Calculation of energy deposition distributions for simple geometries
NASA Technical Reports Server (NTRS)
Watts, J. W., Jr.
1973-01-01
When high-energy charged particles pass through a thin detector, the ionization energy loss in that detector is subject to fluctuations or straggling which must be considered in interpreting the data. Under many conditions, which depend upon the charge and energy of the incident particle and the detector geometry, the ionization energy lost by the particle is significantly different from the energy deposited in the detector. This problem divides naturally into a calculation of the energy loss that results in excitation and low-energy secondary electrons which do not travel far from their production points, and a calculation of energy loss that results in high-energy secondary electrons which can escape from the detector. The first calculation is performed using a modification of the Vavilov energy loss distribution. A cutoff energy is introduced above which all electrons are ignored and energy transferred to low energy particles is assumed to be equivalent to the energy deposited by them. For the second calculation, the trajectory of the primary particle is considered as a source of secondary high-energy electrons. The electrons from this source are transported using Monte Carlo techniques and multiple scattering theory, and the energy deposited by them in the detector is calculated. The results of the two calculations are then combined to predict the energy deposition distribution. The results of these calculations are used to predict the charge resolution of parallel-plate pulse ionization chambers that are being designed to measure the charge spectrum of heavy nuclei in the galactic cosmic-ray flux.
Nuclear data processing for energy release and deposition calculations in the MC21 Monte Carlo code
Trumbull, T. H.
2013-07-01
With the recent emphasis in performing multiphysics calculations using Monte Carlo transport codes such as MC21, the need for accurate estimates of the energy deposition-and the subsequent heating - has increased. However, the availability and quality of data necessary to enable accurate neutron and photon energy deposition calculations can be an issue. A comprehensive method for handling the nuclear data required for energy deposition calculations in MC21 has been developed using the NDEX nuclear data processing system and leveraging the capabilities of NJOY. The method provides a collection of data to the MC21 Monte Carlo code supporting the computation of a wide variety of energy release and deposition tallies while also allowing calculations with different levels of fidelity to be performed. Detailed discussions on the usage of the various components of the energy release data are provided to demonstrate novel methods in borrowing photon production data, correcting for negative energy release quantities, and adjusting Q values when necessary to preserve energy balance. Since energy deposition within a reactor is a result of both neutron and photon interactions with materials, a discussion on the photon energy deposition data processing is also provided. (authors)
Comparison between calculation and measurement of energy deposited by 800 MeV protons
Loewe, W.E.
1980-04-03
The High Energy Transport Code, HETC, was obtained from the Radiation Shielding Information Center (RSIC) at Oak Ridge National Laboratory and altered as necessary to run on a CDC 7600 using the LTSS software in use at LLNL. HETC was then used to obtain calculated estimates of energy deposited, for comparison with a series of benchmark experiments done by LLNL. These experiments used proton beams of various energies incident on well-defined composite targets in good geometry. In this report, two aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam are discussed. Both aspects involve the fact that workers at SAI had previously used their version of HETC to calculate this experiment and reported their comparison with the measured data. The first aspect addressed is that their calculated data and LLNL calculations do not agree, suggesting an error in the conversion process from the RSIC code. The second aspect is not independent of the first, but is of sufficient importance to merit separate emphasis. It is that the SAI calculations agree well with experiments at the detector plate located some distance from the shower plate, whereas the LLNL calculations show a clearcut discrepancy there in comparison with the experiment. A contract was let in January 1980 by LLNL with SAI in order to obtain full details on the two cited aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam. The ensuing discussion is based on the final report of that contracted work.
Calculation of the Frequency Distribution of the Energy Deposition in DNA Volumes by Heavy Ions
NASA Technical Reports Server (NTRS)
Plante, Ianik; Cicinotta, Francis A.
2012-01-01
Radiation quality effects are largely determined by energy deposition in small volumes of characteristic sizes less than 10 nm representative of short-segments of DNA, the DNA nucleosome, or molecules initiating oxidative stress in the nucleus, mitochondria, or extra-cellular matrix. On this scale, qualitatively distinct types of molecular damage are possible for high linear energy transfer (LET) radiation such as heavy ions compared to low LET radiation. Unique types of DNA lesions or oxidative damages are the likely outcome of the energy deposition. The frequency distribution for energy imparted to 1-20 nm targets per unit dose or particle fluence is a useful descriptor and can be evaluated as a function of impact parameter from an ions track. In this work, the simulation of 1-Gy irradiation of a cubic volume of 5 micron by: 1) 450 (1)H(+) ions, 300 MeV; 2) 10 (12)C(6+) ions, 290 MeV/amu and 3) (56)Fe(26+) ions, 1000 MeV/amu was done with the Monte-Carlo simulation code RITRACKS. Cylindrical targets are generated in the irradiated volume, with random orientation. The frequency distribution curves of the energy deposited in the targets is obtained. For small targets (i.e. <25 nm size), the probability of an ion to hit a target is very small; therefore a large number of tracks and targets as well as a large number of histories are necessary to obtain statistically significant results. This simulation is very time-consuming and is difficult to perform by using the original version of RITRACKS. Consequently, the code RITRACKS was adapted to use multiple CPU on a workstation or on a computer cluster. To validate the simulation results, similar calculations were performed using targets with fixed position and orientation, for which experimental data are available [5]. Since the probability of single- and double-strand breaks in DNA as function of energy deposited is well know, the results that were obtained can be used to estimate the yield of DSB, and can be extended
Monte Carlo calculation of energy deposition in ionization chambers for tritium measurements
NASA Astrophysics Data System (ADS)
Zhilin, Chen; Shuming, Peng; Dan, Meng; Yuehong, He; Heyi, Wang
2014-10-01
Energy deposition in ionization chambers for tritium measurements has been theoretically studied using Monte Carlo code MCNP 5. The influence of many factors, including carrier gas, chamber size, wall materials and gas pressure, has been evaluated in the simulations. It is found that β rays emitted by tritium deposit much more energy into chambers flowing through with argon than with deuterium in them, as much as 2.7 times higher at pressure 100 Pa. As chamber size gets smaller, energy deposition decreases sharply. For an ionization chamber of 1 mL, β rays deposit less than 1% of their energy at pressure 100 Pa and only 84% even if gas pressure is as high as 100 kPa. It also indicates that gold plated ionization chamber results in the highest deposition ratio while aluminum one leads to the lowest. In addition, simulations were validated by comparison with experimental data. Results show that simulations agree well with experimental data.
Comparison of energy deposition calculations by the LAHET Code System with experimental results
Beard, C.A.; Lisowski, P.W.; Russell, G.J.; Waters, L.S.
1993-08-01
A comparison was performed between the energy deposition predicted by the LAHET Code System (LCS) with experimental values determined by Belyakov-Bodin et al. for 800, 1000, and 1200 MeV protons on targets composed of lead, bismuth, beryllium, carbon, and aluminum. The lead and bismuth showed agreement within approximately 10% at locations throughout the targets, and the agreement of the total energy deposited over the axial length of the targets ranged from 1% to 25%. For the lead and bismuth cases, the LCS predictions were always greater than the experimental results. For the lighter materials, the agreement at locations throughout the target only agreed within approximately 20%. No definable trend could be determined for the lighter materials since some LCS predictions were greater than the experimental results, some were less than the experimental results, and some showed very good agreement. The total energy deposited over the axial length of the targets was not compared for the lighter materials since it was not explicitly given with the experimental data.
Energy-Deposition and Damage Calculations in Core-Vessel Inserts at the Spallation Neutron Source
Murphy, B.D.
2002-06-25
Heat-deposition and damage calculations are described for core-vessel inserts in the target area of the Spallation Neutron Source. Two separate designs for these inserts (or neutron beam tubes) were studied; a single-unit insert and a multi-unit insert. The single unit contains a neutron guide; the multi unit does not. Both units are constructed of stainless steel. For the single unit, separate studies were carried out with the guide composed of stainless steel, glass, and aluminum. Results are also reported for an aluminum window on the front of the insert, a layer of nickel on the guide, a cadmium shield surrounding the guide, and a stainless steel plug in the beam-tube opening. The locations of both inserts were the most forward positions to be occupied by each design respectively thus ensuring that the calculations are conservative.
Calculation of electron trajectory and energy deposition in no screening region
NASA Astrophysics Data System (ADS)
Kia, Mohammad Reza; Noshad, Houshyar
2016-01-01
The probability density function (PDF) of energy for inelastic collision is obtained by solving the integro-differential form of the quantity equation with the Bhabha differential cross section for particles with spin 1/2. Hence, the total PDF in no screening region is determined by folding theory with the following two assumptions: (1) the electron loses energy by collision and radiation and (2) the electron velocity does not change with a thin absorber. Therefore, a set of coupled stochastic differential equations based on the deviation and energy loss PDFs for electron is presented to obtain the electron trajectory inside the target. The energy PDFs for an electron beam with incident energy of 15.7 MeV inside aluminum and copper are calculated. Besides, the dose distributions for an electron beam with incident energies of 20, 10.2, 6, and 0.5 MeV in water are obtained. The results are in excellent agreement with the experimental data reported in the literature.
NASA Astrophysics Data System (ADS)
Tkachenko, E. A.; Postnikov, D. V.; Blesman, A. I.; Polonyankin, D. A.
2016-02-01
The paper justifies the usefulness of preliminary ion implantation before forming the protective coating by magnetron sputtering in order to improve its adhesion and hence the coating durability. The important characteristics of coatings include the adhesion force and energy. To select the optimal modes of coatings formation, materials and equipment it is proposed the theoretical method of the adhesion force calculation in binary metallic systems. The adhesion force and energy depend on the elemental distribution in the depth of the coating and on the single bond force as in the substrate and in the coating. In addition the adhesion force is also determined by the coefficient taking into account the reduction of the possible bond number and depending on the surface purity and the structural defects presence. The developed model includes all of the above factors. The elements distribution over the depth of the coating was estimated using a kinetic model of mass transfer by vacancy mechanism. The paper presents the results of the adhesion force calculation for the chromium coating on the surface of A21382 steel.
NASA Astrophysics Data System (ADS)
Ploc, Ondrej; Uchihori, Yukio; Kitamura, H.; Kodaira, S.; Dachev, Tsvetan; Spurny, Frantisek; Jadrnickova, Iva; Mrazova, Zlata; Kubancak, Jan
Liulin type detectors are recently used in a wide range of cosmic radiation measurements, e.g. at alpine observatories, onboard aircrafts and spacecrafts. They provide energy deposition spectra up to 21 MeV, higher energy deposition events are stored in the last (overflow) channel. Their main advantages are portability (about the same size as a pack of cigarettes) and ability to record spectra as a function of time, so they can be used as personal dosimeters. Their well-known limitations are: (i) the fact that they are not tissue equivalent, (ii) they can be used as LET spectrometer only under specific conditions (e.g. broad parallel beam), and (iii) that the energy deposition event from particles of LETH20¿35 keV/µm is stored in the overflow bin only so the spectral information is missing. Tissue equivalent proportional counter (TEPC) Hawk has no of these limitations but on the other hand, it cannot be used as personal dosimeter because of its big size (cylinder of 16 cm diameter and 34 cm long). An important fraction of dose equivalent onboard spacecrafts is caused by heavy ions. This contribution presents results from intercomparison measurements with Liulin and Hawk at Heavy Ion Medical Accelerator in Chiba (HIMAC) and cyclotron beams, and related calculations with PHITS (Particle and Heavy-ion Transport code System). Following particles/ions and energies were used: protons 70 MeV, He 150 MeV, Ne 400 MeV, C 135 MeV, C 290 MeV, and Fe 500 MeV. Calculations of LET spectra by PHITS were performed for both, Liulin and Hawk. In case of Liulin, the dose equivalent was calculated using simulations in which several tissue equivalent materials were used as active volume instead of the silicon diode. Dose equivalents calculated in such way was compared with that measured with Hawk. LET spectra measured with Liulin and Hawk were compared for each ion at several points behind binary filters along the Brag curve. Good agreement was observed for some configurations; for
Heat Deposit Calculation in Spallation Unit
NASA Astrophysics Data System (ADS)
Karmanov, F. I.; Travleev, A. A.; Latysheva, L. N.; Vecchi, M.
