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.

Calculation of intrinsic stresses in the diamond-like coatings produced by plasma ion deposition in modes of DC and pulse bias potentials

NASA Astrophysics Data System (ADS)

Kalinichenko, A. A.; Perepelkin, S. S.; Strel'nitskij, V. E.

2015-04-01

The formula derivation for calculation of intrinsic stress in diamond-like coatings deposited from the ion flux in modes of continuous and pulsed potentials in view of process of defects formation is given. The criterion of applicability of obtained formula allowing to determine critical parameters of the pulsed potential mode is suggested. Results of calculation of stresses in diamond-like coatings at deposition of low-energy ions C+ from filtered vacuum arc plasma are adduced. The influence of the bias potential, repetition frequency and pulse duration, on the value of intrinsic stress is discussed. Qualitative agreement of calculated stress and experimental data is stated. The important role of deposition temperature in control of intrinsic stress in deposited coating is noted.

Energy deposition and thermal effects of runaway electrons in ITER-FEAT plasma facing components

NASA Astrophysics Data System (ADS)

Maddaluno, G.; Maruccia, G.; Merola, M.; Rollet, S.

2003-03-01

The profile of energy deposited by runaway electrons (RAEs) of 10 or 50 MeV in International Thermonuclear Experimental Reactor-Fusion Energy Advanced Tokamak (ITER-FEAT) plasma facing components (PFCs) and the subsequent temperature pattern have been calculated by using the Monte Carlo code FLUKA and the finite element heat conduction code ANSYS. The RAE energy deposition density was assumed to be 50 MJ/m 2 and both 10 and 100 ms deposition times were considered. Five different configurations of PFCs were investigated: primary first wall armoured with Be, with and without protecting CFC poloidal limiters, both port limiter first wall options (Be flat tile and CFC monoblock), divertor baffle first wall, armoured with W. The analysis has outlined that for all the configurations but one (port limiter with Be flat tile) the heat sink and the cooling tube beneath the armour are well protected for both RAE energies and for both energy deposition times. On the other hand large melting (W, Be) or sublimation (C) of the surface layer occurs, eventually affecting the PFCs lifetime.

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.

Levelized Cost of Energy Calculator | Energy Analysis | NREL

Science.gov Websites

Levelized Cost of Energy Calculator Levelized Cost of Energy Calculator Transparent Cost Database Button The levelized cost of energy (LCOE) calculator provides a simple calculator for both utility-scale need to be included for a thorough analysis. To estimate simple cost of energy, use the slider controls

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.

Excitation and Ionization Cross Sections for Electron-Beam Energy Deposition in High Temperature Air

DTIC Science & Technology

1987-07-09

are given and compared to existing experimental results or other theoretical approaches. This information can readily be used as input for a deposition...of the doubly-differential, singly- differential and total ionization cross sections which subsequently served to guide theoretical calculations on...coworkers have been leaders in developing a theoretical base for studying electron production and energy deposition in atmospheric gases such as He, N2

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, J; Followill, D; Howell, R

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, titaniummore » 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

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

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.

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.

Auger electron and characteristic energy loss spectra for electro-deposited americium-241

NASA Astrophysics Data System (ADS)

Varma, Matesh N.; Baum, John W.

1983-07-01

Auger electron energy spectra for electro-deposited americium-241 on platinum substrate were obtained using a cylindrical mirror analyzer. Characteristic energy loss spectra for this sample were also obtained at primary electron beam energies of 990 and 390 eV. From these measurements PI, PII, and PIII energy levels for americium-241 are determined. Auger electron energies are compared with theoretically calculated values. Minimum detectability under the present condition of sample preparation and equipment was estimated at approximately 1.2×10-8 g/cm2 or 3.9×10-8 Ci/cm2. Minimum detectability for plutonium-239 under similar conditions was estimated at about 7.2×10-10 Ci/cm2.

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%.

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.

Energy deposition and ion production from thermal oxygen ion precipitation during Cassini's T57 flyby

NASA Astrophysics Data System (ADS)

Snowden, Darci; Smith, Michael; Jimson, Theodore; Higgins, Alex

2018-05-01

Cassini's Radio Science Investigation (RSS) and Langmuir Probe observed abnormally high electron densities in Titan's ionosphere during Cassini's T57 flyby. We have developed a three-dimensional model to investigate how the precipitation of thermal magnetospheric O+ may have contributed to enhanced ion production in Titan's ionosphere. The three-dimensional model builds on previous work because it calculates both the flux of oxygen through Titan's exobase and the energy deposition and ion production rates in Titan's atmosphere. We find that energy deposition rates and ion production rates due to thermal O+ precipitation have a similar magnitude to the rates from magnetospheric electron precipitation and that the simulated ionization rates are sufficient to explain the abnormally high electron densities observed by RSS and Cassini's Langmuir Probe. Globally, thermal O+ deposits less energy in Titan's atmosphere than solar EUV, suggesting it has a smaller impact on the thermal structure of Titan's neutral atmosphere. However, our results indicate that thermal O+ precipitation can have a significant impact on Titan's ionosphere.

Thermal energy storage in granular deposits

NASA Astrophysics Data System (ADS)

Ratuszny, Paweł

2017-10-01

Energy storage technology is crucial for the development of the use of renewable energy sources. This is a substantial constraint, however it can, to some extent, be solved by storing energy in its various forms: electrical, mechanical, chemical and thermal. This article presents the results of research in thermal properties of granular deposits. Correlation between temperature changes in the stores over a period of time and their physical properties has been studied. The results of the research have practical application in designing thermal stores based on bulk materials and ground deposits. Furthermore, the research results are significant for regeneration of the lower ground sources for heat pumps and provide data for designing ground heat exchangers for ventilation systems.

Genetic Algorithm-Based Optimization to Match Asteroid Energy Deposition Curves

NASA Technical Reports Server (NTRS)

Tarano, Ana; Mathias, Donovan; Wheeler, Lorien; Close, Sigrid

2018-01-01

An asteroid entering Earth's atmosphere deposits energy along its path due to thermal ablation and dissipative forces that can be measured by ground-based and spaceborne instruments. Inference of pre-entry asteroid properties and characterization of the atmospheric breakup is facilitated by using an analytic fragment-cloud model (FCM) in conjunction with a Genetic Algorithm (GA). This optimization technique is used to inversely solve for the asteroid's entry properties, such as diameter, density, strength, velocity, entry angle, and strength scaling, from simulations using FCM. The previous parameters' fitness evaluation involves minimizing error to ascertain the best match between the physics-based calculated energy deposition and the observed meteors. This steady-state GA provided sets of solutions agreeing with literature, such as the meteor from Chelyabinsk, Russia in 2013 and Tagish Lake, Canada in 2000, which were used as case studies in order to validate the optimization routine. The assisted exploration and exploitation of this multi-dimensional search space enables inference and uncertainty analysis that can inform studies of near-Earth asteroids and consequently improve risk assessment.

Investigating energy deposition within cell populations using Monte Carlo simulations.

PubMed

Oliver, Patricia A K; Thomson, Rowan M

2018-06-27

In this work, we develop multicellular models of healthy and cancerous human soft tissues, which are used to investigate energy deposition in subcellular targets, quantify the microdosimetric spread in a population of cells, and determine how these results depend on model details. Monte Carlo (MC) tissue models combining varying levels of detail on different length scales are developed: microscopically-detailed regions of interest (>1500 explicitly-modelled cells) are embedded in bulk tissue phantoms irradiated by photons (20 keV to 1.25 MeV). Specific energy (<i>z</i>; energy imparted per unit mass) is scored in nuclei and cytoplasm compartments using the EGSnrc user-code egs_chamber; specific energy mean, <<i>z</i>>, standard deviation, <i>σ</i>_<i>z</i>, and distribution, <i>f</i>(<i>z</i>,<i>D</i>), are calculated for a variety of macroscopic doses, <i>D</i>. MC-calculated <i>f</i>(<i>z</i>,<i>D</i>) are compared with normal distributions having the same mean and standard deviation. For mGy doses, there is considerable variation in energy deposition (microdosimetric spread) throughout a cell population: <i>e</i>.<i>g</i>., for 30 keV photons irradiating melanoma with 7.5 μm cell radius and 3 μm nuclear radius, <i>σ</i>_<i>z</i>/<<i>z</i>> for nuclear targets is 170%, and the fraction of nuclei receiving no energy deposition, <i>f</i>_<i>z</i>=0, is 0.31 for a dose of 10 mGy. If cobalt-60 photons are considered instead, then <i>σ</i>_<i>z</i>/<<i>z</i>> decreases to 84%, and <i>f</i>_<i>z</i>=0 decreases to 0.036. These results correspond to randomly

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

Ionizing Energy Depositions After Fast Neutron Interactions in Silicon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bergmann, Benedikt; Pospisil, Stanislav; Caicedo, Ivan

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

Investigation of energy deposited by femtosecond electron transfer in collisions using hydrated ion nanocalorimetry.

PubMed

Holm, Anne I S; Donald, William A; Hvelplund, Preben; Larsen, Mikkel K; Nielsen, Steen Brøndsted; Williams, Evan R

2008-10-30

Ion nanocalorimetry is used to investigate the internal energy deposited into M (2+)(H 2O) n , M = Mg ( n = 3-11) and Ca ( n = 3-33), upon 100 keV collisions with a Cs or Ne atom target gas. Dissociation occurs by loss of water molecules from the precursor (charge retention) or by capture of an electron to form a reduced precursor (charge reduction) that can dissociate either by loss of a H atom accompanied by water molecule loss or by exclusively loss of water molecules. Formation of bare CaOH (+) and Ca (+) by these two respective dissociation pathways occurs for clusters with n up to 33 and 17, respectively. From the threshold dissociation energies for the loss of water molecules from the reduced clusters, obtained from binding energies calculated using a discrete implementation of the Thomson liquid drop model and from quantum chemistry, estimates of the internal energy deposition can be obtained. These values can be used to establish a lower limit to the maximum and average energy deposition. Not taking into account effects of a kinetic shift, over 16 eV can be deposited into Ca (2+)(H 2O) 33, the minimum energy necessary to form bare CaOH (+) from the reduced precursor. The electron capture efficiency is at least a factor of 40 greater for collisions of Ca (2+)(H 2O) 9 with Cs than with Ne, reflecting the lower ionization energy of Cs (3.9 eV) compared to Ne (21.6 eV). The branching ratio of the two electron capture dissociation pathways differs significantly for these two target gases, but the distributions of water molecules lost from the reduced precursors are similar. These results suggest that the ionization energy of the target gas has a large effect on the electron capture efficiency, but relatively little effect on the internal energy deposited into the ion. However, the different branching ratios suggest that different electronic excited states may be accessed in the reduced precursor upon collisions with these two different target gases.

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.

Mars proton aurora: energy deposition and Lyman-α line profile

NASA Astrophysics Data System (ADS)

Gérard, JC; Hubert, B.; Bisikalo, D. V.; Shematovich, V. I.

2017-09-01

Enhancements of the Lyman-alpha dayglow have been occasionally observed with IUVS on board MAVEN during periods of increased solar wind activity. They are interpreted as signatures of the penetration of energetic protons and H atoms into the Martian atmosphere. We present the results of Monte Carlo simulations of the energy deposition of the proton/H atom beam and the subsequent Lyman-alpha emission. We compare the observed brightness and the altitude of the emission peak with those calculated based on in-situ measurements of the incident energetic protons.

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

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.

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

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.

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.

Simple Levelized Cost of Energy (LCOE) Calculator Documentation | Energy

Science.gov Websites

Analysis | NREL Simple Levelized Cost of Energy (LCOE) Calculator Documentation Simple Levelized Cost of Energy (LCOE) Calculator Documentation Transparent Cost Database Button This is a simple : 1). Cost and Performance Adjust the sliders to suitable values for each of the cost and performance

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.

Mathematical Calculations Of Heat Transfer For The CNC Deposition Platform Based On Chemical Thermal Method

NASA Astrophysics Data System (ADS)

Essa, Mohammed Sh.; Chiad, Bahaa T.; Hussein, Khalil A.

2018-05-01

Chemical thermal deposition techniques are highly depending on deposition platform temperature as well as surface substrate temperatures, so in this research thermal distribution and heat transfer was calculated to optimize the deposition platform temperature distribution, determine the power required for the heating element, to improve thermal homogeneity. Furthermore, calculate the dissipated thermal power from the deposition platform. Moreover, the thermal imager (thermal camera) was used to estimate the thermal destitution in addition to, the temperature allocation over 400cm2 heated plate area. In order to reach a plate temperature at 500 oC, a plate supported with an electrical heater of power (2000 W). Stainless steel plate of 12mm thickness was used as a heated plate and deposition platform and subjected to lab tests using element analyzer X-ray fluorescence system (XRF) to check its elemental composition and found the grade of stainless steel and found to be 316 L. The total heat losses calculated at this temperature was 612 W. Homemade heating element was used to heat the plate and can reach 450 oC with less than 15 min as recorded from the system.as well as the temperatures recorded and monitored using Arduino/UNO microcontroller with cold-junction-compensated K-thermocouple-to-digital converter type MAX6675.

Good practices in free-energy calculations.

PubMed

Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christophe

2010-08-19

As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in a wide range of research areas. Yet, the reliability of these calculations can often be improved significantly if a number of precepts, or good practices, are followed. Although the theory upon which these good practices rely has largely been known for many years, it is 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. In this contribution, the current best practices for carrying out free-energy calculations using free energy perturbation and nonequilibrium work methods are discussed, demonstrating that at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. 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.

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.

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.

Investigation on the correlation between energy deposition and clustered DNA damage induced by low-energy electrons.

PubMed

Liu, Wei; Tan, Zhenyu; Zhang, Liming; Champion, Christophe

2018-05-01

This study presents the correlation between energy deposition and clustered DNA damage, based on a Monte Carlo simulation of the spectrum of direct DNA damage induced by low-energy electrons including the dissociative electron attachment. Clustered DNA damage is classified as simple and complex in terms of the combination of single-strand breaks (SSBs) or double-strand breaks (DSBs) and adjacent base damage (BD). The results show that the energy depositions associated with about 90% of total clustered DNA damage are below 150 eV. The simple clustered DNA damage, which is constituted of the combination of SSBs and adjacent BD, is dominant, accounting for 90% of all clustered DNA damage, and the spectra of the energy depositions correlating with them are similar for different primary energies. One type of simple clustered DNA damage is the combination of a SSB and 1-5 BD, which is denoted as SSB + BD. The average contribution of SSB + BD to total simple clustered DNA damage reaches up to about 84% for the considered primary energies. In all forms of SSB + BD, the SSB + BD including only one base damage is dominant (above 80%). In addition, for the considered primary energies, there is no obvious difference between the average energy depositions for a fixed complexity of SSB + BD determined by the number of base damage, but average energy depositions increase with the complexity of SSB + BD. In the complex clustered DNA damage constituted by the combination of DSBs and BD around them, a relatively simple type is a DSB combining adjacent BD, marked as DSB + BD, and it is of substantial contribution (on average up to about 82%). The spectrum of DSB + BD is given mainly by the DSB in combination with different numbers of base damage, from 1 to 5. For the considered primary energies, the DSB combined with only one base damage contributes about 83% of total DSB + BD, and the average energy deposition is about 106 eV. However, the

Optimization design of energy deposition on single expansion ramp nozzle

NASA Astrophysics Data System (ADS)

Ju, Shengjun; Yan, Chao; Wang, Xiaoyong; Qin, Yupei; Ye, Zhifei

2017-11-01

Optimization design has been widely used in the aerodynamic design process of scramjets. The single expansion ramp nozzle is an important component for scramjets to produces most of thrust force. A new concept of increasing the aerodynamics of the scramjet nozzle with energy deposition is presented. The essence of the method is to create a heated region in the inner flow field of the scramjet nozzle. In the current study, the two-dimensional coupled implicit compressible Reynolds Averaged Navier-Stokes and Menter's shear stress transport turbulence model have been applied to numerically simulate the flow fields of the single expansion ramp nozzle with and without energy deposition. The numerical results show that the proposal of energy deposition can be an effective method to increase force characteristics of the scramjet nozzle, the thrust coefficient CT increase by 6.94% and lift coefficient CN decrease by 26.89%. Further, the non-dominated sorting genetic algorithm coupled with the Radial Basis Function neural network surrogate model has been employed to determine optimum location and density of the energy deposition. The thrust coefficient CT and lift coefficient CN are selected as objective functions, and the sampling points are obtained numerically by using a Latin hypercube design method. The optimized thrust coefficient CT further increase by 1.94%, meanwhile, the optimized lift coefficient CN further decrease by 15.02% respectively. At the same time, the optimized performances are in good and reasonable agreement with the numerical predictions. The findings suggest that scramjet nozzle design and performance can benefit from the application of energy deposition.

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.

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

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…

Energy deposition measurements of single 1H, 4He and 12C ions of therapeutic energies in a silicon pixel detector

NASA Astrophysics Data System (ADS)

Gehrke, T.; Burigo, L.; Arico, G.; Berke, S.; Jakubek, J.; Turecek, D.; Tessonnier, T.; Mairani, A.; Martišíková, M.

2017-04-01

In the field of ion-beam radiotherapy and space applications, measurements of the energy deposition of single ions in thin layers are of interest for dosimetry and imaging. The present work investigates the capability of a pixelated detector Timepix to measure the energy deposition of single ions in therapeutic proton, helium- and carbon-ion beams in a 300 μm-thick sensitive silicon layer. For twelve different incident beams, the measured energy deposition distributions of single ions are compared to the expected energy deposition spectra, which were predicted by detailed Monte Carlo simulations using the FLUKA code. A methodology for the analysis of the measured data is introduced in order to identify and reject signals that are either degraded or caused by multiple overlapping ions. Applying a newly proposed linear recalibration, the energy deposition measurements are in good agreement with the simulations. The twelve measured mean energy depositions between 0.72 MeV/mm and 56.63 MeV/mm in a partially depleted silicon sensor do not deviate more than 7% from the corresponding simulated values. Measurements of energy depositions above 10 MeV/mm with a fully depleted sensor are found to suffer from saturation effects due to the too high per-pixel signal. The utilization of thinner sensors, in which a lower signal is induced, could further improve the performance of the Timepix detector for energy deposition measurements.

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.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2010-12-07

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

SPH Calculations of Comet Shoemaker-Levy-9/Jupiter Impact

NASA Astrophysics Data System (ADS)

Wingate, C. A.; Hoffman, N. M.; Stellingwerf, R. F.

1994-05-01

The impact of Comet Shoemaker-Levy 9 has been simulated in 2D axisymmetric geometry and full 3D using the Los Alamos Smooth Particle Hydrodynamics code (SPHINX). The objective of this study is to calculate energy deposition profiles and fireball evolution histories for a range of comet parameters. We hope to use these results to infer comet properties from observations. The modeling proceeds in two phases. In Phase I, the collision of the incoming fragment, or bolide, is calculated, and its kinetic energy profile is differentiated to give an energy deposition profile. The deposition profile is used as input to Phase II (see companion paper by Stellingwerf et al.) in which the fireball evolution is calculated. Two different bolide densities were simulated, 0.2 g/cm(3) and 0.92 g/cm(3) . The incoming bolide velocity was 60 km/sec and the impact angle was taken to be 45 degrees. Since the calculation is 2D, this means simply that the bolide's depth in the atmosphere is equal to its distance traveled times the cosine of 45 degrees. The baseline calculation assumed a spherical bolide with a diameter of 1 km. Various physical models were used for the bolide including perfect gas equations of state (eos), more realistic eos's and strength of materials. The model for the Jupiter atmosphere was a fit to the Orton atmosphere. The eos for the atmosphere for most of the calculations was taken to be a perfect gas with a gamma of 1.2. A sesame tabular eos was also used. Rather than modeling the entire atmosphere, small sections were modeled using blocks of particles with blocks being shuffled in and out as the calculation progressed. Calculations were done with different size sections to test the sensitivity of the results to this procedure. The results indicate energy deposition for the 0.2 density, 1 km diameter case occurring between 50-200 km. The penetration is seen to increase somewhat as the bolide resolution is improved.

Preliminary topical report on comparison reactor disassembly calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLaughlin, T.P.

1975-11-01

Preliminary results of comparison disassembly calculations for a representative LMFBR model (2100-l voided core) and arbitrary accident conditions are described. The analytical methods employed were the computer programs: FX2- POOL, PAD, and VENUS-II. The calculated fission energy depositions are in good agreement, as are measures of the destructive potential of the excursions, kinetic energy, and work. However, in some cases the resulting fuel temperatures are substantially divergent. Differences in the fission energy deposition appear to be attributable to residual inconsistencies in specifying the comparison cases. In contrast, temperature discrepancies probably stem from basic differences in the energy partition models inherentmore » in the codes. Although explanations of the discrepancies are being pursued, the preliminary results indicate that all three computational methods provide a consistent, global characterization of the contrived disassembly accident. (auth)« less

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

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

PubMed

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

2014-02-01

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

Calculation versus measurement of total energy expenditure.

PubMed

van Lanschot, J J; Feenstra, B W; Vermeij, C G; Bruining, H A

1986-11-01

In acutely ill patients both hypo- and hyperalimentation must be avoided by adjusting caloric intake to total energy expenditure (TEE). We determined the discrepancy between basal energy expenditure (BEE) calculated from the basic Harris-Benedict formula and TEE measured by continuous indirect calorimetry in a heterogeneous group of mechanically ventilated surgical patients. We also compared the accuracy of TEE calculated from the corrected Harris-Benedict formula or estimated by intermittent indirect calorimetry to that of TEE measured by continuous indirect calorimetry. The poor correlation between calculated BEE and measured TEE was significantly (p less than .05) improved by a correction factor based on each patient's clinical condition. The mean absolute difference between calculated TEE and measured TEE was 8.9 +/- 9.6 (SD) %. Calculations were significantly (p less than .05) improved by estimating TEE from two 5-min recording periods, which suggests that continuous indirect calorimetry may not always be necessary to guide caloric replacement.

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

NASA Astrophysics Data System (ADS)

Robertson Handford, C.

1990-08-01

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

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·sin 2β + B·cos 2β, 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

Atomistic calculations of dislocation core energy in aluminium

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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·sin 2β + B·cos 2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

18 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 THE...

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 THE...

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 THE...

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 THE...

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 THE...

Effect of heat treatment on the characteristics of tool steel deposited by the directed energy deposition process

NASA Astrophysics Data System (ADS)

Park, Jun Seok; Lee, Min-Gyu; Cho, Yong-Jae; Sung, Ji Hyun; Jeong, Myeong-Sik; Lee, Sang-Kon; Choi, Yong-Jin; Kim, Da Hye

2016-01-01

The directed energy deposition process has been mainly applied to re-work and the restoration of damaged steel. Differences in material properties between the base and the newly deposited materials are unavoidable, which may affect the mechanical properties and durability of the part. We investigated the effect of heat treatment on the characteristics of tool steel deposited by the DED process. We prepared general tool steel materials of H13 and D2 that were deposited onto heat-treated substrates of H13 and D2, respectively, using a direct metal tooling process. The hardness and microstructure of the deposited steel before and after heat treatment were investigated. The hardness of the deposited H13 steel was higher than that of wrought H13 steel substrate, while that of the deposited D2 was lower than that of wrought D2. The evolution of the microstructures by deposition and heat treatment varied depending on the materials. In particular, the microstructure of the deposited D2 steel after heat treatment consisted of fine carbides in tempered martensite and it is expected that the deposited D2 steel will have isotropic properties and high hardness after heat treatment.

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.

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.

A Lagrangian Approach for Calculating Microsphere Deposition in a One-Dimensional Lung-Airway Model.

PubMed

Vaish, Mayank; Kleinstreuer, Clement

2015-09-01

Using the open-source software openfoam as the solver, a novel approach to calculate microsphere transport and deposition in a 1D human lung-equivalent trumpet model (TM) is presented. Specifically, for particle deposition in a nonlinear trumpetlike configuration a new radial force has been developed which, along with the regular drag force, generates particle trajectories toward the wall. The new semi-empirical force is a function of any given inlet volumetric flow rate, micron-particle diameter, and lung volume. Particle-deposition fractions (DFs) in the size range from 2 μm to 10 μm are in agreement with experimental datasets for different laminar and turbulent inhalation flow rates as well as total volumes. Typical run times on a single processor workstation to obtain actual total deposition results at comparable accuracy are 200 times less than that for an idealized whole-lung geometry (i.e., a 3D-1D model with airways up to 23rd generation in single-path only).

An introduction to best practices in free energy calculations.

PubMed

Shirts, Michael R; Mobley, David L

2013-01-01

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

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.

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.

Studies on the high electronic energy deposition in polyaniline thin films

NASA Astrophysics Data System (ADS)

Deshpande, N. G.; Gudage, Y. G.; Vyas, J. C.; Singh, F.; Sharma, Ramphal

2008-05-01

We report here the physico-chemical changes brought about by high electronic energy deposition of gold ions in HCl doped polyaniline (PANI) thin films. PANI thin films were synthesized by in situ polymerization technique. The as-synthesized PANI thin films of thickness 160 nm were irradiated using Au7+ ion of 100 MeV energy at different fluences, namely, 5 × 1011 ions/cm2 and 5 × 1012 ions/cm2, respectively. A significant change was seen after irradiation in electrical and photo conductivity, which may be related to increased carrier concentration, and structural modifications in the polymer film. In addition, the high electronic energy deposition showed other effects like cross-linking of polymer chains, bond breaking and creation of defect sites. AFM observations revealed mountainous type features in all (before and after irradiation) PANI samples. The average size (diameter) and density of such mountainous clusters were found to be related with the ion fluence. The AFM profiles also showed change in the surface roughness of the films with respect to irradiation, which is one of the peculiarity of the high electronic energy deposition technique.

Energy levels and life times calculations of Mo XXXI

NASA Astrophysics Data System (ADS)

Wajid, Abdul; Jabeen, S.; Husain, Abid

2018-05-01

Fine-structure energy levels belonging to 2p63s2, 2p63s3p, 2p63p2 and 2p63p3d for Mo XXXI have been calculated using the multi-configuration Dirac-Fock method including Quantum electrodynamics (QED) corrections. Most of our calculations of energy levels show good agreement with experimental data available on NIST. Lifetimes for excited levels have also been calculated.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Zongqian; Wang, Kun; Shi, Yuanjie

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 ismore » ∼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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Zongqian; Shi, Yuanjie; Wang, Kun

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, shuntingmore » 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.« less

Light Pipe Energy Savings Calculator

NASA Astrophysics Data System (ADS)

Owens, Erin; Behringer, Ernest R.

