10-01

    The fundamentals of energy deposition, heat flow, and rapid solidification during energy deposition from lasers and electron beams is reviewed. Emphasis is placed on the deposition of energy from pulsed sources (10 to 100 ns pulse duration time) in order to achieve high heating and cooling rates (10/sup 8/ to 10/sup 10/ /sup 0/C/s) in the near surface region. The response of both metals and semiconductors to pulsed energy deposition is considered. Guidelines are presented for the choice of energy source, wavelength, and pulse duration time.

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

    PubMed

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

    2013-11-01

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

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

    PubMed

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

    2009-01-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  17. Energy deposition study of low-energy cosmic radiation at sea level

    NASA Astrophysics Data System (ADS)

    Wijesinghe, Pushpa

    In this dissertation work, a computer simulation model based on the Geant4 simulation package has been designed and developed to study the energy deposition and track structures of cosmic muons and their secondary electrons in tissue-like materials. The particle interactions in a cubic water volume were first simulated. To analyze the energy deposition and tracks in small structures, with the intention of studying the energy localization in nanometric structures such as DNA, the chamber was sliced in three dimentions. Validation studies have been performed by comparing the results with experimental, theoretical, and other simulation results to test the accuracy of the simulation model. A human body phantom in sea-level muon environment was modeled to measure the yearly dose to a human from cosmic muons. The yearly dose in this phantom is about 22 millirems. This is close to the accepted value for the yearly dose from cosmic radiation at sea level. Shielding cosmic muons with a concrete slab from 0 to 2 meters increased the dose received by the body. This dissertation presents an extensive study on the interactions of secondary electrons created by muons in water. Index words. Radiation Dosimetry Simulation, Track Structures, Sea-Level muon Flux, Energy Deposition

  18. A new calculation on the stopping power and mean free path for low energy electrons in toluene over energy range of 20-10000 eV.

    PubMed

    Tan, Zhenyu; Xia, Yueyuan; Liu, Xiangdong; Zhao, Mingwen; Zhang, Liming

    2009-04-01

    A new calculation of the stopping powers (SP) and inelastic mean free paths (IMFP) for electrons in toluene at energies below 10 keV has been presented. The calculation is based on the dielectric model and on an empirical evaluation approach of optical energy loss function (OELF). The reliability for the evaluated OELFs of several hydrocarbons with available experimental optical data has been systematically checked. For toluene, using the empirical OELF, the evaluated mean ionization potential, is compared with that given by Bragg's rule, and the calculated SP at 10 keV is also compared with the Bethe-Bloch prediction. The present results for SP and IMFP provide an alternative basic data for the study on the energy deposition of low-energy electrons transport through toluene, and also show that the method used in this work may be a good one for evaluating the SP and IMFP for hydrocarbons.

  19. Control of MR to RR Transition by Pulsed Energy Deposition

    NASA Astrophysics Data System (ADS)

    Yan, Hong; Adelgren, Russell; Elliott, Gregory; Knight, Doyle

    2003-11-01

    This paper presents a study of the effect of a single laser energy pulse on the transition from a Mach Reflection (MR) to a Regular Reflection (RR) in the Dual Solution Domain (DSD). The freestream Mach number is 3.45 and two oblique shock waves are formed by two symmetric 22 degree wedges. These conditions correspond to a point midway within the DSD. A steady MR was first obtained experimentally and numerically, then a single laser pulse was deposited above the horizontal center plane. For the steady MR, the simulation showed the variation of Mach stem height along the span due to side effects. The predicted spanwise averaged Mach stem height was 1.96 mm within 2 percent of the experimental value of 2 mm. The experiment showed that the Mach stem height decreased to 30 percent of its original height due to the interaction with the laser spot and then returned to its original height by 300 microsec. That the Mach stem returned to its original height was most likely due to freestream turbulence in the wind tunnel. The numerical simulation successfully predicted the reverse transition from a stable MR to a stable RR and the stable RR persisted across the span. This study showed the capability of a laser energy pulse to control the reverse transition of MR -> RR within the Dual Solution Domain.

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

  1. 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

  2. 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%.

  3. Energy deposition in low power coaxial plasma thrusters

    NASA Astrophysics Data System (ADS)

    Myers, Roger Metcalf

    The energy deposition in steady-state, low power, coaxial plasma thrusters operated between 10 and 30 kW with argon and nitrogen propellants was studied experimentally and analytically. The major energy sinks were found to be electrode losses (primarily anode), propellant ionization, and thrust. Performance measurements showed the efficiency and specific impulse to vary between two and ten percent and 500 and 1200 seconds, respectively, as functions of thruster current level, propellant flow rate, and thruster geometry. Thrust was found to increase quadratically with current, in agreement with theoretical models of self-field electromagnetic thrusters. Spectroscopic studies of the plasma exhaust with argon propellant showed it to consist primarily of singly and doubly ionized argon, with an electron temperature between 1.2 and 1.7 eV and electron densities between 2 x 10 (exp 13) cu cm and 5 x 10 (exp 13) cu cm. Floating potential measurements showed the anode fall voltage to be between 65 and 95 percent of the total thruster voltage depending on thruster geometry, propellant, and current level. Non-intrusive cathode surface temperature and erosion measurements revealed that the cathode energy balance was governed by electron cooling, surface radiation and conduction through the cathode base. Comparisons of these new results with data from megawatt class, quasi-steady magnetoplasmadynamic thrusters revealed similarities between the plasma properties and acceleration mechanisms of the devices, but showed they have dramatically different anode power fractions. Attempts to increase thruster efficiency by decreasing the chamber radius were not successful, indicating that major changes in thruster design and/or power level will be required to achieve high efficiency, high specific impulse operation.

  4. 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''.

  5. 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.

  6. Energy deposition around swift proton tracks in polymethylmethacrylate: How much and how far

    NASA Astrophysics Data System (ADS)

    Dapor, Maurizio; Abril, Isabel; de Vera, Pablo; Garcia-Molina, Rafael

    2017-08-01

    The use of proton beams in several modern technologies to probe or modify the properties of materials, such as proton beam lithography or ion beam cancer therapy, requires us to accurately know the extent to which the energy lost by the swift projectiles in the medium is redistributed radially around their tracks, since this determines several endpoints, such as the resolution of imaging or manufacturing techniques, or even the biological outcomes of radiotherapy. In this paper, the radial distribution of the energy deposited around swift-proton tracks in polymethylmethacrylate (PMMA) by the transport of secondary electrons is obtained by means of a detailed Monte Carlo simulation. The initial energy and angular distributions of the secondary electrons generated by proton impact, as well as the electronic cross sections for the ejection of these electrons, are reliably calculated in the framework of the dielectric formalism, where a realistic electronic excitation spectrum of PMMA is accounted for. The cascade of all secondary electrons generated in PMMA is simulated taking into account the main interactions that occur between these electrons and the condensed phase target. After analyzing the influence that several angular distributions of the electrons generated by the proton beam have on the resulting radial profiles of deposited energy, we conclude that the widely used Rudd and Kim formula should be replaced by the simpler isotropic angular distribution, which leads to radial energy distributions comparable to the ones obtained from more realistic angular distributions. By studying the dependence of the radial dose on the proton energy we recommend lower proton energies than previously published for reducing proximity effects around a proton track. The obtained results are of relevance for assessing the resolution limits of proton beam based imaging and manufacturing techniques.

  7. 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…

  8. 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…

  9. 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.

  10. On the calculation of absolute macromolecular binding free energies

    PubMed Central

    Luo, Hengbin; Sharp, Kim

    2002-01-01

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

  11. Path-breaking schemes for nonequilibrium free energy calculations

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  12. 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.

  13. 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.

  14. Energy deposition of quasi-two temperature relativistic electrons in fast-shock ignition scenario

    NASA Astrophysics Data System (ADS)

    Ghasemi, Seyed Abolfazl; Farahbod, Amir Hossein

    2016-10-01

    Previous calculations from Solodov et al. (2008) indicate that classical stopping and scattering dominate electrons energy deposition and transport when the electrons reach the dense plasma in FSI inertial confinement fusion concept [1]. Our calculations show that, by using quasi- two temperature electrons energy distribution function [2] in comparison with exponential [3] or monoenergetic distribution function and also increasing fast electrons energy to about 7 MeV, the ratio of beam blooming to straggling definitely decreases. Our analytical analysis shows that for fuel mass more than 1 mg and for fast ignitor wavelength λif > 0.53 μ m, straggling and beam blooming increases. Meanwhile, by reducing fast ignitor wavelength from 0.53 to 0.35 micron, and for fuel mass about 2 mg, electron penetration into the dense fuel slightly increases. Therefore, reduction of scattering (blooming and straggling) of electrons and enhancement of electron penetration into the dense fuel, can be obtained in relativistic regime with high energy fast electrons of the order of 5 Mev and more. Such derivations can be used in theoretical studies of the ignition conditions and PIC simulations of the electron transport in fast ignition scenario.

  15. 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.

  16. 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.

  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. Relative Binding Free Energy Calculations Applied to Protein Homology Models.

    PubMed

    Cappel, Daniel; Hall, Michelle Lynn; Lenselink, Eelke B; Beuming, Thijs; Qi, Jun; Bradner, James; Sherman, Woody

    2016-12-27

    A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with

  20. 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.

  1. Investigating oceanic tidal energy dissipation on deep time scales using short tidal deposit sequences

    NASA Astrophysics Data System (ADS)

    Coughenour, C.

    2012-12-01

    One of the enduring problems in physical oceanography has been that of tidal dynamics and the effective tidal torque that serves to slow Earth's axial rotation. In the late 20th century, with the aid of satellite altimetry and other technologies, a suite of reliable estimates was finally placed on the magnitude of this torque and other, related parameters in the current epoch. Tidal drag accounts for a 20 microsecond/year increase in mean day length, a 3.5 terawatt dissipation of energy in the oceans (Kantha et al., 1998), and a lunar retreat rate of 3.82 cm/yr (Dickey et al., 1994). Despite these significant advances, however, the problem of tidal dissipation in the geologic past remains largely unresolved. This is due, in part, to difficulties in numerical modeling of past tidal regimes that stem from uncertainties in ocean basin configurations and lunar distances. Tidal deposits can record, to high resolution, the primary astronomical periodicities responsible for the generation of the tidal currents under which transport and deposition occur. With reliable lunar orbital period data obtained from tidal deposits, the past Earth-Moon distance and length of day can be calculated. This task requires careful spectral analysis and consideration of sedimentological factors that may add noise and/or discontinuities to the signal. For deposits representing less than one year of deposition, the necessary assumptions are that Earth's moment of inertia has not changed significantly over the time interval of interest and that the solar component of tidal dissipation can be well-approximated. With consideration of the total angular momentum of the Earth-Moon couplet, we derive a method to calculate lunar distance and length of day. The efficacy of this method and its assumptions is tested via the multi-year sequence of data obtained from the late Precambrian Elatina Formation of Australia and comparing results obtained from the full suite of data by Williams (2000). We go on

  2. An automatic system using mobile-agent software to model the calculation process of a chemical vapor deposition film deposition simulator.