2001-11-01
The present study concerns the calculation of the heat deposition in one of the EAP-80 basic units - the spallation module including the beam window, lead-bismuth spallation target and primary liquid metal cooling system. It is assumed that the model of sub-critical reactor under investigation is based on ANSALDO-INFN-ENEA-CRS4 reference configuration1. The calculation have been done by means of a couple computer codes: INCC 2 and GEANT3.21 3. These codes have been preliminary tested on the experimental data obtained in 4 for the case of interaction of proton beam and lead-bismuth targets at the energy Ep= 800MeV which is close to energy range relevant for ADS configuration.
NASA Astrophysics Data System (ADS)
Plante, Ianik; Ponomarev, Artem L.; Cucinotta, Francis A.
2013-09-01
The biological effects of high-linear energy transfer (LET) radiation are different from those caused by low-LET radiation due to the difference in the patterns of energy deposition in cells. In this work, we studied the role of the track structure in the spatial distribution of radiation-induced double-strand breaks (DSBs). In the first part, the irradiation of a cubic volume of 12 µm of side by 300 MeV protons (LET ˜0.3 keV µm-1) and by 1 GeV/amu iron ion particles (LET˜150 keV µm-1) was simulated with the Monte Carlo code RITRACKS (relativistic ion tracks) and the dose was calculated in voxels of different sizes. In the second part, dose calculations were combined with chromosomes simulated by a random walk (RW) model to assess the formation of DSBs. The number of DSBs was calculated as a function of the dose and particle fluence for 1 GeV protons, 293 MeV/u carbon, and 1 GeV/u iron particles. Finally, the DSB yield was obtained as a function of the LET for protons, helium, and carbon. In general, the number and distribution of calculated DSBs were similar to experimental DNA repair foci data. From this study, we concluded that a stochastic model combining nanoscopic dose calculations and chromosomes simulated by RWs is a useful approach to study radiation-induced DSBs.
Plante, Ianik; Ponomarev, Artem L; Cucinotta, Francis A
2013-09-21
The biological effects of high-linear energy transfer (LET) radiation are different from those caused by low-LET radiation due to the difference in the patterns of energy deposition in cells. In this work, we studied the role of the track structure in the spatial distribution of radiation-induced double-strand breaks (DSBs). In the first part, the irradiation of a cubic volume of 12 µm of side by 300 MeV protons (LET ∼0.3 keV µm(-1)) and by 1 GeV/amu iron ion particles (LET∼150 keV µm(-1)) was simulated with the Monte Carlo code RITRACKS (relativistic ion tracks) and the dose was calculated in voxels of different sizes. In the second part, dose calculations were combined with chromosomes simulated by a random walk (RW) model to assess the formation of DSBs. The number of DSBs was calculated as a function of the dose and particle fluence for 1 GeV protons, 293 MeV/u carbon, and 1 GeV/u iron particles. Finally, the DSB yield was obtained as a function of the LET for protons, helium, and carbon. In general, the number and distribution of calculated DSBs were similar to experimental DNA repair foci data. From this study, we concluded that a stochastic model combining nanoscopic dose calculations and chromosomes simulated by RWs is a useful approach to study radiation-induced DSBs. PMID:23999659
Energy deposition in STARFIRE reactor components
Gohar, Y.; Brooks, J.N.
1985-04-01
The energy deposition in the STARFIRE commercial tokamak reactor was calculated based on detailed models for the different reactor components. The heat deposition and the 14 MeV neutron flux poloidal distributions in the first wall were obtained. The poloidal surface heat load distribution in the first wall was calculated from the plasma radiation. The Monte Carlo method was used for the calculation to allow an accurate modeling for the reactor geometry.
Model calculates was deposition for North Sea oils
Majeed, A.; Bringedal, B.; Overa, S. )
1990-06-18
A model for calculation of wax formation and deposition in pipelines and process equipment has been developed along with a new method for wax-equilibrium calculations using input from TBP distillation cuts. Selected results from the wax formation and deposition model have been compared with laboratory data from wax equilibrium and deposition experiments, and there have been some field applications of the model.
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
Calculation of wet deposition from radioactive plumes
Brenk, H.D.; Vogt, K.J.
1981-05-01
A reevaluation of the current wet deposition models for radioactive plumes of the Gaussian type is presented. The application of the methodology to routine and accidental activity releases from nuclear facilities is discussed. A set of washout parameters for a simplified model has been included.
Energy deposition and dynamic response of materials
NASA Astrophysics Data System (ADS)
Perry, Frank C.
1993-07-01
We are exploring new applications of the technology of energy deposition and dynamic response. Early studies involved analytical solutions of the coupled thermal and elastic response of materials to pulsed energy deposition. Experiments designed to test the theory led to determinations of thermal pressure coefficients for a variety of materials and an understanding of the effects of the time dependence of the energy source on dynamic response. Subsequent experiments at higher deposited energies required analysis by an energy deposition-wave propagation code to explain the observed elastic-plastic behavior. Instrumentation included laser interferometry and holographic interferometry for multi- dimensional response. A possible application of this technology to Biomedical Science is a technique to measure ion transport in biological material. It requires a combination of holographic interferometry and spectroscopy, namely, Resonant Holographic Interferometry Spectroscopy (RHIS). The technique involves the absorption and refraction of light near absorption lines. Stress waves arising from the absorbed light can be assessed with the energy deposition-wave propagation code. Such calculations will require the inclusion of appropriate biomaterial properties.
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.
MCNPX benchmark of in-beam proton energy deposition
Corzine, K.; Ferguson, P.; Morgan, G.; Quintana, D.; Waters, L.; Cooper, R.; Liljestrand, R.; Whiteson, A.
2000-07-01
The MCNPX code is being used to calculate energy deposition in the accelerator production of tritium (APT) target/blanket system components. To ensure that these components are properly designed, the code must be validated. An energy deposition experiment was designed to aid in the code validation using thermocouple sensors in-beam and thermistor-type sensors in decoupler- and blanketlike regions. This paper focuses on the in-beam thermocouple sensors.
NASA Technical Reports Server (NTRS)
Marshall, Paul; Reed, Robert; Fodness, Bryan; Jordan, Tom; Pickel, Jim; Xapsos, Michael; Burke, Ed
2004-01-01
This slide presentation examines motivation for Monte Carlo methods, charge deposition in sensor arrays, displacement damage calculations, and future work. The discussion of charge deposition sensor arrays includes Si active pixel sensor APS arrays and LWIR HgCdTe FPAs. The discussion of displacement damage calculations includes nonionizing energy loss (NIEL), HgCdTe NIEL calculation results including variance, and implications for damage in HgCdTe detector arrays.
Modeling Atmospheric Energy Deposition (by energetic ions)
NASA Astrophysics Data System (ADS)
Parkinson, C. D.; Brain, D. A.; Lillis, R. J.; Liemohn, M. W.; Bougher, S. W.
2011-12-01
The structure, dynamics, chemistry, and evolution of planetary upper atmospheres are in large part determined by the available sources of energy. In addition to the solar EUV flux, the solar wind and solar energetic particle (SEP) events are also important sources. Both of these particle populations can significantly affect an atmosphere, causing atmospheric loss and driving chemical reactions. Attention has been paid to these sources from the standpoint of the radiation environment for humans and electronics, but little work has been done to evaluate their impact on planetary atmospheres. At unmagnetized planets or those with crustal field anomalies, in particular, the solar wind and SEPs of all energies have direct access to the atmosphere and so provide a more substantial energy source than at planets having protective global magnetic fields. Additionally, solar wind and energetic particle fluxes should be more significant for planets orbiting more active stars, such as is the case in the early history of the solar system for paleo-Venus and Mars. Therefore quantification of the atmospheric energy input from the solar wind and SEP events is an important component of our understanding of the processes that control their state and evolution. Such modeling has been previously done for Earth, Mars and Jupiter using a guiding center precipitation model with extensive collisional physics. Currently, this code is only valid for particles with small gyroradii in strong uniform magnetic fields. There is a clear necessity for a Lorentz formulation that can perform calculations for cases where there is only a weak or nonexistent magnetic field that includes detailed physical interaction with the atmosphere (i.e. collisional physics). We show initial efforts to apply a full Lorentz motion particle transport model to study the effects of particle precipitation in the upper atmospheres of Venus, Mars, and Titan. A systematic study of the ionization, excitation, and energy
Nuclear stopping and energy deposition into the central rapidity region
Zingman, J.A.
1987-08-03
Nuclear stopping and energy deposition into the central rapidity region of ultrarelativistic heavy-ion collisions are studied through the application of a model incorporating hydrodynamic baryon flow coupled to a self-consistent field calculated in the flux tube model. Ultrarelativistic heavy ion collisions are modeled in which the nuclei have passed through each other and as a result are charged and heated.
Localized flow control with energy deposition
NASA Astrophysics Data System (ADS)
Adelgren, Russell Gene
A series of experiments with energy deposition via laser-induced optical breakdown of air, i.e., a laser spark, have been performed. These experiments have demonstrated the possibility of using a laser spark for supersonic flow control. In the first of these experiments, Rayleigh scattering flow visualization was taken for energy deposition into quiescent air. A time sequence of images showed the post breakdown fluid motion created by the laser spark for different laser energy levels. Blast wave radius and wave speed measurements were made and correlated to five different laser energy deposition levels. Laser energy was deposited upstream of a sphere in Mach 3.45 flow. The energy was deposited one sphere diameter and 0.6 diameters upstream of the front of the sphere. The frontal surface pressure on the sphere was recorded as the laser spark perturbed region interacted with the flow about the sphere. Tests for three different energy levels and two different incident laser beam diameters were completed. It has been demonstrated that the peak surface pressure associated with the Edney IV interaction can be momentarily reduced by 30% by the interaction with the thermal spot created by the laser spark. The effects of laser energy deposition on another shock interaction phenomena were studied. Laser energy deposition was used to modify the shock structure formed by symmetric wedges at Mach 3.45 within the dual solution domain. It was demonstrated experimentally that the Mach reflection could be reduced by 80% momentarily. The numerical simulations show a transition from the stable Mach reflection to a stable regular reflection. Two energy deposition methods (electric arcing and laser energy deposition) were used to force and control compressible mixing layers of axisymmetric jets. The energy deposition forcing methods have been experimentally investigated with the schlieren technique, particle image velocimetry, Mie scattering, and static pressure probe diagnostic
Theoretical study of energy deposition in ionization chambers for tritium measurements
NASA Astrophysics Data System (ADS)
Chen, Zhilin; Peng, Shuming; Meng, Dan; He, Yuehong; Wang, Heyi
2013-10-01
Energy deposition in ionization chambers has been theoretically studied for tritium measurements in gaseous form. A one-dimension model is introduced to establish the quantitative relationship between energy deposition rate and many factors, including carrier gas, gas pressure, wall material, chamber size, and gas temperature. Energy deposition rate has been calculated at pressure varying from 5 kPa to 500 kPa based on some approximations. It is found that energy deposition rate varies greatly for different parameters, especially at low gas pressure. For the same chamber, energy deposition rate in argon is much higher than in deuterium, as much as 70.7% higher at 5 kPa. Gold plated chamber gives highest energy deposition rate in the calculations while aluminum chamber results in the lowest. As chamber size gets smaller, β ray emitted by tritium will deposit less energy in the sensitive region of the chamber. For chambers flowing through with the same gas, energy deposition rate in a 10 L chamber is 23.9% higher than in a 0.05 L chamber at 5 kPa. Gas temperature also places slight influence on energy deposition rate, and 373 K will lead to 6.7% lower deposition rate than 233 K at 5 kPa. In addition, experiments have been performed to obtain energy deposition rate in a gold plated chamber, which show good accordance with theoretical calculations.