2009-04-01

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

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

NASA Astrophysics Data System (ADS)

Dingfelder, Michael

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

SU-G-TeP3-13: The Role of Nanoscale Energy Deposition in the Development of Gold Nanoparticle-Enhanced Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirkby, C; The University of Calgary, Calgary, AB; Koger, B

2016-06-15

Purpose: Gold nanoparticles (GNPs) can enhance radiotherapy effects. The high photoelectric cross section of gold relative to tissue, particularly at lower energies, leads to localized dose enhancement. However in a clinical context, photon energies must also be sufficient to reach a target volume at a given depth. These properties must be balanced to optimize such a therapy. Given that nanoscale energy deposition patterns around GNPs play a role in determining biological outcomes, in this work we seek to establish their role in this optimization process. Methods: The PENELOPE Monte Carlo code was used to generate spherical dose deposition kernels inmore » 1000 nm diameter spheres around 50 nm diameter GNPs in response to monoenergetic photons incident on the GNP. Induced “lesions” were estimated by either a local effect model (LEM) or a mean dose model (MDM). The ratio of these estimates was examined for a range of photon energies (10 keV to 2 MeV), for three sets of linear-quadratic parameters. Results: The models produce distinct differences in expected lesion values, the lower the alpha-beta ratio, the greater the difference. The ratio of expected lesion values remained constant within 5% for energies of 40 keV and above across all parameter sets and rose to a difference of 35% for lower energies only for the lowest alpha-beta ratio. Conclusion: Consistent with other work, these calculations suggest nanoscale energy deposition patterns matter in predicting biological response to GNP-enhanced radiotherapy. However the ratio of expected lesions between the different models is largely independent of energy, indicating that GNP-enhanced radiotherapy scenarios can be optimized in photon energy without consideration of the nanoscale patterns. Special attention may be warranted for energies of 20 keV or below and low alpha-beta ratios.« less

Recipes for free energy calculations in biomolecular systems.

PubMed

Moradi, Mahmoud; Babin, Volodymyr; Sagui, Celeste; Roland, Christopher

2013-01-01

During the last decade, several methods for sampling phase space and calculating various free energies in biomolecular systems have been devised or refined for molecular dynamics (MD) simulations. Thus, state-of-the-art methodology and the ever increasing computer power allow calculations that were forbidden a decade ago. These calculations, however, are not trivial as they require knowledge of the methods, insight into the system under study, and, quite often, an artful combination of different methodologies in order to avoid the various traps inherent in an unknown free energy landscape. In this chapter, we illustrate some of these concepts with two relatively simple systems, a sugar ring and proline oligopeptides, whose free energy landscapes still offer considerable challenges. In order to explore the configurational space of these systems, and to surmount the various free energy barriers, we combine three complementary methods: a nonequilibrium umbrella sampling method (adaptively biased MD, or ABMD), replica-exchange molecular dynamics (REMD), and steered molecular dynamics (SMD). In particular, ABMD is used to compute the free energy surface of a set of collective variables; REMD is used to improve the performance of ABMD, to carry out sampling in space complementary to the collective variables, and to sample equilibrium configurations directly; and SMD is used to study different transition mechanisms.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

1995-12-01

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

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

PubMed Central

Klimovich, Pavel V.; Mobley, David L.

2015-01-01

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 [14], 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 [16]. Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations. PMID:26487189

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.

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

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

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.

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.

An analytical model for calculating microdosimetric distributions from heavy ions in nanometer site targets.

PubMed

Czopyk, L; Olko, P

2006-01-01

The analytical model of Xapsos used for calculating microdosimetric spectra is based on the observation that straggling of energy loss can be approximated by a log-normal distribution of energy deposition. The model was applied to calculate microdosimetric spectra in spherical targets of nanometer dimensions from heavy ions at energies between 0.3 and 500 MeV amu(-1). We recalculated the originally assumed 1/E(2) initial delta electrons spectrum by applying the Continuous Slowing Down Approximation for secondary electrons. We also modified the energy deposition from electrons of energy below 100 keV, taking into account the effective path length of the scattered electrons. Results of our model calculations agree favourably with results of Monte Carlo track structure simulations using MOCA-14 for light ions (Z = 1-8) of energy ranging from E = 0.3 to 10.0 MeV amu(-1) as well as with results of Nikjoo for a wall-less proportional counter (Z = 18).

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

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.

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.

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 Nb 3Sn 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 5×10 34 cm -2s -1.more » 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.« less

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.

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.

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.

S -matrix calculations of energy levels of sodiumlike ions

DOE PAGES

Sapirstein, J.; Cheng, K. T.

2015-06-24

A recent S -matrix-based QED calculation of energy levels of the lithium isoelectronic sequence is extended to the general case of a valence electron outside an arbitrary filled core. Emphasis is placed on modifications of the lithiumlike formulas required because more than one core state is present, and an unusual feature of the two-photon exchange contribution involving autoionizing states is discussed. Here, the method is illustrated with a calculation of the energy levels of sodiumlike ions, with results for 3s 1/2, 3p 1/2, and 3p 3/2 energies tabulated for the range Z = 30 – 100 . Comparison with experimentmore » and other calculations is given, and prospects for extension of the method to ions with more complex electronic structure discussed.« less

Calculating Potential Energy Curves with Quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Powell, Andrew D.; Dawes, Richard

2014-06-01

Quantum Monte Carlo (QMC) is a computational technique that can be applied to the electronic Schrödinger equation for molecules. QMC methods such as Variational Monte Carlo (VMC) and Diffusion Monte Carlo (DMC) have demonstrated the capability of capturing large fractions of the correlation energy, thus suggesting their possible use for high-accuracy quantum chemistry calculations. QMC methods scale particularly well with respect to parallelization making them an attractive consideration in anticipation of next-generation computing architectures which will involve massive parallelization with millions of cores. Due to the statistical nature of the approach, in contrast to standard quantum chemistry methods, uncertainties (error-bars) are associated with each calculated energy. This study focuses on the cost, feasibility and practical application of calculating potential energy curves for small molecules with QMC methods. Trial wave functions were constructed with the multi-configurational self-consistent field (MCSCF) method from GAMESS-US.[1] The CASINO Monte Carlo quantum chemistry package [2] was used for all of the DMC calculations. An overview of our progress in this direction will be given. References: M. W. Schmidt et al. J. Comput. Chem. 14, 1347 (1993). R. J. Needs et al. J. Phys.: Condensed Matter 22, 023201 (2010).

Changes in the frequency distribution of energy deposited in short pathlengths as a function of energy degradation of the primary beam.

NASA Technical Reports Server (NTRS)

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

1972-01-01

The frequency distributions of event size in the deposition of energy over small pathlengths have been measured after penetration of 44.3 MeV protons through various thicknesses of tissue-equivalent material. Results show that particle energy straggling of an initially monoenergetic proton beam after passage through an absorber causes the frequency distributions of energy deposited in short pathlengths of low atomic number materials to remain broad. In all cases investigated, the ratio of the most probable to the average energy losses has been significantly less than unity.

Mechanism and kinetics of electrophoretic deposition of Al{sub 2}O{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarkar, P.; Nicholson, P.S.

1996-06-01

The four main electrophoretic deposition (EPD) mechanisms are discussed and their shortcomings pointed out. The Hamaker constant for Al{sub 2}O{sub 3} in ethanol suspension is determined by modelling the relationship between particle interaction energy and suspension stability. The Derjagun-Landau-Verwey-Overbeek (DLVO) interaction energy curve for Al{sub 2}O{sub 3} particles in ethanol suspension is calculated and the minimum deposition voltage determined. Three probe dc measurements were conducted to explain discrepancies between the calculated and experimentally-observed voltage. A mechanism proposed is based on the DLVO theory and particle-lyosphere destortion/thinning. Kinetic equations for EPD are developed for constant current and constant voltage deposition usingmore » mass balance conditions and verified by experimental data.« less

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brun, J.; Reynard-Carette, C.; Tarchalski, M.

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 themore » 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

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amharrak, H.; Reynard-Carette, C.; Carette, M.

calorimeter were 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)« less

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.

Airfoil deposition model

NASA Technical Reports Server (NTRS)

Kohl, F. J.

1982-01-01

The methodology to predict deposit evolution (deposition rate and subsequent flow of liquid deposits) as a function of fuel and air impurity content and relevant aerodynamic parameters for turbine airfoils is developed in this research. The spectrum of deposition conditions encountered in gas turbine operations includes the mechanisms of vapor deposition, small particle deposition with thermophoresis, and larger particle deposition with inertial effects. The focus is on using a simplified version of the comprehensive multicomponent vapor diffusion formalism to make deposition predictions for: (1) simple geometry collectors; and (2) gas turbine blade shapes, including both developing laminar and turbulent boundary layers. For the gas turbine blade the insights developed in previous programs are being combined with heat and mass transfer coefficient calculations using the STAN 5 boundary layer code to predict vapor deposition rates and corresponding liquid layer thicknesses on turbine blades. A computer program is being written which utilizes the local values of the calculated deposition rate and skin friction to calculate the increment in liquid condensate layer growth along a collector surface.

Free energy calculations of glycosaminoglycan-protein interactions.

PubMed

Gandhi, Neha S; Mancera, Ricardo L

2009-10-01

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Calculations of absorbed fractions in small water spheres for low-energy monoenergetic electrons and the Auger-emitting radionuclides (123)Ι and (125)Ι.

PubMed

Bousis, Christos; Emfietzoglou, Dimitris; Nikjoo, Hooshang

2012-12-01

To calculate the absorbed fraction (AF) of low energy electrons in small tissue-equivalent spherical volumes by Monte Carlo (MC) track structure simulation and assess the influence of phase (liquid water versus density-scaled water vapor) and of the continuous-slowing-down approximation (CSDA) used in semi-analytic calculations. An event-by-event MC code simulating the transport of electrons in both the vapor and liquid phase of water using appropriate electron-water interaction cross sections was used to quantify the energy deposition of low-energy electrons in spherical volumes. Semi-analytic calculations within the CSDA using a convolution integral of the Howell range-energy expressions are also presented for comparison. The AF for spherical volumes of radii from 10-1000 nm are presented for monoenergetic electrons over the energy range 100-10,000 eV and the two Auger-emitting radionuclides (125)I and (123)I. The MC calculated AF for the liquid phase are found to be smaller than those of the (density scaled) gas phase by up to 10-20% for the monoenergetic electrons and 10% for the two Auger-emitters. Differences between the liquid-phase MC results and the semi-analytic CSDA calculations are up to ∼ 55% for the monoenergetic electrons and up to ∼ 35% for the two Auger-emitters. Condensed-phase effects in the inelastic interaction of low-energy electrons with water have a noticeable but relatively small impact on the AF for the energy range and target sizes examined. Depending on the electron energies, the semi-analytic approach may lead to sizeable errors for target sizes with linear dimensions below 1 micron.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lashkov, V. A., E-mail: valerial180150@gmail.com; Karpenko, A. G., E-mail: aspera.2003.ru@mail.ru; Khoronzhuk, R. S.

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 bymore » 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.« less

A Complete Reporting of MCNP6 Validation Results for Electron Energy Deposition in Single-Layer Extended Media for Source Energies <= 1-MeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, David A.; Hughes, Henry Grady

In this paper, we expand on previous validation work by Dixon and Hughes. That is, we present a more complete suite of validation results with respect to to the well-known Lockwood energy deposition experiment. Lockwood et al. measured energy deposition in materials including beryllium, carbon, aluminum, iron, copper, molybdenum, tantalum, and uranium, for both single- and multi-layer 1-D geometries. Source configurations included mono-energetic, mono-directional electron beams with energies of 0.05-MeV, 0.1-MeV, 0.3- MeV, 0.5-MeV, and 1-MeV, in both normal and off-normal angles of incidence. These experiments are particularly valuable for validating electron transport codes, because they are closely represented bymore » simulating pencil beams incident on 1-D semi-infinite slabs with and without material interfaces. Herein, we include total energy deposition and energy deposition profiles for the single-layer experiments reported by Lockwood et al. (a more complete multi-layer validation will follow in another report).« less

Using the fast fourier transform in binding free energy calculations.

PubMed

Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L

2018-04-30

According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Scalable free energy calculation of proteins via multiscale essential sampling

NASA Astrophysics Data System (ADS)

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2010-12-01

A multiscale simulation method, "multiscale essential sampling (MSES)," is proposed for calculating free energy surface of proteins in a sizable dimensional space with good scalability. In MSES, the configurational sampling of a full-dimensional model is enhanced by coupling with the accelerated dynamics of the essential degrees of freedom. Applying the Hamiltonian exchange method to MSES can remove the biasing potential from the coupling term, deriving the free energy surface of the essential degrees of freedom. The form of the coupling term ensures good scalability in the Hamiltonian exchange. As a test application, the free energy surface of the folding process of a miniprotein, chignolin, was calculated in the continuum solvent model. Results agreed with the free energy surface derived from the multicanonical simulation. Significantly improved scalability with the MSES method was clearly shown in the free energy calculation of chignolin in explicit solvent, which was achieved without increasing the number of replicas in the Hamiltonian exchange.

A Theoretical Approach to the Calculation of Annealed Impurity Profiles of Ion Implanted Boron into Silicon.

DTIC Science & Technology

1977-06-01

determined experimentally) and the distribution of energy deposited into nuclear processes by the boron ions. Damage is a product of this energy distri...energy deposited into nuclear processes, k is a constant adjusted to produce the total number of vacancies calculated in Fig. 11, and Tda m in the...profile computed from the energy depos- ited into nuclear processes = time constant for the release of vacancies fr( ,-, vacancy 1.- t ers C (liilibriul

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

NASA Astrophysics Data System (ADS)

Alaei, Parham

2000-11-01

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

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.

Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

PubMed

Nagata, Yuki

2010-02-01

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

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.

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.

Microdosimetry of low-energy electrons.

PubMed

Liamsuwan, Thiansin; Emfietzoglou, Dimitris; Uehara, Shuzo; Nikjoo, Hooshang

2012-12-01

To investigate differences in energy depositions and microdosimetric parameters of low-energy electrons in liquid and gaseous water using Monte Carlo track structure simulations. KURBUC-liq (Kyushu University and Radiobiology Unit Code for liquid water) was used for simulating electron tracks in liquid water. The inelastic scattering cross sections of liquid water were obtained from the dielectric response model of Emfietzoglou et al. (Radiation Research 2005;164:202-211). Frequencies of energy deposited in nanometre-size cylindrical targets per unit absorbed dose and associated lineal energies were calculated for 100-5000 eV monoenergetic electrons and the electron spectrum of carbon K edge X-rays. The results for liquid water were compared with those for water vapour. Regardless of electron energy, there is a limit how much energy electron tracks can deposit in a target. Phase effects on the frequencies of energy depositions are largely visible for the targets with diameters and heights smaller than 30 nm. For the target of 2.3 nm by 2.3 nm (similar to dimension of DNA segments), the calculated frequency- and dose-mean lineal energies for liquid water are up to 40% smaller than those for water vapour. The corresponding difference is less than 12% for the targets with diameters ≥ 30 nm. Condensed-phase effects are non-negligible for microdosimetry of low-energy electrons for targets with sizes smaller than a few tens of nanometres, similar to dimensions of DNA molecular structures and nucleosomes.

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.

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 pK as 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 pKmore » a 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.« less

Measuring the energy deposited by muon bundles of inclined EAS in the NEVOD-DECOR experiment

NASA Astrophysics Data System (ADS)

Kokoulin, R. P.; Bogdanov, A. G.; Barbashina, N. S.; Dushkin, L. I.; Kindin, V. V.; Kompaniets, K. G.; Mannocchi, G.; Petrukhin, A. A.; Saavedra, O.; Trinchero, G.; Khomyakov, V. A.; Khokhlov, S. S.; Chernov, D. V.; Shutenko, V. V.; Yurina, E. A.; Yashin, I. I.

2018-01-01

As part of an in-depth investigation of the muon excess observed in ultrahigh-energy cosmic rays, one needs to measure the energy characteristics of muon component of extensive air showers (EAS). The mean muon energy can be estimated from the energy deposited in the detector by the muon bundles. In the NEVOD-DECOR experiment, the local muon density and the shower-arrival direction are measured with a track-coordinate detector, and the deposited energy is measured in the Cherenkov calorimeter. The results of the measurements carried out in 17400 h of detector operation are compared with those of the simulation based on the CORSIKA package.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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)

SU-E-T-491: Importance of Energy Dependent Protons Per MU Calibration Factors in IMPT Dose Calculations Using Monte Carlo Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Randeniya, S; Mirkovic, D; Titt, U

2014-06-01

Purpose: In intensity modulated proton therapy (IMPT), energy dependent, protons per monitor unit (MU) calibration factors are important parameters that determine absolute dose values from energy deposition data obtained from Monte Carlo (MC) simulations. Purpose of this study was to assess the sensitivity of MC-computed absolute dose distributions to the protons/MU calibration factors in IMPT. Methods: A “verification plan” (i.e., treatment beams applied individually to water phantom) of a head and neck patient plan was calculated using MC technique. The patient plan had three beams; one posterior-anterior (PA); two anterior oblique. Dose prescription was 66 Gy in 30 fractions. Ofmore » the total MUs, 58% was delivered in PA beam, 25% and 17% in other two. Energy deposition data obtained from the MC simulation were converted to Gy using energy dependent protons/MU calibrations factors obtained from two methods. First method is based on experimental measurements and MC simulations. Second is based on hand calculations, based on how many ion pairs were produced per proton in the dose monitor and how many ion pairs is equal to 1 MU (vendor recommended method). Dose distributions obtained from method one was compared with those from method two. Results: Average difference of 8% in protons/MU calibration factors between method one and two converted into 27 % difference in absolute dose values for PA beam; although dose distributions preserved the shape of 3D dose distribution qualitatively, they were different quantitatively. For two oblique beams, significant difference in absolute dose was not observed. Conclusion: Results demonstrate that protons/MU calibration factors can have a significant impact on absolute dose values in IMPT depending on the fraction of MUs delivered. When number of MUs increases the effect due to the calibration factors amplify. In determining protons/MU calibration factors, experimental method should be preferred in MC dose calculations

Center for the Built Environment: Setpoint Energy Savings Calculator

Science.gov Websites

. Arens, and H. Zhang, 2014. Extending air temperature setpoints: Simulated energy savings and design Near-ZNE Buildings Setpoint Energy Savings Calculator UFAD Case Studies UFAD Cooling Design Tool UFAD Cost Analysis UFAD Design Guide UFAD East End UFAD Energy Modeling UFAD Plenum Performance UFAD

Impact of parametric uncertainty on estimation of the energy deposition into an irradiated brain tumor

NASA Astrophysics Data System (ADS)

Taverniers, Søren; Tartakovsky, Daniel M.

2017-11-01

Predictions of the total energy deposited into a brain tumor through X-ray irradiation are notoriously error-prone. We investigate how this predictive uncertainty is affected by uncertainty in both the location of the region occupied by a dose-enhancing iodinated contrast agent and the agent's concentration. This is done within the probabilistic framework in which these uncertain parameters are modeled as random variables. We employ the stochastic collocation (SC) method to estimate statistical moments of the deposited energy in terms of statistical moments of the random inputs, and the global sensitivity analysis (GSA) to quantify the relative importance of uncertainty in these parameters on the overall predictive uncertainty. A nonlinear radiation-diffusion equation dramatically magnifies the coefficient of variation of the uncertain parameters, yielding a large coefficient of variation for the predicted energy deposition. This demonstrates that accurate prediction of the energy deposition requires a proper treatment of even small parametric uncertainty. Our analysis also reveals that SC outperforms standard Monte Carlo, but its relative efficiency decreases as the number of uncertain parameters increases from one to three. A robust GSA ameliorates this problem by reducing this number.

Electron energy deposition in N2 gas

NASA Technical Reports Server (NTRS)

Fox, J. L.; Victor, G. A.

1988-01-01

The processes by which energetic electrons lose energy in a weakly ionized gas of molecular nitrogen are analyzed and calculations are carried out taking into account the discrete nature of the excitation processes. The excitation, ionization, dissociation and heating efficiencies are computed for energies up to 200 eV absorbed in a gas with fractional ionizations varying from 10(-6) to 10(-2). Individual vibrational excitations up to the seventh vibrational level are presented.

Study of microdosimetric energy deposition patterns in tissue-equivalent medium due to low-energy neutron fields using a graphite-walled proportional counter.

PubMed

Waker, A J; Aslam

2011-06-01

To improve radiation protection dosimetry for low-energy neutron fields encountered in nuclear power reactor environments, there is increasing interest in modeling neutron energy deposition in metrological instruments such as tissue-equivalent proportional counters (TEPCs). Along with these computational developments, there is also a need for experimental data with which to benchmark and test the results obtained from the modeling methods developed. The experimental work described in this paper is a study of the energy deposition in tissue-equivalent (TE) medium using an in-house built graphite-walled proportional counter (GPC) filled with TE gas. The GPC is a simple model of a standard TEPC because the response of the counter at these energies is almost entirely due to the neutron interactions in the sensitive volume of the counter. Energy deposition in tissue spheres of diameter 1, 2, 4 and 8 µm was measured in low-energy neutron fields below 500 keV. We have observed a continuously increasing trend in microdosimetric averages with an increase in neutron energy. The values of these averages decrease as we increase the simulated diameter at a given neutron energy. A similar trend for these microdosimetric averages has been observed for standard TEPCs and the Rossi-type, TE, spherical wall-less counter filled with propane-based TE gas in the same energy range. This implies that at the microdosimetric level, in the neutron energy range we employed in this study, the pattern of average energy deposited by starter and insider proton recoil events in the gas is similar to those generated cumulatively by crosser and stopper events originating from the counter wall plus starter and insider recoil events originating in the sensitive volume of a TEPC.

Energy deposition evaluation for ultra-low energy electron beam irradiation systems using calibrated thin radiochromic film and Monte Carlo simulations.

PubMed

Matsui, S; Mori, Y; Nonaka, T; Hattori, T; Kasamatsu, Y; Haraguchi, D; Watanabe, Y; Uchiyama, K; Ishikawa, M

2016-05-01

For evaluation of on-site dosimetry and process design in industrial use of ultra-low energy electron beam (ULEB) processes, we evaluate the energy deposition using a thin radiochromic film and a Monte Carlo simulation. The response of film dosimeter was calibrated using a high energy electron beam with an acceleration voltage of 2 MV and alanine dosimeters with uncertainty of 11% at coverage factor 2. Using this response function, the results of absorbed dose measurements for ULEB were evaluated from 10 kGy to 100 kGy as a relative dose. The deviation between the responses of deposit energy on the films and Monte Carlo simulations was within 15%. As far as this limitation, relative dose estimation using thin film dosimeters with response function obtained by high energy electron irradiation and simulation results is effective for ULEB irradiation processes management.

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

Maximizing energy deposition by shaping few-cycle laser pulses

NASA Astrophysics Data System (ADS)

Gateau, Julien; Patas, Alexander; Matthews, Mary; Hermelin, Sylvain; Lindinger, Albrecht; Kasparian, Jérôme; Wolf, Jean-Pierre

2018-07-01

We experimentally investigate the impact of pulse shape on the dynamics of laser-generated plasma in rare gases. Fast-rising triangular pulses with a slower decay lead to early ionization of the gas and depose energy more efficiently than their temporally reversed counterparts. As a result, in both argon and krypton, the induced shockwave as well as the plasma luminescence are stronger. This is due to an earlier availability of free electrons to undergo inverse Bremsstrahlung on the pulse trailing edge. Our results illustrate the ability of adequately tailored pulse shapes to optimize the energy deposition in gas plasmas.

Energy deposition evaluation for ultra-low energy electron beam irradiation systems using calibrated thin radiochromic film and Monte Carlo simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsui, S., E-mail: smatsui@gpi.ac.jp; Mori, Y.; Nonaka, T.

2016-05-15

For evaluation of on-site dosimetry and process design in industrial use of ultra-low energy electron beam (ULEB) processes, we evaluate the energy deposition using a thin radiochromic film and a Monte Carlo simulation. The response of film dosimeter was calibrated using a high energy electron beam with an acceleration voltage of 2 MV and alanine dosimeters with uncertainty of 11% at coverage factor 2. Using this response function, the results of absorbed dose measurements for ULEB were evaluated from 10 kGy to 100 kGy as a relative dose. The deviation between the responses of deposit energy on the films andmore » Monte Carlo simulations was within 15%. As far as this limitation, relative dose estimation using thin film dosimeters with response function obtained by high energy electron irradiation and simulation results is effective for ULEB irradiation processes management.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riesen, T.K.; Gottofrey, J.; Heiz, H.J.

1996-12-01

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

Injected ion energy dependence of SiC film deposited by low-energy SiC3H9+ ion beam produced from hexamethyldisilane

NASA Astrophysics Data System (ADS)

Yoshimura, Satoru; Sugimoto, Satoshi; Takeuchi, Takae; Murai, Kensuke; Kiuchi, Masato

2018-04-01

We mass-selected SiC3H9+ ions from various fragments produced through the decomposition of hexamethyldisilane, and finally produced low-energy SiC3H9+ ion beams. The ion beams were injected into Si(1 0 0) substrates and the dependence of deposited films on injected ion energy was then investigated. Injected ion energies were 20, 100, or 200 eV. Films obtained were investigated with X-ray diffraction, X-ray photoelectron spectroscopy, and Raman spectroscopy. X-ray diffraction and X-ray photoelectron spectroscopy of the substrates obtained following the injection of 20 eV ions demonstrated the occurrence of silicon carbide film (3C-SiC) deposition. On the other hand, Raman spectroscopy showed that the films deposited by the injection of 100 or 200 eV ions included 3C-SiC plus diamond-like carbon. Ion beam deposition using hexamethyldisilane-derived 20 eV SiC3H9+ ions is an efficient technique for 3C-SiC film formation on Si substrates.

Measuring the dependence of the decay curve on the electron energy deposit in NaI(Tl)

NASA Astrophysics Data System (ADS)

Choong, W.-S.; Bizarri, G.; Cherepy, N. J.; Hull, G.; Moses, W. W.; Payne, S. A.

2011-08-01

We report on the first measurement of the decay times of NaI(Tl) as a function of the deposited electron energy. It has been suggested that the decay curve depends on the ionization density, which is correlated with the electron energy deposit in the scintillator. The ionization creates excitation states, which can decay radiatively and non-radiatively through a number of competing processes. As a result, the rate at which the excitation decays depends on the ionization density. A measurement of the decay curve as a function of the ionization density will allow us to probe the kinetic rates of the competing processes. The Scintillator Light Yield Non-proportionality Characterization Instrument (SLYNCI) measures the electron response of scintillators utilizing fast sampling ADCs to digitize the raw signals from the detectors, and so can provide a measurement of the light pulse shape from the scintillator. Using data collected with the SLYNCI instrument, the intrinsic scintillation profile is extracted on an event-by-event basis by deconvolving the raw signal with the impulse response of the system. Scintillation profiles with the same electron energy deposit are summed to obtain decay curves as a function of the deposited electron energy. The decay time constants are obtained by fitting the decay curves with a two-component exponential decay. While a slight dependence of the decay time constants on the electron energy deposit is observed, the results are not statistically significant.