    PubMed

    Takahashi, Takahiro; Fukui, Noriyuki; Arakawa, Masamoto; Funatsu, Kimito; Ema, Yoshinori

    2011-09-01

    We have developed an automatic modeling system for calculation processes of the simulator to reproduce experimental results of chemical vapor deposition (CVD), in order to decrease the calculation cost of the simulator. Replacing the simulator by the mathematical models proposed by the system will contribute towards decreasing the calculation costs for predicting the experimental results. The system consists of a mobile agent and two software resources in computer networks, that is, generalized modeling software and a simulator reproducing cross-sections of the deposited films on the substrates with the micrometer- or nanometer-sized trenches. The mobile agent autonomously creates appropriate models by moving to and then operating the software resources. The models are calculated by partial least squares regression (PLS), quadratic PLS (QPLS) and error back propagation (BP) methods using artificial neural networks (ANN) and expresses by mathematical formulas to reproduce the calculated results of the simulator. The models show good reproducibility and predictability both for uniformity and filling properties of the films calculated by the simulator. The models using the BP method yield the best performance. The filling property data are more suitable to modeling than film uniformity.

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

    SciTech Connect

    Handford, C.R. )

    1990-08-01

    Subaqueous deposits of aragonite, gypsum, and halite are accumulating in shallow solar salt ponds constructed in the Pekelmeer, a sea-level salina on Bonaire, Netherlands Antilles. Several halite facies are deposited in the crystallizer ponds in response to difference 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 {approximately} 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.

  4. 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.

  5. 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.

  6. 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.

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

    PubMed Central

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

    2013-01-01

    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

  8. 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

  9. 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).

  10. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Auroral energy deposition rate, characteristic electron energy, and ionospheric parameters derived from Dynamics Explorer 1 images

    NASA Technical Reports Server (NTRS)

    Rees, M. H.; Lummerzheim, D.; Roble, R. G.; Winningham, J. D.; Craven, J. D.

    1988-01-01

    Auroral images obtained by the Spin Scan Auroral Imager (SAI) aboard the DE-1 satellite were used to derive auroral energy deposition rate, characteristic electron energy, and ionospheric parameters. The principles involved in the imaging technique and the physical mechanisms that underlie the relationship between the spectral images and the geophysical parameters are discussed together with the methodology for implementing such analyses. It is shown that images obtained with the SAI provide global parameters at 12-min temporal resolution; the spatial resolution is limited by the field of view of a pixel. The analysis of the 12-min images presented yielded a representation of ionospheric parameters that was better than can be obtained using empirical models based on local measurements averaged over long periods of time.

  12. Subtleties in Energy Calculations in the Image Method

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  13. Subtleties in Energy Calculations in the Image Method

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Abdel-Baki, Manal; El-Diasty, Fouad

    2016-04-01

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

  17. Calculation of Dissociation Energies Using Many-Body Perturbation Theory

    DTIC Science & Technology

    1981-08-01

    formyl radical , HCO, carbon monoxide, CO, and the SCF energy for the hydrogen atom. Table 2 also contains the zero- point vibrational energy for each... formyl radical [ 19]. To compare the theoretical predictions with these heat of reaction data, we must estimate the effect of the rotational and...obtained by considering the elimination of the hydrogen molecule from the methoxy radical , giving the formyl radical and H2 as products. The pertinent

  18. Comparison of calculated internal tide energy flux with microstructure measurements

    NASA Astrophysics Data System (ADS)

    Falahat, Saeed; Nycander, Jonas

    2013-04-01

    A comparison of the model-derived vertical energy flux from the internal tide with micro-structure measurements is undertaken. The latter data set originates from two field surveys during the Brazil Basin Tracer Release experiment (BBTRE1, BBTRE2) as well as from a third field cruise of the LArval Dispersal along the Deep East-Pacific Rise project (LADDER3). The model for estimating the time-dependent vertical energy flux is based on linear wave theory, and takes into account the the finite depth of the ocean, the spatial variations of the bathymetry and the spatio-temporal variations of the barotropic tide. The temporal average of the vertical energy flux over a limited period (a few days) immediately before the observational time is compared with the depth-integrated observed energy dissipation rate. A rather good correlation was found between the theoretical predictions and the microstructure data from the BBTRE2 field survey, while the comparison made for the BBTRE1 survey yields a low correlation, The model-based estimates of the vertical energy flux are of the correct order of magnitude, and imply that about one third of the internal wave energy dissipates locally. In the case of LADDER3, the comparison between the observations and the model predictions shows a significant correlation, whereas the modelled energy flux is much higher than the observed dissipation, implying a very low dissipation efficiency. A possible explanation is that the sharp topography at the East-Pacific Rise consists of a few isolated seamounts, which should mean that the general background level of internal wave energy is low. If nonlinear wave interaction is essential for wave dissipation, the wave dissipation should then be less local in this region than in the eastern Brazil Basin, with very extended rough topography.

  19. Comparison of Calibration of Sensors Used for the Quantification of Nuclear Energy Rate Deposition

    SciTech Connect

    Brun, J.; Reynard-Carette, C.; Tarchalski, M.; Pytel, K.; Lyoussi, A.; Fourmentel, D.; Villard, J.F.; Jagielski, J.

    2015-07-01

    This present work deals with a collaborative program called GAMMA-MAJOR 'Development and qualification of a deterministic scheme for the evaluation of GAMMA heating in MTR reactors with exploitation as example MARIA reactor and Jules Horowitz Reactor' between the National Centre for Nuclear Research of Poland, the French Atomic Energy and Alternative Energies Commission and Aix Marseille University. One of main objectives of this program is to optimize the nuclear heating quantification thanks to calculation validated from experimental measurements of radiation energy deposition carried out in irradiation reactors. The quantification of the nuclear heating is a key data especially for the thermal, mechanical design and sizing of irradiation experimental devices in specific irradiated conditions and locations. The determination of this data is usually performed by differential calorimeters and gamma thermometers such as used in the experimental multi-sensors device called CARMEN 'Calorimetric en Reacteur et Mesures des Emissions Nucleaires'. In the framework of the GAMMA-MAJOR program a new calorimeter was designed for the nuclear energy deposition quantification. It corresponds to a single-cell calorimeter and it is called KAROLINA. This calorimeter was recently tested during an irradiation campaign inside MARIA reactor in Poland. This new single-cell calorimeter differs from previous CALMOS or CARMEN type differential calorimeters according to three main points: its geometry, its preliminary out-of-pile calibration, and its in-pile measurement method. The differential calorimeter, which is made of two identical cells containing heaters, has a calibration method based on the use of steady thermal states reached by simulating the nuclear energy deposition into the calorimeter sample by Joule effect; whereas the single-cell calorimeter, which has no heater, is calibrated by using the transient thermal response of the sensor (heating and cooling steps). The paper will

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  1. Free energy calculation from umbrella sampling using Bayesian inference

    NASA Astrophysics Data System (ADS)

    Bernstein, Noam; Stecher, Thomas; Csányi, Gábor

    2013-03-01

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

  2. 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.

  3. 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.

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

    NASA Technical Reports Server (NTRS)

    Stecker, F

    2008-01-01

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

  5. 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}

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  7. 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.

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

    PubMed

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

    2010-10-12

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

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

    SciTech Connect

    H. Marr; M.J. Anderson

    2001-02-08

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

  10. 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.

  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. 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.

  14. 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.

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

    DTIC Science & Technology

    1982-12-01

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

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

    PubMed

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

    2009-05-28

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

  18. Calculation of energy of atomization in silicate tetrahedron Si4(4-)

    NASA Astrophysics Data System (ADS)

    Kurlov, S. P.; Lepinskikh, B. M.; Bukhtoyarov, O. I.

    The energy of particle interaction was examined by the method of superposition integrals in the elementary silicate anion SiOh4(-4). The Milliken formula, which breaks down the complete energy of atomization into individual contributions, was used in calculation. The three main contributions to the energy of atomization are the energy of interaction of valency electrons, the repulsion energy between non-bonding pairs of electrons in each atom, and the energy of the ionic fraction of the bond.

  19. Monte Carlo study of radial energy deposition from primary and secondary particles for narrow and large proton beamlet source models.

    PubMed

    Peeler, Christopher R; Titt, Uwe

    2012-06-21

    In spot-scanning intensity-modulated proton therapy, numerous unmodulated proton beam spots are delivered over a target volume to produce a prescribed dose distribution. To accurately model field size-dependent output factors for beam spots, the energy deposition at positions radial to the central axis of the beam must be characterized. In this study, we determined the difference in the central axis dose for spot-scanned fields that results from secondary particle doses by investigating energy deposition radial to the proton beam central axis resulting from primary protons and secondary particles for mathematical point source and distributed source models. The largest difference in the central axis dose from secondary particles resulting from the use of a mathematical point source and a distributed source model was approximately 0.43%. Thus, we conclude that the central axis dose for a spot-scanned field is effectively independent of the source model used to calculate the secondary particle dose.

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

    NASA Astrophysics Data System (ADS)

    Xu, Yan; Wu, SiZhong; Zheng, WuDi

    2015-04-01

    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.

  1. 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.

  2. A fragment-cloud model for asteroid breakup and atmospheric energy deposition

    NASA Astrophysics Data System (ADS)

    Wheeler, Lorien F.; Register, Paul J.; Mathias, Donovan L.

    2017-10-01

    As asteroids break up during atmospheric entry, they deposit energy that can be seen in flares of light and, if substantial enough, can produce damaging blast waves. Analytic models of asteroid breakup and energy deposition processes are needed in order to assess potential airburst hazards, and to enable inferences about asteroid properties or breakup physics to be made from comparisons with observed meteors. This paper presents a fragment-cloud model (FCM) that is able to represent a broad range of breakup behaviors and the resulting variations in energy deposition in ways that make it a useful tool for both applications. Sensitivity studies are performed to investigate how variations the model's fragmentation parameters affect the energy deposition results for asteroids 20-500 m in diameter. The model is also used to match observational data from the Chelyabinsk meteor and infer potential asteroid properties and representative modeling parameter ranges. Results illustrate how the model's fragmentation parameters can introduce different energy deposition features, and how much they affect the overall energy deposition rates, magnitudes, and altitudes that would drive ground damage for risk assessment applications.