Theoretical study of energy deposition in ionization chambers for tritium measurements
Chen, Zhilin; Peng, Shuming; Meng, Dan; He, Yuehong; Wang, Heyi
2013-10-15
Energy deposition in ionization chambers has been theoretically studied for tritium measurements in gaseous form. A one-dimension model is introduced to establish the quantitative relationship between energy deposition rate and many factors, including carrier gas, gas pressure, wall material, chamber size, and gas temperature. Energy deposition rate has been calculated at pressure varying from 5 kPa to 500 kPa based on some approximations. It is found that energy deposition rate varies greatly for different parameters, especially at low gas pressure. For the same chamber, energy deposition rate in argon is much higher than in deuterium, as much as 70.7% higher at 5 kPa. Gold plated chamber gives highest energy deposition rate in the calculations while aluminum chamber results in the lowest. As chamber size gets smaller, β ray emitted by tritium will deposit less energy in the sensitive region of the chamber. For chambers flowing through with the same gas, energy deposition rate in a 10 L chamber is 23.9% higher than in a 0.05 L chamber at 5 kPa. Gas temperature also places slight influence on energy deposition rate, and 373 K will lead to 6.7% lower deposition rate than 233 K at 5 kPa. In addition, experiments have been performed to obtain energy deposition rate in a gold plated chamber, which show good accordance with theoretical calculations.
Global Auroral Energy Deposition Compared with Magnetic Indices
NASA Technical Reports Server (NTRS)
Brittnacher, M. J.; Fillingim, M. O.; Elsen, R.; Parks, G. K.; Germany, G. A.; Spann, J. F., Jr.
1997-01-01
Measurement of the global rate of energy deposition in the ionosphere via auroral particle precipitation is one of the primary goals of the Polar UVI program and is an important component of the ISTP program. The instantaneous rate of energy deposition for the entire month of January 1997 has been calculated by applying models to the UVI images and is presented by Fillingim et al. in this session. Magnetic indices, such as Kp, AE, and Dst, which are sensitive to variations in magnetospheric current systems have been constructed from ground magnetometer measurements and employed as measures of activity. The systematic study of global energy deposition raises the possibility of constructing a global magnetospheric activity index explicitly based on particle precipitation to supplement magnetic indices derived from ground magnetometer measurements. The relationship between global magnetic activity as measured by these indices and the rate of total global energy loss due to precipitation is not known at present. We study the correlation of the traditional magnetic index of Kp for the month of January 1997 with the energy deposition derived from the UVI images. We address the question of whether the energy deposition through particle precipitation generally matches the Kp and AE indices, or the more exciting, but distinct, possibility that this particle-derived index may provide an somewhat independent measure of global magnetospheric activity that could supplement traditional magnetically-based activity indices.
Calculation of Dose Deposition in 3D Voxels by Heavy Ions
NASA Technical Reports Server (NTRS)
Plante, Ianik; Cucinotta, Francis A.
2010-01-01
The biological response to high-LET radiation is very different from low-LET radiation, and can be partly attributed to the energy deposition by the radiation. Several experiments, notably detection of gamma-H2AX foci by immunofluorescence, has revealed important differences in the nature and in the spatial distribution of double-strand breaks (DSB) induced by low- and high-LET radiations. Many calculations, most of which are based on amorphous track models with radial dose, have been combined with chromosome models to calculate the number and distribution of DSB within nuclei and chromosome aberrations. In this work, the Monte-Carlo track structure simulation code RITRACKS have been used to calculate directly the energy deposition in voxels (3D pixels). A cubic volume of 5 micrometers of side was irradiated by 1) 450 (1)H+ ions of 300 MeV (LET is approximately 0.3 keV/micrometer) and 2) by 1 (56)Fe26+ ion of 1 GeV/amu (LET is approximately 150 keV/micrometer). In both cases, the dose deposited in the volume is approximately 1 Gy. All energy deposition events are recorded and dose is calculated in voxels of 20 micrometers of side. The voxels are then visualized in 3D by using a color scale to represent the intensity of the dose in a voxel. This simple approach has revealed several important points which may help understand experimental observations. In both simulations, voxels which receive low dose are the most numerous, and those corresponding to electron track ends received a dose which is in the higher range. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. The distribution of the voxels shows major differences for the (56)Fe26+ ion. The track structure can still be seen, and voxels with much higher dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and may be responsible for DSB that are more difficult to
Calculation of Dose Deposition in Nanovolumes and Simulation of gamma-H2AX Experiments
NASA Technical Reports Server (NTRS)
Plante, Ianik
2010-01-01
Monte-Carlo track structure simulations can accurately simulate experimental data: a) Frequency of target hits. b) Dose per event. c) Dose per ion. d) Radial dose. The dose is uniform in micrometers sized voxels; at the nanometer scale, the difference in energy deposition between high and low-LET radiations appears. The calculated 3D distribution of dose voxels, combined with chromosomes simulated by random walk is very similar to the distribution of DSB observed with gamma-H2AX experiments. This is further evidenced by applying a visualization threshold on dose.
Reactivity of adducts relevant to the deposition of hexagonal BN from first-principles calculations
NASA Astrophysics Data System (ADS)
Freitas, R. R. Q.; Gueorguiev, G. K.; de Brito Mota, F.; de Castilho, C. M. C.; Stafström, S.; Kakanakova-Georgieva, A.
2013-09-01
First-principles calculations, which also implement the nudged elastic band (NEB) code, are performed to investigate (i) the stability of the (C2H5)3B:NH3 adduct formed by the initial precursor molecules triethylborane (C2H5)3B and ammonia NH3 in the metal-chemical-vapor-deposition (MOCVD) of hexagonal BN, and (ii) the energy barrier to the first ethane elimination through consistent unimolecular, ammonia-assisted, and adduct-assisted reaction pathways. Comparison is done with the reference case of the (CH3)3Al:NH3 adduct, notoriously known for its high degree of stability and reactivity, which determines an overall severe parasitic gas-phase chemical reaction mechanism in the deposition of AlN.
Calculation of neutral beam deposition accounting for excited states
Gianakon, T.A.
1992-09-01
Large-scale neutral-beam auxillary heating of plasmas has led to new plasma operational regimes which are often dominated by fast ions injected via the absorption of an energetic beam of hydrogen neutrals. An accurate simulation of the slowing down and transport of these fast ions requires an intimate knowledge of the hydrogenic neutral deposition on each flux surface of the plasma. As a refinement to the present generation of transport codes, which base their beam deposition on ground-state reaction rates, a new set of routines, based on the excited states of hydrogen, is presented as mechanism for computing the attenuation and deposition of a beam of energetic neutrals. Additionally, the numerical formulations for the underlying atomic physics for hydrogen impacting on the constiuent plasma species is developed and compiled as a numerical database. Sample results based on this excited state model are compared with the ground-state model for simple plasma configurations.
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.
BEAM INDUCED ENERGY DEPOSITION IN MUON STORAGE RINGS.
MOKHOV,N.V.; JOHNSTONE,C.J.; PARKER,B.L.
2001-06-18
Beam-induced radiation effects have been simulated for 20 and 50 GeV muon storage rings designed for a Neutrino Factory. It is shown that by appropriately shielding the superconducting magnets, quench stability, acceptable dynamic heat loads, and low residual dose rates can be achieved. Alternatively, if a specially-designed skew focusing magnet without superconducting coils on the magnet's mid-plane is used, then the energy is deposited preferentially in the warm iron yoke or outer cryostat layers and internal shielding may not be required. In addition to the component irradiation analysis, shielding studies have been performed. Calculations of the external radiation were done for both designs but the internal energy deposition calculations for the 20 GeV Study-2 lattice are still in progress.
Beam-induced energy deposition in muon storage rings
Nikolai V. Mokhov; Carol J. Johnstone; Brett Parker
2001-06-22
Beam-induced radiation effects have been simulated for 20 and 50 GeV muon storage rings designed for a Neutrino Factory. It is shown that by appropriately shielding the superconducting magnets, quench stability, acceptable dynamic heat loads, and low residual dose rates can be achieved. Alternatively, if a specially-designed skew focusing magnet without superconducting coils on the magnet's mid-plane is used, then the energy is deposited preferentially in the warm iron yoke or outer cryostat layers and internal shielding may not be required. In addition to the component irradiation analysis, shielding studies have been performed. Calculations of the external radiation were done for both designs but the internal energy deposition calculations for the 20 GeV Study-2 lattice are still in progress.
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
Calculations of turbidite deposits and tsunamis from submarine landslides
Gisler, Galen R; Weaver, Robert P; Gittings, Michael L
2009-01-01
Great underwater landslides like Storegga off the Norwegian coast leave massive deposits on the seafloor and must produce enormous tsunamis. Such events have occurred on continental slopes worldwide, and continue to do so. Triggers for such slides include earthquakes, gas hydrate releases, and underwater volcanos. We have petformed a numerical study of such landslides using the multi-material compressible hydrocode Sage in order to understand the relationship between the rheology of the slide material, the configuration of the resulting deposits on the seafloor, and the tsunami that is produced. Instabilities in the fluid-fluid mixing between slide material and seawater produce vortices and swirls with sizes that depend on the rheology of the slide material. These dynamical features of the flow may be preserved as ridges when the sliding material finally stops. Thus studying the configuration of the ridges in prehistoric slides may give us measures of the circumstances under which the slide was initiated. As part of this study, we have also done a convergence test showing that the slide velocity is sensitive to the resolution adopted in the simulation, but that extrapolation to infinite resolution is possible, and can yield good velocities. We will present two-dimensional simulations of schematic underwater slides for our study of rheology, and a three-dimensional simulation in bathymetric conditions that resemble the pre-Storegga Norwegian margin.
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.
Predicting proteinase specificities from free energy calculations.
Mekonnen, Seble Merid; Olufsen, Magne; Smalås, Arne O; Brandsdal, Bjørn O
2006-10-01
The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96). PMID:16386933
Niobium Thin Film Properties Affected by Deposition Energy during Vacuum Deposition
Genfa Wu; H. Phillips; Ronald Sundelin; Anne-Marie Valente
2003-05-01
In order to understand and improve the super-conducting performance of niobium thin films at cryogenic temperatures, an energetic vacuum deposition system has been developed to study deposition energy effects on the properties of niobium thin films on various substrates. Ultra high vacuum avoids the gaseous inclusions in thin films commonly seen in sputtering deposition. A retarding field energy analyzer is used to measure the kinetic energy of niobium ions at the substrate location. A biased substrate holder controls the deposition energy. Transition temperature and residual resistivity ratio (RRR) of the niobium thin films at several deposition energies are obtained together with crystal orientation measurements and atomic force microscope (AFM) inspection, and the results show that there exists a preferred deposition energy around 115eV (the average deposition energy 64 eV plus the 51 V bias voltage).
Metting, N.F.; Braby, L.A.; Rossi, H.H.; Kliauga, P.J.; Howard, J.; Schimmerling, W.; Wong, M.; Rapkin, M.
1986-08-01
The microscopic spatial distribution of energy deposition in irradiated tissue plays a significant role in the final biological effect produced. Therefore, it is important to have accurate microdosimetric spectra of radiation fields used for radiobiology and radiotherapy. The experiments desribed here were designed to measure the distributions of energy deposition around high energy heavy ion tracks generated at Lawrence Berkeley Laboratory's Bevalac Biomedical Facility. A small proportional counter mounted in a large (0.6 by 2.5 m) vacuum chamber was used to measure energy deposition distributions as a function of the distance between detector and primary ion track. The microdosimetric distributions for a homogeneous radiation field were then calculated by integrating over radial distance. This thesis discusses the rationale of the experimental design and the analysis of measurements on 600 MeV/amu iron tracks. 53 refs., 19 figs.