Quantitative study on the chemical solution deposition of zinc oxysulfide

DOE PAGES

Reinisch, Michael; Perkins, Craig L.; Steirer, K. Xerxes

2015-11-21

Zinc Oxysulfide (ZnOS) has demonstrated potential in the last decade to replace CdS as a buffer layer material since it is a wide-band-gap semiconductor with performance advantages over CdS (E g = 2.4 eV) in the near UV-range for solar energy conversion. However, questions remain on the growth mechanisms of chemical bath deposited ZnOS. In this study, a detailed model is employed to calculate solubility diagrams that describe simple conditions for complex speciation control using only ammonium hydroxide without additional base. For these conditions, ZnOS is deposited via aqueous solution deposition on a quartz crystal microbalance in a continuous flowmore » cell. Data is used to analyze the growth rate dependence on temperature and also to elucidate the effects of dimethylsulfoxide (DMSO) when used as a co-solvent. Activation energies (EA) of ZnOS are calculated for different flow rates and solution compositions. As a result, the measured EA relationships are affected by changes in the primary growth mechanism when DMSO is included.« less

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.

PubMed

Gapsys, Vytautas; de Groot, Bert L

2017-12-12

Nucleotide-sequence-dependent interactions between proteins and DNA are responsible for a wide range of gene regulatory functions. Accurate and generalizable methods to evaluate the strength of protein-DNA binding have long been sought. While numerous computational approaches have been developed, most of them require fitting parameters to experimental data to a certain degree, e.g., machine learning algorithms or knowledge-based statistical potentials. Molecular-dynamics-based free energy calculations offer a robust, system-independent, first-principles-based method to calculate free energy differences upon nucleotide mutation. We present an automated procedure to set up alchemical MD-based calculations to evaluate free energy changes occurring as the result of a nucleotide mutation in DNA. We used these methods to perform a large-scale mutation scan comprising 397 nucleotide mutation cases in 16 protein-DNA complexes. The obtained prediction accuracy reaches 5.6 kJ/mol average unsigned deviation from experiment with a correlation coefficient of 0.57 with respect to the experimentally measured free energies. Overall, the first-principles-based approach performed on par with the molecular modeling approaches Rosetta and FoldX. Subsequently, we utilized the MD-based free energy calculations to construct protein-DNA binding profiles for the zinc finger protein Zif268. The calculation results compare remarkably well with the experimentally determined binding profiles. The software automating the structure and topology setup for alchemical calculations is a part of the pmx package; the utilities have also been made available online at http://pmx.mpibpc.mpg.de/dna_webserver.html .

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.

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.

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.

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.

Atmospheric Energy Deposition Modeling and Inference for Varied Meteoroid Structures

NASA Technical Reports Server (NTRS)

Wheeler, Lorien; Mathias, Donovan; Stokan, Edward; Brown, Peter

2018-01-01

Asteroids populations are highly diverse, ranging from coherent monoliths to loosely-bound rubble piles with a broad range of material and compositional properties. These different structures and properties could significantly affect how an asteroid breaks up and deposits energy in the atmosphere, and how much ground damage may occur from resulting blast waves. We have previously developed a fragment-cloud model (FCM) for assessing the atmospheric breakup and energy deposition of asteroids striking Earth. The approach represents ranges of breakup characteristics by combining progressive fragmentation with releases of variable fractions of debris and larger discrete fragments. In this work, we have extended the FCM to also represent asteroids with varied initial structures, such as rubble piles or fractured bodies. We have used the extended FCM to model the Chelyabinsk, Benesov, Kosice, and Tagish Lake meteors, and have obtained excellent matches to energy deposition profiles derived from their light curves. These matches provide validation for the FCM approach, help guide further model refinements, and enable inferences about pre-entry structure and breakup behavior. Results highlight differences in the amount of small debris vs. discrete fragments in matching the various flare characteristics of each meteor. The Chelyabinsk flares were best represented using relatively high debris fractions, while Kosice and Benesov cases were more notably driven by their discrete fragmentation characteristics, perhaps indicating more cohesive initial structures. Tagish Lake exhibited a combination of these characteristics, with lower-debris fragmentation at high altitudes followed by sudden disintegration into small debris in the lower flares. Results from all cases also suggest that lower ablation coefficients and debris spread rates may be more appropriate for the way in which debris clouds are represented in FCM, offering an avenue for future model refinement.

Simulated Martian pressure cycle based on the sublimation and deposition of polar CO2

NASA Astrophysics Data System (ADS)

Kemppinen, Osku; Paton, Mark; Savijärvi, Hannu; Harri, Ari-Matti

2014-05-01

The Martian atmospheric pressure cycle is driven by sublimation and deposition of CO2 at polar caps. In the thin atmosphere of Mars the surface energy balance and thus the phase changes of CO2 are dominated by radiation. Additionally, because the atmosphere is so thin, the annual polar cap cycle can have a large relative effect on the pressure. In this work we utilize radiative transfer models to calculate the amount of radiation incoming to Martian polar latitudes over each sol of the year, as well as the amount of energy lost from the surface due to thermal radiation. The energy budget calculated in this way allows us to estimate the amount of CO2 sublimating and depositing at each hour of the Martian year. Since virtually all of the sublimated CO2 is believed to enter and stay in the atmosphere until depositing, this estimate allows us to calculate the annual pressure cycle, assuming that the CO2 is distributed approximately evenly over the planet. The model is running with physically plausible parameters and producing encouragingly good fits to in situ measured data made by e.g. Viking landers. In the next phase we will validate the simulation runs against polar ice cap thickness measurements as well as compare the calculated CO2 source and sink strengths to the sources and sinks of global atmospheric models.

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.

Progress in calculating the potential energy surface of H3+.

PubMed

Adamowicz, Ludwik; Pavanello, Michele

2012-11-13

The most accurate electronic structure calculations are performed using wave function expansions in terms of basis functions explicitly dependent on the inter-electron distances. In our recent work, we use such basis functions to calculate a highly accurate potential energy surface (PES) for the H(3)(+) ion. The functions are explicitly correlated Gaussians, which include inter-electron distances in the exponent. Key to obtaining the high accuracy in the calculations has been the use of the analytical energy gradient determined with respect to the Gaussian exponential parameters in the minimization of the Rayleigh-Ritz variational energy functional. The effective elimination of linear dependences between the basis functions and the automatic adjustment of the positions of the Gaussian centres to the changing molecular geometry of the system are the keys to the success of the computational procedure. After adiabatic and relativistic corrections are added to the PES and with an effective accounting of the non-adiabatic effects in the calculation of the rotational/vibrational states, the experimental H(3)(+) rovibrational spectrum is reproduced at the 0.1 cm(-1) accuracy level up to 16,600 cm(-1) above the ground state.

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.

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

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

PubMed

Ogata, Koji; Hatakeyama, Makoto; Nakamura, Shinichiro

2018-02-15

The octanol-water partition coefficient (log P ow ) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the log P ow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆ G water values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of log P ow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted log P ow values.

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

PubMed

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

2014-07-01

The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides. Absorbed dose and stopping cross section for the Auger electrons of 5-18 eV emitted by(125)I within DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure-response curves for induction of DNA strand breaks. For a single decay of(125)I within DNA, the Auger electrons of 5-18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm(3) volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break. Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such

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)

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

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.

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

PubMed

Baudin, Pablo; Kristensen, Kasper

2017-06-07

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).

AFM investigation and optical band gap study of chemically deposited PbS thin films

NASA Astrophysics Data System (ADS)

Zaman, S.; Mansoor, M.; Abubakar; Asim, M. M.

2016-08-01

The interest into deposition of nanocrystalline PbS thin films, the potential of designing and tailoring both the topographical features and the band gap energy (Eg) by controlling growth parameters, has significant technological importance. Nanocrystalline thin films of lead sulfide were grown onto glass substrates by chemical bath deposition (CBD) method. The experiments were carried out by varying deposition temperature. We report on the modification of structural and optical properties as a function of deposition temperature. The morphological changes of the films were analyzed by using SEM and AFM. AFM was also used to calculate average roughness of the films. XRD spectra indicated preferred growth of cubic phase of PbS films in (200) direction with increasing deposition time. Optical properties have been studied by UV-Spectrophotometer. From the diffused reflectance spectra we have calculated the optical Eg shift from 0.649-0.636 eV with increasing deposition time.

Zr-ZrO2 cermet solar coatings designed by modelling calculations and deposited by dc magnetron sputtering

NASA Astrophysics Data System (ADS)

Zhang, Qi-Chu; Hadavi, M. S.; Lee, K.-D.; Shen, Y. G.

2003-03-01

High solar performance Zr-ZrO2 cermet solar coatings were designed using a numerical computer model and deposited experimentally. The layer thickness and Zr metal volume fraction for the Zr-ZrO2 cermet solar selective coatings on a Zr or Al reflector with a surface ZrO2 or Al2O3 anti-reflection layer were optimized to achieve maximum photo-thermal conversion efficiency at 80°C under concentration factors of 1-20 using the downhill simplex method in multi-dimensions in the numerical calculation. The dielectric function and the complex refractive index of Zr-ZrO2 cermet materials were calculated using Sheng's approximation. Optimization calculations show that Al2O3/Zr-ZrO2/Al solar coatings with two cermet layers and three cermet layers have nearly identical solar absorptance, emittance and photo-thermal conversion efficiency that are much better than those for films with one cermet layer. The optimized Al2O3/Zr-ZrO2/Al solar coating film with two cermet layers has a high solar absorptance value of 0.97 and low hemispherical emittance value of 0.05 at 80°C for a concentration factor of 2. The Al2O3/Zr-ZrO2/Al solar selective coatings with two cermet layers were deposited using dc magnetron sputtering technology. During the deposition of Zr-ZrO2 cermet layer, a Zr metallic target was run in a gas mixture of argon and oxygen. By control of oxygen flow rate the different metal volume fractions in the cermet layers were achieved using dc reactive sputtering. A solar absorptance of 0.96 and normal emittance of 0.05 at 80°C were achieved.

A new parallel algorithm of MP2 energy calculations.

PubMed

Ishimura, Kazuya; Pulay, Peter; Nagase, Shigeru

2006-03-01

A new parallel algorithm has been developed for second-order Møller-Plesset perturbation theory (MP2) energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2-16) show that the program has high CPU and parallel efficiency. Timings are presented for two relatively large molecules, taxol (C(47)H(51)NO(14)) and luciferin (C(11)H(8)N(2)O(3)S(2)), the former with the 6-31G* and 6-311G** basis sets (1,032 and 1,484 basis functions, 164 correlated orbitals), and the latter with the aug-cc-pVDZ and aug-cc-pVTZ basis sets (530 and 1,198 basis functions, 46 correlated orbitals). An MP2 energy calculation on C(130)H(10) (1,970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors.

The effect of laser energy on V2O5 thin film growth prepared by laser assisted molecular beam deposition

NASA Astrophysics Data System (ADS)

Abdel Samad, B.; Ashrit, P. V.

2014-09-01

Vanadium pentoxide V2O5 thin films were grown on glass substrates by the LAMBD deposition system with different laser energies. The structure, composition and optical properties of the films have been investigated with atomic force microscopy, x-ray photoemission spectroscopy, ellipsometry and the transmittance analysis. Upon the increase of laser energy, the results showed that the changes in the optical constants are consistent with the thickness changes of the film. The refractive index increases and the absorption coefficient increases when the laser energy increases. The AFM analysis showed a change of the roughness and structure of the deposited films at different laser energies. The prepared films deposited by LAMBD showed interesting properties with correct V2O5 phase without need of annealing after deposition.

Calculation and Measurement of Low-Energy Radiative Moller Scattering

NASA Astrophysics Data System (ADS)

Epstein, Charles; DarkLight Collaboration

2017-09-01

A number of current nuclear physics experiments have come to rely on precise knowledge of electron-electron (Moller) and positron-electron (Bhabha) scattering. Some of these experiments, having lepton beams on targets containing atomic electrons, use these purely-QED processes as normalization. In other scenarios, with electron beams at low energy and very high intensity, Moller scattering and radiative Moller scattering have such enormous cross-sections that the backgrounds they produce must be understood. In this low-energy regime, the electron mass is also not negligible in the calculation of the cross section. This is important, for example, in the DarkLight experiment (100 MeV). As a result, we have developed a new event generator for the radiative Moller and Bhabha processes, with new calculations that keep all terms of the electron mass. The MIT High Voltage Research Laboratory provides us a unique opportunity to study this process experimentally and compare it with our work, at a low beam energy of 2.5 MeV where the effects of the electron mass are significant. We are preparing a dedicated apparatus consisting of a magnetic spectrometer in order to directly measure this process. An overview of the calculation and the status of the experiment will be presented.

Fracture Analysis of MWCNT/Epoxy Nanocomposite Film Deposited on Aluminum Substrate.

PubMed

Her, Shiuh-Chuan; Chien, Pao-Chu

2017-04-13

Multi-walled carbon nanotube (MWCNT) reinforced epoxy films were deposited on an aluminum substrate by a hot-pressing process. Three-point bending tests were performed to determine the Young's modulus of MWCNT reinforced nanocomposite films. Compared to the neat epoxy film, nanocomposite film with 1 wt % of MWCNT exhibits an increase of 21% in the Young's modulus. Four-point-bending tests were conducted to investigate the fracture toughness of the MWCNT/epoxy nanocomposite film deposited on an aluminum substrate with interfacial cracks. Based on the Euler-Bernoulli beam theory, the strain energy in a film/substrate composite beam is derived. The difference of strain energy before and after the propagation of the interfacial crack are calculated, leading to the determination of the strain energy release rate. Experimental test results show that the fracture toughness of the nanocomposite film deposited on the aluminum substrate increases with the increase in the MWCNT content.

Factors affecting energy deposition and expansion in single wire low current experiments

NASA Astrophysics Data System (ADS)

Duselis, Peter U.; Vaughan, Jeffrey A.; Kusse, Bruce R.

2004-08-01

Single wire experiments were performed on a low current pulse generator at Cornell University. A 220 nF capacitor charged to 15-25 kV was used to drive single wire experiments. The capacitor and wire holder were connected in series through an external variable inductor to control the current rise rate. This external series inductance was adjustable from 0.2 to 2 μH. When coupled with the range of charging voltages this results in current rise rates from 5 to 50 A/ns. The current heated the wire through liquid and vapor phases until plasma formed around the wire. Energy deposition and expansion rates were measured as functions of the current rise rate. These results indicated better energy deposition and higher expansion rates with faster current rise rates. Effects of the wire-electrode connection method and wire polarity were also studied.

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

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.

Effect of substrate roughness on the apparent surface free energy of sputter deposited superhydrophobic polytetrafluoroethylene coatings: A comparison of experimental data with different theoretical models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Selvakumar, N.; Barshilia, Harish C.; Rajam, K. S.

2010-07-15

We have studied the effect of substrate roughness on the wettability and the apparent surface free energy (SFE) of sputter deposited polytetrafluoroethylene (PTFE) coatings deposited on untreated glass (average roughness, R{sub a}=2.0 nm), plasma etched glass (R{sub a}=7.4 nm), and sandblasted glass (R{sub a}=4500 nm) substrates. The wettability of the PTFE coatings deposited on substrates with varying roughnesses was evaluated by measuring the apparent contact angle (CA) using a series of probe liquids from nonpolar aprotic to polar protic. The wettability measurements indicate that an apparent water CA of 152 deg. with a sliding angle of 8 deg. was achievedmore » for PTFE coatings deposited on a substrate with R{sub a}=4500 nm. The superhydrophobicity observed in these coatings is attributed to the presence of dual scale roughness, densely packed microstructure and the presence of CF{sub 3} groups. Unlike the bulk PTFE which is mainly dispersive, the sputter deposited PTFE coatings are expected to have some degree of polar component due to the plasma treatment. In order to calculate the dispersive SFE of PTFE coatings, we have used the Girifalco-Good-Fowkes (GGF) method and validated it with the Zisman model. Furthermore, the Owens-Wendt model has been used to calculate the dispersive and the polar components of the apparent SFE of the PTFE coatings. These results are further corroborated using the Fowkes method. Finally, an ''equation of state'' theory proposed by Neumann has been used to calculate the apparent SFE values of the PTFE coatings. The results indicate that the apparent SFE values of the PTFE coatings obtained from the Owens-Wendt and the Fowkes methods are comparable to those obtained from the Neumann's method. The analyses further demonstrate that the GGF and the Zisman methods underestimate the apparent SFE values of the sputter deposited PTFE coatings.« less

Monte Carlo calculation of the sensitivity of a commercial dose calibrator to gamma and beta radiation.

PubMed

Laedermann, Jean-Pascal; Valley, Jean-François; Bulling, Shelley; Bochud, François O

2004-06-01

The detection process used in a commercial dose calibrator was modeled using the GEANT 3 Monte Carlo code. Dose calibrator efficiency for gamma and beta emitters, and the response to monoenergetic photons and electrons was calculated. The model shows that beta emitters below 2.5 MeV deposit energy indirectly in the detector through bremsstrahlung produced in the chamber wall or in the source itself. Higher energy beta emitters (E > 2.5 MeV) deposit energy directly in the chamber sensitive volume, and dose calibrator sensitivity increases abruptly for these radionuclides. The Monte Carlo calculations were compared with gamma and beta emitter measurements. The calculations show that the variation in dose calibrator efficiency with measuring conditions (source volume, container diameter, container wall thickness and material, position of the source within the calibrator) is relatively small and can be considered insignificant for routine measurement applications. However, dose calibrator efficiency depends strongly on the inner-wall thickness of the detector.

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

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.

IMF Control of Alfvénic Energy Transport and Deposition at High Latitudes

NASA Astrophysics Data System (ADS)

Hatch, Spencer M.; LaBelle, James; Lotko, William; Chaston, Christopher C.; Zhang, Binzheng

2017-12-01

We investigate the influence of the interplanetary magnetic field (IMF) clock angle ϕIMF on high-latitude inertial Alfvén wave (IAW) activity in the magnetosphere-ionosphere transition region using Fast Auroral SnapshoT (FAST) satellite observations. We find evidence that negative IMF Bz coincides with nightside IAW power generation and enhanced rates of IAW-associated electron energy deposition, while positive IMF Bz coincides with enhanced dayside wave and electron energy deposition. Large (≳ 5 nT) negative IMF By coincides with enhanced postnoon IAW power, while large positive IMF By coincides with enhanced but relatively weaker prenoon IAW power. For each ϕIMF orientation we compare IAW Poynting flux and IAW-associated electron energy flux distributions with previously published distributions of Alfvénic Poynting flux over ˜2-22 mHz, as well as corresponding wave-driven electron energy deposition derived from Lyon-Fedder-Mobarry global MHD simulations. We also compare IAW Poynting flux distributions with distributions of broad and diffuse electron number flux, categorized using an adaptation of the Newell et al. (2009) precipitation scheme for FAST. Under negative IMF Bz in the vicinity of the cusp (9.5-14.5 magnetic local time), regions of intense dayside IAW power correspond to enhanced diffuse electron number flux but relatively weaker broadband electron precipitation. Differences between cusp region IAW activity and broadband precipitation illustrate the need for additional information, such as fields or pitch angle measurements, to identify the physical mechanisms associated with electron precipitation in the vicinity of the cusp.

Calculations of acceptor ionization energies in GaN

NASA Astrophysics Data System (ADS)

Wang, H.; Chen, A.-B.

2001-03-01

The k.p Hamiltonian and a model potential are used to deduce the acceptor ionization energies in GaN from a systematic study of the chemical trend in GaAs, GaP, and InP. The acceptors studied include Be, Mg, Ca, Zn, and Cd on the cation sites and C, Si, and Ge on the anion sites. Our calculated acceptor ionization energies are estimated to be accurate to better than 10% across the board. The ionization energies of C and Be (152 and 187 meV, respectively) in wurtzite GaN are found to be lower than that of Mg (224 meV). The C was found to behave like the hydrogenic acceptor in all systems and it has the smallest ionization energy among all the acceptors studied.

Removing the barrier to the calculation of activation energies

DOE PAGES

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.

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

PubMed

Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

2016-06-27

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

Calculation of dose contributions of electron and charged heavy particles inside phantoms irradiated by monoenergetic neutron.

PubMed

Satoh, Daiki; Takahashi, Fumiaki; Endo, Akira; Ohmachi, Yasushi; Miyahara, Nobuyuki

2008-09-01

The radiation-transport code PHITS with an event generator mode has been applied to analyze energy depositions of electrons and charged heavy particles in two spherical phantoms and a voxel-based mouse phantom upon neutron irradiation. The calculations using the spherical phantoms quantitatively clarified the type and energy of charged particles which are released through interactions of neutrons with the phantom elements and contribute to the radiation dose. The relative contribution of electrons increased with an increase in the size of the phantom and with a decrease in the energy of the incident neutrons. Calculations with the voxel-based mouse phantom for 2.0-MeV neutron irradiation revealed that the doses to different locations inside the body are uniform, and that the energy is mainly deposited by recoil protons. The present study has demonstrated that analysis using PHITS can yield dose distributions that are accurate enough for RBE evaluation.

Optical model calculations of heavy-ion target fragmentation

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Wilson, J. W.; Cucinotta, F. A.; Norbury, J. W.

1986-01-01

The fragmentation of target nuclei by relativistic protons and heavy ions is described within the context of a simple abrasion-ablation-final-state interaction model. Abrasion is described by a quantum mechanical formalism utilizing an optical model potential approximation. Nuclear charge distributions of the excited prefragments are calculated by both a hypergeometric distribution and a method based upon the zero-point oscillations of the giant dipole resonance. Excitation energies are estimated from the excess surface energy resulting from the abrasion process and the additional energy deposited by frictional spectator interactions of the abraded nucleons. The ablation probabilities are obtained from the EVA-3 computer program. Isotope production cross sections for the spallation of copper targets by relativistic protons and for the fragmenting of carbon targets by relativistic carbon, neon, and iron projectiles are calculated and compared with available experimental data.

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.

Measurement of energy deposited by charged particle beams in composite targets. [0. 5 to 28. 5 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crase, K.; Farley, W.E.; Kruger, H.

1977-11-03

The energies deposited in composite targets by proton beams from 0.8 to 28.5 GeV energy and by an electron beam at 0.5 GeV energy were measured. The targets consisted of various thicknesses of /sup 238/U shower plates backed by a composite detector plate consisting of a 5-cm-thick CH/sub 2/ moderator and a 0.635-cm /sup 238/U plate. The spacing between the shower and detector plates was varied to allow different spreading of the shower between plates. Passive detectors (thermoluminescence dosimeters, Lexan fission track recorders, photographic emulsions, and removable /sup 238/U pieces) were used to measure the fission-fragment dose and the nonfissionmore » dose at various depths and radial positions in the targets. Plots and numerical values of the measured doses are presented for comparison with computer code calculations. To provide a basis for comparison of the effects of different particle beam energies, data along the beam axes are presented as specific dose (cal/g per incident integrated kJ/cm/sup 2/). In general, the higher the incident proton energy, the larger is the dose in the back of the target relative to that in the front.« less

Efficient calculation of the energy of a molecule in an arbitrary electric field

NASA Astrophysics Data System (ADS)

Pulay, Peter; Janowski, Tomasz

In thermodynamic (e.g., Monte Carlo) simulations with electronic embedding, the energy of the active site or solute must be calculated for millions of configurations of the environment (solvent or protein matrix) to obtain reliable statistics. This precludes the use of accurate but expensive ab initio and density functional techniques. Except for the immediate neighbors, the effect of the environment is electrostatic. We show that the energy of a molecule in the irregular field of the environment can be determined very efficiently by expanding the electric potential in known functions, and precalculating the first and second order response of the molecule to the components of the potential. These generalized multipole moments and polarizabilities allow the calculation of the energy of the system without further ab initio calculations. Several expansion functions were explored: polynomials, distributed inverse powers, and sine functions. The latter provide the numerically most stable fit but require new types of integrals. Distributed inverse powers can be simulated using dummy atoms, and energies calculated this way provide a very good approximation to the actual energies in the field of the environment.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Development of a quantum mechanics-based free-energy perturbation method: use in the calculation of relative solvation free energies.

PubMed

Reddy, M Rami; Singh, U C; Erion, Mark D

2004-05-26

Free-energy perturbation (FEP) is considered the most accurate computational method for calculating relative solvation and binding free-energy differences. Despite some success in applying FEP methods to both drug design and lead optimization, FEP calculations are rarely used in the pharmaceutical industry. One factor limiting the use of FEP is its low throughput, which is attributed in part to the dependence of conventional methods on the user's ability to develop accurate molecular mechanics (MM) force field parameters for individual drug candidates and the time required to complete the process. In an attempt to find an FEP method that could eventually be automated, we developed a method that uses quantum mechanics (QM) for treating the solute, MM for treating the solute surroundings, and the FEP method for computing free-energy differences. The thread technique was used in all transformations and proved to be essential for the successful completion of the calculations. Relative solvation free energies for 10 structurally diverse molecular pairs were calculated, and the results were in close agreement with both the calculated results generated by conventional FEP methods and the experimentally derived values. While considerably more CPU demanding than conventional FEP methods, this method (QM/MM-based FEP) alleviates the need for development of molecule-specific MM force field parameters and therefore may enable future automation of FEP-based calculations. Moreover, calculation accuracy should be improved over conventional methods, especially for calculations reliant on MM parameters derived in the absence of experimental data.

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

NASA Astrophysics Data System (ADS)

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

1982-06-01

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

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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

PubMed

Muddana, Hari S; Gilson, Michael K

2012-06-12

The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

Monte Carlo charged-particle tracking and energy deposition on a Lagrangian mesh.

PubMed

Yuan, J; Moses, G A; McKenty, P W

2005-10-01

A Monte Carlo algorithm for alpha particle tracking and energy deposition on a cylindrical computational mesh in a Lagrangian hydrodynamics code used for inertial confinement fusion (ICF) simulations is presented. The straight line approximation is used to follow propagation of "Monte Carlo particles" which represent collections of alpha particles generated from thermonuclear deuterium-tritium (DT) reactions. Energy deposition in the plasma is modeled by the continuous slowing down approximation. The scheme addresses various aspects arising in the coupling of Monte Carlo tracking with Lagrangian hydrodynamics; such as non-orthogonal severely distorted mesh cells, particle relocation on the moving mesh and particle relocation after rezoning. A comparison with the flux-limited multi-group diffusion transport method is presented for a polar direct drive target design for the National Ignition Facility. Simulations show the Monte Carlo transport method predicts about earlier ignition than predicted by the diffusion method, and generates higher hot spot temperature. Nearly linear speed-up is achieved for multi-processor parallel simulations.

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

NASA Astrophysics Data System (ADS)

Dalal, Shakeel; Fakhraai, Zahra; Ediger, Mark

2014-03-01

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

Influence of Biochar on Deposition and Release of Clay Colloids in Saturated Porous Media.