  3. 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.

  4. 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.

  5. Fluorocarbon thin-film deposition on polymer surfaces from low-energy polyatomic ion beams

    NASA Astrophysics Data System (ADS)

    Wijesundara, Muthu Bandage Jayathilaka

    Low energy polyatomic ion deposition is attractive for selective surface modification of advanced materials. Surface modification by fluorocarbon (FC) thin film deposition is widely used for many technological applications. Thus, polymer surface modification by FC thin film deposition was carried out using mass-separated low energy FC ion beams. X-ray photoelectron spectroscopy, atomic force microscopy and air/water contact angles were employed to examine how the FC film chemistry, morphology, and long term stability depend on incident ion structure, kinetic energy, and fluence. Molecular dynamics simulations were performed to support experimental data. 25--100 eV CF3+ and C3F 5+ ion deposition on polystyrene (PS) surface was examined. CF3+ and C3F5+ each formed a distribution of different FC functional groups on PS in amounts dependent upon the incident ion energy, structure, and fluence. Both ions deposited mostly intact upon the surface at 25 eV. The total fluorine and fluorinated carbon content were increased with ion energy. The fluorination efficiency was higher for the larger ion. The simulations revealed that the fragmentation behavior depends on the incident ion structure and its energy. The simulations also confirmed that FC ions only penetrated a few angstroms into the surface. The compositional changes of 25--100 eV CF3+ and C3F5+ ion-modified PS surfaces were examined after being exposed to atmosphere for four and eight weeks. The FC films oxidized in atmospheric conditions. Oxygen incorporation into the ion-modified surfaces increased with ion energy due to higher surface bond breakage and active site formation at high collision energy. Overall, the aging process of these ion-deposited films appeared similar to that of plasma-deposited films. Mass-selected 50 eV C3F5+ ion deposition was employed to create chemical gradient thin films on polymethylmethacrylate (PMMA) by variation of the ion fluence across the substrate surface. The surface chemistry

  6. 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

  7. 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.

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

    PubMed

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

    2015-01-22

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

  9. 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.

  10. Engineering Properties of Superhard Films with Ion Energy and Post-Deposition Processing

    SciTech Connect

    Monteiro, Othon R.; Delplancke-Ogletree, Marie-Paule

    2003-08-26

    Recent developments in plasma synthesis of hard materials using energetic ions are described. Metal Plasma Immersion Ion Implantation and Deposition (MePIIID) has been used to prepare several hard films: from diamondlike carbon (DLC) to carbides, from nitrides to oxides. The energy of the depositing species is controlled to maximize adhesion as well as to change the physical and chemical properties of the films. Adhesion is promoted by the creation of a graded interface between the film and the substrate. The energy of the depositing ions is also used to modify and control the intrinsic stresses and the microstructure of the films. The deposition is carried out at room temperature, which is important for temperature sensitive substrates. A correlation between intrinsic stresses and the energetics of the deposition is presented for the case of DLC films, and means to reduce stress levels are discussed.

  11. Engineering properties of superhard films with ion energy and post-deposition processing

    SciTech Connect

    Monteiro, Othon R.; Delplancke-Ogletree, Mari-Paule

    2002-10-14

    Recent developments in plasma synthesis of hard materials using energetic ions are described. Metal Plasma Immersion Ion Implantation and Deposition (MePIIID) has been used to prepare several hard films: from diamondlike carbon (DLC) to carbides, from nitrides to oxides. The energy of the depositing species is controlled to maximize adhesion as well as to change the physical and chemical properties of the films. Adhesion is promoted by the creation of a graded interface between the film and the substrate. The energy of the depositing ions is also used to modify and control the intrinsic stresses and the microstructure of the films. The deposition is carried out at room temperature, which is important for temperature sensitive substrates. A correlation between intrinsic stresses and the energetics of the deposition is presented for the case of DLC films, and means to reduce stress levels are discussed.

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

    PubMed

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

    2015-02-15

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

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

    DOE PAGES

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

    2015-05-06

    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-2s-1. For the anticipated lifetimemore » 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.« less

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Dawei

    2017-03-01

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

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

    PubMed Central

    Zhang, Dawei

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Topping, David; Alibay, Irfan; Bane, Michael

    2017-04-01

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

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

    SciTech Connect

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

    2005-10-26

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

  19. Point-by-point near-field optical energy deposition around plasmonic nanospheres in absorbing media.

    PubMed

    Harrison, R K; Ben-Yakar, Adela

    2015-08-01

    Here we investigate the effects of absorbing media on plasmon-enhanced near-field optical energy deposition. We find that increasing absorption by the medium results in increased particle scattering at the expense of particle absorption, and that much of this increased particle scattering is absorbed by the medium close to the particle surface. We present an analytical method for evaluating the spatial distribution of near-field enhanced absorption surrounding plasmonic metal nanospheres in absorbing media using a new point-by-point method. We propose criteria to define relevant near-field boundaries and calculate the properties of the local absorption enhancement, which redistributes absorption to the near-field and decays asymptotically as a function of the distance from the particle to background levels. Using this method, we performed a large-scale parametric study to understand the effect of particle size and wavelength on the near-field absorption for gold nanoparticles in aqueous media and silicon, and identified conditions that are relevant to enhanced local infrared absorption in silicon. The presented approach provides insight into the local energy transfer around plasmonic nanoparticles for predicting near-field effects for advanced concepts in optical sensing, thin-film solar cells, nonlinear imaging, and photochemical applications.

  20. 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.

  1. 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.

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

    PubMed

    Wang, He; Vassiliev, Oleg N

    2014-07-21

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

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

    NASA Astrophysics Data System (ADS)

    Wang, He; Vassiliev, Oleg N.

    2014-07-01

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

  4. Advanced Materials Enabled by Atomic Layer Deposition for High Energy Density Rechargeable Batteries

    NASA Astrophysics Data System (ADS)

    Chen, Lin

    In order to meet the ever increasing energy needs of society and realize the US Department of Energy (DOE)'s target for energy storage, acquiring a fundamental understanding of the chemical mechanisms in batteries for direct guidance and searching novel advanced materials with high energy density are critical. To realize rechargeable batteries with superior energy density, great cathodes and excellent anodes are required. LiMn2O4 (LMO) has been considered as a simpler surrogate for high energy cathode materials like NMC. Previous studies demonstrated that Al2O3 coatings prepared by atomic layer deposition (ALD) improved the capacity of LMO cathodes. This improvement was attributed to a reduction in surface area and diminished Mn dissolution. However, here we propose a different mechanism for ALD Al 2O3 on LMO based on in-situ and ex-situ investigations coupled with density functional theory calculations. We discovered that Al2O 3 not only coats the LMO, but also dopes the LMO surface with Al leading to changes in the Mn oxidation state. Different thicknesses of Al2O 3 were deposited on nonstoichiometric LiMn2O4 for electrochemical measurements. The LMO treated with one cycle of ALD Al2O3 (1xAl 2O3 LMO) to produce a sub-monolayer coating yielded a remarkable initial capacity, 16.4% higher than its uncoated LMO counterpart in full cells. The stability of 1xAl2O3 LMO is also much better as a result of stabilized defects with Al species. Furthermore, 4xAl 2O3 LMO demonstrates remarkable capacity retention. Stoichiometric LiMn2O4 was also evaluated with similar improved performance achieved. All superior results, accomplished by great stability and reduced Mn dissolution, is thanks to the synergetic effects of Al-doping and ALD Al2O 3 coating. Turning our attention to the anode, we again utilized aluminum oxide ALD to form conformal films on lithium. We elaborately designed and studied, for the first time, the growth mechanism during Al2O3 ALD on lithium metal in

  5. 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.

  6. Efficient Energy Deposition for an Electron Beam Pumped KrF Laser

    NASA Astrophysics Data System (ADS)

    Hegeler, F.; Myers, M. C.; Friedman, M.; Sethian, J. D.; Swanekamp, S. B.; Rose, D. V.; Welch, D. R.

    2002-11-01

    Electra is a repetitively pulsed, electron beam pumped krypton fluoride (KrF) laser that will develop the technologies that can meet the Inertial Fusion Energy (IFE) requirements for durability, efficiency, and cost. The Electra laser is pumped with two opposing electron beams each with parameters of 500 kV, 90 kA, with a 100 ns flat-top pulse duration, and a cathode area of 27 x 97 cm^2. The e-beam propagates through a hibachi structure, which supports a thin foil that isolates the vacuum diode from the high-pressure (>1 atm) laser gas. It has been demonstrated that segmenting the beam into strips to miss the hibachi support ribs significantly increases the electron beam deposition efficiency. The energy deposition efficiency is defined as the ratio of energy deposited in the laser gas over the vacuum diode e-beam energy. Energy deposition efficiencies of 75have been achieved with a 500 keV e-beam. In addition, 1-D and 3-D codes have simulated the e-beam propagation through the hibachi, and 1-D codes predict a maximum energy deposition efficiency of 81

  7. Mechanisms of ignition by transient energy deposition: Regimes of combustion wave propagation

    NASA Astrophysics Data System (ADS)

    Kiverin, A. D.; Kassoy, D. R.; Ivanov, M. F.; Liberman, M. A.

    2013-03-01

    Regimes of chemical reaction wave propagating in reactive gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied depending on the characteristics of a transient thermal energy deposition localized in a finite volume of reactive gas. Different regimes of the reaction wave propagation are initiated depending on the amount of deposited thermal energy, power of the source, and the size of the hot spot. The main parameters which define regimes of the combustion waves facilitated by the transient deposition of thermal energy are acoustic time scale, duration of the energy deposition, ignition time scale, and size of the hot spot. The interplay between these parameters specifies the role of gasdynamical processes, the formation and steepness of the temperature gradient, and speed of the spontaneous wave. The obtained results show how ignition of one or another combustion regime depends on the value of energy, rate of the energy deposition, and size of the hot spot, which is important for the practical use and for risk assessment.

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

    PubMed

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

    2017-03-30

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

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

    PubMed

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

    2012-07-10

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

  10. 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.

  11. 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.

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

    PubMed

    Neuhauser, Daniel; Rabani, Eran; Baer, Roi

    2013-04-04

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

  13. 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.

  14. 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.

  15. On the role of energy deposition in triggering SEGR in power MOSFETs

    SciTech Connect

    Selva, L.E.; Swift, G.M.; Taylor, W.A.; Edmonds, L.D.