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 and Radiological Studies for the LBNF Hadron Absorber
Rakhno, I. L.; Mokhov, N. V.; Tropin, I. S.; Eidelman, Y. I.
2015-06-25
Results of detailed Monte Carlo energy deposition and radiological studies performed for the LBNF hadron absorber with the MARS15 code are described. The model of the entire facility, that includes a pion-production target, focusing horns, target chase, decay channel, hadron absorber system – all with corresponding radiation shielding – was developed using the recently implemented ROOT-based geometry option in the MARS15 code. Both normal operation and accidental conditions were studied. Results of detailed thermal calculations with the ANSYS code helped to select the most viable design options.
Electron energy deposition in carbon monoxide gas
NASA Technical Reports Server (NTRS)
Liu, Weihong; Victor, G. A.
1994-01-01
A comprehensive set of electron impact cross sections for carbon monoxide molecules is presented on the basis of the most recent experimental measurements and theoretical calculations. The processes by which energetic electrons lose energy in CO gas are analyzed with these input cross sections. The efficiencies are computed of vibrational and electronic excitation, dissociation, ionization, and heating for CO gas with fractional ionization ranging from 0% to 10%. The calculated mean energy per ion pair for neutral CO gas is 32.3 eV, which is in excellent agreement with the experimental value of 32.2 eV. It increases to 35.6 eV at a fractional ionization of 1%, typical of supernovae ejecta.
Zero energy scattering calculation in Euclidean space
NASA Astrophysics Data System (ADS)
Carbonell, J.; Karmanov, V. A.
2016-03-01
We show that the Bethe-Salpeter equation for the scattering amplitude in the limit of zero incident energy can be transformed into a purely Euclidean form, as it is the case for the bound states. The decoupling between Euclidean and Minkowski amplitudes is only possible for zero energy scattering observables and allows determining the scattering length from the Euclidean Bethe-Salpeter amplitude. Such a possibility strongly simplifies the numerical solution of the Bethe-Salpeter equation and suggests an alternative way to compute the scattering length in Lattice Euclidean calculations without using the Luscher formalism. The derivations contained in this work were performed for scalar particles and one-boson exchange kernel. They can be generalized to the fermion case and more involved interactions.
NASA Astrophysics Data System (ADS)
Litsarev, Mikhail S.
2013-02-01
A description of the DEPOSIT computer code is presented. The code is intended to calculate total and m-fold electron-loss cross-sections (m is the number of ionized electrons) and the energy T(b) deposited to the projectile (positive or negative ion) during a collision with a neutral atom at low and intermediate collision energies as a function of the impact parameter b. The deposited energy is calculated as a 3D integral over the projectile coordinate space in the classical energy-deposition model. Examples of the calculated deposited energies, ionization probabilities and electron-loss cross-sections are given as well as the description of the input and output data. Program summaryProgram title: DEPOSIT Catalogue identifier: AENP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENP_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 8726 No. of bytes in distributed program, including test data, etc.: 126650 Distribution format: tar.gz Programming language: C++. Computer: Any computer that can run C++ compiler. Operating system: Any operating system that can run C++. Has the code been vectorised or parallelized?: An MPI version is included in the distribution. Classification: 2.4, 2.6, 4.10, 4.11. Nature of problem: For a given impact parameter b to calculate the deposited energy T(b) as a 3D integral over a coordinate space, and ionization probabilities Pm(b). For a given energy to calculate the total and m-fold electron-loss cross-sections using T(b) values. Solution method: Direct calculation of the 3D integral T(b). The one-dimensional quadrature formula of the highest accuracy based upon the nodes of the Yacobi polynomials for the cosθ=x∈[-1,1] angular variable is applied. The Simpson rule for the φ∈[0,2π] angular variable is used. The Newton-Cotes pattern of the seventh order
MCNPX benchmark of out-of-beam energy deposition in LiAl
Corzine, K.; Ferguson, P.; Morgan, G.; Quintana, D.; Waters, L.; Cooper, R.; Liljestrand, R.; Whiteson, A.
2000-07-01
The MCNPX code is currently being used to calculate energy deposition in the accelerator production of tritium (APT) target/blanket system components. To ensure that these components are properly designed, the code must be validated. An energy deposition experiment was designed to aid in the code validation using thermocouple sensors in-beam and thermistor-type sensors in decoupler- and blanketlike regions. This paper focuses on the out-of-beam thermistor sensors constructed of LiAl.
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.
A simple model for calculating tsunami flow speed from tsunami deposits
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.
NASA Astrophysics Data System (ADS)
Tan, Zhenyu; Dong, Lei; Tang, Fule
2012-08-01
The calculations of the characteristic quantities of low-energy electron (⩽20 keV) irradiation to the five typical spacecraft dielectrics, i.e. epoxy, kapton, mylar, polyethylene, and teflon, have been performed by means of Monte Carlo method. These characteristic quantities include the electron backscattering coefficient, the depth distributions of both energy deposition and deposited electrons, and the maximum penetration depth of deposited electrons in the dielectrics. A Monte Carlo model has been specifically constructed for simulating the transport of low-energy electrons in spacecraft dielectrics (organic materials). In this model, the description of the inelastic scattering of energetic electron is based on the dielectric approach developed previously and the Born-Ochkur's exchange correction is included. Especially, the optical energy loss functions of organic materials can be obtained using an empirical evaluation. In addition, the mean cross section based on the Mott model is proposed for calculating the elastic scattering of energetic electrons in organic materials for high simulation efficiency. The constructed Monte Carlo model has been examined by a series of calculations and comparisons with the reported experiments and other theoretical results. For the dielectrics under consideration and in the energy range of E0 ⩽ 20 keV, the calculated electron backscattering coefficients and the extrapolated range of deposited electrons are listed at selected energies in numerical form for convenient use, and an empirical expression of estimating the extrapolated range in the energy range of 1-20 keV is given. The distribution characteristics of both energy deposition and deposited electrons are presented, and it is found that kapton and mylar present the close characteristic quantities for each other, which is of significance for the choice of the dielectrics in design of spacecraft. The characteristic quantity calculations presented in this work are a
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
NASA Astrophysics Data System (ADS)
Rodkin, M. V.; Shatakhtsyan, A. R.
2015-05-01
The method for calculating the fractal correlation dimension is applied for analyzing the data on the locations of large and extralarge ore deposits. The approach implemented in this study differs by a few of important points from that commonly used, e.g., in the calculations of the correlation dimension for a set of the epicenters (hypocenters) of the earthquakes. Firstly, we demonstrate the possibility and advisability of obtaining different dimension estimates for different spatial scales. Such a separation turned out to be useful in distinguishing between the regularities in the location of ore deposits on the scale of an ore cluster, ore province, and entire continent. Secondly, we introduce a new notion, a mixed correlation dimension, and use it for different types of the objects (e.g., Au and Ag). The standard formula for calculating the correlation dimension is trivially generalized on this case. It is shown that the values of the correlation dimension can be lower and higher than the dimension of the hosting medium. The cases when the correlation dimension is higher than that of the hosting medium are interpreted as a "mutual repulsion" of the deposits of the two mentioned types. In contrast, the small correlation dimensions indicate that the deposits of the corresponding types tend to have spatially close locations. The calculations are conducted for the spherical Earth. The method is applied to the data on the large and extralarge world-class ore deposits from the Largest Mineral Deposits of the World (LMDs) geoinformation system (GIS). Different patterns of the studied behavior are illustrated by the model examples.
GIS supported calculations of (137)Cs deposition in Sweden based on precipitation data.
Almgren, Sara; Nilsson, Elisabeth; Erlandsson, Bengt; Isaksson, Mats
2006-09-15
It is of interest to know the spatial variation and the amount of (137)Cs e.g. in case of an accident with a radioactive discharge. In this study, the spatial distribution of the quarterly (137)Cs deposition over Sweden due to nuclear weapons fallout (NWF) during the period 1962-1966 was determined by relating the measured deposition density at a reference site to the amount of precipitation. Measured quarterly values of (137)Cs deposition density per unit precipitation at three reference sites and quarterly precipitation at 62 weather stations distributed over Sweden were used in the calculations. The reference sites were assumed to represent areas with different quarterly mean precipitation. The extent of these areas was determined from the distribution of the mean measured precipitation between 1961 and 1990 and varied according to seasonal variations in the mean precipitation pattern. Deposition maps were created by interpolation within a geographical information system (GIS). Both integrated (total) and cumulative (decay corrected) deposition densities were calculated. The lowest levels of NWF (137)Cs deposition density were noted in north-eastern and eastern parts of Sweden and the highest levels in the western parts of Sweden. Furthermore the deposition density of (137)Cs, resulting from the Chernobyl accident was determined for an area in western Sweden based on precipitation data. The highest levels of Chernobyl (137)Cs in western Sweden were found in the western parts of the area along the coast and the lowest in the east. The sum of the deposition densities from NWF and Chernobyl in western Sweden was then compared to the total activity measured in soil samples at 27 locations. Comparisons between the predicted values of this study show a good agreement with measured values and other studies. PMID:16647743
Estimating the energy deposition based on anisotropic fluxes measured by POES MEPED
NASA Astrophysics Data System (ADS)
Sandanger, Marit Irene; Stadsnes, Johan; Nesse Tyssøy, Hilde; Glesnes Ødegaard, Linn-Kristine; Åsnes, Arne
2015-04-01
The Medium Energy Proton and Electron Detector (MEPED) onboard the Polar Orbiting Operational Environmental Satellites (POES) consists of two electron telescopes, one viewing nearly radially outward from Earth (the 0o detector) and the other viewing antiparallel to the satellite's velocity (the 90o detector). Energetic particle measurements from POES are often used to estimate the energy deposition in the mesosphere. The electron fluxes usually show strong pitch angle anisotropy. Until now, it has been customary to derive a lower estimate of the energy deposition in the mesosphere from the 0o detector, while an upper estimate is derived from the 90odetector. We have developed a method using measurements from both the 0o and 90o telescopes in a combination with theoretically determined pitch angle distributions, in order to give a more precise estimate of the energy deposition in the upper atmosphere. The derived anisotropic flux distributions are used to calculate the energy deposition during Relativistic Electron Precipitation (REP) events.
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2010 CFR
2010-04-01
... calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... FEDERAL POWER ACT Charges for Headwater Benefits § 11.13 Energy gains calculations. (a) Energy gains at a... not complex or in which headwater benefits are expected to be small, calculations will be made...
Griesheimer, D. P.; Stedry, M. H.
2013-07-01
A rigorous treatment of energy deposition in a Monte Carlo transport calculation, including coupled transport of all secondary and tertiary radiations, increases the computational cost of a simulation dramatically, making fully-coupled heating impractical for many large calculations, such as 3-D analysis of nuclear reactor cores. However, in some cases, the added benefit from a full-fidelity energy-deposition treatment is negligible, especially considering the increased simulation run time. In this paper we present a generalized framework for the in-line calculation of energy deposition during steady-state Monte Carlo transport simulations. This framework gives users the ability to select among several energy-deposition approximations with varying levels of fidelity. The paper describes the computational framework, along with derivations of four energy-deposition treatments. Each treatment uses a unique set of self-consistent approximations, which ensure that energy balance is preserved over the entire problem. By providing several energy-deposition treatments, each with different approximations for neglecting the energy transport of certain secondary radiations, the proposed framework provides users the flexibility to choose between accuracy and computational efficiency. Numerical results are presented, comparing heating results among the four energy-deposition treatments for a simple reactor/compound shielding problem. The results illustrate the limitations and computational expense of each of the four energy-deposition treatments. (authors)
Energy deposition studies for the LBNE beam absorber
Rakhno, Igor L.; Mokhov, Nikolai V.; Tropin, Igor S.