PubMed

Haque, Muhammad Emdadul; Shen, Chongyang; Li, Tiantian; Chu, Haoxue; Wang, Hong; Li, Zhen; Huang, Yuanfang

2017-11-01

Although the potential application of biochar in soil remediation has been recognized, the effect of biochar on the transport of clay colloids, and accordingly the fate of colloid-associated contaminants, is unclear to date. This study conducted saturated column experiments to systematically examine transport of clay colloids in biochar-amended sand porous media in different electrolytes at different ionic strengths. The obtained breakthrough curves were simulated by the convection-diffusion equation, which included a first-order deposition and release terms. The deposition mechanisms were interpreted by calculating Derjaguin-Landau-Verwey-Overbeek interaction energies. A linear relationship between the simulated deposition rate or the attachment efficiency and the fraction of biochar was observed ( ≥ 0.91), indicating more favorable deposition in biochar than in sand. The interaction energy calculations show that the greater deposition in biochar occurs because the half-tube-like cavities on the biochar surfaces favor deposition in secondary minima and the nanoscale physical and chemical heterogeneities on the biochar surfaces increase deposition in primary minima. The deposited clay colloids in NaCl can be released by reduction of ionic strength, whereas the presence of a bivalent cation (Ca) results in irreversible deposition due to the formation of cation bridging between the colloids and biochar surfaces. The deposition and release of clay colloids on or from biochar surfaces not only change their mobilizations in the soil but also influence the efficiency of the biochar for removal of pollutants. Therefore, the influence of biochar on clay colloid transport must be considered before application of the biochar in soil remediation. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Comparison of feed energy costs of maintenance, lean deposition, and fat deposition in three lines of mice selected for heat loss.

PubMed

Eggert, D L; Nielsen, M K

2006-02-01

Three replications of mouse selection populations for high heat loss (MH), low heat loss (ML), and a nonselected control (MC) were used to estimate the feed energy costs of maintenance and gain and to test whether selection had changed these costs. At 21 and 49 d of age, mice were weighed and subjected to dual x-ray densitometry measurement for prediction of body composition. At 21 d, mice were randomly assigned to an ad libitum, an 80% of ad libitum, or a 60% of ad libitum feeding group for 28-d collection of individual feed intake. Data were analyzed using 3 approaches. The first approach was an attempt to partition energy intake between costs for maintenance, fat deposition, and lean deposition for each replicate, sex, and line by multiple regression of feed intake on the sum of daily metabolic weight (kg(0.75)), fat gain, and lean gain. Approach II was a less restrictive attempt to partition energy intake between costs for maintenance and total gain for each replicate, sex, and line by multiple regression of feed intake on the sum of daily metabolic weight and total gain. Approach III used multiple regression on the entire data set with pooled regressions on fat and lean gains, and subclass regressions for maintenance. Contrasts were conducted to test the effect of selection (MH - ML) and asymmetry of selection [(MH + ML)/2 - MC] for the various energy costs. In approach I, there were no differences between lines for costs of maintenance, fat deposition, or protein deposition, but we question our ability to estimate these accurately. In approach II, selection changed both cost of maintenance (P = 0.03) and gain (P = 0.05); MH mice had greater per unit costs than ML mice for both. Asymmetry of the selection response was found in approach II for the cost of maintenance (P = 0.06). In approach III, the effect of selection (P < 0.01) contributed to differences in the maintenance cost, but asymmetry of selection (P > 0.17) was not evident. Sex effects were found for

Light absorption and excitation energy transfer calculations in primitive photosynthetic bacteria

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

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.

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.

Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems

NASA Astrophysics Data System (ADS)

Swinburne, Thomas D.; Marinica, Mihai-Cosmin

2018-03-01

The calculation of free energy differences for thermally activated mechanisms in the solid state are routinely hindered by the inability to define a set of collective variable functions that accurately describe the mechanism under study. Even when possible, the requirement of descriptors for each mechanism under study prevents implementation of free energy calculations in the growing range of automated material simulation schemes. We provide a solution, deriving a path-based, exact expression for free energy differences in the solid state which does not require a converged reaction pathway, collective variable functions, Gram matrix evaluations, or probability flux-based estimators. The generality and efficiency of our method is demonstrated on a complex transformation of C 15 interstitial defects in iron and double kink nucleation on a screw dislocation in tungsten, the latter system consisting of more than 120 000 atoms. Both cases exhibit significant anharmonicity under experimentally relevant temperatures.

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.

Texturing effects in molybdenum and aluminum nitride films correlated to energetic bombardment during sputter deposition

NASA Astrophysics Data System (ADS)

Drüsedau, T. P.; Koppenhagen, K.; Bläsing, J.; John, T.-M.

Molybdenum films sputter-deposited at low pressure show a (110) to (211) texture turnover with increasing film thickness, which is accompanied by a transition from a fiber texture to a mosaic-like texture. The degree of (002) texturing of sputtered aluminum nitride (AlN) films strongly depends on nitrogen pressure in Ar/N2 or in a pure N2 atmosphere. For the understanding of these phenomena, the power density at the substrate during sputter deposition was measured by a calorimetric method and normalized to the flux of deposited atoms. For the deposition of Mo films and various other elemental films, the results of the calorimetric measurements are well described by a model. This model takes into account the contributions of plasma irradiation, the heat of condensation and the kinetic energy of sputtered atoms and reflected Ar neutrals. The latter two were calculated by TRIM.SP Monte Carlo simulations. An empirical rule is established showing that the total energy input during sputter deposition is proportional to the ratio of target atomic mass to sputtering yield. For the special case of a circular planar magnetron the radial dependence of the Mo and Ar fluxes and related momentum components at the substrate were calculated. It is concluded that mainly the lateral inhomogeneous radial momentum component of the Mo atoms is the cause of the in-plane texturing. For AlN films, maximum (002) texturing appears at about 250 eV per atom energy input.

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

Improvements to the nuclear model code GNASH for cross section calculations at higher energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, P.G.; Chadwick, M.B.

1994-05-01

The nuclear model code GNASH, which in the past has been used predominantly for incident particle energies below 20 MeV, has been modified extensively for calculations at higher energies. The model extensions and improvements are described in this paper, and their significance is illustrated by comparing calculations with experimental data for incident energies up to 160 MeV.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezaee, Mohammad, E-mail: Mohammad.Rezaee@USherbrooke.ca; Hunting, Darel J.; Sanche, Léon

2014-07-15

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

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

PubMed Central

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

2015-01-01

dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide. PMID:24989405

High voltage electrophoretic deposition for electrochemical energy storage and other applications

NASA Astrophysics Data System (ADS)

Santhanagopalan, Sunand

High voltage electrophoretic deposition (HVEPD) has been developed as a novel technique to obtain vertically aligned forests of one-dimensional nanomaterials for efficient energy storage. The ability to control and manipulate nanomaterials is critical for their effective usage in a variety of applications. Oriented structures of one-dimensional nanomaterials provide a unique opportunity to take full advantage of their excellent mechanical and electrochemical properties. However, it is still a significant challenge to obtain such oriented structures with great process flexibility, ease of processing under mild conditions and the capability to scale up, especially in context of efficient device fabrication and system packaging. This work presents HVEPD as a simple, versatile and generic technique to obtain vertically aligned forests of different one-dimensional nanomaterials on flexible, transparent and scalable substrates. Improvements on material chemistry and reduction of contact resistance have enabled the fabrication of high power supercapacitor electrodes using the HVEPD method. The investigations have also paved the way for further enhancements of performance by employing hybrid material systems and AC/DC pulsed deposition. Multi-walled carbon nanotubes (MWCNTs) were used as the starting material to demonstrate the HVEPD technique. A comprehensive study of the key parameters was conducted to better understand the working mechanism of the HVEPD process. It has been confirmed that HVEPD was enabled by three key factors: high deposition voltage for alignment, low dispersion concentration to avoid aggregation and simultaneous formation of holding layer by electrodeposition for reinforcement of nanoforests. A set of suitable parameters were found to obtain vertically aligned forests of MWCNTs. Compared with their randomly oriented counterparts, the aligned MWCNT forests showed better electrochemical performance, lower electrical resistance and a capability to

The effect of energy and momentum transfer during magnetron sputter deposition of yttrium oxide thin films

NASA Astrophysics Data System (ADS)

Xia, Jinjiao; Liang, Wenping; Miao, Qiang; Depla, Diederik

2018-05-01

The influence of the ratio between the energy and the deposition flux, or the energy per arriving atom, on the growth of Y2O3 sputter deposited thin films has been studied. The energy per arriving atom has been varied by the adjustment of the discharge power, and/or the target-to-substrate distance. The relationship between the energy per arriving atom and the phase evolution, grain size, microstructure, packing density and residual stress was investigated in detail. At low energy per arriving atom, the films consist of the monoclinic B phase with a preferential (1 1 1) orientation. A minority cubic C phase appears at higher energy per arriving atom. A study of the thin film cross sections showed for all films straight columns throughout the thickness, typically for a zone II microstructure. The intrinsic stress is compressive, and increases with increasing energy per atom. The same trend is observed for the film density. Simulations show that the momentum transfer per arriving atom also scales with the energy per arriving atom. Hence, the interpretation of the observed trends as a function of the energy per arriving atom must be treated with care.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

PubMed

Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-03-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

NASA Astrophysics Data System (ADS)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Storm phase-partitioned rates and budgets of global Alfvénic energy deposition, electron precipitation, and ion outflow

NASA Astrophysics Data System (ADS)

Hatch, Spencer M.; LaBelle, James; Chaston, Christopher C.

2018-01-01

We review the role of Alfvén waves in magnetosphere-ionosphere coupling during geomagnetically active periods, and use three years of high-latitude FAST satellite observations of inertial Alfvén waves (IAWs) together with 55 years of tabulated measurements of the Dst index to answer the following questions: 1) How do global rates of IAW-related energy deposition, electron precipitation, and ion outflow during storm main phase and storm recovery phase compare with global rates during geomagnetically quiet periods? 2) What fraction of net IAW-related energy deposition, electron precipitation, and ion outflow is associated with storm main phase and storm recovery phase; that is, how are these budgets partitioned by storm phase? We find that during the period between October 1996 and November 1999, rates of IAW-related energy deposition, electron precipitation, and ion outflow during geomagnetically quiet periods are increased by factors of 4-5 during storm phases. We also find that ∼62-68% of the net Alfvénic energy deposition, electron precipitation, and ion outflow in the auroral ionosphere occurred during storm main and recovery phases, despite storm phases comprising only 31% of this period. In particular storm main phase, which comprised less than 14% of the three-year period, was associated with roughly a third of the total Alfvénic energy input and ion outflow in the auroral ionosphere. Measures of geomagnetic activity during the IAW study period fall near corresponding 55-year median values, from which we conclude that each storm phase is associated with a fraction of total Alfvénic energy, precipitation, and outflow budgets in the auroral ionosphere that is, in the long term, probably as great or greater than the fraction associated with geomagnetic quiescence for all times except possibly those when geomagnetic activity is protractedly weak, such as solar minimum. These results suggest that the budgets of IAW-related energy deposition, electron

4He binding energy calculation including full tensor-force effects

NASA Astrophysics Data System (ADS)

Fonseca, A. C.

1989-09-01

The four-body equations of Alt, Grassberger, and Sandhas are solved in the version where the (2)+(2) subamplitudes are treated exactly by convolution, using one-term separable Yamaguchy nucleon-nucleon potentials in the 1S0 and 3S1-3D1 channels. The resulting jp=1/2+ and (3/2+ three-body subamplitudes are represented in a separable form using the energy-dependent pole expansion. Converged bound-state results are calculated for the first time using the full interaction, and are compared with those obtained from a simplified treatment of the tensor force. The Tjon line that correlates three-nucleon and four-nucleon binding energies is shown using different nucleon-nucleon potentials. In all calculations the Coulomb force has been neglected.

FINITE-DIFFERENCE ELECTROMAGNETIC DEPOSITION/THERMOREGULATORY MODEL: COMPARISON BETWEEN THEORY AND MEASUREMENTS (JOURNAL VERSION)

EPA Science Inventory

The rate of the electromagnetic energy deposition and the resultant thermoregulatory response of a block model of a squirrel monkey exposed to plane-wave fields at 350 MHz were calculated using a finite-difference procedure. Noninvasive temperature measurements in live squirrel m...

Relativistic calculation of correlational energy for a helium-like atom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palchikov, V.G.

This paper presents an analytical method for calculating the firstorder correlational energy from the electron interaction, taking account of lag effects. Explicit analytical expressions are obtained for radial matrix elements. The nonrelativistic limit is investigated. The given method may be used to calculate correlation effects in higher orders of perturbation theory (second and higher orders with respect to 1/z) using the Strum expansion for the Coulomb Green's functions.

Calculation of energy costs of composite biomass stirring at biogas stations

NASA Astrophysics Data System (ADS)

Suslov, D. Yu; Temnikov, D. O.

2018-03-01

The paper is devoted to the study of the equipment to produce biogas fuel from organic wastes. The bioreactor equipped with a combined stirring system ensuring mechanical and bubbling stirring is designed. The method of energy cost calculation of the combined stirring system with original design is suggested. The received expressions were used in the calculation of the stirring system installed in the 10 m3 bioreactor: power consumed by the mixer during the start-up period made Nz =9.03 kW, operating power of the mixer made NE =1.406 kW, compressor power for bubbling stirring made NC =18.5 kW. Taking into account the operating mode of single elements of the stirring system, the energy cost made 4.38% of the total energy received by the biogas station.

Study of Z scaling of runaway electron plateau final loss energy deposition into wall of DIII-D

DOE PAGES

Hollmann, Eric M.; Commaux, Nicolas; Eidietis, Nicholas; ...

2017-06-12

Here, controlled runaway electron (RE) plateau-wall strikes with different initial impurity levels are used to study the effect of background plasma ion charge Z (resistivity) on RE-­wall loss dynamics. It is found that Joule heating (magnetic to kinetic energy conversion) during the final loss does not go up monotonically with increasing Z, but peaks at intermediate Z ~ 6. Joule heating and overall time scales of the RE final loss are found to be reasonably well-described by a basic 0D coupled-circuit model, with only the loss time as a free parameter. This loss time is found to be fairly wellmore » correlated with the avalanche time, possibly suggesting that the RE final loss rate is limited by the avalanche rate. First attempts at measuring total energy deposition to the vessel walls by REs during the final loss are made. At higher plasma impurity levels Z > 5, energy deposition to the wall appears be consistent with modeling, at least within the large uncertainties of the measurement. At low impurity levels Z < 5, however, local energy deposition appears around 5-­20× less than expected, suggesting that the RE energy dissipation at low Z is not fully understood.« less

Study of Z scaling of runaway electron plateau final loss energy deposition into wall of DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hollmann, Eric M.; Commaux, Nicolas; Eidietis, Nicholas

Here, controlled runaway electron (RE) plateau-wall strikes with different initial impurity levels are used to study the effect of background plasma ion charge Z (resistivity) on RE-­wall loss dynamics. It is found that Joule heating (magnetic to kinetic energy conversion) during the final loss does not go up monotonically with increasing Z, but peaks at intermediate Z ~ 6. Joule heating and overall time scales of the RE final loss are found to be reasonably well-described by a basic 0D coupled-circuit model, with only the loss time as a free parameter. This loss time is found to be fairly wellmore » correlated with the avalanche time, possibly suggesting that the RE final loss rate is limited by the avalanche rate. First attempts at measuring total energy deposition to the vessel walls by REs during the final loss are made. At higher plasma impurity levels Z > 5, energy deposition to the wall appears be consistent with modeling, at least within the large uncertainties of the measurement. At low impurity levels Z < 5, however, local energy deposition appears around 5-­20× less than expected, suggesting that the RE energy dissipation at low Z is not fully understood.« less

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.

Scaling of Energy Deposition in Fast Ignition Targets

NASA Astrophysics Data System (ADS)

Campbell, R. B.; Welch, Dale

2005-10-01

We examine the scaling to ignition of the energy deposition of laser generated electrons in compressed fast ignition cores. Relevant cores have densities of several hundred g/cm^3, with a few keV initial temperature. As the laser intensities increase approaching ignition systems, on the order of a few 10^21W/cm^2, the hot electron energies expected to approach 100MeV[1]. Most certainly anomalous processes must play a role in the energy transfer, but the exact nature of these processes, as well as a practical way to model them, remain open issues. Traditional PIC explicit methods are limited to low densities on current and anticipated computing platforms, so the study of relevant parameter ranges has received so far little attention. We use LSP[2] to examine a relativistic electron beam (presumed generated from a laser plasma interaction) of legislated energy and angular distribution is injected into a 3D block of compressed DT. Collective effects will determine the stopping, most likely driven by magnetic field filamentation. The scaling of the stopping as a function of block density and temperature, as well as hot electron current and laser intensity is presented. Sub-grid models may be profitably used and degenerate effects included in the solution of this problem. Sandia is operated by Sandia Corporation, for the USDOE. [1] A. Pukhov, et. al., Phys. Plas. 6, p2847 (1999) [2] D. R. Welch et al., Comput. Phys.Commun. 164, p183 (2004).

Towards accurate free energy calculations in ligand protein-binding studies.

PubMed

Steinbrecher, Thomas; Labahn, Andreas

2010-01-01

Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties of biomolecule binding, would be invaluable in the study of biological systems. In addition, as the mode of action of many pharmaceuticals is based upon their inhibition or activation of biomolecule targets, predictive models of small molecule receptor binding are very helpful tools in rational drug design. Since the goal here is normally to design a new compound with a high inhibition strength, one of the most important thermodynamic properties is the binding free energy DeltaG(0). The prediction of binding constants has always been one of the major goals in the field of computational chemistry, because the ability to reliably assess a hypothetical compound's binding properties without having to synthesize it first would save a tremendous amount of work. The different approaches to this question range from fast and simple empirical descriptor methods to elaborate simulation protocols aimed at putting the computation of free energies onto a solid foundation of statistical thermodynamics. While the later methods are still not suited for the screenings of thousands of compounds that are routinely performed in computational drug design studies, they are increasingly put to use for the detailed study of protein ligand interactions. This review will focus on molecular mechanics force field based free energy calculations and their application to the study of protein ligand interactions. After a brief overview of other popular methods for the calculation of free energies, we will describe recent advances in methodology and a variety of exemplary studies of molecular dynamics

Moderation of near-field pressure over a supersonic flight model using laser-pulse energy deposition

NASA Astrophysics Data System (ADS)

Furukawa, D.; Aoki, Y.; Iwakawa, A.; Sasoh, A.

2016-05-01

The impact of a thermal bubble produced by energy deposition on the near-field pressure over a Mach 1.7 free-flight model was experimentally investigated using an aeroballistic range. A laser pulse from a transversely excited atmospheric (TEA) CO2 laser was sent into a test chamber with 68 kPa ambient pressure, focused 10 mm below the flight path of a conically nosed cylinder with a diameter of 10 mm. The pressure history, which was measured 150 mm below the flight path along the acoustic ray past the bubble, exhibited precursory pressure rise and round-off peak pressure, thereby demonstrating the proof-of-concept of sonic boom alleviation using energy deposition.

Calculation of the effective dose from natural radioactivity in soil using MCNP code.

PubMed

Krstic, D; Nikezic, D

2010-01-01

Effective dose delivered by photon emitted from natural radioactivity in soil was calculated in this work. Calculations have been done for the most common natural radionuclides in soil (238)U, (232)Th series and (40)K. A ORNL human phantoms and the Monte Carlo transport code MCNP-4B were employed to calculate the energy deposited in all organs. The effective dose was calculated according to ICRP 74 recommendations. Conversion factors of effective dose per air kerma were determined. Results obtained here were compared with other authors. Copyright 2009 Elsevier Ltd. All rights reserved.

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

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. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

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

Reconstructing Tsunami Flow Speed from Sedimentary Deposits

NASA Astrophysics Data System (ADS)

Jaffe, B. E.; Gelfenbaum, G. R.

2014-12-01

Paleotsunami deposits contain information about the flow that created them that can be used to reconstruct tsunami flow speed and thereby improving assessment of tsunami hazard. We applied an inverse tsunami sediment transport model to sandy deposits near Sendai Airport, Japan, that formed during the 11 March 2011 Tohoku-oki tsunami to test model performance and explore the spatial variations in tsunami flow speed. The inverse model assumes the amount of suspended sediment in the water column is in equilibrium with local flow speed and that sediment transport convergences, primarily from bedload transport, do not contribute significantly to formation of the portion of the deposit we identify as formed by sediment settling out of suspension. We interpret massive or inversely graded intervals as forming from sediment transport convergences and do not model them. Sediment falling out of suspension forms a specific type of normal grading, termed 'suspension' grading, where the entire grain size distribution shifts to finer sizes higher up in a deposit. Suspension grading is often observed in deposits of high-energy flows, including turbidity currents and tsunamis. The inverse model calculates tsunami flow speed from the thickness and bulk grain size of a suspension-graded interval. We identified 24 suspension-graded intervals from 7 trenches located near the Sendai Airport from ~250-1350 m inland from the shoreline. Flow speeds were highest ~500 m from the shoreline, landward of the forested sand dunes where the tsunami encountered lower roughness in a low-lying area as it traveled downslope. Modeled tsunami flow speeds range from 2.2 to 9.0 m/s. Tsunami flow speeds are sensitive to roughness, which is unfortunately poorly constrained. Flow speed calculated by the inverse model was similar to those calculated from video taken from a helicopter about 1-2 km inland. Deposit reconstructions of suspension-graded intervals reproduced observed upward shifts in grain size

Controlled energy deposition and void-like modification inside transparent solids by two-color tightly focused femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Potemkin, Fedor; Mareev, Evgeniy; Bezsudnova, Yulia; Platonenko, Victor; Bravy, Boris; Gordienko, Vyacheslav

2017-04-01

We report a bulk void-like micromodification of fused silica using two-color μJ-energy level tightly focused (NA = 0.5) co-propagating seeding (visible, 0.62 μm) and heating (near-IR, 1.24 μm) femtosecond laser pulses with online third harmonic diagnostics of created microplasmas as well as subsequent laser-induced void-like defects. It has been shown experimentally and theoretically that production of seeding electrons through multiphoton ionization by visible laser pulses paves the way for controllability of the energy deposition and laser-induced micromodification via carrier heating by delayed infrared laser pulses inside the material. Experimental results demonstrate wide possibilities to increase the density of energy deposited up to 6 kJ cm-3 inside the dielectric by tight focusing of two color fs-laser pulses and elliptical polarization for infrared heating fs-laser pulses. The developed theoretical approach predicts the enhancement of deposited energy density up to 9 kJ cm-3 using longer (mid-IR) wavelengths for heating laser pulses.

Graphical Calculation of Estimated Energy Expenditure in Burn Patients.

PubMed

Egro, Francesco M; Manders, Ernest C; Manders, Ernest K

2018-03-01

Historically, estimated energy expenditure (EEE) has been related to the percent of body surface area burned. Subsequent evaluations of these estimates have indicated that the earlier formulas may overestimate the amount of caloric support necessary for burn-injured patients. Ireton-Jones et al derived 2 equations for determining the EEE required to support burn patients, 1 for ventilator-dependent patients and 1 for spontaneously breathing patients. Evidence has proved their reliability, but they remain challenging to apply in a clinical setting given the difficult and cumbersome mathematics involved. This study aims to introduce a graphical calculation of EEE in burn patients that can be easily used in the clinical setting. The multivariant linear regression analysis from Ireton-Jones et al yielded equations that were rearranged into the form of a simple linear equation of the type y = mx + b. By choosing an energy expenditure and the age of the subject, the weight was calculated. The endpoints were then calculated, and a graph was mapped by means of Adobe FrameMaker. A graphical representation of Ireton-Jones et al's equations was obtained by plotting the weight (kg) on the y axis, the age (years) on the x axis, and a series of parallel lines representing the EEE in burn patients. The EEE has been displayed graphically on a grid to allow rapid determination of the EEE needed for a given patient of a designated weight and age. Two graphs were plotted: 1 for ventilator-dependent patients and 1 for spontaneously breathing patients. Correction factors for sex, the presence of additional trauma, and obesity are indicated on the graphical calculators. We propose a graphical tool to calculate caloric requirements in a fast, easy, and portable manner.

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

NASA Astrophysics Data System (ADS)

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

2000-05-01

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

A Metallurgical Investigation of the Direct Energy Deposition Surface Repair of Ferrous Alloys

NASA Astrophysics Data System (ADS)

Marya, Manuel; Singh, Virendra; Hascoet, Jean-Yves; Marya, Surendar

2018-02-01

Among additive manufacturing (AM) processes, the direct energy deposition (DED) by laser is explored to establish its applicability for the repair of ferrous alloys such as UNS G41400 low-alloy steel, UNS S41000 martensitic stainless steel, UNS S17400 precipitation-strengthened martensitic stainless steel, and UNS S32750 super-duplex stainless steel. Unlike plating, thermal spray, and conventional cladding weld, DED laser powder deposition offers potential advantages, e.g., thin deposits, limited dilutions, narrow heat-affected zones (HAZ), potentially improved surface properties. In this investigation, all AM deposits were completed with an IREPA CLAD™ system using a powder feed of UNS N06625, an alloy largely selected for its outstanding corrosion resistance. This investigation first addresses topological aspects of AM deposits (including visual imperfections) before focusing on changes in microstructure, microhardness, chemical composition across AM deposits and base materials. It has been established that dense, uniform, hard ( 300 HVN), crack-free UNS N06625-compliant AM deposits of fine dendritic microstructures are reliably produced. However, except for the UNS S32750 steel, a significant martensitic hardening was observed in the HAZs of UNS G41400 ( 650 HVN), UNS S41000 ( 500 HVN), and UNS S17400 ( 370 HVN). In summary, this investigation demonstrates that the DED laser repair of ferrous parts with UNS N06625 may restore damaged surfaces, but it also calls for cautions and complementary investigations for alloys experiencing a high HAZ hardening, for which industry standard recommendations are exceeded and lead to an increased risk of delayed cracking in corrosive environments.

10 CFR 2.1019 - Depositions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Depositions. 2.1019 Section 2.1019 Energy NUCLEAR... Geologic Repository § 2.1019 Depositions. (a) Any party or interested governmental participant desiring to take the testimony of any person by deposition on oral examination shall, without leave of the...

10 CFR 2.1019 - Depositions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Depositions. 2.1019 Section 2.1019 Energy NUCLEAR... Geologic Repository § 2.1019 Depositions. (a) Any party or interested governmental participant desiring to take the testimony of any person by deposition on oral examination shall, without leave of the...