    1999-12-01

    Single event gate rupture (SEGR) was studied using three types of power MOSFET devices with ions having incident linear energy transfers (LETs) in silicon from 26 to 82 MeV{center{underscore}dot}cm{sup 2}/mg. Results are: (1) consistent with Wrobel's oxide breakdown for V{sub DS} = 0 volts (for both normal incidence and angle); and (2) when V{sub GS} = 0 volts, energy deposited near the Si/SiO{sub 2} interface is more important than the energy deposited deeper in the epi.

  16. 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.

  17. 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.

  18. 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.

  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. 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.

  1. 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. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

    SciTech Connect

    George, K.; Schweizer, T.

    2008-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-28

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

  5. 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.

  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

    2016-09-02

    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.

  7. Relationship between energy deposition and shock wave phenomenon in an underwater electrical wire explosion

    NASA Astrophysics Data System (ADS)

    Han, Ruoyu; Zhou, Haibin; Wu, Jiawei; Qiu, Aici; Ding, Weidong; Zhang, Yongmin

    2017-09-01

    An experimental study of pressure waves generated by an exploding copper wire in a water medium is performed. We examined the effects of energy deposited at different stages on the characteristics of the resulting shock waves. In the experiments, a microsecond time-scale pulsed current source was used to explode a 300-μm-diameter, 4-cm-long copper wire with initial stored energies ranging from 500 to 2700 J. Our experimental results indicated that the peak pressure (4.5-8.1 MPa) and energy (49-287 J) of the shock waves did not follow a simple relationship with any electrical parameters, such as peak voltage or deposited energy. Conversely, the impulse had a quasi-linear relationship with the parameter Π. We also found that the peak pressure was mainly influenced by the energy deposited before separation of the shock wave front and the discharge plasma channel (DPC). The decay time constant of the pressure waveform was affected by the energy injection after the separation. These phenomena clearly demonstrated that the deposited energy influenced the expansion of the DPC and affected the shock wave characteristics.

  8. 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.

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

    SciTech Connect

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

    2003-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Mamedov, Bahtiyar Akber; Copuroglu, Ebru

    2017-02-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    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/Ld), 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 Å) as measured by superlattice x-ray diffraction techniques. The value of D*(0) was found to increase from 3×10-17 to 1×10-16 cm2/sec as the applied substrate bias was increased from 0 to -75 V. However even at Va=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 Ld of the ion bombardment created defects was ˜1000 Å. Enhanced diffusion also has a significiant effect on the altered layer thickness xe and the total sputtering time te (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 xe and te in single-phase binary alloys were considered. The results show that both xe and te are considerably larger using a depth dependent D*(x), when Ld

  14. 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.

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

    PubMed Central

    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 (Xe22+ to Xe30+) 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

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

    NASA Astrophysics Data System (ADS)

    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.

    2014-07-01

    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 (Xe22+ to Xe30+) 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.

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

    NASA Astrophysics Data System (ADS)

    Klimovich, Pavel V.; Mobley, David L.

    2015-11-01

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

  18. 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.

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

    PubMed

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

    1983-01-01

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

  20. 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.

  1. Effect of Mach number on the efficiency of microwave energy deposition in supersonic flow

    NASA Astrophysics Data System (ADS)

    Lashkov, V. A.; Karpenko, A. G.; Khoronzhuk, R. S.; Mashek, I. Ch.

    2016-05-01

    The article is devoted to experimental and numerical studies of the efficiency of microwave energy deposition into a supersonic flow around the blunt cylinder at different Mach numbers. Identical conditions for energy deposition have been kept in the experiments, thus allowing to evaluate the pure effect of varying Mach number on the pressure drop. Euler equations are solved numerically to model the corresponding unsteady flow compressed gas. The results of numerical simulations are compared to the data obtained from the physical experiments. It is shown that the momentum, which the body receives during interaction of the gas domain modified by microwave discharge with a shock layer before the body, increases almost linearly with rising of Mach number and the efficiency of energy deposition also rises.

  2. 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.

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

    PubMed

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

    2013-08-15

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

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

    PubMed

    Michalski; Hardy; Saramago

    1998-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1987-12-01

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

  6. Strong shock generation by fast electron energy deposition

    SciTech Connect

    Fox, T. E.; Pasley, J.; Robinson, A. P. L.

    2013-12-15

    It has been suggested that fast electrons may play a beneficial role in the formation of the ignitor shock in shock ignition owing to the high areal density of the fuel at the time of the ignitor pulse. In this paper, we extend previous studies which have focused on monoenergetic electron sources to populations with extended energy distributions. In good agreement with analytic scalings, we show that strong shocks can be produced with peak pressures of a few hundred Mbar to over 1 Gbar using fast electron intensities of 1–10 PW/cm{sup 2} in a uniform deuterium-tritium plasma at 10 g/cm{sup 3}. However, the length required for shock formation increases with fast electron temperature. As this shock formation distance becomes comparable to the target size, the shock is not able to fully develop, and this implies a limit on the ability of fast electrons to aid shock formation.

  7. 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.

  8. Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Koppisetty, Chaitanya A. K.; Frank, Martin; Lyubartsev, Alexander P.; Nyholm, Per-Georg

    2015-01-01

    Accurate estimation of protein-carbohydrate binding energies using computational methods is a challenging task. Here we report the use of expanded ensemble molecular dynamics (EEMD) simulation with double decoupling for estimation of binding energies of hevein, a plant lectin with its monosaccharide and disaccharide ligands GlcNAc and (GlcNAc)2, respectively. In addition to the binding energies, enthalpy and entropy components of the binding energy are also calculated. The estimated binding energies for the hevein-carbohydrate interactions are within the range of ±0.5 kcal of the previously reported experimental binding data. For comparison, binding energies were also estimated using thermodynamic integration, molecular dynamics end point calculations (MM/GBSA) and the expanded ensemble methodology is seen to be more accurate. To our knowledge, the method of EEMD simulations has not been previously reported for estimating biomolecular binding energies.

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

    PubMed Central

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

    2014-01-01

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

  10. 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)).

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

    SciTech Connect

    Younes, W; Gogny, D

    2011-10-03

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

  12. Extended bulk defects induced by low-energy ions during partially ionized beam deposition

    SciTech Connect

    Lee, W.I.; Wong, J.; Borrego, J.M.; Lu, T.

    1988-08-15

    The study of possible defects generated by low-energy ions during partially ionized beam (PIB) depositions was performed. No defects were observed when acceleration voltage was set lower than 1 kV. Surprisingly, several deep levels were detected up to the depth of 4000 A in the 3-kV sample. However, these levels can be annealed out at a relatively low temperature of 400 /sup 0/C. It is concluded in this study that, by properly choosing the ion energy range, PIB deposition will not cause severe damage to the substrate and can be a viable technique for growing heterostructures.

  13. 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.

  14. 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.

  15. Amorphization due to electronic energy deposition in defective strontium titanate

    DOE PAGES

    Xue, Haizhou; Zarkadoula, Eva; Liu, Peng; ...

    2017-01-27

    The synergistic interaction of electronic energy loss by ions with ion-induced defects created by elastic nuclear scattering processes has been investigated for single crystal SrTiO3. An initial pre-damaged defect state corresponding to a relative disorder level of 0.10–0.15 sensitizes the SrTiO3 to amorphous track formation along the ion path of 12 and 20 MeV Ti, 21 MeV Cl and 21 MeV Ni ions, where Ti, Cl and Ni ions otherwise do not produce amorphous or damage tracks in pristine SrTiO3. The electronic stopping power threshold for amorphous ion track formation is found to be 6.7 keV/nm for the pre-damaged defectmore » state studied in this work. Lastly, these results suggest the possibility of selectively producing nanometer scale, amorphous ion tracks in thin films of epitaxial SrTiO3.« less

  16. 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.

  17. 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

  18. Plasma engineering of silicon quantum dots and their properties through energy deposition and chemistry.

    PubMed

    Sahu, Bibhuti Bhusan; Yin, Yongyi; Gauter, Sven; Han, Jeon Geon; Kersten, Holger

    2016-09-21

    The characterization of plasma and atomic radical parameters along with the energy influx from plasma to the substrate during plasma enhanced chemical vapor deposition (PECVD) of Si quantum dot (QD) films is presented and discussed. In particular, relating to the Si QD process optimization and control of film growth, the necessity to control the deposition environment by inducing the effect of the energy of the key plasma species is realized. In this contribution, we report dual frequency PECVD processes for the low-temperature and high-rate deposition of Si QDs by chemistry and energy control of the key plasma species. The dual frequency plasmas can effectively produce a very high plasma density and atomic H and N densities, which are found to be crucial for the growth and nucleation of QDs. Apart from the study of plasma chemistry, the crucial role of the energy imparted due to these plasma activated species on the substrate is determined in light of QD formation. Various plasma diagnostics and film analysis methods are integrated to correlate the effect of plasma and energy flux on the properties of the deposited films prepared in the reactive mixtures of SiH4/NH3 at various pressures. The present results are highly relevant to the development of the next-generation plasma process for devices that rely on effective control of the QD size and film properties.

  19. Internal energy deposition with silicon nanoparticle-assisted laser desorption/ionization (SPALDI) mass spectrometry

    NASA Astrophysics Data System (ADS)

    Dagan, Shai; Hua, Yimin; Boday, Dylan J.; Somogyi, Arpad; Wysocki, Ronald J.; Wysocki, Vicki H.

    2009-06-01

    The use of silicon nanoparticles for laser desorption/ionization (LDI) is a new appealing matrix-less approach for the selective and sensitive mass spectrometry of small molecules in MALDI instruments. Chemically modified silicon nanoparticles (30 nm) were previously found to require very low laser fluence in order to induce efficient LDI, which raised the question of internal energy deposition processes in that system. Here we report a comparative study of internal energy deposition from silicon nanoparticles to previously explored benzylpyridinium (BP) model compounds during LDI experiments. The internal energy deposition in silicon nanoparticle-assisted laser desorption/ionization (SPALDI) with different fluorinated linear chain modifiers (decyl, hexyl and propyl) was compared to LDI from untreated silicon nanoparticles and from the organic matrix, [alpha]-cyano-4-hydroxycinnamic acid (CHCA). The energy deposition to internal vibrational modes was evaluated by molecular ion survival curves and indicated that the ions produced by SPALDI have an internal energy threshold of 2.8-3.7 eV. This is slightly lower than the internal energy induced using the organic CHCA matrix, with similar molecular survival curves as previously reported for LDI off silicon nanowires. However, the internal energy associated with desorption/ionization from the silicon nanoparticles is significantly lower than that reported for desorption/ionization on silicon (DIOS). The measured survival yields in SPALDI gradually decrease with increasing laser fluence, contrary to reported results for silicon nanowires. The effect of modification of the silicon particle surface with semifluorinated linear chain silanes, including fluorinated decyl (C10), fluorinated hexyl (C6) and fluorinated propyl (C3) was explored too. The internal energy deposited increased with a decrease in the length of the modifier alkyl chain. Unmodified silicon particles exhibited the highest analyte internal energy

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

    ERIC Educational Resources Information Center

    Barbiric, Dora; Tribe, Lorena; Soriano, Rosario

    2015-01-01

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

  1. 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…

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

    EPA Science Inventory

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

  3. 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...