2015-01-29
Results of detailed Monte Carlo energy deposition studies performed for the LBNE absorber core and the surrounding shielding with the MARS15 code are described. The model of the entire facility, that includes a pion-production target, focusing horns, target chase, decay channel, hadron absorber system – all with corresponding radiation shielding – was developed using the recently implemented ROOT-based geometry option in the MARS15 code. This option provides substantial flexibility and automation when developing complex geometry models. Both normal operation and accidental conditions were studied. Various design options were considered, in particular the following: (i) filling the decay pipe with air or helium; (ii) the absorber mask material and shape; (iii) the beam spoiler material and size. Results of detailed thermal calculations with the ANSYS code helped to select the most viable absorber design options.
Study of the energy deposit of muon bundles in the NEVOD detector
NASA Astrophysics Data System (ADS)
Bogdanov, A. G.; Dushkin, L. I.; Khokhlov, S. S.; Khomyakov, V. A.; Kindin, V. V.; Kokoulin, R. P.; Kovylyaeva, E. A.; Mannocchi, G.; Petrukhin, A. A.; Saavedra, O.; Shutenko, V. V.; Trinchero, G.; Yashin, I. I.
2015-08-01
In several cosmic ray experiments, an excess of multi-muon events in comparison with calculations performed in frame of the widely used hadron interaction models was found. In order to solve this puzzle, investigations of muon energy characteristics in EAS are required. An experiment on the measurement of the energy deposit of muon bundles in water has been started with the NEVOD-DECOR experimental complex. The results of the analysis of the first experimental data are discussed. It has been found that the average specific energy deposit in the Cherenkov calorimeter appreciably increases with zenith angle, thus reflecting the increase of the mean muon energy in the bundles. A possible evidence for an increase of the energy deposit at primary energies above 1017 eV is observed.
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.
Energy Band Calculations for Maximally Even Superlattices
NASA Astrophysics Data System (ADS)
Krantz, Richard; Byrd, Jason
2007-03-01
Superlattices are multiple-well, semiconductor heterostructures that can be described by one-dimensional potential wells separated by potential barriers. We refer to a distribution of wells and barriers based on the theory of maximally even sets as a maximally even superlattice. The prototypical example of a maximally even set is the distribution of white and black keys on a piano keyboard. Black keys may represent wells and the white keys represent barriers. As the number of wells and barriers increase, efficient and stable methods of calculation are necessary to study these structures. We have implemented a finite-element method using the discrete variable representation (FE-DVR) to calculate E versus k for these superlattices. Use of the FE-DVR method greatly reduces the amount of calculation necessary for the eigenvalue problem.
Modeling Atmospheric Energy Deposition (by energetic ions): New Results
NASA Astrophysics Data System (ADS)
Parkinson, C.; Brain, D. A.; Lillis, R. J.; Liemohn, M. W.; Bougher, S. W.
2012-12-01
The structure, dynamics, chemistry, and evolution of planetary upper atmospheres are in large part determined by the available sources of energy. In addition to the solar EUV flux, the solar wind and solar energetic particle (SEP) events are also important sources. Both of these particle populations can significantly affect an atmosphere, causing atmospheric loss and driving chemical reactions. Attention has been paid to these sources from the standpoint of the radiation environment for humans and electronics, but little work has been done to evaluate their impact on planetary atmospheres. At unmagnetized planets or those with crustal field anomalies, in particular, the solar wind and SEPs of all energies have direct access to the atmosphere and so provide a more substantial energy source than at planets having protective global magnetic fields. Additionally, solar wind and energetic particle fluxes should be more significant for planets orbiting more active stars, such as is the case in the early history of the solar system for paleo-Venus and Mars. Therefore quantification of the atmospheric energy input from the solar wind and SEP events is an important component of our understanding of the processes that control their state and evolution. Such modeling has been previously done for Earth, Mars and Jupiter using a guiding center precipitation model with extensive collisional physics. Currently, this code is only valid for particles with small gyroradii in strong uniform magnetic fields. There is a clear necessity for a Lorentz formulation that can perform calculations for cases where there is only a weak or nonexistent magnetic field that includes detailed physical interaction with the atmosphere (i.e. collisional physics). We show initial efforts to apply a full Lorentz motion particle transport model to study the effects of particle precipitation in the upper atmospheres of Venus, Mars, and Titan. A systematic study of the ionization, excitation, and energy
NASA Astrophysics Data System (ADS)
Patashova, T.
2009-04-01
Calculation of mineral resources and their proper assessment is relevant, since the stock of resources determines the economic independence of the state. I would like present the work wherein discusses gravel and sand deposits of different genetic type (kames, eskers, marginal glaciofluvial ridges, sandurs, glaciofluvial deltas and redrifted glaciofluvial aeolian formations). Their geological structure and formation conditions have been assessed; quality characteristics of mineral resources have been analysed; calculation of resources has been performed by applying most popular resources calculating methods used in Lithuania up to now, such as those of geological blocks, profiles and isolines, as well as the up-to-date GRID method created on the basis of triangle method in GIS environment. Comparison of resources assessed by different methods has revealed their advantages and disadvantages, their availability subject to deposits‘genetic types.
Low-energy calculations for nuclear photodisintegration
NASA Astrophysics Data System (ADS)
Deflorian, S.; Efros, V. D.; Leidemann, W.
2016-03-01
In the Standard Solar Model a central role in the nucleosynthesis is played by reactions of the kind {}{Z_1}{A_1}{X_1} + {}{Z_2}{A_2}{X_2} to {}{Z_1 + {Z_2}}{A_1 + {A_2}}Y + γ , which enter the proton-proton chains. These reactions can also be studied through the inverse photodisintegration reaction. One option is to use the Lorentz Integral Transform approach, which transforms the continuum problem into a bound state-like one. A way to check the reliability of such methods is a direct calculation, for example using the Kohn Variational Principle to obtain the scattering wave function and then directly calculate the response function of the reaction.
A Lagrangian Approach for Calculating Microsphere Deposition in a One-Dimensional Lung-Airway Model.
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). PMID:26141916
Stochastic spatial energy deposition profiles for MeV protons and keV electrons
NASA Astrophysics Data System (ADS)
Udalagama, C.; Bettiol, A. A.; Watt, F.
2009-12-01
With the rapid advances being made in novel high-energy ion-beam techniques such as proton beam writing, single-ion-event effects, ion-beam-radiation therapy, ion-induced fluorescence imaging, proton/ion microscopy, and ion-induced electron imaging, it is becoming increasingly important to understand the spatial energy-deposition profiles of energetic ions as they penetrate matter. In this work we present the results of comprehensive yet straightforward event-by-event Monte Carlo calculations that simulate ion/electron propagation and secondary electron ( δ ray) generation to yield spatial energy-deposition data. These calculations combine SRIM/TRIM features, EEDL97 data and volume-plasmon-localization models with a modified version of one of the newer δ ray generation models, namely, the Hansen-Kocbach-Stolterfoht. The development of the computer code DEEP (deposition of energy due to electrons and protons) offers a unique means of studying the energy-deposition/redistribution problem while still retaining the important stochastic nature inherent in these processes which cannot be achieved with analytical modeling. As an example of an application of DEEP we present results that compare the energy-deposition profiles of primary MeV protons and primary keV electrons in polymethymethacrylate. Such data are important when comparing proximity effects in the direct write lithography processes of proton-beam writing and electron-beam writing. Our calculations demonstrate that protons are able to maintain highly compact spatial energy-deposition profiles compared with electrons.
Calculation of molecular free energies in classical potentials
NASA Astrophysics Data System (ADS)
Farhi, Asaf; Singh, Bipin
2016-02-01
Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.
NASA Astrophysics Data System (ADS)
Sommer, S. G.; Østergård, H. S.; Løfstrøm, P.; Andersen, H. V.; Jensen, L. S.
Substantial emission of ammonia (NH 3) from animal houses and the related high local deposition of NH 3-N are a threat to semi-natural nitrogen-deficient ecosystems situated near the NH 3 source. In Denmark, there are regulations limiting the level of NH 3 emission from livestock houses near N-deficient ecosystems that are likely to change due to nitrogen (N) enrichment caused by NH 3 deposition. The models used for assessing NH 3 emission from livestock production, therefore, need to be precise, as the regulation will affect both the nature of the ecosystem and the economy of the farmer. Therefore a study was carried out with the objective of validating the Danish model used to monitor NH 3 transport, dispersion and deposition from and in the neighbourhood of a chicken farm. In the study we measured NH 3 emission with standard flux measuring methods, NH 3 concentrations at increasing distances from the chicken houses using passive diffusion samplers and deposition using 15N-enriched biomonitors and field plot studies. The dispersion and deposition of NH 3 were modelled using the Danish OML-DEP model. It was also shown that model calculations clearly reflect the measured NH 3 concentration and N deposition. Deposition of N measured by biomonitors clearly reflected the variation in NH 3 concentrations and showed that deposition was not significantly different from zero ( P < 0.05) at distances greater than 150-200 m from these chicken houses. Calculations confirmed this, as calculated N deposition 320 m away from the chicken farm was only marginally affected by the NH 3 emission from the farm. There was agreement between calculated and measured deposition showing that the model gives true estimates of the deposition in the neighbourhood of a livestock house emitting NH 3.
Global Auroral Energy Deposition Derived from Polar UVI Images
NASA Technical Reports Server (NTRS)
Fillingim, M. O.; Brittnacher, M. J.; Elsen, R.; Parks, G. K.; Spann, J. F., Jr.; Germany, G. A.
1997-01-01
Quantitative measurement of the transfer of energy and momentum to the ionosphere from the solar wind is one of the main objectives of the ISTP program. Global measurement of auroral energy deposition derived from observations of the longer wavelength LBH band emissions made by the Ultraviolet Imager on the Polar spacecraft is one of the key elements in this satellite and ground-based instrument campaign. These "measurements" are inferred by combining information from consecutive images using different filters and have a time resolution on the average of three minutes and are made continuously over a 5 to 8 hour period during each 18 hour orbit of the Polar spacecraft. The energy deposition in the ionosphere from auroral electron precipitation augments are due to Joule heating associated with field aligned currents. Assuming conjugacy of energy deposition between the two hemispheres the total energy input to the ionosphere through electron precipitation can be determined at high time resolution. Previously, precipitating particle measurements along the tracks of low altitude satellites provided only local measurements and the global energy precipitation could be inferred through models but not directly measured. We use the UVI images for the entire month of January 1997 to estimate the global energy deposition at high time resolution. We also sort the energy deposition into sectors to find possible trends, for example, on the dayside and nightside, or the dawn and dusk sides.
Energetic particle energy deposition in Titan's upper atmosphere
NASA Astrophysics Data System (ADS)
Westlake, J. H.; Smith, H. T.; Mitchell, D. G.; Paranicas, C. P.; Rymer, A. M.; Bell, J. M.; Waite, J. H., Jr.; Mandt, K. E.