Sustainable manufacturing by calculating the energy demand during turning of AISI 1045 steel

NASA Astrophysics Data System (ADS)

Nur, R.; Nasrullah, B.; Suyuti, M. A.; Apollo

2018-01-01

Sustainable development will become important issues for many fields, including production, industry, and manufacturing. In order to achieve sustainable development, industry should be able to perform of sustainable production processes and environmentally friendly. Therefore, there is need to minimize the energy demand in the machining process. This paper presents a calculation method of energy consumption in the machining process, especially turning process which calculated by summing the number of energy consumption, such as the electric energy consumed during the machining preparation, the electrical energy during the cutting processes, and the electrical energy to produce a cutting tool. A case study was performed on dry turning of mild carbon steel using coated carbide. This approach can be used to determine the total amount of electrical energy consumed in the specific machining process. It concluded that the energy consumption will be an increase for using the high cutting speed as well as for the feed rate was increased.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Deposit model for volcanogenic uranium deposits

USGS Publications Warehouse

Breit, George N.; Hall, Susan M.

2011-01-01

The International Atomic Energy Agency's tabulation of volcanogenic uranium deposits lists 100 deposits in 20 countries, with major deposits in Russia, Mongolia, and China. Collectively these deposits are estimated to contain uranium resources of approximately 500,000 tons of uranium, which amounts to 6 percent of the known global resources. Prior to the 1990s, these deposits were considered to be small (less than 10,000 tons of uranium) with relatively low to moderate grades (0.05 to 0.2 weight percent of uranium). Recent availability of information on volcanogenic uranium deposits in Asia highlighted the large resource potential of this deposit type. For example, the Streltsovskoye district in eastern Russia produced more than 100,000 tons of uranium as of 2005; with equivalent resources remaining. Known volcanogenic uranium deposits within the United States are located in Idaho, Nevada, Oregon, and Utah. These deposits produced an estimated total of 800 tons of uranium during mining from the 1950s through the 1970s and have known resources of 30,000 tons of uranium. The most recent estimate of speculative resources proposed an endowment of 200,000 tons of uranium.

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.

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.

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

PubMed

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

2014-10-14

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

10 CFR 590.307 - Depositions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Depositions. 590.307 Section 590.307 Energy DEPARTMENT OF... RESPECT TO THE IMPORT AND EXPORT OF NATURAL GAS Procedures § 590.307 Depositions. (a) Upon motion filed by... witness by deposition. Unless otherwise directed in the authorization issued, a witness being deposed may...

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

PubMed

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

2007-01-15

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

Impact of surface strain on the spin dynamics of deposited Co nanowires

NASA Astrophysics Data System (ADS)

Polyakov, O. P.; Korobova, J. G.; Stepanyuk, O. V.; Bazhanov, D. I.

2017-01-01

Tailoring the magnetic properties at atomic-scale is essential in the engineering of modern spintronics devices. One of the main concerns in the novel nanostructured materials design is the decrease of the paid energy in the way of functioning, but allowing to switch between different magnetic states with a relative low-cost energy at the same time. Magnetic anisotropy (MA) energy defines the stability of a spin in the preferred direction and is a fundamental variable in magnetization switching processes. Transition-metal wires are known to develop large, stable spin and orbital magnetic moments together with MA energies that are orders of magnitude larger than in the corresponding solids. Different ways of controlling the MA have been exploited such as alloying, surface charging, and external electrical fields. Here we investigate from a first-principle approach together with dynamic calculations, the surface strain driven mechanism to tune the magnetic properties of deposited nanowires. We consider as a prototype system, the monoatomic Co wires deposited on strained Pt(111) and Au(111) surfaces. Our first-principles calculations reveal a monotonic increase/decrease of MA energy under compressive/tensile strain in supported Co wire. Moreover, the spin dynamics studies based on solving the Landau-Lifshitz-Gilbert equation show that the induced surface-strain leads to a substantial decrease of the required external magnetic field magnitude for magnetization switching in Co wire.

Shaping thin film growth and microstructure pathways via plasma and deposition energy: a detailed theoretical, computational and experimental analysis.

PubMed

Sahu, Bibhuti Bhusan; Han, Jeon Geon; Kersten, Holger

2017-02-15

Understanding the science and engineering of thin films using plasma assisted deposition methods with controlled growth and microstructure is a key issue in modern nanotechnology, impacting both fundamental research and technological applications. Different plasma parameters like electrons, ions, radical species and neutrals play a critical role in nucleation and growth and the corresponding film microstructure as well as plasma-induced surface chemistry. The film microstructure is also closely associated with deposition energy which is controlled by electrons, ions, radical species and activated neutrals. The integrated studies on the fundamental physical properties that govern the plasmas seek to determine their structure and modification capabilities under specific experimental conditions. There is a requirement for identification, determination, and quantification of the surface activity of the species in the plasma. Here, we report a detailed study of hydrogenated amorphous and crystalline silicon (c-Si:H) processes to investigate the evolution of plasma parameters using a theoretical model. The deposition processes undertaken using a plasma enhanced chemical vapor deposition method are characterized by a reactive mixture of hydrogen and silane. Later, various contributions of energy fluxes on the substrate are considered and modeled to investigate their role in the growth of the microstructure of the deposited film. Numerous plasma diagnostic tools are used to compare the experimental data with the theoretical results. The film growth and microstructure are evaluated in light of deposition energy flux under different operating conditions.

Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, H.; Kato, M.; Ishimaru, T.

2014-02-20

Organometallic chemical vapor deposition of silicon nitride films enhanced by atomic nitrogen generated from surface-wave plasma is investigated. Feasibility of precursors of triethylsilane (TES) and bis(dimethylamino)dimethylsilane (BDMADMS) is discussed based on a calculation of bond energies by computer simulation. Refractive indices of 1.81 and 1.71 are obtained for deposited films with TES and BDMADMS, respectively. X-ray photoelectron spectroscopy (XPS) analysis of the deposited film revealed that TES-based film coincides with the stoichiometric thermal silicon nitride.

Buoyancy driven mixing of miscible fluids by volumetric energy deposition of microwaves.

PubMed

Wachtor, Adam J; Mocko, Veronika; Williams, Darrick J; Goertz, Matthew P; Jebrail, Farzaneh F

2013-01-01

An experiment that seeks to investigate buoyancy driven mixing of miscible fluids by microwave volumetric energy deposition is presented. The experiment involves the use of a light, non-polar fluid that initially rests on top of a heavier fluid which is more polar. Microwaves preferentially heat the polar fluid, and its density decreases due to thermal expansion. As the microwave heating continues, the density of the lower fluid eventually becomes less than that of the upper, and buoyancy driven Rayleigh-Taylor mixing ensues. The choice of fluids is crucial to the success of the experiment, and a description is given of numerous fluid combinations considered and characterized. After careful consideration, the miscible pair of toluene/tetrahydrofuran (THF) was determined as having the best potential for successful volumetric energy deposition buoyancy driven mixing. Various single fluid calibration experiments were performed to facilitate the development of a heating theory. Thereafter, results from two-fluid mixing experiments are presented that demonstrate the capability of this novel Rayleigh-Taylor driven experiment. Particular interest is paid to the onset of buoyancy driven mixing and unusual aspects of the experiment in the context of typical Rayleigh-Taylor driven mixing.

Broadband infrared absorption enhancement by electroless-deposited silver nanoparticles

NASA Astrophysics Data System (ADS)

Gritti, Claudia; Raza, Søren; Kadkhodazadeh, Shima; Kardynal, Beata; Malureanu, Radu; Mortensen, N. Asger; Lavrinenko, Andrei V.

2017-01-01

Decorating semiconductor surfaces with plasmonic nanoparticles (NPs) is considered a viable solution for enhancing the absorptive properties of photovoltaic and photodetecting devices. We propose to deposit silver NPs on top of a semiconductor wafer by a cheap and fast electroless plating technique. Optical characterization confirms that the random array of electroless-deposited NPs improves absorption by up to 20% in a broadband of near-infrared frequencies from the bandgap edge to 2000 nm. Due to the small filling fraction of particles, the reflection in the visible range is practically unchanged, which points to the possible applications of such deposition method for harvesting photons in nanophotonics and photovoltaics. The broadband absorption is a consequence of the resonant behavior of particles with different shapes and sizes, which strongly localize the incident light at the interface of a high-index semiconductor substrate. Our hypothesis is substantiated by examining the plasmonic response of the electroless-deposited NPs using both electron energy loss spectroscopy and numerical calculations.

Electrophoretic deposition (EPD): Mechanisms, kinetics, and application to ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarkar, P.; Nicholson, P.S.

1996-08-01

The mechanisms of electrophoretic deposition (EPD) are discussed and their shortcomings identified. The kinetics of the processes involved are analyzed for constant-current and constant-voltage conditions. A method of determining the Hamaker constant of suspended particles is developed by modeling the relationship between the particle interaction energy and the suspension stability. A three-probe dc technique is used to map the voltage profile around the depositing electrode, and the results are used to explain discrepancies between the calculated and experimentally observed voltage drops during deposition. A mechanism of deposition is proposed based on DLVO theory and particle double-layer distortion/thinning on application ofmore » a dc field to the suspension. Kinetic equations are developed for constant-current and constant-voltage EPD using mass balance conditions; these are verified by experiments. After the phenomenon is introduced and discussed, a critique of the application of EPD to the synthesis of ceramic shapes and coatings is given.« less

The role of low-energy electrons in focused electron beam induced deposition: four case studies of representative precursors

PubMed Central

Thorman, Rachel M; Kumar T. P., Ragesh; Fairbrother, D Howard

2015-01-01

Summary Focused electron beam induced deposition (FEBID) is a single-step, direct-write nanofabrication technique capable of writing three-dimensional metal-containing nanoscale structures on surfaces using electron-induced reactions of organometallic precursors. Currently FEBID is, however, limited in resolution due to deposition outside the area of the primary electron beam and in metal purity due to incomplete precursor decomposition. Both limitations are likely in part caused by reactions of precursor molecules with low-energy (<100 eV) secondary electrons generated by interactions of the primary beam with the substrate. These low-energy electrons are abundant both inside and outside the area of the primary electron beam and are associated with reactions causing incomplete ligand dissociation from FEBID precursors. As it is not possible to directly study the effects of secondary electrons in situ in FEBID, other means must be used to elucidate their role. In this context, gas phase studies can obtain well-resolved information on low-energy electron-induced reactions with FEBID precursors by studying isolated molecules interacting with single electrons of well-defined energy. In contrast, ultra-high vacuum surface studies on adsorbed precursor molecules can provide information on surface speciation and identify species desorbing from a substrate during electron irradiation under conditions more representative of FEBID. Comparing gas phase and surface science studies allows for insight into the primary deposition mechanisms for individual precursors; ideally, this information can be used to design future FEBID precursors and optimize deposition conditions. In this review, we give a summary of different low-energy electron-induced fragmentation processes that can be initiated by the secondary electrons generated in FEBID, specifically, dissociative electron attachment, dissociative ionization, neutral dissociation, and dipolar dissociation, emphasizing the

The role of low-energy electrons in focused electron beam induced deposition: four case studies of representative precursors.

PubMed

Thorman, Rachel M; Kumar T P, Ragesh; Fairbrother, D Howard; Ingólfsson, Oddur

2015-01-01

Focused electron beam induced deposition (FEBID) is a single-step, direct-write nanofabrication technique capable of writing three-dimensional metal-containing nanoscale structures on surfaces using electron-induced reactions of organometallic precursors. Currently FEBID is, however, limited in resolution due to deposition outside the area of the primary electron beam and in metal purity due to incomplete precursor decomposition. Both limitations are likely in part caused by reactions of precursor molecules with low-energy (<100 eV) secondary electrons generated by interactions of the primary beam with the substrate. These low-energy electrons are abundant both inside and outside the area of the primary electron beam and are associated with reactions causing incomplete ligand dissociation from FEBID precursors. As it is not possible to directly study the effects of secondary electrons in situ in FEBID, other means must be used to elucidate their role. In this context, gas phase studies can obtain well-resolved information on low-energy electron-induced reactions with FEBID precursors by studying isolated molecules interacting with single electrons of well-defined energy. In contrast, ultra-high vacuum surface studies on adsorbed precursor molecules can provide information on surface speciation and identify species desorbing from a substrate during electron irradiation under conditions more representative of FEBID. Comparing gas phase and surface science studies allows for insight into the primary deposition mechanisms for individual precursors; ideally, this information can be used to design future FEBID precursors and optimize deposition conditions. In this review, we give a summary of different low-energy electron-induced fragmentation processes that can be initiated by the secondary electrons generated in FEBID, specifically, dissociative electron attachment, dissociative ionization, neutral dissociation, and dipolar dissociation, emphasizing the different

Energy deposition and neutron flux study in a gravity-driven dense granular target (DGT) with GEANT4 toolkit

NASA Astrophysics Data System (ADS)

Zhao, Qiang; Cui, Wenjuan; He, Zhiyong; Zhang, Xueying; Ma, Wenjing

2018-07-01

China initiative Accelerator Driven System (CiADS) has been approved as a strategic plan to build an ADS demonstration facility in the next few years. It proposed a new concept for a high-power spallation target: the gravity-driven dense granular target (DGT). As the same with a monolithic target (MT), both solid and liquid target, energy deposition and neutron flux are two critical issues. In this paper, we focus on these two issues and long for some valuable results for the project. Unlike a solid target, the internal geometry structure of a DGT is very complicated. To be as much as closer with the reality, we designed an algorithm and firstly packed the grains randomly in a cylindrical container in GEANT4 software. The packing result was in great agreement with the experimentally measured results. It shows that the algorithm is practicable. In the next step, all the simulations about energy deposition and neutron flux of a DGT were performed with the GEANT4 codes, and the results were compared with the data of a MT. Compared to a MT, a DGT has inarguable advantages in both terms of energy deposition and neutron flux. In addition, the simulations with different radius of grains were also performed. Finally, we found that both the energy deposition and neutron flux are nearly irrelevant to the radius of the grains in the range of 0.5 mm-5 mm when the packing density is same by analyzing the results meticulously.

Ionized cluster beam deposition

NASA Technical Reports Server (NTRS)

Kirkpatrick, A. R.

1983-01-01

Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

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.

Monte Carlo calculations of initial energies of electrons in water irradiated by photons with energies up to 1GeV.

PubMed

Todo, A S; Hiromoto, G; Turner, J E; Hamm, R N; Wright, H A

1982-12-01

Previous calculations of the initial energies of electrons produced in water irradiated by photons are extended to 1 GeV by including pair and triplet production. Calculations were performed with the Monte Carlo computer code PHOEL-3, which replaces the earlier code, PHOEL-2. Tables of initial electron energies are presented for single interactions of monoenergetic photons at a number of energies from 10 keV to 1 GeV. These tables can be used to compute kerma in water irradiated by photons with arbitrary energy spectra to 1 GeV. In addition, separate tables of Compton-and pair-electron spectra are given over this energy range. The code PHOEL-3 is available from the Radiation Shielding Information Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830.

10 CFR 590.307 - Depositions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Depositions. 590.307 Section 590.307 Energy DEPARTMENT OF ENERGY (CONTINUED) NATURAL GAS (ECONOMIC REGULATORY ADMINISTRATION) ADMINISTRATIVE PROCEDURES WITH RESPECT TO THE IMPORT AND EXPORT OF NATURAL GAS Procedures § 590.307 Depositions. (a) Upon motion filed by...

Non-linear, non-monotonic effect of nano-scale roughness on particle deposition in absence of an energy barrier: Experiments and modeling

PubMed Central

Jin, Chao; Glawdel, Tomasz; Ren, Carolyn L.; Emelko, Monica B.

2015-01-01

Deposition of colloidal- and nano-scale particles on surfaces is critical to numerous natural and engineered environmental, health, and industrial applications ranging from drinking water treatment to semi-conductor manufacturing. Nano-scale surface roughness-induced hydrodynamic impacts on particle deposition were evaluated in the absence of an energy barrier to deposition in a parallel plate system. A non-linear, non-monotonic relationship between deposition surface roughness and particle deposition flux was observed and a critical roughness size associated with minimum deposition flux or “sag effect” was identified. This effect was more significant for nanoparticles (<1 μm) than for colloids and was numerically simulated using a Convective-Diffusion model and experimentally validated. Inclusion of flow field and hydrodynamic retardation effects explained particle deposition profiles better than when only the Derjaguin-Landau-Verwey-Overbeek (DLVO) force was considered. This work provides 1) a first comprehensive framework for describing the hydrodynamic impacts of nano-scale surface roughness on particle deposition by unifying hydrodynamic forces (using the most current approaches for describing flow field profiles and hydrodynamic retardation effects) with appropriately modified expressions for DLVO interaction energies, and gravity forces in one model and 2) a foundation for further describing the impacts of more complicated scales of deposition surface roughness on particle deposition. PMID:26658159

Non-linear, non-monotonic effect of nano-scale roughness on particle deposition in absence of an energy barrier: Experiments and modeling

NASA Astrophysics Data System (ADS)

Jin, Chao; Glawdel, Tomasz; Ren, Carolyn L.; Emelko, Monica B.

2015-12-01

Deposition of colloidal- and nano-scale particles on surfaces is critical to numerous natural and engineered environmental, health, and industrial applications ranging from drinking water treatment to semi-conductor manufacturing. Nano-scale surface roughness-induced hydrodynamic impacts on particle deposition were evaluated in the absence of an energy barrier to deposition in a parallel plate system. A non-linear, non-monotonic relationship between deposition surface roughness and particle deposition flux was observed and a critical roughness size associated with minimum deposition flux or “sag effect” was identified. This effect was more significant for nanoparticles (<1 μm) than for colloids and was numerically simulated using a Convective-Diffusion model and experimentally validated. Inclusion of flow field and hydrodynamic retardation effects explained particle deposition profiles better than when only the Derjaguin-Landau-Verwey-Overbeek (DLVO) force was considered. This work provides 1) a first comprehensive framework for describing the hydrodynamic impacts of nano-scale surface roughness on particle deposition by unifying hydrodynamic forces (using the most current approaches for describing flow field profiles and hydrodynamic retardation effects) with appropriately modified expressions for DLVO interaction energies, and gravity forces in one model and 2) a foundation for further describing the impacts of more complicated scales of deposition surface roughness on particle deposition.

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

NASA Astrophysics Data System (ADS)

Hošek, Petr; Spiwok, Vojtěch

2016-01-01

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

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

How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

PubMed

Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

2015-06-09

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

PubMed Central

2016-01-01

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

Validation of Ground-based Optical Estimates of Auroral Electron Precipitation Energy Deposition

NASA Astrophysics Data System (ADS)

Hampton, D. L.; Grubbs, G. A., II; Conde, M.; Lynch, K. A.; Michell, R.; Zettergren, M. D.; Samara, M.; Ahrns, M. J.

2017-12-01

One of the major energy inputs into the high latitude ionosphere and mesosphere is auroral electron precipitation. Not only does the kinetic energy get deposited, the ensuing ionization in the E and F-region ionosphere modulates parallel and horizontal currents that can dissipate in the form of Joule heating. Global models to simulate these interactions typically use electron precipitation models that produce a poor representation of the spatial and temporal complexity of auroral activity as observed from the ground. This is largely due to these precipitation models being based on averages of multiple satellite overpasses separated by periods much longer than typical auroral feature durations. With the development of regional and continental observing networks (e.g. THEMIS ASI), the possibility of ground-based optical observations producing quantitative estimates of energy deposition with temporal and spatial scales comparable to those known to be exhibited in auroral activity become a real possibility. Like empirical precipitation models based on satellite overpasses such optics-based estimates are subject to assumptions and uncertainties, and therefore require validation. Three recent sounding rocket missions offer such an opportunity. The MICA (2012), GREECE (2014) and Isinglass (2017) missions involved detailed ground based observations of auroral arcs simultaneously with extensive on-board instrumentation. These have afforded an opportunity to examine the results of three optical methods of determining auroral electron energy flux, namely 1) ratio of auroral emissions, 2) green line temperature vs. emission altitude, and 3) parametric estimates using white-light images. We present comparisons from all three methods for all three missions and summarize the temporal and spatial scales and coverage over which each is valid.

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

NASA Astrophysics Data System (ADS)

Mey, Antonia S. J. S.; Jiménez, Jordi Juárez; Michel, Julien

2018-01-01

The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKechnie, Scott; Booth, George H.; Cohen, Aron J.

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 ionizationmore » 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.« less

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

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2016-01-01

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations. PMID:27453631

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

PubMed

Miao, Yinglong; McCammon, J Andrew

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

Enhanced calculation of eigen-stress field and elastic energy in atomistic interdiffusion of alloys

NASA Astrophysics Data System (ADS)

Cecilia, José M.; Hernández-Díaz, A. M.; Castrillo, Pedro; Jiménez-Alonso, J. F.

2017-02-01

The structural evolution of alloys is affected by the elastic energy associated to eigen-stress fields. However, efficient calculations of the elastic energy in evolving geometries are actually a great challenge in promising atomistic simulation techniques such as Kinetic Monte Carlo (KMC) methods. In this paper, we report two complementary algorithms to calculate the eigen-stress field by linear superposition (a.k.a. LSA, Lineal Superposition Algorithm) and the elastic energy modification in atomistic interdiffusion of alloys (the Atom Exchange Elastic Energy Evaluation (AE4) Algorithm). LSA is shown to be appropriated for fast incremental stress calculation in highly nanostructured materials, whereas AE4 provides the required input for KMC and, additionally, it can be used to evaluate the accuracy of the eigen-stress field calculated by LSA. Consequently, they are suitable to be used on-the-fly with KMC. Both algorithms are massively parallel by their definition and thus well-suited for their parallelization on modern Graphics Processing Units (GPUs). Our computational studies confirm that we can obtain significant improvements compared to conventional Finite Element Methods, and the utilization of GPUs opens up new possibilities for the development of these methods in atomistic simulation of materials.

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

PubMed Central

2016-01-01

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

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

PubMed

Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L

2017-06-13

λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.

TH-CD-201-07: Experimentally Investigating Proton Energy Deposition On the Microscopic Scale Using Fluorescence Nuclear Track Detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Underwood, T; University College London, London; McFadden, C

Purpose: In order to further understand the interplay between proton physics and radiobiology it is necessary to consider proton energy deposition on the microscopic scale. In this work we used Fluorescent Nuclear Track Detectors (FNTDs) to experimentally investigate proton energy deposition, track-by-track. Methods: We irradiated 8×4×0.5mm{sup 3} FNTD chips (Landauer Inc) at seven water depths along a pristine proton Bragg peak with range=12cm. After irradiation, the FNTDs were scanned using a confocal microscope (FV1200, Olympus) with a high-power red laser and an oil-immersion objective lens (UPLSAPO60XO, NA=1.35). 10 slice image stacks were acquired with a slice-thickness of 2µm at multiplemore » positions across each FNTD. Image-based analyses of track radius and track “mass” (integrated signal intensity) were performed using trackpy. For comparison, Monte Carlo simulated data were obtained using TOPAS and TOPAS-nBio. Results: Excellent correlation was observed between median track mass and TOPAS dose-averaged linear energy transfer. The resolution of the imaging system was determined insufficient to detect a relationship between track radius and exposure depth. Histograms of track mass (i) displayed strong repeatability across positions within an FNTD and (ii) varied in peak position and shape as a function of depth. TOPAS-nBio simulations implemented on the nanometer scale using physics lists from GEANT4-DNA yielded energy deposition distributions for individual protons and electrons scored within a virtual FNTD. Good agreement was found between these simulated datasets and the FNTD track mass distributions. Conclusion: Robust experimental measurements of the integral energy deposited by individual proton tracks can be performed using FNTDs. Monte Carlo simulations offer an exceedingly powerful approach to the quantification of proton energy deposition on the microscopic scale, but whilst they have been well validated at the macroscopic level, their

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

USDA-ARS?s Scientific Manuscript database

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

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

PubMed

Harada, Ryuhei; Kitao, Akio

2011-07-14

The folding process for a β-hairpin miniprotein, chignolin, was investigated by free energy landscape (FEL) calculations using the recently proposed multiscale free energy landscape calculation method (MSFEL). First, coarse-grained molecular dynamics simulations searched a broad conformational space, then multiple independent, all-atom molecular dynamics simulations with explicit solvent determined the detailed local FEL using massively distributed computing. The combination of the two models enabled efficient calculation of the free energy landscapes. The MSFEL analysis showed that chignolin has an intermediate state as well as a misfolded state. The folding process is initiated by the formation of a β-hairpin turn, followed by the formation of contacts in the hydrophobic core between Tyr2 and Trp9. Furthermore, mutation of Tyr2 shifts the population to the misfolded conformation. The results indicate that the hydrophobic core plays an important role in stabilizing the native state of chignolin. © 2011 American Chemical Society

An investigation of nonuniform dose deposition from an electron beam

NASA Astrophysics Data System (ADS)

Lilley, William; Luu, Kieu X.

1994-08-01

In a search for an explanation of nonuniform electron-beam dose deposition, the integrated tiger series (ITS) of coupled electron/photon Monte Carlo transport codes was used to calculate energy deposition in the package materials of an application-specific integrated circuit (ASIC) while the thicknesses of some of the materials were varied. The thicknesses of three materials that were in the path of an electron-beam pulse were varied independently so that analysis could determine how the radiation dose measurements using thermoluminescent dosimeters (TLD's) would be affected. The three materials were chosen because they could vary during insertion of the die into the package or during the process of taking dose measurements. The materials were aluminum, HIPEC (a plastic), and silver epoxy. The calculations showed that with very small variations in thickness, the silver epoxy had a large effect on the dose uniformity over the area of the die.

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.

Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations

NASA Astrophysics Data System (ADS)

McCarrick, Margaret A.; Kollman, Peter A.

1999-03-01

The relative binding free energies in HIV protease of haloperidol thioketal (THK) and three of its derivatives were examined with free energy calculations. THK is a weak inhibitor (IC50 = 15 μM) for which two cocrystal structures with HIV type 1 proteases have been solved [Rutenber, E. et al., J. Biol. Chem., 268 (1993) 15343]. A THK derivative with a phenyl group on C2 of the piperidine ring was expected to be a poor inhibitor based on experiments with haloperidol ketal and its 2- phenyl derivative (Caldera, P., personal communication). Our calculations predict that a 5-phenyl THK derivative, suggested based on examination of the crystal structure, will bind significantly better than THK. Although there are large error bars as estimated from hysteresis, the calculations predict that the 5-phenyl substituent is clearly favored over the 2-phenyl derivative as well as the parent compound. The unfavorable free energies of solvation of both phenyl THK derivatives relative to the parent compound contributed to their predicted binding free energies. In a third simulation, the change in binding free energy for 5-benzyl THK relative to THK was calculated. Although this derivative has a lower free energy in the protein, its decreased free energy of solvation increases the predicted ΔΔG(bind) to the same range as that of the 2-phenyl derivative.

Additive Manufacturing of AlSi10Mg Alloy Using Direct Energy Deposition: Microstructure and Hardness Characterization

NASA Astrophysics Data System (ADS)

Javidani, M.; Arreguin-Zavala, J.; Danovitch, J.; Tian, Y.; Brochu, M.