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

    PubMed

    Xie, Zhen; Bowman, Joel M

    2006-04-27

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

  5. 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)

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Wortman, D.

    1983-07-01

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

  8. 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.

  9. Atomic physics calculations in support of studies for high energy density plasmas

    SciTech Connect

    Wang, P.; MacFarlane, J.J.; Moses, G.A.; Mehlhorn, T.A.

    1995-12-31

    The studies of high energy density plasmas require basic atomic data, equations of state, opacities, and stopping power. Unfortunately, the related experimental data are very limited. To obtain these data for a wide domain of plasma conditions, one must rely on theoretical calculations. The authors have developed an atomic physics calculation package which can provide high quality atomic data for numerical simulations of high energy density plasmas. In this paper, they give detailed descriptions of physics models used in the package. Particular emphasis will be on a hybrid model for equations of state, a self-consistent field model for ion stopping power, and opacity calculations.

  10. Hiking down the energy landscape: progress toward the Kauzmann temperature via vapor deposition.

    PubMed

    Kearns, Kenneth L; Swallen, Stephen F; Ediger, M D; Wu, Tian; Sun, Ye; Yu, Lian

    2008-04-24

    Physical vapor deposition was employed to prepare amorphous samples of indomethacin and 1,3,5-(tris)naphthylbenzene. By depositing onto substrates held somewhat below the glass transition temperature and varying the deposition rate from 15 to 0.2 nm/s, glasses with low enthalpies and exceptional kinetic stability were prepared. Glasses with fictive temperatures that are as much as 40 K lower than those prepared by cooling the liquid can be made by vapor deposition. As compared to an ordinary glass, the most stable vapor-deposited samples moved about 40% toward the bottom of the potential energy landscape for amorphous materials. These results support the hypothesis that enhanced surface mobility allows stable glass formation by vapor deposition. A comparison of the enthalpy content of vapor-deposited glasses with aged glasses was used to evaluate the difference between bulk and surface dynamics for indomethacin; the dynamics in the top few nanometers of the glass are about 7 orders of magnitude faster than those in the bulk at Tg - 20 K.

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

    SciTech Connect

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

    2012-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  13. Vibrational energy transfer in molecular collisions andvan der Waals clusters: Experiments and trajectory calculations

    NASA Astrophysics Data System (ADS)

    Yoder, Laurie Miller

    2000-09-01

    Polyatomic molecules with significant amounts of vibrational energy have high state densities that preclude state-to-state energy transfer observations. Both experiments and calculations are used to quantify energy transfer within this energy continuum. The work focuses on vibrationally excited aromatic molecules containing 10 to 15 atoms (pyrazine, benzene, methylpyrazine, toluene, pyrimidine, and aniline). In collisional experiments, the average vibrational energy of hot molecules was monitored by infrared fluorescence as they were deactivated by collisions with the bath. The experimental data were modeled with master equation simulations. The results for pyrazine show that the temperature dependence of the energy transfer is weak, and the average energy transferred per collision is approximately linearly dependent on vibrational energy. The experimental data cannot be modeled without invoking a biexponential collision step-size distribution, which implies that ``supercollisions,'' or very strongly deactivating collisions, are important. Additional information on the dynamics of energy transfer can be obtained through the vibrational predissociation of van der Waals dimers, which is the half-collision analog of a full collision. The ion imaging technique and a velocity-resolved time-of-flight technique were used to quantify the recoil energy released in the vibrational predissociation of triplet state mixed van der Waals dimers which contain ~2000 to ~8000 cm-1 of vibrational energy. The resulting recoil energy distributions peak near zero energy and are monotonically decreasing functions of energy. The fraction of initially available vibrational energy that appears as recoil energy is small. The average recoil energy is not strongly dependent on the initial vibrational energy or the density of states of the aromatic donor. Completely statistical models are unable to describe the results. Vibrational energy transfer both in van der Waals cluster predissociation

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

    PubMed

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

    2013-01-16

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

  16. 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.

  17. 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.

  18. Energy deposition through radiative processes in absorbers irradiated by electron beams

    NASA Astrophysics Data System (ADS)

    Tatsuo, Tabata; Pedro, Andreo; Kunihiko, Shinoda; Rinsuke, Ito

    1994-09-01

    The component of energy deposition due to radiative processes (bremsstrahlung component) in absorbers irradiated by electron beams has been computed together with the total energy deposition by using the ITS Monte Carlo system version 3.0. Plane-parallel electron beams with energies from 0.1 to 100 MeV have been assumed to be incident normally on the slab absorber, whose thickness is 2.5 times the continuous slowing-down approximation (csda) range of the incident electrons. Absorber materials considered are elemental solids with atomic numbers between 4 and 92 (Be, C, Al, Cu, Ag, Au and U). An analytic formula is given to express the depth profile of the bremsstrahlung component as a function of scaled depth (depth in units of the csda range), incident-electron energy and absorber atomic number. It is also applicable to compounds.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  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. Correlated natural transition orbital framework for low-scaling excitation energy calculations (CorNFLEx)

    NASA Astrophysics Data System (ADS)

    Baudin, Pablo; Kristensen, Kasper

    2017-06-01

    We present a new framework for calculating coupled cluster (CC) excitation energies at a reduced computational cost. It relies on correlated natural transition orbitals (NTOs), denoted CIS(D')-NTOs, which are obtained by diagonalizing generalized hole and particle density matrices determined from configuration interaction singles (CIS) information and additional terms that represent correlation effects. A transition-specific reduced orbital space is determined based on the eigenvalues of the CIS(D')-NTOs, and a standard CC excitation energy calculation is then performed in that reduced orbital space. The new method is denoted CorNFLEx (Correlated Natural transition orbital Framework for Low-scaling Excitation energy calculations). We calculate second-order approximate CC singles and doubles (CC2) excitation energies for a test set of organic molecules and demonstrate that CorNFLEx yields excitation energies of CC2 quality at a significantly reduced computational cost, even for relatively small systems and delocalized electronic transitions. In order to illustrate the potential of the method for large molecules, we also apply CorNFLEx to calculate CC2 excitation energies for a series of solvated formamide clusters (up to 4836 basis functions).

  2. Energy bandgap variation in oblique angle-deposited indium tin oxide

    SciTech Connect

    Kim, Kyurin; Kim, Hyunsoo; Cho, Jaehee; Park, Jun Hyuk; Kim, Jong Kyu; Fred Schubert, E.

    2016-01-25

    Indium tin oxide (ITO) thin films deposited using the oblique angle deposition (OAD) technique exhibit a strong correlation between structural and optical properties, especially the optical bandgap energy. The microstructural properties of ITO thin films are strongly influenced by the tilt angle used during the OAD process. When changing the tilt angle, the refractive index, porosity, and optical bandgap energy of ITO films also change due to the existence of a preferential growth direction at the interface between ITO and the substrate. Experiments reveal that the ITO film's optical bandgap varies from 3.98 eV (at normal incident deposition) to 3.87 eV (at a 60° tilt angle)

  3. 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.

  4. Reduced energy bandgap of a-Si:H films deposited by PECVD at elevating temperatures

    NASA Astrophysics Data System (ADS)

    Cahyono, Yoyok; Maslakah, Umi; Muttaqin, Fuad Darul; Darminto

    2017-01-01

    The hydrogenated amorphous silicon (a-Si:H) films with the thickness of several hundreds nanometer have successfully been grown on the glass substrates by plasma enhanced (PE) chemical vapor deposition (CVD), employing SiH4 gas with H2 dilution. The deposition temperatures being set from 150°C up to 250°C was intended to induce nanocrystalline clusters in the amorphous structure, to reduce dangling bond and to recover defect states in the gap, in order to obtain films with reduced energy band gap. The X-ray diffractometry, UV-Vis spectrometric and atomic force microscopic examinations were conducted to structurally study the samples. The reduction of energy bandgap from 1.89 eV down to 1.03 eV was obtained from the deposited films.

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

    NASA Astrophysics Data System (ADS)

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

    1993-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

  7. 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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  11. 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.

  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 (HF), second-order Møller-Plesset perturbation theory (MP2) 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 diff 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. 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.

  14. Recent Development of Advanced Electrode Materials by Atomic Layer Deposition for Electrochemical Energy Storage.

    PubMed

    Guan, Cao; Wang, John

    2016-10-01

    Electrode materials play a decisive role in almost all electrochemical energy storage devices, determining their overall performance. Proper selection, design and fabrication of electrode materials have thus been regarded as one of the most critical steps in achieving high electrochemical energy storage performance. As an advanced nanotechnology for thin films and surfaces with conformal interfacial features and well controllable deposition thickness, atomic layer deposition (ALD) has been successfully developed for deposition and surface modification of electrode materials, where there are considerable issues of interfacial and surface chemistry at atomic and nanometer scale. In addition, ALD has shown great potential in construction of novel nanostructured active materials that otherwise can be hardly obtained by other processing techniques, such as those solution-based processing and chemical vapor deposition (CVD) techniques. This review focuses on the recent development of ALD for the design and delivery of advanced electrode materials in electrochemical energy storage devices, where typical examples will be highlighted and analyzed, and the merits and challenges of ALD for applications in energy storage will also be discussed.

  15. 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.

  16. Recent Development of Advanced Electrode Materials by Atomic Layer Deposition for Electrochemical Energy Storage

    PubMed Central

    2016-01-01

    Electrode materials play a decisive role in almost all electrochemical energy storage devices, determining their overall performance. Proper selection, design and fabrication of electrode materials have thus been regarded as one of the most critical steps in achieving high electrochemical energy storage performance. As an advanced nanotechnology for thin films and surfaces with conformal interfacial features and well controllable deposition thickness, atomic layer deposition (ALD) has been successfully developed for deposition and surface modification of electrode materials, where there are considerable issues of interfacial and surface chemistry at atomic and nanometer scale. In addition, ALD has shown great potential in construction of novel nanostructured active materials that otherwise can be hardly obtained by other processing techniques, such as those solution‐based processing and chemical vapor deposition (CVD) techniques. This review focuses on the recent development of ALD for the design and delivery of advanced electrode materials in electrochemical energy storage devices, where typical examples will be highlighted and analyzed, and the merits and challenges of ALD for applications in energy storage will also be discussed. PMID:27840793

  17. Atmospheric Breakup and Energy Deposition Modeling for Asteroid Impact Risk Assessmen

    NASA Astrophysics Data System (ADS)

    Wheeler, L.; Mathias, D.