2012-04-01
Titan’s upper atmosphere has been observed to be variable on a pass-by-pass basis. During the nominal mission where the Cassini Ion and Neutral Mass Spectrometer (INMS) only sampled the northern hemisphere this variability was initially believed to be tied to solar drivers manifest in latitudinal variations in the thermal structure of the upper atmosphere. However, when Cassini delved into the southern hemisphere the latitudinal dependence was not present in the data. Recently, Westlake et al. (2011) showed that the pass-by-pass variability is correlated with the deviations in the plasma environment as identified by Rymer et al. (2009) and Simon et al. (2010). Furthermore, the studies of Westlake et al. (2011) and Bell et al. (2011) showed that Titan’s upper atmosphere responds to changes in the ambient magnetospheric plasma on timescales of roughly one Titan day (16 Earth days). We report on recent studies of energy deposition in Titan’s upper atmosphere. Previous studies by Smith et al. (2009), Cravens et al. (2008), Tseng et al. (2008), and Shah et al. (2009) reported on energetic proton and oxygen ion precipitation. Back of the envelope calculations by Sittler et al. (2009) showed that magnetospheric energy inputs are expected to be of the order of or greater than the solar processes. We report on further analysis of the plasma environment around Titan during the flybys that the INMS has good data. We utilize data from the Magnetospheric Imaging Instrument to determine how the magnetospheric particle population varies from pass to pass and how this influences the net magnetospheric energy input prior to the flyby. We also report on enhanced energetic neutral atom emissions during select highly energetic passes. References: Bell, J., et al.: “Simulating the time-dependent response of Titan's upper atmosphere to periods of magnetospheric forcing”. Geophys. Res. Lett., Vol. 38, L06202, 2011. Rymer, A. M., et al.: “Discrete classification and electron
NASA Astrophysics Data System (ADS)
Patašova, Tatjana; Jurgaitis, Algirdas
2008-01-01
Calculation of mineral resources and their proper assessment is relevant, since the stock of resources determines the economic independence of the state. The present work discusses gravel and sand deposits of different genetic type (kames, eskers, marginal glaciofluvial ridges, sandurs, glaciofluvial deltas and redrifted glaciofluvial aeolian formations). Their geological structure and formation conditions have been assessed; quality characteristics of mineral resources have been analysed; calculation of resources has been performed by applying old methods used in Lithuania up to now, such as those of geological blocks, profiles and isolines, as well as the up-to-date GRID method created on the basis of the triangle method in GIS environment. Comparison of resources assessed by different methods has revealed their advantages and disadvantages.
Calculation of Modulated Transport Coefficients for Recovery of ECH Deposition Profiles
NASA Astrophysics Data System (ADS)
Brookman, M. W.; Austin, M. E.; Horton, C. W.; Petty, C. C.
2015-11-01
Ray tracing of ECRF power through fixed plasma profiles may significantly underestimate the ECH and ECCD deposition profile width. Density fluctuations present in tokamak plasmas modify the path of radiation on a fluctuation timescale, spreading the heating power over a wide area. Deposition is hard to measure as transport quickly spreads power, and transport effects are difficult to separate from a truly broadened profile. While the total power deposited should be unchanged in an ITER-like scenario, tearing mode suppression is sensitive to the alignment and width of the ECCD profile. A novel integral method for calculating thermal transport coefficients based on ECE measurements of Te is presented and applied to DIII-D data. These are compared with computational predictions of broadening from the ray tracing code C3PO and distribution code LUKE. This work will provide the analytical framework for measuring fluctuation broadening in a future DIII-D experiment. Supported by the US DOE under DE-FG03-97ER54415 & DE-FG02-04ER54761.
Simulation of proton-induced energy deposition in integrated circuits
NASA Technical Reports Server (NTRS)
Fernald, Kenneth W.; Kerns, Sherra E.
1988-01-01
A time-efficient simulation technique was developed for modeling the energy deposition by incident protons in modern integrated circuits. To avoid the excessive computer time required by many proton-effects simulators, a stochastic method was chosen to model the various physical effects responsible for energy deposition by incident protons. Using probability density functions to describe the nuclear reactions responsible for most proton-induced memory upsets, the simulator determines the probability of a proton hit depositing the energy necessary for circuit destabilization. This factor is combined with various circuit parameters to determine the expected error-rate in a given proton environment. An analysis of transient or dose-rate effects is also performed. A comparison to experimental energy-disposition data proves the simulator to be quite accurate for predicting the expected number of events in certain integrated circuits.
A nuclear fragmentation energy deposition model
NASA Technical Reports Server (NTRS)
Ngo, D. M.; Wilson, J. W.; Fogarty, T. N.; Buck, W. W.; Townsend, L. W. (Principal Investigator)
1991-01-01
A formalism for target fragment transport is presented with application to energy loss spectra in thin silicon devices. A nuclear data base is recommended that agrees well with the measurements of McNulty et al. using surface barrier detectors. High-energy events observed by McNulty et al., which are not predicted by intranuclear cascade models, are well represented by the present work.
The measurement and calculation of nanodosimetric energy distributions for electrons and photons
NASA Astrophysics Data System (ADS)
Evans, Thomas Michael
1997-09-01
Low dose and low dose rate fields constitute the majority of radiation exposure scenarios in radiation protection. Conversely, very little epidemiological or physical data are available at these levels. This situation exists because the parameters characterizing low dose and low dose rate environments are difficult to assess at cellular levels where the fundamental biological effects from radiation insults occur. The quantities required for a complete biological assessment are the distribution of energy deposition in biological targets and the cellular response to such insults. A new detector to measure physical energy depositions on nanometer scales was developed in this thesis. A computational tool was also developed to calculate clustered distributions of energy deposition from electrons and photons. A dosimeter has been developed which characterizes energy depositions from charged particles in nanometer dimensions. The dosimeter is a threshold-type detector based on the temperature response of the superheated liquid droplet detector (SLDD). SLDDs based on Freon-115 have been designed and tested. A data acquisition system that measures the acoustic signals from bubble nucleation events has been developed. An original electron track code, ESLOW3.1, has been developed. The code simulates electron tracks on an event-by-event basis down to an absolute minimum of 20 eV. The transport medium is water vapor. The cross sections have been compared with published data and theoretical models where available. Trial calculations of pertinent quantities are in good agreement with published results. A new operational quantity, the cluster spectrum, given the symbol c(/varepsilon), has been defined. This quantity is measured by the SLDD operated in nanodosimetry mode. The performance of the SLDD has been tested with a 60Co point source. The effective measurement range of the nanodosimeter is between 60 and 500 eV of energy deposition. Measured values of c(/varepsilon) are
Guidelines for the analysis of free energy calculations.
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. PMID:25808134
Guidelines for the analysis of free energy calculations
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
System to quantify gamma-ray radial energy deposition in semiconductor detectors
Kammeraad, Judith E.; Blair, Jerome J.
2001-01-01
A system for measuring gamma-ray radial energy deposition is provided for use in conjunction with a semiconductor detector. The detector comprises two electrodes and a detector material, and defines a plurality of zones within the detecting material in parallel with the two electrodes. The detector produces a charge signal E(t) when a gamma-ray interacts with the detector. Digitizing means are provided for converting the charge signal E(t) into a digitized signal. A computational means receives the digitized signal and calculates in which of the plurality of zones the gamma-ray deposited energy when interacting with the detector. The computational means produces an output indicating the amount of energy deposited by the gamma-ray in each of the plurality of zones.
Biological consequences of nanoscale energy deposition near irradiated heavy atom nanoparticles
NASA Astrophysics Data System (ADS)
McMahon, Stephen J.; Hyland, Wendy B.; Muir, Mark F.; Coulter, Jonathan A.; Jain, Suneil; Butterworth, Karl T.; Schettino, Giuseppe; Dickson, Glenn R.; Hounsell, Alan R.; O'Sullivan, Joe M.; Prise, Kevin M.; Hirst, David G.; Currell, Fred J.
2011-06-01
Gold nanoparticles (GNPs) are being proposed as contrast agents to enhance X-ray imaging and radiotherapy, seeking to take advantage of the increased X-ray absorption of gold compared to soft tissue. However, there is a great discrepancy between physically predicted increases in X-ray energy deposition and experimentally observed increases in cell killing. In this work, we present the first calculations which take into account the structure of energy deposition in the nanoscale vicinity of GNPs and relate this to biological outcomes, and show for the first time good agreement with experimentally observed cell killing by the combination of X-rays and GNPs. These results are not only relevant to radiotherapy, but also have implications for applications of heavy atom nanoparticles in biological settings or where human exposure is possible because the localised energy deposition high-lighted by these results may cause complex DNA damage, leading to mutation and carcinogenesis.
Biological consequences of nanoscale energy deposition near irradiated heavy atom nanoparticles
McMahon, Stephen J.; Hyland, Wendy B.; Muir, Mark F.; Coulter, Jonathan A.; Jain, Suneil; Butterworth, Karl T.; Schettino, Giuseppe; Dickson, Glenn R.; Hounsell, Alan R.; O'Sullivan, Joe M.; Prise, Kevin M.; Hirst, David G.; Currell, Fred J.
2011-01-01
Gold nanoparticles (GNPs) are being proposed as contrast agents to enhance X-ray imaging and radiotherapy, seeking to take advantage of the increased X-ray absorption of gold compared to soft tissue. However, there is a great discrepancy between physically predicted increases in X-ray energy deposition and experimentally observed increases in cell killing. In this work, we present the first calculations which take into account the structure of energy deposition in the nanoscale vicinity of GNPs and relate this to biological outcomes, and show for the first time good agreement with experimentally observed cell killing by the combination of X-rays and GNPs. These results are not only relevant to radiotherapy, but also have implications for applications of heavy atom nanoparticles in biological settings or where human exposure is possible because the localised energy deposition high-lighted by these results may cause complex DNA damage, leading to mutation and carcinogenesis. PMID:22355537
Spectroscopically Accurate Calculations of the Rovibrational Energies of Diatomic Hydrogen
NASA Astrophysics Data System (ADS)
Perry, Jason
2005-05-01
The Born-Oppenheimer approximation has been used to calculate the rotational and vibrational states of diatomic hydrogen. Because it is an approximation, our group now wants to use a Born-Oppenheimer potential to calculate the electronic energy that has been corrected to match closely with spectroscopic results. We are using a code that has corrections for adiabatic, relativistic, radiative, and non-adiabatic effects. The rovibrational energies have now been calculated for both bound and quasi-bound states. We also want to compute quadrupole transition probabilities for diatomic hydrogen. These calculations aspire to investigate diatomic hydrogen in astrophysical environments.
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...
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...
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...
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...
New approach to calculating the potential energy of colliding nuclei
Kurmanov, R. S.; Kosenko, G. I.
2014-12-15
The differential method proposed by the present authors earlier for the reduction of volume integrals in calculating the potential energy of a compound nucleus is generalized to the case of two interacting nuclei. The Coulomb interaction energy is obtained for the cases of a sharp and a diffuse boundary of nuclei, while the nuclear interaction energy is found only for nuclei with a sharp boundary, the finiteness of the nuclear-force range being taken into account. The present method of calculations permits reducing the time it takes to compute the potential energy at least by two orders of magnitude.
Transonic flow control by means of local energy deposition
NASA Astrophysics Data System (ADS)
Aul'Chenko, S. M.; Zamuraev, V. P.; Kalinina, A. P.
2011-11-01
Experimental data for the feasibility of transonic flow control by means of energy deposition are generalized. Energy supplied to the immediate vicinity of a body in stream before a compression shock is found to result in the nonlinear interaction of introduced disturbances with the shock and the surface in zones extended along the surface. A new, explosive gasdynamic mechanism behind the shift of the compression shock is discovered. It is shown that the nonlinear character of the interaction may considerably decrease the wave resistance of, e.g., transonic airfoils. It is found that energy supply from without stabilizes a transonic flow about an airfoil—the effect similar to the Khristianovich stabilization effect. The dependence of the energy deposition optimal frequency on the energy source parameters and Mach number of the incoming flow at which the resistance drops to the greatest extent is obtained. The influence of the real thermodynamic properties and viscosity of air is studied.
Calculation of Rydberg energy levels for the francium atom
NASA Astrophysics Data System (ADS)
Huang, Shi-Zhong; Chu, Jin-Min
2010-06-01
Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of the np2Po1/2 (n = 7-50) and np2Po3/2 (n = 7-50) spectrum series for the francium atom are calculated. The calculated results are in excellent agreement with the 48 measured levels, and 40 energy levels for highly excited states are predicted.