2017-04-01

This paper aims to study the manufacturing of the AlSi10Mg alloy with direct energy deposition (DED) process. Following fabrication, the macro- and microstructural evolution of the as-processed specimens was initially investigated using optical microscopy and scanning electron microscopy. Columnar dendritic structure was the dominant solidification feature of the deposit; nevertheless, detailed microstructural analysis revealed cellular morphology near the substrate and equiaxed dendrites at the top end of the deposit. Moreover, the microstructural morphology in the melt pool boundary of the deposit differed from the one in the core of the layers. The remaining porosity of the deposit was evaluated by Archimedes' principle and by image analysis of the polished surface. Crystallographic texture in the deposit was also assessed using electron backscatter diffraction and x-ray diffraction analysis. The dendrites were unidirectionally oriented at an angle of 80° to the substrate. EPMA line scans were performed to evaluate the compositional variation and elemental segregation in different locations. Eventually, microhardness (HV) tests were conducted in order to study the hardness gradient in the as-DED-processed specimen along the deposition direction. The presented results, which exhibited a deposit with an almost defect free structure, indicate that the DED process can suitable for the deposition of Al-Si-based alloys with a highly consolidated structure.

Effect of deposition temperature on the structural and optical properties of CdSe QDs thin films deposited by CBD method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laatar, F., E-mail: fakher8laatar@gmail.com; Harizi, A.; Smida, A.

2016-06-15

Highlights: • Synthesis of CdSe QDs with L-Cysteine capping agent for applications in nanodevices. • The films of CdSe QDs present uniform and good dispersive particles at the surface. • Effect of bath temperature on the structural and optical properties of CdSe QDs thin films. • Investigation of the optical constants and dispersion parameters of CdSe QDs thin films. - Abstract: Cadmium selenide quantum dots (CdSe QDs) thin films were deposited onto glass substrates by a chemical bath deposition (CBD) method at different temperatures from an aqueous solution containing L-Cysteine (L-Cys) as capping agent. The evolution of the surface morphologymore » and elemental composition of the CdSe films were studied by AFM, SEM, and EDX analyses. Structural and optical properties of CdSe thin films were investigated by XRD, UV–vis and PL spectroscopy. The dispersion behavior of the refractive index is described using the single oscillator Wemple-DiDomenico (W-D) model, and the physical dispersion parameters are calculated as a function of deposition temperature. The dispersive optical parameters such as average oscillator energy (E{sub o}), dispersion energy (E{sub d}), and static refractive index (n{sub o}) were found to vary with the deposition temperature. Besides, the electrical free carrier susceptibility (χ{sub e}) and the carrier concentration of the effective mass ratio (N/m*) were evaluated according to the Spitzer-Fan model.« less

An empirical formula to calculate the full energy peak efficiency of scintillation detectors.

PubMed

Badawi, Mohamed S; Abd-Elzaher, Mohamed; Thabet, Abouzeid A; El-khatib, Ahmed M

2013-04-01

This work provides an empirical formula to calculate the FEPE for different detectors using the effective solid angle ratio derived from experimental measurements. The full energy peak efficiency (FEPE) curves of the (2″(*)2″) NaI(Tl) detector at different seven axial distances from the detector were depicted in a wide energy range from 59.53 to 1408keV using standard point sources. The distinction was based on the effects of the source energy and the source-to-detector distance. A good agreement was noticed between the measured and calculated efficiency values for the source-to-detector distances at 20, 25, 30, 35, 40, 45 and 50cm. Copyright © 2012 Elsevier Ltd. All rights reserved.

New more accurate calculations of the ground state potential energy surface of H(3) (+).

PubMed

Pavanello, Michele; Tung, Wei-Cheng; Leonarski, Filip; Adamowicz, Ludwik

2009-02-21

Explicitly correlated Gaussian functions with floating centers have been employed to recalculate the ground state potential energy surface (PES) of the H(3) (+) ion with much higher accuracy than it was done before. The nonlinear parameters of the Gaussians (i.e., the exponents and the centers) have been variationally optimized with a procedure employing the analytical gradient of the energy with respect to these parameters. The basis sets for calculating new PES points were guessed from the points already calculated. This allowed us to considerably speed up the calculations and achieve very high accuracy of the results.

Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm.

PubMed

Famulari, Gabriel; Pater, Piotr; Enger, Shirin A

2017-07-07

The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(>E)/f(>0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2004-02-01

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

Extended wave-packet model to calculate energy-loss moments of protons in matter

NASA Astrophysics Data System (ADS)

Archubi, C. D.; Arista, N. R.

2017-12-01

In this work we introduce modifications to the wave-packet method proposed by Kaneko to calculate the energy-loss moments of a projectile traversing a target which is represented in terms of Gaussian functions for the momentum distributions of electrons in the atomic shells. These modifications are introduced using the Levine and Louie technique to take into account the energy gaps corresponding to the different atomic levels of the target. We use the extended wave-packet model to evaluate the stopping power, the energy straggling, the inverse mean free path, and the ionization cross sections for protons in several targets, obtaining good agreements for all these quantities on an extensive energy range that covers low-, intermediate-, and high-energy regions. The extended wave-packet model proposed here provides a method to calculate in a very straightforward way all the significant terms of the inelastic interaction of light ions with any element of the periodic table.

Potential energy surface interpolation with neural networks for instanton rate calculations

NASA Astrophysics Data System (ADS)

Cooper, April M.; Hallmen, Philipp P.; Kästner, Johannes

2018-03-01

Artificial neural networks are used to fit a potential energy surface (PES). We demonstrate the benefits of using not only energies but also their first and second derivatives as training data for the neural network. This ensures smooth and accurate Hessian surfaces, which are required for rate constant calculations using instanton theory. Our aim was a local, accurate fit rather than a global PES because instanton theory requires information on the potential only in the close vicinity of the main tunneling path. Elongations along vibrational normal modes at the transition state are used as coordinates for the neural network. The method is applied to the hydrogen abstraction reaction from methanol, calculated on a coupled-cluster level of theory. The reaction is essential in astrochemistry to explain the deuteration of methanol in the interstellar medium.

Deposition and reentrainment of Brownian particles in porous media under unfavorable chemical conditions: some concepts and applications.

PubMed

Hahn, Melinda W; O'Meliae, Charles R

2004-01-01

The deposition and reentrainment of particles in porous media have been examined theoretically and experimentally. A Brownian Dynamics/Monte Carlo (MC/BD) model has been developed that simulates the movement of Brownian particles near a collector under "unfavorable" chemical conditions and allows deposition in primary and secondary minima. A simple Maxwell approach has been used to estimate particle attachment efficiency by assuming deposition in the secondary minimum and calculating the probability of reentrainment. The MC/BD simulations and the Maxwell calculations support an alternative view of the deposition and reentrainment of Brownian particles under unfavorable chemical conditions. These calculations indicate that deposition into and subsequent release from secondary minima can explain reported discrepancies between classic model predictions that assume irreversible deposition in a primary well and experimentally determined deposition efficiencies that are orders of magnitude larger than Interaction Force Boundary Layer (IFBL) predictions. The commonly used IFBL model, for example, is based on the notion of transport over an energy barrier into the primary well and does not address contributions of secondary minimum deposition. A simple Maxwell model based on deposition into and reentrainment from secondary minima is much more accurate in predicting deposition rates for column experiments at low ionic strengths. It also greatly reduces the substantial particle size effects inherent in IFBL models, wherein particle attachment rates are predicted to decrease significantly with increasing particle size. This view is consistent with recent work by others addressing the composition and structure of the first few nanometers at solid-water interfaces including research on modeling water at solid-liquid interfaces, surface speciation, interfacial force measurements, and the rheological properties of concentrated suspensions. It follows that deposition under these

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

USGS Publications Warehouse

Woolway, R. Iestyn; Jones, Ian D; Hamilton, David P.; Maberly, Stephen C; Muroaka, Kohji; Read, Jordan S.; Smyth, Robyn L; Winslow, Luke A.

2015-01-01

Lake Heat Flux Analyzer is a program used for calculating the surface energy fluxes in lakes according to established literature methodologies. The program was developed in MATLAB for the rapid analysis of high-frequency data from instrumented lake buoys in support of the emerging field of aquatic sensor network science. To calculate the surface energy fluxes, the program requires a number of input variables, such as air and water temperature, relative humidity, wind speed, and short-wave radiation. Available outputs for Lake Heat Flux Analyzer include the surface fluxes of momentum, sensible heat and latent heat and their corresponding transfer coefficients, incoming and outgoing long-wave radiation. Lake Heat Flux Analyzer is open source and can be used to process data from multiple lakes rapidly. It provides a means of calculating the surface fluxes using a consistent method, thereby facilitating global comparisons of high-frequency data from lake buoys.

Mesoscale energy deposition footprint model for kiloelectronvolt cluster bombardment of solids.

PubMed

Russo, Michael F; Garrison, Barbara J

2006-10-15

Molecular dynamics simulations have been performed to model 5-keV C60 and Au3 projectile bombardment of an amorphous water substrate. The goal is to obtain detailed insights into the dynamics of motion in order to develop a straightforward and less computationally demanding model of the process of ejection. The molecular dynamics results provide the basis for the mesoscale energy deposition footprint model. This model provides a method for predicting relative yields based on information from less than 1 ps of simulation time.

Calculation of Quasi-Particle Energies of Aromatic Self-Assembled Monolayers on Au(111).

PubMed

Li, Yan; Lu, Deyu; Galli, Giulia

2009-04-14

We present many-body perturbation theory calculations of the electronic properties of phenylene diisocyanide self-assembled monolayers (SAMs) on a gold surface. Using structural models obtained within density functional theory (DFT), we have investigated how the SAM molecular energies are modified by self-energy corrections and how they are affected by the presence of the surface. We have employed a combination of GW (G = Green's function; W = screened Coulomb interaction) calculations of the SAM quasi-particle energies and a semiclassical image potential model to account for surface polarization effects. We find that it is essential to include both quasi-particle corrections and surface screening in order to provide a reasonable estimate of the energy level alignment at a SAM-metal interface. In particular, our results show that within the GW approximation the energy distance between phenylene diisocyanide SAM energy levels and the gold surface Fermi level is much larger than that found within DFT, e.g., more than double in the case of low packing densities of the SAM.

Prediction of Combustion Gas Deposit Compositions

NASA Technical Reports Server (NTRS)

Kohl, F. J.; Mcbride, B. J.; Zeleznik, F. J.; Gordon, S.

1985-01-01

Demonstrated procedure used to predict accurately chemical compositions of complicated deposit mixtures. NASA Lewis Research Center's Computer Program for Calculation of Complex Chemical Equilibrium Compositions (CEC) used in conjunction with Computer Program for Calculation of Ideal Gas Thermodynamic Data (PAC) and resulting Thermodynamic Data Base (THDATA) to predict deposit compositions from metal or mineral-seeded combustion processes.

Excited state free energy calculations of Cy3 in different environments

NASA Astrophysics Data System (ADS)

Sawangsang, Pilailuk; Buranachai, Chittanon; Punwong, Chutintorn

2015-05-01

Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

Site energies and charge transfer rates near pentacene grain boundaries from first-principles calculations

NASA Astrophysics Data System (ADS)

Kobayashi, Hajime; Tokita, Yuichi

2015-03-01

Charge transfer rates near pentacene grain boundaries are derived by calculating the site energies and transfer integrals of 37 pentacene molecules using first-principles calculations. The site energies decrease considerably near the grain boundaries, and electron traps of up to 300 meV and hole barriers of up to 400 meV are generated. The charge transfer rates across the grain boundaries are found to be reduced by three to five orders of magnitude with a grain boundary gap of 4 Å because of the reduction in the transfer integrals. The electron traps and hole barriers also reduce the electron and hole transfer rates by factors of up to 10 and 50, respectively. It is essential to take the site energies into consideration to determine charge transport near the grain boundaries. We show that the complex site energy distributions near the grain boundaries can be represented by an equivalent site energy difference, which is a constant for any charge transfer pass. When equivalent site energy differences are obtained for various grain boundary structures by first-principles calculations, the effects of the grain boundaries on the charge transfer rates are introduced exactly into charge transport simulations, such as the kinetic Monte Carlo method.

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

PubMed

Gericke, D O; Schlanges, M

2003-03-01

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

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.

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

X-alpha calculation of transition energies in multiply ionized atoms

NASA Technical Reports Server (NTRS)

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

1974-01-01

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

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

Hanson-Heine, Magnus W. D.; George, Michael W.; Besley, Nicholas A.

2018-05-01

Core-electron binding energies (CEBEs) computed within a Δ self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z + 1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy.

Studies of Niobium Thin Film Produced by Energetic Vacuum Deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genfa Wu; Anne-Marie Valente; H. Phillips

2004-05-01

An energetic vacuum deposition system has been used to study deposition energy effects on the properties of niobium thin films on copper and sapphire substrates. The absence of working gas avoids the gaseous inclusions commonly seen with sputtering deposition. A biased substrate holder controls the deposition energy. Transition temperature and residual resistivity ratio of the niobium thin films at several deposition energies are obtained together with surface morphology and crystal orientation measurements by AFM inspection, XRD and TEM analysis. The results show that niobium thin films on sapphire substrate exhibit the best cryogenic properties at deposition energy around 123 eV.more » The TEM analysis revealed that epitaxial growth of film was evident when deposition energy reaches 163 eV for sapphire substrate. Similarly, niobium thin film on copper substrate shows that film grows more oriented with higher deposition energy and grain size reaches the scale of the film thickness at the deposition energy around 153 eV.« less

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

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.

Residual energy deposition in dental enamel during IR laser ablation at 2.79, 2.94, 9.6, and 10.6 μm

NASA Astrophysics Data System (ADS)

Ragadio, Jerome N.; Lee, Christian K.; Fried, Daniel

2000-03-01

The objective of this study was to measure the residual heat deposition during laser ablation at those IR laser wavelengths best suited for the removal of dental caries. The principal factor limiting the rate of laser ablation of dental hard tissue is the risk of excessive heat accumulation in the tooth, which has the potential for causing damage to the pulp. Optimal laser ablation systems minimize the residual energy deposition in the tooth by transferring deposited laser energy to kinetic and internal energy of ejected tissue components. The residual heat deposition in the tooth was measured at laser wavelengths of 2.79, 2.94, 9.6 and 10.6 micrometer and pulse widths of 150 ns - 150 microsecond(s) . The residual energy was at a minimum for fluences well above the ablation threshold where it saturates at values from 25 - 70% depending on pulse duration and wavelength for the systems investigated. The lowest values of the residual energy were measured for short (less than 20 microseconds) CO2 laser pulses at 9.6 micrometer and for Q-switched erbium laser pulses. This work was supported by NIH/NIDCR R29DE12091 and the Center for Laser Applications in Medicine, DOE DEFG0398ER62576.

Quasiclassical trajectory calculations to evaluate a kinematic constraint on internal energy in suprathreshold collision energy abstraction reactions

NASA Astrophysics Data System (ADS)

Shuman, Nicholas S.; Mihok, Morgan; Fistik, Margaret; Valentini, James J.

2005-08-01

Experimentally observed product quantum state distributions across a wide range of abstraction reactions at suprathreshold collision energies have shown a strong bias against product internal energy. Only a fraction, sometimes quite a small fraction, of the energetically accessible product quantum states are populated. Picconatto et al. [J. Chem. Phys. 114, 1663 (2001)] noted a simple mathematical relationship between the highest-energy rovibrational states observed and the kinematics of the reaction system. They proposed a reaction model based on reaction kinematics that quantitatively explains this behavior. The model is in excellent agreement with measured quantum state distributions. The assumptions of the model invoke detailed characteristics of reactive trajectories at suprathreshold collision energies. Here we test those assumptions using quasiclassical trajectory calculations for the abstraction reactions H +HCl→H2+Cl, D +HCl→HD+Cl, and H +DCl→HD+Cl. Trajectories were run on a potential-energy surface calculated with a London-Eyring-Polyani-Sato function with a localized 3-center term (LEPS-3C) previously shown to accurately reproduce experimentally observed product state distributions for the H +HCl abstraction reaction. The trajectories sample collision energies near threshold and also substantially above it. Although the trajectories demonstrate some aspects of the model, they show that it is not valid. However, the inadequacy of the proposed model does not invalidate the apparent kinematic basis of the observed energy constraint. The present results show that there must be some other molecular behavior rooted in the reaction kinematics that is the explanation and the source of the constraint.

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.

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)

Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues

NASA Astrophysics Data System (ADS)

Fiorentini, Raffaele; Kremer, Kurt; Potestio, Raffaello; Fogarty, Aoife C.

2017-06-01

The calculation of free energy differences is a crucial step in the characterization and understanding of the physical properties of biological molecules. In the development of efficient methods to compute these quantities, a promising strategy is that of employing a dual-resolution representation of the solvent, specifically using an accurate model in the proximity of a molecule of interest and a simplified description elsewhere. One such concurrent multi-resolution simulation method is the Adaptive Resolution Scheme (AdResS), in which particles smoothly change their resolution on-the-fly as they move between different subregions. Before using this approach in the context of free energy calculations, however, it is necessary to make sure that the dual-resolution treatment of the solvent does not cause undesired effects on the computed quantities. Here, we show how AdResS can be used to calculate solvation free energies of small polar solutes using Thermodynamic Integration (TI). We discuss how the potential-energy-based TI approach combines with the force-based AdResS methodology, in which no global Hamiltonian is defined. The AdResS free energy values agree with those calculated from fully atomistic simulations to within a fraction of kBT. This is true even for small atomistic regions whose size is on the order of the correlation length, or when the properties of the coarse-grained region are extremely different from those of the atomistic region. These accurate free energy calculations are possible because AdResS allows the sampling of solvation shell configurations which are equivalent to those of fully atomistic simulations. The results of the present work thus demonstrate the viability of the use of adaptive resolution simulation methods to perform free energy calculations and pave the way for large-scale applications where a substantial computational gain can be attained.

Use of the VIP-Man model to calculate energy imparted and effective dose for x-ray examinations.

PubMed

Winslow, Mark; Huda, Walter; Xu, X George; Chao, T C; Shi, C Y; Ogden, Kent M; Scalzetti, Ernest M

2004-02-01

A male human tomographic model was used to calculate values of energy imparted (epsilon) and effective dose (E) for monoenergetic photons (30-150 keV) in radiographic examinations. Energy deposition in the organs and tissues of the human phantom were obtained using Monte Carlo simulations. Values of E/epsilon were obtained for three common projections [anterior-posterior (AP), posterior-anterior (PA), and lateral (LAT)] of the head, cervical spine, chest, and abdomen, respectively. For head radiographs, all three projections yielded similar E/epsilon values. At 30 keV, the value of E/epsilon was approximately 1.6 mSv J(-1), which is increased to approximately 7 mSv J(-1) for 150 keV photons. The AP cervical spine was the only projection investigated where the value of E/epsilon decreased with increasing photon energy. Above 70 keV, cervical spine E/epsilon values showed little energy dependence and ranged between approximately 8.5 mSv J(-1) for PA projections and approximately 17 mSv J(-1) for AP projections. The values of E/epsilon for AP chest examinations showed very little variation with photon energy, and had values of approximately 23 mSv J(-1). Values of E/epsilon for PA and LAT chest projections were substantially lower than the AP projections and increased with increasing photon energy. For abdominal radiographs, differences between the PA and LAT projections were very small. All abdomen projections showed an increase in the E/epsilon ratio with increasing photon energy, and reached a maximum value of approximately 13.5 mSv J(-1) for AP projections, and approximately 9.5 mSv J(-1) for PA/lateral projections. These monoenergetic E/epsilon values can generate values of E/epsilon for any x-ray spectrum, and can be used to convert values of energy imparted into effective dose for patients undergoing common head and body radiological examinations.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto

2014-09-21

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

Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass.

PubMed

Wright, Katherine E; Williamson, Charles; Grasby, Stephen E; Spear, John R; Templeton, Alexis S

2013-01-01

We combined free enenergy calculations and metagenomic analyses of an elemental sulfur (S(0)) deposit on the surface of Borup Fiord Pass Glacier in the Canadian High Arctic to investigate whether the energy available from different redox reactions in an environment predicts microbial metabolism. Many S, C, Fe, As, Mn, and [Formula: see text] oxidation reactions were predicted to be energetically feasible in the deposit, and aerobic oxidation of S(0) was the most abundant chemical energy source. Small subunit ribosomal RNA (SSU rRNA) gene sequence data showed that the dominant phylotypes were Sulfurovum and Sulfuricurvum, both Epsilonproteobacteria known to be capable of sulfur lithotrophy. Sulfur redox genes were abundant in the metagenome, but sox genes were significantly more abundant than reverse dsr (dissimilatory sulfite reductase)genes. Interestingly, there appeared to be habitable niches that were unoccupied at the depth of genome coverage obtained. Photosynthesis and [Formula: see text] oxidation should both be energetically favorable, but we found few or no functional genes for oxygenic or anoxygenic photosynthesis, or for [Formula: see text] oxidation by either oxygen (nitrification) or nitrite (anammox). The free energy, SSU rRNA gene and quantitative functional gene data are all consistent with the hypothesis that sulfur-based chemolithoautotrophy by Epsilonproteobacteria (Sulfurovum and Sulfuricurvum) is the main form of primary productivity at this site, instead of photosynthesis. This is despite the presence of 24-h sunlight, and the fact that photosynthesis is not known to be inhibited by any of the environmental conditions present. This is the first time that Sulfurovum and Sulfuricurvum have been shown to dominate a sub-aerial environment, rather than anoxic or sulfidic settings. We also found that Flavobacteria dominate the surface of the sulfur deposits. We hypothesize that this aerobic heterotroph uses enough oxygen to create a microoxic

Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass

PubMed Central

Wright, Katherine E.; Williamson, Charles; Grasby, Stephen E.; Spear, John R.; Templeton, Alexis S.

2013-01-01

We combined free enenergy calculations and metagenomic analyses of an elemental sulfur (S0) deposit on the surface of Borup Fiord Pass Glacier in the Canadian High Arctic to investigate whether the energy available from different redox reactions in an environment predicts microbial metabolism. Many S, C, Fe, As, Mn, and NH4+ oxidation reactions were predicted to be energetically feasible in the deposit, and aerobic oxidation of S0 was the most abundant chemical energy source. Small subunit ribosomal RNA (SSU rRNA) gene sequence data showed that the dominant phylotypes were Sulfurovum and Sulfuricurvum, both Epsilonproteobacteria known to be capable of sulfur lithotrophy. Sulfur redox genes were abundant in the metagenome, but sox genes were significantly more abundant than reverse dsr (dissimilatory sulfite reductase)genes. Interestingly, there appeared to be habitable niches that were unoccupied at the depth of genome coverage obtained. Photosynthesis and NH4+ oxidation should both be energetically favorable, but we found few or no functional genes for oxygenic or anoxygenic photosynthesis, or for NH4+ oxidation by either oxygen (nitrification) or nitrite (anammox). The free energy, SSU rRNA gene and quantitative functional gene data are all consistent with the hypothesis that sulfur-based chemolithoautotrophy by Epsilonproteobacteria (Sulfurovum and Sulfuricurvum) is the main form of primary productivity at this site, instead of photosynthesis. This is despite the presence of 24-h sunlight, and the fact that photosynthesis is not known to be inhibited by any of the environmental conditions present. This is the first time that Sulfurovum and Sulfuricurvum have been shown to dominate a sub-aerial environment, rather than anoxic or sulfidic settings. We also found that Flavobacteria dominate the surface of the sulfur deposits. We hypothesize that this aerobic heterotroph uses enough oxygen to create a microoxic environment in the sulfur below, where the

Mechanical properties improvement of pulsed laser-deposited hydroxyapatite thin films by high energy ion-beam implantation

NASA Astrophysics Data System (ADS)

Nelea, V.; Pelletier, H.; Müller, D.; Broll, N.; Mille, P.; Ristoscu, C.; Mihailescu, I. N.

2002-01-01

Major problems in the hydroxyapatite (HA), Ca 5(PO 4) 3OH, thin films processing still keep the poor mechanical properties and the lack in density. We present a study on the feasibility of high energy ion-beam implantation technique to densify HA bioceramic films. Crystalline HA films were grown by pulsed laser deposition (PLD) method using an excimer KrF ∗ laser ( λ=248 nm, τ FWHM≥20 ns). The films were deposited on Ti-5Al-2.5Fe alloys substrates previously coated with a ceramic TiN buffer layer. After deposition the films were implanted with Ar + ions at high energy. Optical microscopy (OM), white light confocal microscopy (WLCM), grazing incidence X-ray diffraction (GIXRD) and Berkovich nanoindentation in normal and scratch options have been applied for the characterization of the obtained structures. We put into evidence an enhancement of the mechanical characteristics after implantation, while GIXRD measurements confirm that the crystalline structure of HA phase is preserved. The improvement in mechanical properties is an effect of a densification after ion treatment as a result of pores elimination and grains regrowth.

An ab initio potential energy surface for the formic acid dimer: zero-point energy, selected anharmonic fundamental energies, and ground-state tunneling splitting calculated in relaxed 1-4-mode subspaces.

PubMed

Qu, Chen; Bowman, Joel M

2016-09-14

We report a full-dimensional, permutationally invariant potential energy surface (PES) for the cyclic formic acid dimer. This PES is a least-squares fit to 13475 CCSD(T)-F12a/haTZ (VTZ for H and aVTZ for C and O) energies. The energy-weighted, root-mean-square fitting error is 11 cm -1 and the barrier for the double-proton transfer on the PES is 2848 cm -1 , in good agreement with the directly-calculated ab initio value of 2853 cm -1 . The zero-point vibrational energy of 15 337 ± 7 cm -1 is obtained from diffusion Monte Carlo calculations. Energies of fundamentals of fifteen modes are calculated using the vibrational self-consistent field and virtual-state configuration interaction method. The ground-state tunneling splitting is computed using a reduced-dimensional Hamiltonian with relaxed potentials. The highest-level, four-mode coupled calculation gives a tunneling splitting of 0.037 cm -1 , which is roughly twice the experimental value. The tunneling splittings of (DCOOH) 2 and (DCOOD) 2 from one to three mode calculations are, as expected, smaller than that for (HCOOH) 2 and consistent with experiment.

Computational Model of D-Region Ion Production Caused by Energetic Electron Precipitations Based on General Monte Carlo Transport Calculations

NASA Astrophysics Data System (ADS)

Kouznetsov, A.; Cully, C. M.

2017-12-01

During enhanced magnetic activities, large ejections of energetic electrons from radiation belts are deposited in the upper polar atmosphere where they play important roles in its physical and chemical processes, including VLF signals subionospheric propagation. Electron deposition can affect D-Region ionization, which are estimated based on ionization rates derived from energy depositions. We present a model of D-region ion production caused by an arbitrary (in energy and pitch angle) distribution of fast (10 keV - 1 MeV) electrons. The model relies on a set of pre-calculated results obtained using a general Monte Carlo approach with the latest version of the MCNP6 (Monte Carlo N-Particle) code for the explicit electron tracking in magnetic fields. By expressing those results using the ionization yield functions, the pre-calculated results are extended to cover arbitrary magnetic field inclinations and atmospheric density profiles, allowing ionization rate altitude profile computations in the range of 20 and 200 km at any geographic point of interest and date/time by adopting results from an external atmospheric density model (e.g. NRLMSISE-00). The pre-calculated MCNP6 results are stored in a CDF (Common Data Format) file, and IDL routines library is written to provide an end-user interface to the model.