    2016-12-01

    The Asteroid Threat Assessment Project (ATAP) team at NASA Ames Research Center is developing physics-based models to assess the risk posed by potential asteroid strikes on Earth. As part of this effort, an analytic asteroid fragmentation model has been developed to model the atmospheric energy deposition of asteroids with a range of compositional properties and entry conditions. The resulting energy deposition profiles are used to estimate airburst altitudes and blast overpressure damage on the ground. The model approach combines successive fragmentation of larger independent pieces with the release of aggregate clouds of debris. A wide range of potential breakup behaviors can be assessed by varying the number and masses of fragments produced, the fraction of mass released as debris clouds, and the size-strength scaling used to increase the durability of smaller fragments. The initial asteroid body can also be seeded with a distribution of independent fragment sizes and remaining debris mass to represent a variety of structural types, from rubble piles to coherent monoliths. The model is able to reproduce key energy deposition features, such as multiple flares, high-altitude regolith blow-off, or initial disruption of loosely bound conglomerations followed by more energetic breakup of the constituent boulders. These capabilities provide a means to investigate sensitivities of energy deposition to potential variations in asteroid structure, while also maintaining a level of fidelity appropriate for the large numbers of cases needed for statistical risk assessment.

  18. Energy deposition in scintillation detectors and the triggers formation in the GAMMA-400 experiment

    NASA Astrophysics Data System (ADS)

    Arkhangelskaja, Irene; Yurkin, Yuri T.; Arkhangelsky, Andrey; Topchiev, Nikolay; Kheymits, Maxim; Chasovikov, Evgeniy; Galper, Arkady; Chistyakov, Pavel

    In this paper, some details of the GAMMA-400 trigger system construction are presented. The comparison between relativistic electron, proton, and gamma-ray energy deposition is described and methods of on-board triggers and trigger markers formation for discrimination between each of other are proposed.

  19. 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.

  20. 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.

  1. 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

  2. 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)

  3. 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)

  4. Classification of processes for the atomic layer deposition of metals based on mechanistic information from density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Elliott, S. D.; Dey, G.; Maimaiti, Y.

    2017-02-01

    Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.

  5. Classification of processes for the atomic layer deposition of metals based on mechanistic information from density functional theory calculations.

    PubMed

    Elliott, S D; Dey, G; Maimaiti, Y

    2017-02-07

    Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.

  6. Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain.

    PubMed

    Anisimov, Victor M; Cavasotto, Claudio N

    2011-07-30

    The accurate and efficient calculation of binding free energies is essential in computational biophysics. We present a linear-scaling quantum mechanical (QM)-based end-point method termed MM/QM-COSMO to calculate binding free energies in biomolecular systems, with an improved description of entropic changes. Molecular dynamics trajectories are re-evaluated using a semiempirical Hamiltonian and a continuum solvent model; translational and rotational entropies are calculated using configurational integrals, and internal entropy is calculated using the harmonic oscillator approximation. As an application, we studied the binding of a series of phosphotyrosine tetrapeptides to the human Lck SH2 domain, a key component in intracellular signal transduction, modulation of which can have therapeutic relevance in the treatment of cancer, osteoporosis, and autoimmune diseases. Calculations with molecular mechanics Poisson-Boltzmann, and generalized Born surface area methods showed large discrepancies with experimental data stemming from the enthalpic component, in agreement with an earlier report. The empirical force field-based solvent interaction energy scoring function yielded improved results, with average unsigned error of 3.6 kcal/mol, and a better ligand ranking. The MM/QM-COSMO method exhibited the best agreement both for absolute (average unsigned error = 0.7 kcal/mol) and relative binding free energy calculations. These results show the feasibility and promise of a full QM-based end-point method with an adequate balance of accuracy and computational efficiency. Copyright © 2011 Wiley Periodicals, Inc.

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

    PubMed

    Fouda, Adam; Ryde, Ulf

    2016-11-08

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Yang, Xue; Hassanein, Ahmed

    2014-02-01

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

  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

    2016-03-08

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

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

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

    1996-01-15

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

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

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel; Khishchenko, Konstantin

    2012-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  15. 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.

  16. Kinetic-energy induced smoothening and delay of epitaxial breakdown in pulsed-laser deposition

    SciTech Connect

    Shin, Byungha; Aziz, Michael J.

    2007-08-15

    We have isolated the effect of kinetic energy of depositing species from the effect of flux pulsing during pulsed-laser deposition (PLD) on surface morphology evolution of Ge(001) homoepitaxy at low temperature (100 deg. C). Using a dual molecular beam epitaxy (MBE) PLD chamber, we compare morphology evolution from three different growth methods under identical experimental conditions except for the differing nature of the depositing flux: (a) PLD with average kinetic energy 300 eV (PLD-KE); (b) PLD with suppressed kinetic energy comparable to thermal evaporation energy (PLD-TH); and (c) MBE. The thicknesses at which epitaxial breakdown occurs are ranked in the order PLD-KE>MBE>PLD-TH; additionally, the surface is smoother in PLD-KE than in MBE. The surface roughness of the films grown by PLD-TH cannot be compared due to the early epitaxial breakdown. These results demonstrate convincingly that kinetic energy is more important than flux pulsing in the enhancement of epitaxial growth, i.e., the reduction in roughness and the delay of epitaxial breakdown.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Vessally, Esmail; Aryana, Soma

    2016-01-01

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2004-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  6. 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.

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

    PubMed

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

    2015-03-07

    A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)(-2) type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.

  8. 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.

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

    SciTech Connect

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

    2012-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

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

    DTIC Science & Technology

    1993-11-04

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

  12. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.

    PubMed

    Miller, Bill R; McGee, T Dwight; Swails, Jason M; Homeyer, Nadine; Gohlke, Holger; Roitberg, Adrian E

    2012-09-11

    MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.

  13. Assessing Locations of Energy Transfer/Deposit in the Ionosphere-Thermosphere System

    NASA Astrophysics Data System (ADS)

    Tu, J.; Song, P.

    2014-12-01

    It has long been believed that most of energy transferred from the magnetosphere and deposited in the ionosphere-thermosphere system occurs in the auroral zone, the region of strong field-aligned current density. Recent observations of the Poynting flux to the ionosphere and theoretical investigations of the magnetosphere-ionosphere coupling show that the strongest energy transfer may be in the polar cap proper where the plasma flow speed is high and not where the flow reverses. This implies that the field-aligned current is not the primary agent of the energy transfer into the ionosphere-thermosphere system and that other physical progresses are at play. Recent simulation studies using an inductive-dynamic approach (including self-consistent solutions of Faraday's law and retaining inertia terms in the ion momentum equations) on the magnetosphere-ionosphere-thermosphere coupling indicate that the energy transfer is through Alfven waves propagating to the ionosphere/thermosphere and the energy deposition is via the frictional heating caused by relative motion between ions and neutrals. In this study we assess the locations of the energy transfer and deposition by employing a self-consistent inductive-dynamic ionosphere-thermosphere model. In a 2-D numerical simulation (dawn-dusk meridian plane), we solve the continuity, momentum, and energy equations for multiple species of ions and neutrals including photochemistry and Maxwell's equations. By simulating responses of the ionosphere-thermosphere system to enhanced magnetosphere convection, we show that the strongest energy transfer occurs in the polar cap proper instead of the auroral zone.

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

    PubMed

    Łusakowski, A; Bogusławski, P; Story, T

    2015-06-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  16. High-Level Calculations on Nitrosooxyalanes: Possible New High-Energy Materials?

    NASA Astrophysics Data System (ADS)

    Stouffer, Michael L.; Ball, David W.

    2010-06-01

    As part of our survey of new potential high-energy materials, we have calculated the structures, vibrational frequencies and spectra, and various enthalpies of reaction for nitrosooxy-, dinitrosooxy-, and trinitrosooxyalane. Although the initial intent was to determine the properties of nitroalanes, in all cases the bonding to the central aluminum atom was through an oxygen atom of the NO2 group. All molecules optimized to a near planar structure. Calculations of their reaction energies showed that the higher the nitrosooxy content, the more negative the enthalpies of formation, with enthalpies of combustion or decomposition falling precipitously.

  17. MCNP6 updated proton-induced fission cross section calculations at intermediate energies

    NASA Astrophysics Data System (ADS)

    Kerby, Leslie; Mashnik, Stepan; Mulvaney, John

    2017-09-01

    MCNP6 has been Validated and Verified against intermediate- and high-energy fission cross-section experimental data. Recent improvements contained in CEM03.03F and MCNP6-F to consider precompound emission of heavy clusters up to 28Mg has necessitated a re-calculation of fission cross sections. With our re-calculation, we find that CEM03.03F, which is used in MCNP6-F, predicts fission cross sections in good agreement with available experimental data for reactions induced by protons on both subactinide and actinide nuclei at incident energies from several tens of MeV to several GeV.

  18. Quantum scattering calculation for reaction Br + H2 on two potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Quan, Wei-Long; Tang, Ping-Ying; Tang, Bi-Yu

    Three-dimensional time-dependent quantum wave packet calculations have been carried out for Br + H2 on a new global ab initio and a semi-empirical extended London-Eyring-Polanyi-Sato potential energy surface. It is shown that on the ab initio surface, the threshold energy is much lower, and the reaction probabilities, cross sections, and rate constants are much larger. The effects of the initial rovibrational excitation have also been studied. Comparison of rate constants with experimental measurement implies that the ab initio surface is more suitable for quantum dynamic calculation. The possible reasons and mechanism for the dynamical difference on the two PES are analyzed and discussed.

  19. 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.

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

    SciTech Connect

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

    1995-12-31

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

  1. Calculation of Positron Binding Energies and Implications for Feshbach-Resonant Positron-Uracil Annihilation

    NASA Astrophysics Data System (ADS)

    Wanniarachchi, Indika; Morgan, Caroline

    2010-04-01

    Here we investigate by first-principles calculations the possible role of vibrational Feshbach resonances in enhancing positron annihilation for low-energy positron beams incident on uracil, a base found in RNA. Geometries, vibrational polarizabilities, and dipole moments for uracil and 5-halouracils are calculated with density functional theory, DFT-B3LYP with a 6-31G+(d, p) basis set, and are used to determine positron-uracil and positron-5-halouracil binding energies. The energy of the Feshbach resonances is then determined by the law of energy conservation. Experimental work on positron interactions with uracil and 5-halouracils in conjunction with the theoretical work reported here is underway.