The EXPURT model for calculating external gamma doses from deposited material in inhabited areas.
Jones, J A; Singer, L N; Brown, J
2006-01-01
EXPURT, NRPB's model for calculating external gamma doses in inhabited areas, was originally developed in the mid-1980s. Deposition on surfaces in the area, the subsequent transfer of material between different surfaces or its removal from the system, and dose rates in various locations from material on the different surfaces are modelled. The model has been updated to take account of more recent experimental data on the transfer rates between surfaces and to make it more flexible for use in assessing dose rates following an accidental release. EXPURT is a compartmental model and models the transfer of material between the surfaces using a set of first order differential equations. It enables the impact of the decontamination of surfaces on doses and dose rates to be explored. The paper describes the EXPURT model and presents some preliminary results obtained using it. PMID:16242820
Protein thermostability calculations using alchemical free energy simulations.
Seeliger, Daniel; de Groot, Bert L
2010-05-19
Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design. PMID:20483340
Is ring breaking feasible in relative binding free energy calculations?
Liu, Shuai; Wang, Lingle; Mobley, David L
2015-04-27
Our interest is relative binding free energy (RBFE) calculations based on molecular simulations. These are promising tools for lead optimization in drug discovery, computing changes in binding free energy due to modifications of a lead compound. However, in the "alchemical" framework for RBFE calculations, some types of mutations have the potential to introduce error into the computed binding free energies. Here we explore the magnitude of this error in several different model binding calculations. We find that some of the calculations involving ring breaking have significant errors, and these errors are especially large in bridged ring systems. Since the error is a function of ligand strain, which is unpredictable in advance, we believe that ring breaking should be avoided when possible. PMID:25835054
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.
Free energy calculations for molecular solids using GROMACS
NASA Astrophysics Data System (ADS)
Aragones, J. L.; Noya, E. G.; Valeriani, C.; Vega, C.
2013-07-01
In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.
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.
S-matrix calculations of energy levels of alkalilike ions
NASA Astrophysics Data System (ADS)
Sapirstein, Jonathan; Cheng, K. T.
2013-05-01
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. Formulas are presented that allow calculation of the energy levels of valence ns , np1 / 2 , np3 / 2 , nd3 / 2 , and nd5 / 2 states. Emphasis is placed on modifications of the lithiumlike formulas required because more than one core state is present, and a discussion of an unusual feature of the two-photon exchange contribution involving autoiononizing states is given. The method is illustrated with a calculation of energy levels of the sodium isoelectronic sequence, with results for 3s1 / 2 , 3p1 / 2 , and 3p3 / 2 energies tabulated for the range Z = 20 - 100 . A detailed breakdown of the calculation is given for Z = 74 . Comparison with experiment and other calculations is given, and prospects for extension of the method to ions with more complex electronic structure discussed. The work of JS was supported in part by NSF Grant No. PHY-1068065. The work of KTC was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
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.
Calculating fusion neutron energy spectra from arbitrary reactant distributions
NASA Astrophysics Data System (ADS)
Eriksson, J.; Conroy, S.; Andersson Sundén, E.; Hellesen, C.
2016-02-01
The Directional Relativistic Spectrum Simulator (DRESS) code can perform Monte-Carlo calculations of reaction product spectra from arbitrary reactant distributions, using fully relativistic kinematics. The code is set up to calculate energy spectra from neutrons and alpha particles produced in the D(d, n)3He and T(d, n)4He fusion reactions, but any two-body reaction can be simulated by including the corresponding cross section. The code has been thoroughly tested. The kinematics calculations have been benchmarked against the kinematics module of the ROOT Data Analysis Framework. Calculated neutron energy spectra have been validated against tabulated fusion reactivities and against an exact analytical expression for the thermonuclear fusion neutron spectrum, with good agreement. The DRESS code will be used as the core of a detailed synthetic diagnostic framework for neutron measurements at the JET and MAST tokamaks.
Lead Optimization Mapper: Automating free energy calculations for lead optimization
Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P.; Summa, Christopher M.; Jaber, Vivian R.; Lim, Nathan M.; Mobley, David L.
2013-01-01
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce Lead Optimization Mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license. PMID:24072356
NASA Astrophysics Data System (ADS)
Stadsnes, Johan; Sandanger, Marit; Nesse Tyssoy, Hilde; Odegaard, Linn-Kristine; Asnes, Arne
Data from the MEPED particle spectrometers on the Polar Orbiting Operational Environmental Satellites (POES) are often used for estimating the energy deposition in the upper atmosphere from electrons in the energy range 30 keV - 2.5 MeV. MEPED includes two collimated electron detectors, which are pointing approximately towards zenith (0 degree detector) and in the horizontal plane (90 degree detector). At medium and high geomagnetic latitudes the 0 degree detector measures particles within a limited part of the bounce loss cone and the 90 degree detector measures particles outside or near the edge of the loss cone. The electron fluxes often show strong pitch angle anisotropy which causes large uncertainty in the estimate of energy deposition based on these measurements. An upper estimate is derived from the 90 degree detector and a lower estimate from the 0 degree detector. The electron anisotropy is to a large extent determined by wave-particle interactions causing pitch angle diffusion driving electrons into the bounce loss cone. The pitch angle anisotropy is dependent on the strength of the diffusion. We are developing a method for calculating the flux versus pitch angle in the loss cone based on the measured electron fluxes and modeled flux profiles from pitch angle scattering by whistler mode waves. We will present results from calculation of the energy deposition using the derived anisotropic flux distribution during a REP event in 2008.
NASA Astrophysics Data System (ADS)
Burigo, Lucas; Pshenichnov, Igor; Mishustin, Igor; Hilgers, Gerhard; Bleicher, Marcus
2016-05-01
The Geant4-based Monte Carlo model for Heavy-Ion Therapy (MCHIT) was extended to study the patterns of energy deposition at sub-micrometer distance from individual ion tracks. Dose distributions for low-energy 1H, 4He, 12C and 16O ions measured in several experiments are well described by the model in a broad range of radial distances, from 0.5 to 3000 nm. Despite the fact that such distributions are characterized by long tails, a dominant fraction of deposited energy (∼80%) is confined within a radius of about 10 nm. The probability distributions of clustered ionization events in nanoscale volumes of water traversed by 1H, 2H, 4He, 6Li, 7Li, and 12C ions are also calculated. A good agreement of calculated ionization cluster-size distributions with the corresponding experimental data suggests that the extended MCHIT can be used to characterize stochastic processes of energy deposition to sensitive cellular structures.
Total-energy and pressure calculations for random substitutional alloys
Johnson, D.D. ); Nicholson, D.M. ); Pinski, F.J. ); Gyoerffy, B.L. ); Stocks, G.M. )
1990-05-15
We present the details and the derivation of density-functional-based expressions for the total energy and pressure for random substitutional alloys (RSA) using the Korringa-Kohn-Rostoker Green's-function approach in combination with the coherent-potential approximation (CPA) to treat the configurational averaging. This includes algebraic cancellation of various electronic core contributions to the total energy and pressure, as in ordered-solid muffin-tin-potential calculations. Thus, within the CPA, total-energy and pressure calculations for RSA have the same foundation and have been found to have the same accuracy as those obtained in similar calculations for ordered solids. Results of our calculations for the impurity formation energy, and for the bulk moduli, the lattice parameters, and the energy of mixing as a function of concentration in fcc Cu{sub {ital c}}Zn{sub 1{minus}{ital c}} alloys show that this generalized density-functional theory will be useful in studying alloy phase stability.
Ion beam energy spectrum calculation via dosimetry data deconvolution.
Harper-Slaboszewicz, Victor Jozef; Sharp, Andrew Clinton
2010-10-01
The energy spectrum of a H{sup +} beam generated within the HERMES III accelerator is calculated from dosimetry data to refine future experiments. Multiple layers of radiochromic film are exposed to the beam. A graphic user interface was written in MATLAB to align the film images and calculate the beam's dose depth profile. Singular value regularization is used to stabilize the unfolding and provide the H{sup +} beam's energy spectrum. The beam was found to have major contributions from 1 MeV and 8.5 MeV protons. The HERMES III accelerator is typically used as a pulsed photon source to experimentally obtain photon impulse response of systems due to high energy photons. A series of experiments were performed to explore the use of Hermes III to generate an intense pulsed proton beam. Knowing the beam energy spectrum allows for greater precision in experiment predictions and beam model verification.
Calculation of exchange energies using algebraic perturbation theory
Burrows, B. L.; Dalgarno, A.; Cohen, M.
2010-04-15
An algebraic perturbation theory is presented for efficient calculations of localized states and hence of exchange energies, which are the differences between low-lying states of the valence electron of a molecule, formed by the collision of an ion Y{sup +} with an atom X. For the case of a homonuclear molecule these are the gerade and ungerade states and the exchange energy is an exponentially decreasing function of the internuclear distance. For such homonuclear systems the theory is used in conjunction with the Herring-Holstein technique to give accurate exchange energies for a range of intermolecular separations R. Since the perturbation parameter is essentially 1/R, this method is suitable for large R. In particular, exchange energies are calculated for X{sub 2}{sup +} systems, where X is H, Li, Na, K, Rb, or Cs.
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.
NASA Astrophysics Data System (ADS)
Mlynczak, Martin G.; Garcia, Rolando R.; Roble, Raymond G.; Hagan, Maura
2000-07-01
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-μm 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.
Critical energy deposit in heavy ion complete fusion
Fonte, R.; Insolia, A. Dipartimento di Fisica dell'Universita di Catania corso Italia, 57-95129 Catania, Italy)
1991-07-01
In the framework of an {ital l}-window model for complete fusion reactions within a sharp cutoff approximation, the problem of the maximum excitation energy which can be deposited in a compound nucleus is discussed. Predictions about the spin distribution of the compound nucleus are compared with the conclusions of a recent analysis of the {sup 28}Si+{sup 28}Si fusion reaction.
On the calculation of classical vibrational energy exchange
NASA Astrophysics Data System (ADS)
Gibbons, John P.; Stettler, John D.
1982-07-01
A three-dimensional, Monte Carlo classical model for the calculation of vibrational energy relaxation and transfer rates for both diatomic—monatomic and diatomic—diatomic systems was developed, analyzed and implemented. Mediation by internal angular momentum changes was demonstrated to be important in these energy transfer processes. This mechanism was incorporated into the model in order to achieve statistically significant results within reasonable computer running times. This made possible the extension of the model calculations to much lower temperatures than had been previously investigated. This calculational procedure was applied to Ar—O 2, to He—O 2 and to the near resonant CO—N 2 process at several temperatures between room temperature and 4000 K with the use of exponential repulsive intermolecular potential. Three different sets of potential parameters obtained from three independent sources were used. The results were compared to experiment.
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.
Breiland, W.G.; Coltrin, M.E.
1989-10-01
Deposition rates are presented for silicon from silane in a helium carrier gas using a tubular CVD reactor with a two-dimensional flow geometry. Measured surface-temperature profiles, inlet gas velocities, total pressures, and silane/helium concentrations are reported, providing exact boundary conditions that can be used in a two-dimensional numerical CVD model. Comparisons are made between this data and two variations of a model by Coltrin, Kee, and Miller in which different empirical expressions for the silane and disilane reactive sticking coefficient are used.
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.
Accurate calculation of diffraction-limited encircled and ensquared energy.
Andersen, Torben B
2015-09-01
Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873
Calculation of Mg(+)-ligand relative binding energies
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.
1992-01-01
The calculated relative binding energies of 16 organic molecules to Mg(+) are compared with experimental results where available. The geometries of the ligands and the Mg(+)-ligand complexes arc optimized at the self-consistent field level using a 6-31G* basis set. The Mg(+) binding energies are evaluated using second-order perturbation theory and basis sets of triple-sigma quality augmented with two sets of polarization functions. This level of theory is calibrated against higher levels of theory for selected systems. The computed binding energies are accurate to about 2 kcal/mol.