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Absolute binding free energies between T4 lysozyme and 141 small molecules: calculations based on multiple rigid receptor configurations

PubMed Central

Xie, Bing; Nguyen, Trung Hai; Minh, David D. L.

2017-01-01

We demonstrate the feasibility of estimating protein-ligand binding free energies using multiple rigid receptor configurations. Based on T4 lysozyme snapshots extracted from six alchemical binding free energy calculations with a flexible receptor, binding free energies were estimated for a total of 141 ligands. For 24 ligands, the calculations reproduced flexible-receptor estimates with a correlation coefficient of 0.90 and a root mean square error of 1.59 kcal/mol. The accuracy of calculations based on Poisson-Boltzmann/Surface Area implicit solvent was comparable to previously reported free energy calculations. PMID:28430432

An ultrahigh vacuum, low-energy ion-assisted deposition system for III-V semiconductor film growth

NASA Astrophysics Data System (ADS)

Rohde, S.; Barnett, S. A.; Choi, C.-H.

1989-06-01

A novel ion-assisted deposition system is described in which the substrate and growing film can be bombarded with high current densities (greater than 1 mA/sq cm) of very low energy (10-200 eV) ions. The system design philosophy is similar to that used in III-V semiconductor molecular-beam epitaxy systems: the chamber is an all-metal ultrahigh vacuum system with liquid-nitrogen-cooled shrouds, Knudsen-cell evaporation sources, a sample insertion load-lock, and a 30-kV reflection high-energy electron diffraction system. III-V semiconductor film growth is achieved using evaporated group-V fluxes and group-III elemental fluxes sputtered from high-purity targets using ions extracted from a triode glow discharge. Using an In target and an As effusion cell, InAs deposition rates R of 2 microns/h have been obtained. Epitaxial growth of InAs was observed on both GaSb(100) and Si(100) substrates.

The activation energy for nanocrystalline diamond films deposited from an Ar/H2/CH4 hot-filament reactor.

PubMed

Barbosa, D C; Melo, L L; Trava-Airoldi, V J; Corat, E J

2009-06-01

In this work we have investigated the effect of substrate temperature on the growth rate and properties of nanocrystalline diamond thin films deposited by hot filament chemical vapor deposition (HFCVD). Mixtures of 0.5 vol% CH4 and 25 vol% H2 balanced with Ar at a pressure of 50 Torr and typical deposition time of 12 h. We present the measurement of the activation energy by accurately controlling the substrate temperature independently of other CVD parameters. Growth rates have been measured in the temperature range from 550 to 800 degrees C. Characterization techniques have involved Raman spectroscopy, high resolution X-ray difractometry and scanning electron microscopy. We also present a comparison with most activation energy for micro and nanocrystalline diamond determinations in the literature and propose that there is a common trend in most observations. The result obtained can be an evidence that the growth mechanism of NCD in HFCVD reactors is very similar to MCD growth.

Predictive modeling capabilities from incident powder and laser to mechanical properties for laser directed energy deposition

NASA Astrophysics Data System (ADS)

Shin, Yung C.; Bailey, Neil; Katinas, Christopher; Tan, Wenda

2018-05-01

This paper presents an overview of vertically integrated comprehensive predictive modeling capabilities for directed energy deposition processes, which have been developed at Purdue University. The overall predictive models consist of vertically integrated several modules, including powder flow model, molten pool model, microstructure prediction model and residual stress model, which can be used for predicting mechanical properties of additively manufactured parts by directed energy deposition processes with blown powder as well as other additive manufacturing processes. Critical governing equations of each model and how various modules are connected are illustrated. Various illustrative results along with corresponding experimental validation results are presented to illustrate the capabilities and fidelity of the models. The good correlations with experimental results prove the integrated models can be used to design the metal additive manufacturing processes and predict the resultant microstructure and mechanical properties.

Predictive modeling capabilities from incident powder and laser to mechanical properties for laser directed energy deposition

NASA Astrophysics Data System (ADS)

Shin, Yung C.; Bailey, Neil; Katinas, Christopher; Tan, Wenda

2018-01-01

This paper presents an overview of vertically integrated comprehensive predictive modeling capabilities for directed energy deposition processes, which have been developed at Purdue University. The overall predictive models consist of vertically integrated several modules, including powder flow model, molten pool model, microstructure prediction model and residual stress model, which can be used for predicting mechanical properties of additively manufactured parts by directed energy deposition processes with blown powder as well as other additive manufacturing processes. Critical governing equations of each model and how various modules are connected are illustrated. Various illustrative results along with corresponding experimental validation results are presented to illustrate the capabilities and fidelity of the models. The good correlations with experimental results prove the integrated models can be used to design the metal additive manufacturing processes and predict the resultant microstructure and mechanical properties.

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

PubMed

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

2016-01-01

We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.

PubMed Central

Soares, C M; Martel, P J; Mendes, J; Carrondo, M A

1998-01-01

The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. Instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. Given these stability problems, a partially restrained model, which avoids destruction of the structure, was created with the objective of performing free energy calculations of heme reduction, studies that require long simulations. With this model, the free energy of reduction of each individual heme was calculated. A correction in the long-range electrostatic interactions of charge groups belonging to the redox centers had to be made in order to make the system physically meaningful. Correlation is obtained between the calculated free energies and the experimental data for three of four hemes. However, the relative scale of the calculated energies is different from the scale of the experimental free energies. Reasons for this are discussed. In addition to the free energy calculations, this model allows the study of conformational changes upon reduction. Even if the precise details of the structural changes that take place in this system upon individual heme reduction are probably out of the reach of this study, it appears that these structural changes are small, similarly to what is observed for other redox proteins. This does not mean that their effect is minor, and one example is the conformational change observed in propionate D from heme I when heme II becomes reduced. A motion of this kind could be the basis of the experimentally observed cooperativity effects between heme reduction, namely positive cooperativity. PMID:9545034

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

PubMed

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

2015-05-01

Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

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

PubMed Central

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

2015-01-01

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

Analysis of dose-LET distribution in the human body irradiated by high energy hadrons.

PubMed

Sato, T; Tsuda, S; Sakamoto, Y; Yamaguchi, Y; Niita, K

2003-01-01

For the purposes of radiological protection, it is important to analyse profiles of the particle field inside a human body irradiated by high energy hadrons, since they can produce a variety of secondary particles which play an important role in the energy deposition process, and characterise their radiation qualities. Therefore Monte Carlo calculations were performed to evaluate dose distributions in terms of the linear energy transfer of ionising particles (dose-LET distribution) using a newly developed particle transport code (Particle and Heavy Ion Transport code System, PHITS) for incidences of neutrons, protons and pions with energies from 100 MeV to 200 GeV. Based on these calculations, it was found that more than 80% and 90% of the total deposition energies are attributed to ionisation by particles with LET below 10 keV microm(-1) for the irradiations of neutrons and the charged particles, respectively.

Constraining Depositional Slope From Sedimentary Structures in Sandy Braided Streams

NASA Astrophysics Data System (ADS)

Lynds, R. M.; Mohrig, D.; Heller, P. L.

2003-12-01

Determination of paleoslopes in ancient fluvial systems has potentially broad application to quantitatively constraining the history of tectonics and paleoclimate in continental sequences. Our method for calculating paleoslopes for sandy braided streams is based upon a simple physical model that establishes depositional skin-frictional shear stresses from assemblages of sedimentary structures and their associated grain size distributions. The addition of a skin-frictional shear stress, with a geometrically determined form-drag shear stress results in a total boundary shear stress which is directly related to water-surface slope averaged over an appropriate spatial scale. In order to apply this model to ancient fluvial systems, it is necessary to measure the following: coarsest suspended sediment size, finest grain size carried in bed load, flow depth, dune height, and dune length. In the rock record, suspended load and bed load can be accurately assessed by well-preserved suspended load deposits ("low-energy" ripples) and bed load deposits (dune foresets). This model predicts an average slope for the North Loup River near Taylor, Nebraska (modern case study) of 2.7 x 10-3. The measured reach-averaged water surface slope for the same reach of the river is 1.37 x 10-3. We suggest that it is possible to calculate the depositional slope of a sandy fluvial system by a factor of approximately two. Additionally, preliminary application of this model to the Lower Jurassic Kayenta Formation throughout the Colorado Plateau provides a promising and consistent evaluation of paleoslope in an ancient and well-preserved, sandy braided stream deposit.

Ab initio calculation of reaction energies. III. Basis set dependence of relative energies on the FH2 and H2CO potential energy surfaces

NASA Astrophysics Data System (ADS)

Frisch, Michael J.; Binkley, J. Stephen; Schaefer, Henry F., III

1984-08-01

The relative energies of the stationary points on the FH2 and H2CO nuclear potential energy surfaces relevant to the hydrogen atom abstraction, H2 elimination and 1,2-hydrogen shift reactions have been examined using fourth-order Møller-Plesset perturbation theory and a variety of basis sets. The theoretical absolute zero activation energy for the F+H2→FH+H reaction is in better agreement with experiment than previous theoretical studies, and part of the disagreement between earlier theoretical calculations and experiment is found to result from the use of assumed rather than calculated zero-point vibrational energies. The fourth-order reaction energy for the elimination of hydrogen from formaldehyde is within 2 kcal mol-1 of the experimental value using the largest basis set considered. The qualitative features of the H2CO surface are unchanged by expansion of the basis set beyond the polarized triple-zeta level, but diffuse functions and several sets of polarization functions are found to be necessary for quantitative accuracy in predicted reaction and activation energies. Basis sets and levels of perturbation theory which represent good compromises between computational efficiency and accuracy are recommended.

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

PubMed

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

2017-12-01

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

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.

Reconstruction of Axial Energy Deposition in Magnetic Liner Inertial Fusion Based on PECOS Shadowgraph Unfolds Using the AMR Code FLASH

NASA Astrophysics Data System (ADS)

Adams, Marissa; Jennings, Christopher; Slutz, Stephen; Peterson, Kyle; Gourdain, Pierre; U. Rochester-Sandia Collaboration

2017-10-01

Magnetic Liner Inertial Fusion (MagLIF) experiments incorporate a laser to preheat a deuterium filled capsule before compression via a magnetically imploding liner. In this work, we focus on the blast wave formed in the fuel during the laser preheat component of MagLIF, where approximately 1kJ of energy is deposited in 3ns into the capsule axially before implosion. To model blast waves directly relevant to experiments such as MagLIF, we inferred deposited energy from shadowgraphy of laser-only experiments preformed at the PECOS target chamber using the Z-Beamlet laser. These energy profiles were used to initialize 2-dimensional simulations using by the adaptive mesh refinement code FLASH. Gradients or asymmetries in the energy deposition may seed instabilities that alter the fuel's distribution, or promote mix, as the blast wave interacts with the liner wall. The AMR capabilities of FLASH allow us to study the development and dynamics of these instabilities within the fuel and their effect on the liner before implosion. Sandia Natl Labs is managed by NTES of Sandia, LLC., a subsidiary of Honeywell International, Inc, for the U.S. DOEs NNSA under contract DE-NA0003525.

Enhancing nonlinear energy deposition into transparent solids with an elliptically polarized and mid-IR heating laser pulse under two-color femtosecond impact

NASA Astrophysics Data System (ADS)

Potemkin, F. V.; Mareev, E. I.; Bezsudnova, Yu I.; Platonenko, V. T.; Bravy, B. G.; Gordienko, V. M.

2017-06-01

We report on an enhancement of deposited energy density of up to 10 kJ cm-3 inside transparent solids (fused silica and quartz) from using two-color µJ energy level tightly focused (NA  =  0.5) co-propagating linearly polarized seeding (visible, 0.62 µm) and elliptically polarized heating (near-IR, 1.24 µm) femtosecond laser pulses. The rise in temperature under constant volume causes pressure of up to 12 GPa. It has been shown experimentally and theoretically that the production of seeding electrons through multiphoton ionization by visible laser pulse paves the way for controllability of the energy deposition and laser-induced micromodification via carrier heating by delayed infrared laser pulses inside the material. The developed theoretical approach predicts that the deposited energy density will be enhanced by up to 14 kJ cm-3 when using longer (up to 5 µm) wavelengths for heating laser pulses inside transparent solids.

SU-F-T-376: The Efficiency of Calculating Photonuclear Reaction On High-Energy Photon Therapy by Monte Carlo Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirayama, S; Fujibuchi, T

Purpose: Secondary-neutrons having harmful influences to a human body are generated by photonuclear reaction on high-energy photon therapy. Their characteristics are not known in detail since the calculation to evaluate them takes very long time. PHITS(Particle and Heavy Ion Transport code System) Monte Carlo code since versions 2.80 has the new parameter “pnimul” raising the probability of occurring photonuclear reaction forcibly to make the efficiency of calculation. We investigated the optimum value of “pnimul” on high-energy photon therapy. Methods: The geometry of accelerator head based on the specification of a Varian Clinac 21EX was used for PHITS ver. 2.80. Themore » phantom (30 cm * 30 cm * 30 cm) filled the composition defined by ICRU(International Commission on Radiation Units) was placed at source-surface distance 100 cm. We calculated the neutron energy spectra in the surface of ICRU phantom with “pnimal” setting 1, 10, 100, 1000, 10000 and compared the total calculation time and the behavior of photon using PDD(Percentage Depth Dose) and OCR(Off-Center Ratio). Next, the cutoff energy of photon, electron and positron were investigated for the calculation efficiency with 4, 5, 6 and 7 MeV. Results: The calculation total time until the errors of neutron fluence become within 1% decreased as increasing “pnimul”. PDD and OCR showed no differences by the parameter. The calculation time setting the cutoff energy like 4, 5, 6 and 7 MeV decreased as increasing the cutoff energy. However, the errors of photon become within 1% did not decrease by the cutoff energy. Conclusion: The optimum values of “pnimul” and the cutoff energy were investigated on high-energy photon therapy. It is suggest that using the optimum “pnimul” makes the calculation efficiency. The study of the cutoff energy need more investigation.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olsen, A.R.; Moreno, S.; Deringer, J.

The objective of this report is to provide a source of weather data for direct use with a number of simplified energy calculation methods available today. Complete weather data for a number of cities in the United States are provided for use in the following methods: degree hour, modified degree hour, bin, modified bin, and variable degree day. This report contains sets of weather data for 23 cities using Weather Year for Energy Calculations (WYEC) source weather data. Considerable overlap is present in cities (21) covered by both the TRY and WYEC data. The weather data at each city hasmore » been summarized in a number of ways to provide differing levels of detail necessary for alternative simplified energy calculation methods. Weather variables summarized include dry bulb and wet bulb temperature, percent relative humidity, humidity ratio, wind speed, percent possible sunshine, percent diffuse solar radiation, total solar radiation on horizontal and vertical surfaces, and solar heat gain through standard DSA glass. Monthly and annual summaries, in some cases by time of day, are available. These summaries are produced in a series of nine computer generated tables.« less

The Role of Porosity in the Formation of Coastal Boulder Deposits - Hurricane Versus Tsunami

NASA Astrophysics Data System (ADS)

Spiske, M.; Boeroecz, Z.; Bahlburg, H.

2007-12-01

Coastal boulder deposits are a consequence of high-energy wave impacts, such as storms, hurricanes or tsunami. Distinguishing parameters between storm, hurricane and tsunami origin are distance of a deposit from the coast, boulder weight and inferred wave height. Formulas to calculate minimum wave heights of both storm and tsunami waves depend on accurate determination of boulder dimensions and lithology from the respective deposits. At present however, boulder porosity appears to be commonly neglected, leading to significant errors in determined bulk density, especially when boulders consist of reef or coral limestone. This limits precise calculations of wave heights and hampers a clear distinction between storm, hurricane and tsunami origin. Our study uses Archimedean and optical 3D-profilometry measurements for the determination of porosities and bulk densities of reef and coral limestone boulders from the islands of Aruba, Bonaire and Curaçao (ABC Islands, Netherlands Antilles). Due to the high porosities (up to 68 %) of the enclosed coral species, the weights of the reef rock boulders are as low as 20 % of previously calculated values. Hence minimum calculated heights both for tsunami and hurricane waves are smaller than previously proposed. We show that hurricane action appears to be the likely depositional mechanism for boulders on the ABC Islands, since 1) our calculations result in tsunami wave heights which do not permit the overtopping of coastal platforms on the ABC Islands, 2) boulder fields lie on the windward (eastern) sides of the islands, 3) recent hurricanes transported boulders up to 35 m3 and 4) the scarcity of tsunami events affecting the coasts of the ABC Islands compared to frequent impacts of tropical storms and hurricanes.

Accurate, robust and reliable calculations of Poisson-Boltzmann binding energies

PubMed Central

Nguyen, Duc D.; Wang, Bao

2017-01-01

Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with SESs for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of ΔGel obtained at the grid spacing of 1.0 Å compared to ΔGel at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in ΔΔGel calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. PMID:28211071

On the importance of full-dimensionality in low-energy molecular scattering calculations

PubMed Central

Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof

2016-01-01

Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm−1 in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870

A study of vapor-phase deposition of silicon nitride layers by ammonolysis of dichlorosilane at lowered pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manzha, N. M., E-mail: magazine@miee.ru

2010-12-15

Deposition kinetics of silicon nitride layers at lowered reactor pressures of 10-130 Pa and temperatures in the range 973-1073 K has been studied. The equilibrium constant of the bimolecular reaction of dichlorosilane with ammonia has been calculated. The apparent activation energies calculated taking into account the experimental growth rate nearly coincide with the experimental data. Recommendations for improving the quality of silicon nitride layers are made.

Development of a calculation method for estimating specific energy distribution in complex radiation fields.

PubMed

Sato, Tatsuhiko; Watanabe, Ritsuko; Niita, Koji

2006-01-01

Estimation of the specific energy distribution in a human body exposed to complex radiation fields is of great importance in the planning of long-term space missions and heavy ion cancer therapies. With the aim of developing a tool for this estimation, the specific energy distributions in liquid water around the tracks of several HZE particles with energies up to 100 GeV n(-1) were calculated by performing track structure simulation with the Monte Carlo technique. In the simulation, the targets were assumed to be spherical sites with diameters from 1 nm to 1 microm. An analytical function to reproduce the simulation results was developed in order to predict the distributions of all kinds of heavy ions over a wide energy range. The incorporation of this function into the Particle and Heavy Ion Transport code System (PHITS) enables us to calculate the specific energy distributions in complex radiation fields in a short computational time.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

Effects of Differing Energy Dependences in Three Level-Density Models on Calculated Cross Sections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, C.Y.

2000-07-15

Three level-density formalisms commonly used for cross-section calculations are examined. Residual nuclides in neutron interaction with {sup 58}Ni are chosen to quantify the well-known differences in the energy dependences of the three formalisms. Level-density parameters for the Gilbert and Cameron model are determined from experimental information. Parameters for the back-shifted Fermi-gas and generalized superfluid models are obtained by fitting their level densities at two selected energies for each nuclide to those of the Gilbert and Cameron model, forcing the level densities of the three models to be as close as physically allowed. The remaining differences are in their energy dependencesmore » that, it is shown, can change the calculated cross sections and particle emission spectra significantly, in some cases or energy ranges by a factor of 2.« less

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints

PubMed Central

2017-01-01

Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein–protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task. Moreover, convergence and reversibility of resulting free-energy values remain poorly described. In this work, an easy-to-use, yet robust approach for the calculation of standard-state protein–protein binding free energies using perturbed distance restraints is described. In the binding process the conformations of the proteins were restrained, as suggested earlier. Two approaches to avoid end-state problems upon release of the conformational restraints were compared. The method was evaluated by practical application to a small model complex of ubiquitin and the very flexible ubiquitin-binding domain of human DNA polymerase ι (UBM2). All computed free energy differences were closely monitored for convergence, and the calculated binding free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol–1 from experimental values. Statistical error estimates were in the order of thermal noise. We conclude that the presented method has promising potential for broad applicability to quantitatively describe protein–protein and various other kinds of complex formation. PMID:28898077

Self-energy matrices for electron transport calculations within the real-space finite-difference formalism

NASA Astrophysics Data System (ADS)

Tsukamoto, Shigeru; Ono, Tomoya; Hirose, Kikuji; Blügel, Stefan

2017-03-01

The self-energy term used in transport calculations, which describes the coupling between electrode and transition regions, is able to be evaluated only from a limited number of the propagating and evanescent waves of a bulk electrode. This obviously contributes toward the reduction of the computational expenses in transport calculations. In this paper, we present a mathematical formula for reducing the computational expenses further without using any approximation and without losing accuracy. So far, the self-energy term has been handled as a matrix with the same dimension as the Hamiltonian submatrix representing the interaction between an electrode and a transition region. In this work, through the singular-value decomposition of the submatrix, the self-energy matrix is handled as a smaller matrix, whose dimension is the rank number of the Hamiltonian submatrix. This procedure is practical in the case of using the pseudopotentials in a separable form, and the computational expenses for determining the self-energy matrix are reduced by 90% when employing a code based on the real-space finite-difference formalism and projector-augmented wave method. In addition, this technique is applicable to the transport calculations using atomic or localized basis sets. Adopting the self-energy matrices obtained from this procedure, we present the calculation of the electron transport properties of C20 molecular junctions. The application demonstrates that the electron transmissions are sensitive to the orientation of the molecule with respect to the electrode surface. In addition, channel decomposition of the scattering wave functions reveals that some unoccupied C20 molecular orbitals mainly contribute to the electron conduction through the molecular junction.

Extended calculations of energies, transition rates, and lifetimes for F-like Kr XXVIII

NASA Astrophysics Data System (ADS)

Zhang, C. Y.; Si, R.; Yao, K.; Gu, M. F.; Wang, K.; Chen, C. Y.

2018-02-01

The excitation energies, lifetimes, wavelengths and E1, E2, M1 and M2 transition rates for the lowest 389 levels of the 2l7, 2l63l‧, 2l64l‧, and 2l65l‧ configurations from second-order many-body perturbation theory (MBPT) calculations, and the results for the lowest 200 states of the 2l7, 2l63l‧, and 2l64l‧ configurations from multi-configuration Dirac-Hartree-Fock (MCDHF) calculations in F-like Kr XXVIII are presented in this work. The relative differences between our two sets of level energies are mostly within 0.005% for the lowest 200 levels. Comparisons are made with experimental and other available theoretical results to assess the reliability and accuracy of the present calculations. We believe them to be the most complete and accurate results for Kr XXVIII at present.

Electron propagator calculations on the ionization energies of CrH -, MnH - and FeH -

NASA Astrophysics Data System (ADS)

Lin, Jyh-Shing; Ortiz, J. V.

1990-08-01

Electron propagator calculations with unrestricted Hartree-Fock reference states yield the ionization energies of the title anions. Spin contamination in the anionic reference state is small, enabling the use of second-and third-order self-energies in the Dyson equation. Feynman-Dyson amplitudes for these ionizations are essentially identical to canonical spin-orbitals. For most of the final states, these consist of an antibonding combination of an sp metal hybrid, polarized away from the hydrogen, and hydroegen s functions. In one case, the Feynman-Dyson amplitude consists of nonbonding d functions. Calculated ionization energies are within 0.5 eV of experiment.

Surface free energy of TiC layers deposited by electrophoretic deposition (EPD)

NASA Astrophysics Data System (ADS)

Gorji, Mohammad Reza; Sanjabi, Sohrab

2018-01-01

In this study porous structure coatings of bare TiC (i.e. 20 nm, 0.7 µm and 5/45 µm) and core-shell structures of TiC/NiP synthesized through electroless plating were deposited by EPD. Room temperature surface free energy (i.e. γs) of TiC and TiC/NiP coatings were determined via measuring contact angles of distilled water and diiodemethane liquids. The effect of Ni-P shell on spreading behavior of pure copper on porous EPD structures was also investigated by high temperature wetting experiments. According to the results existence of a Ni-P layer around the TiC particles has led to roughness (i.e. at least 0.1 µm), and porosity mean length (i.e. at least 1 µm) increase. This might be related to various sizes of TiC agglomerates formed during electroless plating. It has been observed that room temperature γs changed from 44.49 to 54.12 mJ.m-2 as a consequence of particle size enlargement for TiC. The highest and lowest (67.25 and 44.49 mJ.m-2) γs were measured for TiC nanoparticles which showed 1.5 times increase in surface free energy after being plated with Ni-P. It was also observed that plating Ni-P altered non-spreading (θs > 100 o) behavior of TiC to full-spreading ((θs 0o)) which can be useful for preparation of hard coatings by infiltration sintering phenomenon. Zeta potential of EPD suspensions, morphology, phase structure and topography of as-EPD layers were investigated through Zetasizer, field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD) and atomic force microscopy (AFM) instruments respectively.

Absolute surface energy calculations of Wurtzite (0001)/(000-1): a study of ZnO and GaN

NASA Astrophysics Data System (ADS)

Zhang, Jingzhao; Zhang, Yiou; Tse, Kinfai; Deng, Bei; Xu, Hu; Zhu, Junyi

The accurate absolute surface energies of (0001)/(000-1) surfaces of wurtzite structures are crucial in determining the thin film growth mode of important energy materials. However, the surface energies still remain to be solved due to the intrinsic difficulty of calculating dangling bond energy of asymmetrically bonded surface atoms. We used a pseudo-hydrogen passivation method to estimate the dangling bond energy and calculate the polar surfaces of ZnO and GaN. The calculations were based on the pseudo chemical potentials obtained from a set of tetrahedral clusters or simple pseudo-molecules, using density functional theory approaches, for both GGA and HSE. And the surface energies of (0001)/(000-1) surfaces of wurtzite ZnO and GaN we obtained showed relatively high self-consistencies. A wedge structure calculation with a new bottom surface passivation scheme of group I and group VII elements was also proposed and performed to show converged absolute surface energy of wurtzite ZnO polar surfaces. Part of the computing resources was provided by the High Performance Cluster Computing Centre, Hong Kong Baptist University. This work was supported by the start-up funding and direct Grant with the Project code of 4053134 at CUHK.

An efficient parallel algorithm for the calculation of canonical MP2 energies.

PubMed

Baker, Jon; Pulay, Peter

2002-09-01

We present the parallel version of a previous serial algorithm for the efficient calculation of canonical MP2 energies (Pulay, P.; Saebo, S.; Wolinski, K. Chem Phys Lett 2001, 344, 543). It is based on the Saebo-Almlöf direct-integral transformation, coupled with an efficient prescreening of the AO integrals. The parallel algorithm avoids synchronization delays by spawning a second set of slaves during the bin-sort prior to the second half-transformation. Results are presented for systems with up to 2000 basis functions. MP2 energies for molecules with 400-500 basis functions can be routinely calculated to microhartree accuracy on a small number of processors (6-8) in a matter of minutes with modern PC-based parallel computers. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1150-1156, 2002

MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO⁺(H₂O) cluster using accurate potential energy and dipole moment surfaces.