  2. 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.

  3. Chemical transport models: the combined non-local diffusion and mixing schemes, and calculation of in-canopy resistance for dry deposition fluxes.

    PubMed

    Mihailovic, Dragutin T; Alapaty, Kiran; Podrascanin, Zorica

    2009-03-01

    Improving the parameterization of processes in the atmospheric boundary layer (ABL) and surface layer, in air quality and chemical transport models. To do so, an asymmetrical, convective, non-local scheme, with varying upward mixing rates is combined with the non-local, turbulent, kinetic energy scheme for vertical diffusion (COM). For designing it, a function depending on the dimensionless height to the power four in the ABL is suggested, which is empirically derived. Also, we suggested a new method for calculating the in-canopy resistance for dry deposition over a vegetated surface. The upward mixing rate forming the surface layer is parameterized using the sensible heat flux and the friction and convective velocities. Upward mixing rates varying with height are scaled with an amount of turbulent kinetic energy in layer, while the downward mixing rates are derived from mass conservation. The vertical eddy diffusivity is parameterized using the mean turbulent velocity scale that is obtained by the vertical integration within the ABL. In-canopy resistance is calculated by integration of inverse turbulent transfer coefficient inside the canopy from the effective ground roughness length to the canopy source height and, further, from its the canopy height. This combination of schemes provides a less rapid mass transport out of surface layer into other layers, during convective and non-convective periods, than other local and non-local schemes parameterizing mixing processes in the ABL. The suggested method for calculating the in-canopy resistance for calculating the dry deposition over a vegetated surface differs remarkably from the commonly used one, particularly over forest vegetation. In this paper, we studied the performance of a non-local, turbulent, kinetic energy scheme for vertical diffusion combined with a non-local, convective mixing scheme with varying upward mixing in the atmospheric boundary layer (COM) and its impact on the concentration of pollutants

  4. High energy conversion efficiency in laser-proton acceleration by controlling laser-energy deposition onto thin foil targets

    NASA Astrophysics Data System (ADS)

    Brenner, C. M.; Robinson, A. P. L.; Markey, K.; Scott, R. H. H.; Gray, R. J.; Rosinski, M.; Deppert, O.; Badziak, J.; Batani, D.; Davies, J. R.; Hassan, S. M.; Lancaster, K. L.; Li, K.; Musgrave, I. O.; Norreys, P. A.; Pasley, J.; Roth, M.; Schlenvoigt, H.-P.; Spindloe, C.; Tatarakis, M.; Winstone, T.; Wolowski, J.; Wyatt, D.; McKenna, P.; Neely, D.

    2014-02-01

    An all-optical approach to laser-proton acceleration enhancement is investigated using the simplest of target designs to demonstrate application-relevant levels of energy conversion efficiency between laser and protons. Controlled deposition of laser energy, in the form of a double-pulse temporal envelope, is investigated in combination with thin foil targets in which recirculation of laser-accelerated electrons can lead to optimal conditions for coupling laser drive energy into the proton beam. This approach is shown to deliver a substantial enhancement in the coupling of laser energy to 5-30 MeV protons, compared to single pulse irradiation, reaching a record high 15% conversion efficiency with a temporal separation of 1 ps between the two pulses and a 5 μm-thick Au foil. A 1D simulation code is used to support and explain the origin of the observation of an optimum pulse separation of ˜1 ps.

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

    NASA Astrophysics Data System (ADS)

    Lu, Nandou

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

  6. Spatial distribution and energy deposition of precipitating Oxygen ions and their relation with the Martian crustal fields

    NASA Astrophysics Data System (ADS)

    Li, Lei; Zhang, Yiteng

    In the electromagnetic environment set by the MHD model (Ma et al.,2004), considering the dynamic feature of O+ ions, the spatial distributions and energy spectra of O+ ions impacting the atmosphere of Mars are calculated by tracing the trajectories of cold O+ ions launched from the sunlit hemisphere. The effects of the crustal fields on the spatial distribution of precipitating O+ ions are investigated by turning on or off the crustal fields. Global maps of precipitating O+ ion flux show that the crustal fields have no significant effect on the spatial distribution of lower energy precipitating ions(<100eV), while the distribution of higher energyprecipitating O+ ions (>100eV) is closely related with the distribution of the crustal fields. Most O+ ions originated in lower exosphere impact day side atmosphere before getting much energy since the electric field is weak there. O+ ions from higher source may impact the atmosphere with higher energy deposition, forming patchy precipitation regions both at dayside and nightside when the crustal fields are present. A precipitation belt formed by high energy O+ ions (around 1keV) is found near the midnight region, revealing that the crustal fields may change the electromagnetic environment near Mars significantly and result in the acceleration of precipitating O+ ions at the nightside. Together with the rotation of the planet, the consequences of the impacting of O+, including heating and sputtering of the atmosphere and ionosphere, should be much more complicated than expected.

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

    NASA Astrophysics Data System (ADS)

    Kryzhanovsky, Boris; Litinskii, Leonid

    2015-01-01

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

  8. The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations.

    PubMed

    Tjong, Harianto; Zhou, Huang-Xiang

    2006-11-28

    The Poisson-Boltzmann equation gives the electrostatic free energy of a solute molecule (with dielectric constant epsilon(l)) solvated in a continuum solvent (with dielectric constant epsilon(s)). Here a simple formula is presented that accurately predicts the electrostatic free energy for all combinations of epsilon(l) and epsilon(s) from the calculation on a single set of epsilon(l) and epsilon(s) values.

  9. Laser energy density, structure and properties of pulsed-laser deposited zinc oxide films

    NASA Astrophysics Data System (ADS)

    Tsoutsouva, M. G.; Panagopoulos, C. N.; Kompitsas, M.

    2011-05-01

    Zinc oxide thin films were deposited on soda lime glass substrates by pulsed laser deposition in an oxygen-reactive atmosphere at 20 Pa and a constant substrate temperature at 300 °C. A pulsed KrF excimer laser, operated at 248 nm with pulse duration 10 ns, was used to ablate the ceramic zinc oxide target. The structure, the optical and electrical properties of the as-deposited films were studied in dependence of the laser energy density in the 1.2-2.8 J/cm 2 range, with the aid of X-ray Diffraction, Atomic Force Microscope, Transmission Spectroscopy techniques, and the Van der Pauw method, respectively. The results indicated that the structural and optical properties of the zinc oxide films were improved by increasing the laser energy density of the ablating laser. The surface roughness of the zinc oxide film increased with the decrease of laser energy density and both the optical bang gap and the electrical resistivity of the film were significantly affected by the laser energy density.

  10. Measurement of Runaway Electron Plateau Final Loss Energy Deposition into Wall of DIII-D

    NASA Astrophysics Data System (ADS)

    Hollmann, E. M.; Bykov, I.; Moyer, R. A.; Rudakov, D. L.; Commaux, N.; Shiraki, D.; Lasnier, C.; Martin-Solis, R.; Cooper, C.; Eidietis, N.; Parks, P.; Paz-Soldan, C.

    2016-10-01

    Intentional runaway electron (RE) plateau-wall strikes with different initial impurity levels are used to study the effect of background plasma relativistic electron Z (as well as plasma resistivity for slow electrons) on RE-wall loss dynamics. RE wall loss time is found to be close to the avalanche time (meC/eE| |) 1 nλ √{ 3 (Z + 5) / π } , consistent with REs being lost by a series of MHD reconnection events, with timescale limited by current profile filling via avalanche. Local kinetic energy deposition is estimated with both hard x-ray emission and with infra-red imaging. At higher plasma impurity levels Z 10 , energy deposition appears to be consistent with power balance estimates, as long as collisional dissipation during the final loss event is included. At low impurity levels Z 1 , however, local energy deposition appears around 10 × less than expected, indicating that the energy dissipation at low Z is still poorly understood. Work supported by the US DOE under DE-FG02-07ER54917, DE-AC05-00OR22725, DE-AC52-07NA27344, DE-FC02-04ER54698.

  11. Influence of emitter temperature on the energy deposition in a low-pressure plasma

    SciTech Connect

    Levko, Dmitry; Raja, Laxminarayan L.

    2016-03-15

    The influence of emitter temperature on the energy deposition into low-pressure plasma is studied by the self-consistent one-dimensional Particle-in-Cell Monte Carlo Collisions model. Depending on the emitter temperature, different modes of discharge operation are obtained. The mode type depends on the plasma frequency and does not depend on the ratio between the densities of beam and plasma electrons. Namely, plasma is stable when the plasma frequency is small. For this plasma, the energy transfer from emitted electrons to plasma electrons is inefficient. The increase in the plasma frequency results first in the excitation of two-stream electron instability. However, since the thermal velocity of plasma electrons is smaller than the electrostatic wave velocity, the resonant wave-particle interaction is inefficient for the energy deposition into the plasma. Further increase in the plasma frequency leads to the distortion of beam of emitted electrons. Then, the electrostatic wave generated due to two-stream instability decays into multiple slower waves. Phase velocities of these waves are comparable with the thermal velocity of plasma electrons which makes possible the resonant wave-particle interaction. This results in the efficient energy deposition from emitted electrons into the plasma.

  12. Evolution of energy deposition during glass cutting with pulsed femtosecond laser radiation

    NASA Astrophysics Data System (ADS)

    Kalupka, C.; Großmann, D.; Reininghaus, M.

    2017-05-01

    We report on investigations of the energy deposition in the volume of thin glass during an ablation cutting process with pulsed femtosecond laser radiation by time-resolved pump-probe shadowgraphy. For a single laser pulse, the temporal evolution of the transient electronic excitation of the glass volume is imaged up to 10 ps after initial excitation. For an increasing number of laser pulses, the spatial excitation of the glass volume significantly changes compared to single pulse irradiation. Sharp spikes are observed, which reduce the transmission of the illuminating probe pulse. This indicates local maxima of the absorption and, therefore, energy deposition of the pump pulse energy in the glass volume. Furthermore, for an increasing number of pulses, different shapes of the surface ablation crater are observed. To study the correlation between the shape of the surface ablation crater and the energy deposition in the glass volume, simulations of the spatial intensity distribution of the pump pulse are executed by means of linear beam propagation method. We show that the transient excitation spikes observed by pump-probe shadowgraphy can be explained by refraction and diffraction of the laser radiation at the surface ablation crater. Our results provide an experimental validation for the physical reason of an ablation stop for an ablation cutting process. Moreover, the simulations allow for the prediction of damage inside the glass volume.