PubMed

Homayoon, Zahra

2014-09-28

A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO(+)(H2O) cluster is reported. The PES is based on fitting of roughly 32,000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO(+)(H2O) and NO(+)(D2O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO(+)(H2O) and NO(+)(D2O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO(+)(H2O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water "antisymmetric" stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO+(H2O) cluster using accurate potential energy and dipole moment surfaces

NASA Astrophysics Data System (ADS)

Homayoon, Zahra

2014-09-01

A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO+(H2O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO+(H2O) and NO+(D2O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO+(H2O) and NO+(D2O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO+(H2O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water "antisymmetric" stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

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

DOE PAGES

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

2017-02-22

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

A combined molecular dynamics and Monte Carlo simulation of the spatial distribution of energy deposition by proton beams in liquid water.

PubMed

Garcia-Molina, Rafael; Abril, Isabel; Heredia-Avalos, Santiago; Kyriakou, Ioanna; Emfietzoglou, Dimitris

2011-10-07

We have evaluated the spatial distribution of energy deposition by proton beams in liquid water using the simulation code SEICS (Simulation of Energetic Ions and Clusters through Solids), which combines molecular dynamics and Monte Carlo techniques and includes the main interaction phenomena between the projectile and the target constituents: (i) the electronic stopping force due to energy loss to target electronic excitations, including fluctuations due to the energy-loss straggling, (ii) the elastic scattering with the target nuclei, with their corresponding energy loss and (iii) the dynamical changes in projectile charge state due to electronic capture and loss processes. An important feature of SEICS is the accurate account of the excitation spectrum of liquid water, based on a consistent solid-state description of its energy-loss-function over the whole energy and momentum space. We analyse how the above-mentioned interactions affect the depth distribution of the energy delivered in liquid water by proton beams with incident energies of the order of several MeV. Our simulations show that the position of the Bragg peak is determined mainly by the stopping power, whereas its width can be attributed to the energy-loss straggling. Multiple elastic scattering processes contribute slightly only at the distal part of the Bragg peak. The charge state of the projectiles only changes when approaching the end of their trajectories, i.e. near the Bragg peak. We have also simulated the proton-beam energy distribution at several depths in the liquid water target, and found that it is determined mainly by the fluctuation in the energy loss of the projectile, evaluated through the energy-loss straggling. We conclude that a proper description of the target excitation spectrum as well as the inclusion of the energy-loss straggling is essential in the calculation of the proton beam depth-dose distribution.

A virtual photon energy fluence model for Monte Carlo dose calculation.

PubMed

Fippel, Matthias; Haryanto, Freddy; Dohm, Oliver; Nüsslin, Fridtjof; Kriesen, Stephan

2003-03-01

The presented virtual energy fluence (VEF) model of the patient-independent part of the medical linear accelerator heads, consists of two Gaussian-shaped photon sources and one uniform electron source. The planar photon sources are located close to the bremsstrahlung target (primary source) and to the flattening filter (secondary source), respectively. The electron contamination source is located in the plane defining the lower end of the filter. The standard deviations or widths and the relative weights of each source are free parameters. Five other parameters correct for fluence variations, i.e., the horn or central depression effect. If these parameters and the field widths in the X and Y directions are given, the corresponding energy fluence distribution can be calculated analytically and compared to measured dose distributions in air. This provides a method of fitting the free parameters using the measurements for various square and rectangular fields and a fixed number of monitor units. The next step in generating the whole set of base data is to calculate monoenergetic central axis depth dose distributions in water which are used to derive the energy spectrum by deconvolving the measured depth dose curves. This spectrum is also corrected to take the off-axis softening into account. The VEF model is implemented together with geometry modules for the patient specific part of the treatment head (jaws, multileaf collimator) into the XVMC dose calculation engine. The implementation into other Monte Carlo codes is possible based on the information in this paper. Experiments are performed to verify the model by comparing measured and calculated dose distributions and output factors in water. It is demonstrated that open photon beams of linear accelerators from two different vendors are accurately simulated using the VEF model. The commissioning procedure of the VEF model is clinically feasible because it is based on standard measurements in air and water. It is

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.

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.

Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

PubMed

Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

2008-02-13

Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

On the energy deposition into the plasma for an inverted fireball geometry

NASA Astrophysics Data System (ADS)

Levko, Dmitry; Gruenwald, Johannes

2017-10-01

Energy deposition into a plasma for an inverted fireball geometry is studied using a self-consistent two-dimensional Particle-in-Cell Monte Carlo collision model. In this model, the cathode is a pin which injects the fixed electron current and the anode is a hollow metal tube covered with the metal grid. We obtain an almost constant ratio between the densities of plasmas generated in the cathode-grid gap and inside the hollow anode. The results of the simulations show that there is no energy exchange between the beam and plasma electrons at low emission currents. For increasing current, however, we observe the increasing coupling between the electron beam and the thermal plasma electrons. This leads to the heating of plasma electrons and the generation of the so-called supra-thermal electrons.

Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design

PubMed Central

Chen, Wei; Chang, Chia-En; Gilson, Michael K.

2004-01-01

The second generation Mining Minima method yields binding affinities accurate to within 0.8 kcal/mol for the associations of α-, β-, and γ-cyclodextrin with benzene, resorcinol, flurbiprofen, naproxen, and nabumetone. These calculations require hours to a day on a commodity computer. The calculations also indicate that the changes in configurational entropy upon binding oppose association by as much as 24 kcal/mol and result primarily from a narrowing of energy wells in the bound versus the free state, rather than from a drop in the number of distinct low-energy conformations on binding. Also, the configurational entropy is found to vary substantially among the bound conformations of a given cyclodextrin-guest complex. This result suggests that the configurational entropy must be accounted for to reliably rank docked conformations in both host-guest and ligand-protein complexes. In close analogy with the common experimental observation of entropy-enthalpy compensation, the computed entropy changes show a near-linear relationship with the changes in mean potential plus solvation energy. PMID:15339804

A Method for Calculating Fermi Energy and Carrier Concentrations in Semiconducts

ERIC Educational Resources Information Center

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

1976-01-01

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

Neutron Capture Energies for Flux Normalization and Approximate Model for Gamma-Smeared Power

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kang Seog; Clarno, Kevin T.; Liu, Yuxuan

The Consortium for Advanced Simulation of Light Water Reactors (CASL) Virtual Environment for Reactor Applications (VERA) neutronics simulator MPACT has used a single recoverable fission energy for each fissionable nuclide assuming that all recoverable energies come only from fission reaction, for which capture energy is merged with fission energy. This approach includes approximations and requires improvement by separating capture energy from the merged effective recoverable energy. This report documents the procedure to generate recoverable neutron capture energies and the development of a program called CapKappa to generate capture energies. Recoverable neutron capture energies have been generated by using CapKappa withmore » the evaluated nuclear data file (ENDF)/B-7.0 and 7.1 cross section and decay libraries. The new capture kappas were compared to the current SCALE-6.2 and the CASMO-5 capture kappas. These new capture kappas have been incorporated into the Simplified AMPX 51- and 252-group libraries, and they can be used for the AMPX multigroup (MG) libraries and the SCALE code package. The CASL VERA neutronics simulator MPACT does not include a gamma transport capability, which limits it to explicitly estimating local energy deposition from fission, neutron, and gamma slowing down and capture. Since the mean free path of gamma rays is typically much longer than that for the neutron, and the total gamma energy is about 10% to the total energy, the gamma-smeared power distribution is different from the fission power distribution. Explicit local energy deposition through neutron and gamma transport calculation is significantly important in multi-physics whole core simulation with thermal-hydraulic feedback. Therefore, the gamma transport capability should be incorporated into the CASL neutronics simulator MPACT. However, this task will be timeconsuming in developing the neutron induced gamma production and gamma cross section libraries. This study is to

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.

PubMed

Miao, Yinglong; Feher, Victoria A; McCammon, J Andrew

2015-08-11

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively.

Size Reduction of Hamiltonian Matrix for Large-Scale Energy Band Calculations Using Plane Wave Bases

NASA Astrophysics Data System (ADS)

Morifuji, Masato

2018-01-01

We present a method of reducing the size of a Hamiltonian matrix used in calculations of electronic states. In the electronic states calculations using plane wave basis functions, a large number of plane waves are often required to obtain precise results. Even using state-of-the-art techniques, the Hamiltonian matrix often becomes very large. The large computational time and memory necessary for diagonalization limit the widespread use of band calculations. We show a procedure of deriving a reduced Hamiltonian constructed using a small number of low-energy bases by renormalizing high-energy bases. We demonstrate numerically that the significant speedup of eigenstates evaluation is achieved without losing accuracy.

Proposed linear energy transfer areal detector for protons using radiochromic film.

PubMed

Mayer, Rulon; Lin, Liyong; Fager, Marcus; Douglas, Dan; McDonough, James; Carabe, Alejandro

2015-04-01

Radiation therapy depends on predictably and reliably delivering dose to tumors and sparing normal tissues. Protons with kinetic energy of a few hundred MeV can selectively deposit dose to deep seated tumors without an exit dose, unlike x-rays. The better dose distribution is attributed to a phenomenon known as the Bragg peak. The Bragg peak is due to relatively high energy deposition within a given distance or high Linear Energy Transfer (LET). In addition, biological response to radiation depends on the dose, dose rate, and localized energy deposition patterns or LET. At present, the LET can only be measured at a given fixed point and the LET spatial distribution can only be inferred from calculations. The goal of this study is to develop and test a method to measure LET over extended areas. Traditionally, radiochromic films are used to measure dose distribution but not for LET distribution. We report the first use of these films for measuring the spatial distribution of the LET deposited by protons. The radiochromic film sensitivity diminishes for large LET. A mathematical model correlating the film sensitivity and LET is presented to justify relating LET and radiochromic film relative sensitivity. Protons were directed parallel to radiochromic film sandwiched between solid water slabs. This study proposes the scaled-normalized difference (SND) between the Treatment Planning system (TPS) and measured dose as the metric describing the LET. The SND is correlated with a Monte Carlo (MC) calculation of the LET spatial distribution for a large range of SNDs. A polynomial fit between the SND and MC LET is generated for protons having a single range of 20 cm with narrow Bragg peak. Coefficients from these fitted polynomial fits were applied to measured proton dose distributions with a variety of ranges. An identical procedure was applied to the protons deposited from Spread Out Bragg Peak and modulated by 5 cm. Gamma analysis is a method for comparing the calculated

Proposed linear energy transfer areal detector for protons using radiochromic film

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Rulon; Lin, Liyong; Fager, Marcus

2015-04-15

Radiation therapy depends on predictably and reliably delivering dose to tumors and sparing normal tissues. Protons with kinetic energy of a few hundred MeV can selectively deposit dose to deep seated tumors without an exit dose, unlike x-rays. The better dose distribution is attributed to a phenomenon known as the Bragg peak. The Bragg peak is due to relatively high energy deposition within a given distance or high Linear Energy Transfer (LET). In addition, biological response to radiation depends on the dose, dose rate, and localized energy deposition patterns or LET. At present, the LET can only be measured atmore » a given fixed point and the LET spatial distribution can only be inferred from calculations. The goal of this study is to develop and test a method to measure LET over extended areas. Traditionally, radiochromic films are used to measure dose distribution but not for LET distribution. We report the first use of these films for measuring the spatial distribution of the LET deposited by protons. The radiochromic film sensitivity diminishes for large LET. A mathematical model correlating the film sensitivity and LET is presented to justify relating LET and radiochromic film relative sensitivity. Protons were directed parallel to radiochromic film sandwiched between solid water slabs. This study proposes the scaled-normalized difference (SND) between the Treatment Planning system (TPS) and measured dose as the metric describing the LET. The SND is correlated with a Monte Carlo (MC) calculation of the LET spatial distribution for a large range of SNDs. A polynomial fit between the SND and MC LET is generated for protons having a single range of 20 cm with narrow Bragg peak. Coefficients from these fitted polynomial fits were applied to measured proton dose distributions with a variety of ranges. An identical procedure was applied to the protons deposited from Spread Out Bragg Peak and modulated by 5 cm. Gamma analysis is a method for comparing the

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.

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...

Studies on high electronic energy deposition in transparent conducting indium tin oxide thin films

NASA Astrophysics Data System (ADS)

Deshpande, N. G.; Gudage, Y. G.; Ghosh, A.; Vyas, J. C.; Singh, F.; Tripathi, A.; Sharma, Ramphal

2008-02-01

We have examined the effect of swift heavy ions using 100 MeV Au8+ ions on the electrical properties of transparent, conducting indium tin oxide polycrystalline films with resistivity of 0.58 × 10-4 Ω cm and optical transmission greater than 78% (pristine). We report on the modifications occurring after high electronic energy deposition. With the increase in fluency, x-ray line intensity of the peaks corresponding to the planes (1 1 0), (4 0 0), (4 4 1) increased, while (3 3 1) remained constant. Surface morphological studies showed a pomegranate structure of pristine samples, which was highly disturbed with a high dose of irradiation. For the high dose, there was a formation of small spherical domes uniformly distributed over the entire surface. The transmittance was seen to be decreasing with the increase in ion fluency. At higher doses, the resistivity and photoluminescence intensity was seen to be decreased. In addition, the carrier concentration was seen to be increased, which was in accordance with the decrease in resistivity. The observed modifications after high electronic energy deposition in these films may lead to fruitful device applications.

Modeling physical vapor deposition of energetic materials

DOE PAGES

Shirvan, Koroush; Forrest, Eric C.

2018-03-28

Morphology and microstructure of organic explosive films formed using physical vapor deposition (PVD) processes strongly depends on local surface temperature during deposition. Currently, there is no accurate means of quantifying the local surface temperature during PVD processes in the deposition chambers. This study focuses on using a multiphysics computational fluid dynamics tool, STARCCM+, to simulate pentaerythritol tetranitrate (PETN) deposition. The PETN vapor and solid phase were simulated using the volume of fluid method and its deposition in the vacuum chamber on spinning silicon wafers was modeled. The model also included the spinning copper cooling block where the wafers are placedmore » along with the chiller operating with forced convection refrigerant. Implicit time-dependent simulations in two- and three-dimensional were performed to derive insights in the governing physics for PETN thin film formation. PETN is deposited at the rate of 14 nm/s at 142.9 °C on a wafer with an initial temperature of 22 °C. The deposition of PETN on the wafers was calculated at an assumed heat transfer coefficient (HTC) of 400 W/m 2 K. This HTC proved to be the most sensitive parameter in determining the local surface temperature during deposition. Previous experimental work found noticeable microstructural changes with 0.5 mm fused silica wafers in place of silicon during the PETN deposition. This work showed that fused silica slows initial wafer cool down and results in ~10 °C difference for the surface temperature at 500 μm PETN film thickness. It was also found that the deposition surface temperature is insensitive to the cooling power of the copper block due to the copper block's very large heat capacity and thermal conductivity relative to the heat input from the PVD process. Future work should incorporate the addition of local stress during PETN deposition. Lastly, based on simulation results, it is also recommended to investigate the impact of wafer

Modeling physical vapor deposition of energetic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirvan, Koroush; Forrest, Eric C.

Morphology and microstructure of organic explosive films formed using physical vapor deposition (PVD) processes strongly depends on local surface temperature during deposition. Currently, there is no accurate means of quantifying the local surface temperature during PVD processes in the deposition chambers. This study focuses on using a multiphysics computational fluid dynamics tool, STARCCM+, to simulate pentaerythritol tetranitrate (PETN) deposition. The PETN vapor and solid phase were simulated using the volume of fluid method and its deposition in the vacuum chamber on spinning silicon wafers was modeled. The model also included the spinning copper cooling block where the wafers are placedmore » along with the chiller operating with forced convection refrigerant. Implicit time-dependent simulations in two- and three-dimensional were performed to derive insights in the governing physics for PETN thin film formation. PETN is deposited at the rate of 14 nm/s at 142.9 °C on a wafer with an initial temperature of 22 °C. The deposition of PETN on the wafers was calculated at an assumed heat transfer coefficient (HTC) of 400 W/m 2 K. This HTC proved to be the most sensitive parameter in determining the local surface temperature during deposition. Previous experimental work found noticeable microstructural changes with 0.5 mm fused silica wafers in place of silicon during the PETN deposition. This work showed that fused silica slows initial wafer cool down and results in ~10 °C difference for the surface temperature at 500 μm PETN film thickness. It was also found that the deposition surface temperature is insensitive to the cooling power of the copper block due to the copper block's very large heat capacity and thermal conductivity relative to the heat input from the PVD process. Future work should incorporate the addition of local stress during PETN deposition. Lastly, based on simulation results, it is also recommended to investigate the impact of wafer

CC2 oscillator strengths within the local framework for calculating excitation energies (LoFEx).

PubMed

Baudin, Pablo; Kjærgaard, Thomas; Kristensen, Kasper

2017-04-14

In a recent work [P. Baudin and K. Kristensen, J. Chem. Phys. 144, 224106 (2016)], we introduced a local framework for calculating excitation energies (LoFEx), based on second-order approximated coupled cluster (CC2) linear-response theory. LoFEx is a black-box method in which a reduced excitation orbital space (XOS) is optimized to provide coupled cluster (CC) excitation energies at a reduced computational cost. In this article, we present an extension of the LoFEx algorithm to the calculation of CC2 oscillator strengths. Two different strategies are suggested, in which the size of the XOS is determined based on the excitation energy or the oscillator strength of the targeted transitions. The two strategies are applied to a set of medium-sized organic molecules in order to assess both the accuracy and the computational cost of the methods. The results show that CC2 excitation energies and oscillator strengths can be calculated at a reduced computational cost, provided that the targeted transitions are local compared to the size of the molecule. To illustrate the potential of LoFEx for large molecules, both strategies have been successfully applied to the lowest transition of the bivalirudin molecule (4255 basis functions) and compared with time-dependent density functional theory.

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.

Topography and surface free energy of DPPC layers deposited on a glass, mica, or PMMA support.

PubMed

Jurak, Malgorzata; Chibowski, Emil

2006-08-15

An investigation of energetic properties of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) layers deposited on glass, mica, and PMMA (poly(methyl methacrylate)) surfaces was carried out by means of contact angles measurements (advancing and receding) for three probe liquids (diiodomethane, water, and formamide). DPPC was deposited on the surfaces from water (on glass and mica) or methanol (on PMMA) solutions. The topography of the tested surfaces was determined with a help of scanning electron microscopy (SEM) and atomic force microscopy (AFM). Using the measured contact angles, the total apparent surface free energy and its components of the studied layers were determined from van Oss et al.'s (Lifshitz-van der Waals and acid-base components, LWAB) and contact angle hysteresis (CAH) approaches. It allowed us to learn about changes in the surface free energy of the layers (hydrophobicity/hydrophilicity) depending on their number and kind of support. It was found that the changes in the energy greatly depended on the surface properties of the substrate as well as the statistical number of monolayers of DPPC. However, principal changes took place for first three monolayers.

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

PubMed

Kaus, Joseph W; Pierce, Levi T; Walker, Ross C; McCammont, J Andrew

2013-09-10

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

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

PubMed Central

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

2013-01-01

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

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters

PubMed Central

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

2013-01-01

Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand’s electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered. PMID:24015114

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perfetti, Christopher M; Rearden, Bradley T

2013-01-01

The TSUNAMI code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, such as quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The CLUTCH and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in themore » CE KENO framework to generate the capability for TSUNAMI-3D to perform eigenvalue sensitivity calculations in continuous-energy applications. This work explores the improvements in accuracy that can be gained in eigenvalue and eigenvalue sensitivity calculations through the use of the SCALE CE KENO and CE TSUNAMI continuous-energy Monte Carlo tools as compared to multigroup tools. The CE KENO and CE TSUNAMI tools were used to analyze two difficult models of critical benchmarks, and produced eigenvalue and eigenvalue sensitivity coefficient results that showed a marked improvement in accuracy. The CLUTCH sensitivity method in particular excelled in terms of efficiency and computational memory requirements.« less

Numerical renormalization group calculation of impurity internal energy and specific heat of quantum impurity models

NASA Astrophysics Data System (ADS)

Merker, L.; Costi, T. A.

2012-08-01

We introduce a method to obtain the specific heat of quantum impurity models via a direct calculation of the impurity internal energy requiring only the evaluation of local quantities within a single numerical renormalization group (NRG) calculation for the total system. For the Anderson impurity model we show that the impurity internal energy can be expressed as a sum of purely local static correlation functions and a term that involves also the impurity Green function. The temperature dependence of the latter can be neglected in many cases, thereby allowing the impurity specific heat Cimp to be calculated accurately from local static correlation functions; specifically via Cimp=(∂Eionic)/(∂T)+(1)/(2)(∂Ehyb)/(∂T), where Eionic and Ehyb are the energies of the (embedded) impurity and the hybridization energy, respectively. The term involving the Green function can also be evaluated in cases where its temperature dependence is non-negligible, adding an extra term to Cimp. For the nondegenerate Anderson impurity model, we show by comparison with exact Bethe ansatz calculations that the results recover accurately both the Kondo induced peak in the specific heat at low temperatures as well as the high-temperature peak due to the resonant level. The approach applies to multiorbital and multichannel Anderson impurity models with arbitrary local Coulomb interactions. An application to the Ohmic two-state system and the anisotropic Kondo model is also given, with comparisons to Bethe ansatz calculations. The approach could also be of interest within other impurity solvers, for example, within quantum Monte Carlo techniques.

Monte Carlo Calculations of Suprathermal Alpha Particles Trajectories in the Rippled Field of TFTR

NASA Astrophysics Data System (ADS)

Punjabi, Alkesh; Lam, Maria; Boozer, Allen

1996-11-01

We study the transport of suprathermal alpha particles and their energy deposition into electrons, deuterons, tritons and carbon-12 impurity in the rippled field of TFTR. The Monte Carlo code (Punjabi A., Boozer A., Lam M., Kim M., and Burke K., J. Plasma Phys.), 44, 405 (1990) developed by Punjabi and Boozer for the transport of plasma particles due to MHD modes in toroidal plasmas is used in conjunction with the SHAF code (White R. B., and Boozer A., PPPL -3094) (1995) of White. we integrate drift Hamiltonian equation of motion in non-canonical, rectangular, Boozer coordinates. The deposition of alpha energy into electrons, deuterons, tritons and C-12 particles is calculated and recorded. The effects of energy and pitch angle scattering are included. The result of this study will be presented. This work is supported by the US DOE. The assistance provided by Professors R. B. White and S. Zweben of PPPL is gratefully acknowledged.

Numerical simulations of energy deposition caused by 50 MeV—50 TeV proton beams in copper and graphite targets

NASA Astrophysics Data System (ADS)

Nie, Y.; Schmidt, R.; Chetvertkova, V.; Rosell-Tarragó, G.; Burkart, F.; Wollmann, D.

2017-08-01

The conceptual design of the Future Circular Collider (FCC) is being carried out actively in an international collaboration hosted by CERN, for the post-Large Hadron Collider (LHC) era. The target center-of-mass energy of proton-proton collisions for the FCC is 100 TeV, nearly an order of magnitude higher than for LHC. The existing CERN accelerators will be used to prepare the beams for FCC. Concerning beam-related machine protection of the whole accelerator chain, it is critical to assess the consequences of beam impact on various accelerator components in the cases of controlled and uncontrolled beam losses. In this paper, we study the energy deposition of protons in solid copper and graphite targets, since the two materials are widely used in magnets, beam screens, collimators, and beam absorbers. Nominal injection and extraction energies in the hadron accelerator complex at CERN were selected in the range of 50 MeV-50 TeV. Three beam sizes were studied for each energy, corresponding to typical values of the betatron function. Specifically for thin targets, comparisons between fluka simulations and analytical Bethe equation calculations were carried out, which showed that the damage potential of a few-millimeter-thick graphite target and submillimeter-thick copper foil can be well estimated directly by the Bethe equation. The paper provides a valuable reference for the quick evaluation of potential damage to accelerator elements over a large range of beam parameters when beam loss occurs.

Rapid calculation of radiative heating rates and photodissociation rates in inhomogeneous multiple scattering atmospheres

NASA Technical Reports Server (NTRS)

Toon, Owen B.; Mckay, C. P.; Ackerman, T. P.; Santhanam, K.

1989-01-01

The solution of the generalized two-stream approximation for radiative transfer in homogeneous multiple scattering atmospheres is extended to vertically inhomogeneous atmospheres in a manner which is numerically stable and computationally efficient. It is shown that solar energy deposition rates, photolysis rates, and infrared cooling rates all may be calculated with the simple modifications of a single algorithm. The accuracy of the algorithm is generally better than 10 percent, so that other uncertainties, such as in absorption coefficients, may often dominate the error in calculation of the quantities of interest to atmospheric studies.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

Variationally Optimized Free-Energy Flooding for Rate Calculation.

PubMed

McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

2015-08-14

We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

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

ERIC Educational Resources Information Center

Woodyard, Jack R., Sr.

1972-01-01

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

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

PubMed Central

2016-01-01

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively. PMID:26300708

System and method for radiation dose calculation within sub-volumes of a monte carlo based particle transport grid

DOEpatents

Bergstrom, Paul M.; Daly, Thomas P.; Moses, Edward I.; Patterson, Jr., Ralph W.; Schach von Wittenau, Alexis E.; Garrett, Dewey N.; House, Ronald K.; Hartmann-Siantar, Christine L.; Cox, Lawrence J.; Fujino, Donald H.

2000-01-01

A system and method is disclosed for radiation dose calculation within sub-volumes of a particle transport grid. In a first step of the method voxel volumes enclosing a first portion of the target mass are received. A second step in the method defines dosel volumes which enclose a second portion of the target mass and overlap the first portion. A third step in the method calculates common volumes between the dosel volumes and the voxel volumes. A fourth step in the method identifies locations in the target mass of energy deposits. And, a fifth step in the method calculates radiation doses received by the target mass within the dosel volumes. A common volume calculation module inputs voxel volumes enclosing a first portion of the target mass, inputs voxel mass densities corresponding to a density of the target mass within each of the voxel volumes, defines dosel volumes which enclose a second portion of the target mass and overlap the first portion, and calculates common volumes between the dosel volumes and the voxel volumes. A dosel mass module, multiplies the common volumes by corresponding voxel mass densities to obtain incremental dosel masses, and adds the incremental dosel masses corresponding to the dosel volumes to obtain dosel masses. A radiation transport module identifies locations in the target mass of energy deposits. And, a dose calculation module, coupled to the common volume calculation module and the radiation transport module, for calculating radiation doses received by the target mass within the dosel volumes.

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

NASA Astrophysics Data System (ADS)

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

2013-06-01

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