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

    NASA Astrophysics Data System (ADS)

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

    1995-08-01

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

  14. Energy Deposition and Condition of the Metal Core in Exploding Wire Experiments

    NASA Astrophysics Data System (ADS)

    Sarkisov, G. S.; Rosenthal, S. E.; Struve, K. W.; McDaniel, D. H.; Waisman, E. M.; Sasorov, P. V.

    2002-11-01

    Measurements of the Joule energy deposition into exploding wire and its relation with condition of the expanding wire core are presented. Wires of nine different metals with diameters of 10-30 microns, have been exploded by fast 150A/ns and slow 20A/ns pulses, in vacuum and in air. It has been shown by interferometry and light emission that expanding wire core has different conditions. The substances with small atomization enthalpy (Ag, Al, Cu, Au) demonstrate full vaporization of the wire core. The refractory metals (Ti, Pt, Mo, W) demonstrates that core consists from vapor and small and hot microparticles. In this case we observe "firework effect" when large radiation from the wire exceed the energy deposition time in a three order of magnitude. For non-refractory metals radiation dropping fast in 100 ns time scale due to effective adiabatic cooling. It is possible if main part of the metal core was vaporized. The interferometrical investigation of the refraction coefficient of expanding metal core is proof this conclusion. It has been shown that energy deposition before surface breakdown dependent strongly from current rate, surface coatings, environment, wire diameter and radial electric field. The regime of wire explosion in vacuum without shunting plasma shell has been realized for fast exploding mode. In this case we observe anomaly high energy deposition in to the wire core exceeding regular value in almost 20 times. The experimental results for Al wire have been compared with ALEGRA 2D MHD simulations. *Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL8500.

  15. An online tool for calculation of free-energy balance for the renal inner medulla.

    PubMed

    Vilbig, Ryan L; Sarkar, Abhijit; Zischkau, Joseph; Knepper, Mark A; Pisitkun, Trairak

    2012-08-01

    Concentrating models of the renal inner medulla can be classified according to external free-energy balance into passive models (positive values) and models that require an external energy source (negative values). Here we introduce an online computational tool that implements the equations of Stephenson and colleagues (Stephenson JL, Tewarson RP, Mejia R. Proc Natl Acad Sci USA 71: 1618-1622, 1974) to calculate external free-energy balance at steady state for the inner medulla (http://helixweb.nih.gov/ESBL/FreeEnergy). Here "external free-energy balance" means the sum of free-energy flows in all streams entering and leaving the inner medulla. The program first assures steady-state mass balance for all components and then tallies net external free-energy balance for the selected flow conditions. Its use is illustrated by calculating external free-energy balance for an example of the passive concentrating model taken from the original paper by Kokko and Rector (Kokko JP, Rector FC Jr. Kidney Int 2: 214-223, 1972).

  16. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions.

    PubMed Central

    Levitt, D G

    1978-01-01

    The electrostatic energy profile of one, two, or three ions in an aqueous channel through a lipid membrane is calculated. It is shown that the previous solution to this problem (based on the assumption that the channel is infinitely long) significantly overestimates the electrostatic energy barrier. For example, for a 3-A radius pore, the energy is 16 kT for the infinite channel and 6.7 kT for an ion in the center of a channel 25 A long. The energy as a function of the position of the ion is also determined. With this energy profile, the rate of crossing the membrane (using the Nernst-Planck equation) was estimated and found to be compatible with the maximum conductance observed for the gramicidin A channel. The total electrostatic energy (as a function of position) required to place two or three ions in the channel is also calculated. The electrostatic interaction is small for two ions at opposite ends of the channel and large for any positioning of the three ions. Finally, the gradient through the channel of an applied potential is calculated. The solution to these problems is based on solving an equivalent problem in which an appropriate surface charge is placed on the boundary between the lipid and aqueous regions. The magnitude of the surface charge is obtained from the numerical solution for a system of coupled integral equations. PMID:656542

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

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2017-03-01

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

  18. 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

  19. Investigation of voxel warping and energy mapping approaches for fast 4D Monte Carlo dose calculations in deformed geometries using VMC++

    NASA Astrophysics Data System (ADS)

    Heath, Emily; Tessier, Frederic; Kawrakow, Iwan

    2011-08-01

    A new deformable geometry class for the VMC++ Monte Carlo code was implemented based on the voxel warping method. Alternative geometries which use tetrahedral sub-elements were implemented and efficiency improvements investigated. A new energy mapping method, based on calculating the volume overlap between deformed reference dose grid and the target dose grid, was also developed. Dose calculations using both the voxel warping and energy mapping methods were compared in simple phantoms as well as a patient geometry. The new deformed geometry implementation in VMC++ increased calculation times by approximately a factor of 6 compared to standard VMC++ calculations in rectilinear geometries. However, the tetrahedron-based geometries were found to improve computational efficiency, relative to the dodecahedron-based geometry, by a factor of 2. When an exact transformation between the reference and target geometries was provided, the voxel and energy warping methods produced identical results. However, when the transformation is not exact, there were discrepancies in the energy deposited on the target geometry which lead to significant differences in the dose calculated by the two methods. Preliminary investigations indicate that these energy differences may correlate with registration errors; however, further work is needed to determine the usefulness of this metric for quantifying registration accuracy.

  20. In-situ monitoring by reflective high energy electron diffraction during pulsed laser deposition

    NASA Astrophysics Data System (ADS)

    Blank, Dave H. A.; Rijnders, Guus J. H. M.; Koster, Gertjan; Rogalla, Horst

    1999-01-01

    Pulsed laser deposition (PLD) has developed during the past decade from a fast but limited preparation tool towards a competitive thin film deposition technique. One of the advantages above other techniques is the possibility of growth at relative high background pressure. There is a large freedom in choosing which kind of gas. Moreover, in a number of applications, the gaseous species in the background pressure are part of the elements to be grown, e.g., oxygen in the case of high Tc superconductors. However, the advantage of relative high pressures leads to restrictions of using standard diagnostics and monitoring of the film growth, e.g., reflective high energy electron diffraction (RHEED). Here, a PLD chamber including an in-situ RHEED system is presented, which makes it possible to monitor and study the growth at standard PLD parameters. Using a two-stages differential pumped, magnetically shielded, extension tube mounted at the electron gun side and a special designed phosphor screen including CCD camera, real time monitoring by observation of RHEED oscillations could be established at pressures up to 50 Pa. In this paper the latest results on applying this technique on SrTiO 3 and YBa 2Cu 3O 7 will be presented. Additional to the usual diagnostics performed with RHEED, another phenomena can be observed. The pulsed way of deposition, characteristic for PLD, leads to relaxations in the intensity of the diffracted pattern due to the mobility of the deposited material. These relaxation times give extra information about relaxation, crystallization, and nucleation of the deposited material. The presented technique leads to a better understanding of the growth during pulsed laser deposition and, because of the possibility to monitor the growth, will make PLD competitive with other deposition techniques.

  1. Monte-Carlo Simulations of the Nuclear Energy Deposition Inside the CARMEN-1P Differential Calorimeter Irradiated into OSIRIS Reactor

    SciTech Connect

    Amharrak, H.; Reynard-Carette, C.; Carette, M.; Lemaire, M.; Vaglio-Gaudard, C.; Fourmentel, D.; Lyoussi, A.

    2015-07-01

    carried out. A preliminary analysis shows that the numerical results overestimate the measurements by about 20 %. A new approach has been developed in order to estimate the nuclear heating by two methods (energy deposition or KERMA) by considering the whole complete geometry of the sensor. This new approach will contribute to the interpretation of the irradiation campaign and will be useful to improve the out-of-pile calibration procedure of the sensor and its thermal response during irradiations. The aim of this paper is to present simulations made by using MCNP5 Monte-Carlo transport code (using ENDF/B-VI nuclear data library) for the nuclear heating inside the different parts of the calorimeter (head, rod and base). Calculations into two steps will be realized. We will use as an input source in the model new spectra (neutrons, prompt-photons and delayed-photons) calculated with the Monte Carlo code TRIPOLI-4{sup R} inside different experimental channels (water) located into the OSIRIS periphery and used during the CARMEN-1P irradiation campaign. We will consider Neutrons- Photons-Electrons and Photons-Electrons modes. We will begin by a brief description of the differential-calorimeter device geometry. Then the MCNP5 model used for the calculations of nuclear heating inside the calorimeter elements will be introduced. The energy deposition due to the prompt-gamma, delayed-gamma and neutrons, the neutron-activation of the device will be considered. The different components of the nuclear heating inside the different parts of the calorimeter will be detailed. Moreover, a comparison between KERMA and nuclear energy deposition estimations will be given. Finally, a comparison between this total nuclear heating Calculation and Experiment in graphite sample will be determined. (authors)

  2. 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.

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

    SciTech Connect

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

    2016-03-15

    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.

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

    NASA Astrophysics Data System (ADS)

    Goldzak, Tamar; Gilary, Ido; Moiseyev, Nimrod

    2012-05-01

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

  5. 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.

  6. 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.

  7. Electron correlation and relative energy characteristics in nonempirical calculations of complex beryllohydrides of light elements

    SciTech Connect

    Charkin, O.P.; Cimiraglia, R.; Persico, M.; Tomasi, J.

    1987-01-01

    Nonempirical ab initio calculations have been carried out for 15 molecules of simple and complex beryllohydrides and their salts in the SCF approximation and with consideration of the electron correlation in the CIPSI, MP3, and CISD approximations with various basis sets from 6-31G to 6-311G**. The importance of the correlation contributions to the relative energy characteristics (the dissociation energies, the relative energies of alternative geometric configurations, etc.) of these molecules has been analyzed. The effectiveness of the additive approach for the description of the correlation contributions has been analyzed in series of closely related compounds.

  8. 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.

  9. 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.

  10. Quantum calculations of vibrational energies of H3O2- on an ab initio potential.

    PubMed

    Huang, Xinchuan; Braams, Bastiaan J; Carter, Stuart; Bowman, Joel M

    2004-04-28

    We report a full-dimensional potential energy surface for H3O2-, based on fitting 66,965 ab initio electronic energies. A major feature of this potential is a barrier of roughly 200 cm-1 to internal rotation of the two hydroxyl groups about a line connecting the two oxygen atoms and the bridging hydrogen atom. The potential is used in calculations of vibrational energies, performed with the "Reaction Path" version of the code "MULTIMODE". The results are compared to recent infrared messenger experiments and are used to propose interpretations of the experimental results.

  11. 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.

  12. 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

  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. 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.

  15. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Castano, F.; And Others

    1983-01-01

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

  17. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Korneva, L. A.

    1975-01-01

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

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

    PubMed

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

    2012-06-01

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

  20. 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…