Three dimensional calculation of flux of low energy atmospheric neutrinos
NASA Technical Reports Server (NTRS)
Lee, H.; Bludman, S. A.
1985-01-01
Results of three-dimensional Monte Carlo calculation of low energy flux of atmospheric neutrinos are presented and compared with earlier one-dimensional calculations 1,2 valid at higher neutrino energies. These low energy neutrinos are the atmospheric background in searching for neutrinos from astrophysical sources. Primary cosmic rays produce the neutrino flux peaking at near E sub=40 MeV and neutrino intensity peaking near E sub v=100 MeV. Because such neutrinos typically deviate by 20 approximately 30 from the primary cosmic ray direction, three-dimensional effects are important for the search of atmospheric neutrinos. Nevertheless, the background of these atmospheric neutrinos is negligible for the detection of solar and supernova neutrinos.
Nassan, L; Abdallah, B; Omar, H; Sarheel, A; Alsomel, N; Ghazi, N
2016-01-01
The focus of this article was on the experimental estimation of the neutron energy spectrum in the inner irradiation site of the miniature neutron source reactor (MNSR), using, for the first time, a selected set of deposited metal films on Teflon (DMFTs) neutron detectors. Gold, copper, zinc, titanium, aluminum, nickel, silver, and chromium were selected because of the dependence of their neutron cross-sections on neutron energy. Emphasis was placed on the usability of this new type of neutron detectors in the total neutron energy spectrum adjustment. The measured saturation activities per target nucleus values of the DMFTs, and the calculated neutron spectrum in the inner irradiation site using the MCNP-4C code were used as an input for the STAY'SL computer code during the adjustment procedure. The agreement between the numerically calculated and experimentally adjusted spectra results was discussed. PMID:26562448
Composite electron propagator methods for calculating ionization energies
NASA Astrophysics Data System (ADS)
Díaz-Tinoco, Manuel; Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V.
2016-06-01
Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules.
Calculating Free Energy Changes in Continuum Solvation Models.
Ho, Junming; Ertem, Mehmed Z
2016-02-25
We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and 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 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. PMID:26878566
Composite electron propagator methods for calculating ionization energies.
Díaz-Tinoco, Manuel; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V
2016-06-14
Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules. PMID:27305999
Energy deposited in the high luminosity inner triplets of the LHC by collision debris
Wildner, E.; Broggi, F.; Cerutti, F.; Ferrari, A.; Hoa, C.; Koutchouk, J.-P.; Mokhov, N.V.; /Fermilab
2008-06-01
The 14 TeV center of mass proton-proton collisions in the LHC produce not only debris interesting for physics but also showers of particles ending up in the accelerator equipment, in particular in the superconducting magnet coils. Evaluations of this contribution to the heat, that has to be transported by the cryogenic system, have been made to guarantee that the energy deposition in the superconducting magnets does not exceed limits for magnet quenching and the capacity of the cryogenic system. The models of the LHC base-line are detailed and include description of, for energy deposition, essential elements like beam-pipes and corrector magnets. The evaluations made using the Monte-Carlo code FLUKA are compared to previous studies using MARS. For the consolidation of the calculations, a dedicated comparative study of these two codes was performed for a reduced setup.
Energy deposition model based on electron scattering cross section data from water molecules
NASA Astrophysics Data System (ADS)
Muñoz, A.; Oiler, J. C.; Blanco, F.; Gorfinkiel, J. D.; Limão-Vieira, P.; Maira-Vidal, A.; Borge, M. J. G.; Tengblad, O.; Huerga, C.; Téllez, M.; García, G.
2008-10-01
A complete set of electrons scattering cross sections by water molecules over a broad energy range, from the me V to the Me V ranges, is presented in this study. These data have been obtained by combining experiments and calculations and cover most relevant processes, both elastic and inelastic, which can take place in the considered energy range. A new Monte Carlo simulation programme has been developed using as input parameter these cross sectional data as well as experimental energy loss spectra. The simulation procedure has been applied to obtain electron tracks and energy deposition plots in water when irradiated by a Ru-106 plaque as those used for brachyteraphy of ocular tumours. Finally, the low energy electron tracks provided by the present model have been compared with those obtained with other codes available in the literature
Binding Energy Calculations for Novel Ternary Ionic Lattices
NASA Astrophysics Data System (ADS)
Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo
2002-03-01
Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.
Ultrasonic energy in liposome production: process modelling and size calculation.
Barba, A A; Bochicchio, S; Lamberti, G; Dalmoro, A
2014-04-21
The use of liposomes in several fields of biotechnology, as well as in pharmaceutical and food sciences is continuously increasing. Liposomes can be used as carriers for drugs and other active molecules. Among other characteristics, one of the main features relevant to their target applications is the liposome size. The size of liposomes, which is determined during the production process, decreases due to the addition of energy. The energy is used to break the lipid bilayer into smaller pieces, then these pieces close themselves in spherical structures. In this work, the mechanisms of rupture of the lipid bilayer and the formation of spheres were modelled, accounting for how the energy, supplied by ultrasonic radiation, is stored within the layers, as the elastic energy due to the curvature and as the tension energy due to the edge, and to account for the kinetics of the bending phenomenon. An algorithm to solve the model equations was designed and the relative calculation code was written. A dedicated preparation protocol, which involves active periods during which the energy is supplied and passive periods during which the energy supply is set to zero, was defined and applied. The model predictions compare well with the experimental results, by using the energy supply rate and the time constant as fitting parameters. Working with liposomes of different sizes as the starting point of the experiments, the key parameter is the ratio between the energy supply rate and the initial surface area. PMID:24647821
Detailed modeling of microwave energy deposition in EBT devices
Batchelor, D.B.; Rasmussen, D.A.; Goldfinger, R.C.
1983-08-01
Ray-tracing studies have been combined with a simple wave power balance model to provide a complete, albeit approximate, description of microwave power deposition in the ELMO Bumpy Torus (EBT-I), EBT-Scale (EBT-S), and EBT Proof-of-Principle (EBT-P) devices. Electron cyclotron absorption of ordinary and extraordinary waves by the combined core plasma and relativistic annuli is calculated using a fully relativistic damping package developed for the RAYS geometrical optics code. The rays are traced in finite-beta bumpy cylinder plasma equilibria that are obtained from the Oak Ridge National Laboratory (ORNL) two-dimensional (2-D) equilibrium code. These results for direct, single-pass absorption are combined with results from a statistical model for the deposition of multiply reflected and mode-converted waves to obtain estimates of the power deposited in the core, surface, and annulus plasma components. Wave absorption by the annuli and by the core components at the fundamental and second harmonic resonances, reflection and Budden tunneling of the extraordinary mode at the right-hand cutoff, and conversion between ordinary and extraordinary modes upon wall reflection are the processes included in the power balance model. Experimental measurements of wave power flux on the cavity wall in EBT-S made with a simple microwave calorimeter are in good agreement with predictions of the model for a variety of operating configurations.
Stone, C.A. IV; Croessmann, C.D.; Whitley, J.B.
1988-01-01
This report describes an energy coupling model that considers electron reflection losses during electron beam heating experiments. This model is embodied on the REFLEX computer code, written in standard FORTRAN 77. REFLEX currently models energy deposition phenomena in three different sample geometries. These configurations include flat, cylindrical shell, and hemispherical shell surfaces. Given the electron beam operating parameters, REFLEX calculates the heat flux profile over a sample's surface, the total amount of energy deposited into a sample, and the percentage of the electron beam energy that is transferred to a sample. This document describes the energy deposition equations used in the REFLEX code; the program is described and detailed instructions are given regarding the input. Results are given for each geometry and possible experimental applications are presented. 3 refs., 20 figs., 11 tabs.
Self-consistent calculations of alpha-decay energies
Tolokonnikov, S. V.; Lutostansky, Yu. S.; Saperstein, E. E.
2013-06-15
On the basis of the self-consistent theory of finite Fermi systems, the energies of alphadecay chains were calculated for several new superheavy nuclei discovered recently in experiments of the Dubna-Livermore Collaboration headed by Yu.Ts. Oganessian. The approach in question is implemented on the basis of the generalized method of the density functional proposed by Fayans and his coauthors. The version used here relies on the functional DF3-a proposed recently for describing a wide array of nuclear data, including data on superheavy nuclei. A detailed comparison of the results obtained on this basis with the predictions of different approaches, including the self-consistent Skyrme-Hartree-Fock method, the micro-macro method in the version developed by Sobiczewski and his coauthors, and the phenomenological method of Liran and his coauthors, is performed. The resulting alpha-decay energies are used to calculate respective lifetimes with the aid of the phenomenological Parkhomenko-Sobiczewski formula.
Improved initial guess for minimum energy path calculations.
Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt; Jónsson, Hannes
2014-06-01
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used. PMID:24907989
Improved initial guess for minimum energy path calculations
Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt
2014-06-07
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.
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
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.
Free energy calculations for a flexible water model.
Habershon, Scott; Manolopoulos, David E
2011-11-28
In this work, we consider the problem of calculating the classical free energies of liquids and solids for molecular models with intramolecular flexibility. We show that thermodynamic integration from the fully-interacting solid of interest to a Debye crystal reference state, with anisotropic harmonic interactions derived from the Hessian of the original crystal, provides a straightforward route to calculating the Gibbs free energy of the solid. To calculate the molecular liquid free energy, it is essential to correctly account for contributions from both intermolecular and intramolecular motion; we employ thermodynamic integration to a Lennard-Jones reference fluid, coupled with direct evaluation of the molecular ro-vibrational partition function. These approaches are used to study the low-pressure classical phase diagram of the flexible q-TIP4P/F water model. We find that, while the experimental ice-I/liquid and ice-III/liquid coexistence lines are described reasonably well by this model, the ice-II phase is predicted to be metastable. In light of this finding, we go on to examine how the coupling between intramolecular flexibility and intermolecular interactions influences the computed phase diagram by comparing our results with those of the underlying rigid-body water model. PMID:21887423
An energy transfer method for 4D Monte Carlo dose calculation
Siebers, Jeffrey V.; Zhong, Hualiang
2008-01-01
This article presents a new method for four-dimensional Monte Carlo dose calculations which properly addresses dose mapping for deforming anatomy. The method, called the energy transfer method (ETM), separates the particle transport and particle scoring geometries: Particle transport takes place in the typical rectilinear coordinate system of the source image, while energy deposition scoring takes place in a desired reference image via use of deformable image registration. Dose is the energy deposited per unit mass in the reference image. ETM has been implemented into DOSXYZnrc and compared with a conventional dose interpolation method (DIM) on deformable phantoms. For voxels whose contents merge in the deforming phantom, the doses calculated by ETM are exactly the same as an analytical solution, contrasting to the DIM which has an average 1.1% dose discrepancy in the beam direction with a maximum error of 24.9% found in the penumbra of a 6 MV beam. The DIM error observed persists even if voxel subdivision is used. The ETM is computationally efficient and will be useful for 4D dose addition and benchmarking alternative 4D dose addition algorithms. PMID:18841862
An energy transfer method for 4D Monte Carlo dose calculation.
Siebers, Jeffrey V; Zhong, Hualiang
2008-09-01
This article presents a new method for four-dimensional Monte Carlo dose calculations which properly addresses dose mapping for deforming anatomy. The method, called the energy transfer method (ETM), separates the particle transport and particle scoring geometries: Particle transport takes place in the typical rectilinear coordinate system of the source image, while energy deposition scoring takes place in a desired reference image via use of deformable image registration. Dose is the energy deposited per unit mass in the reference image. ETM has been implemented into DOSXYZnrc and compared with a conventional dose interpolation method (DIM) on deformable phantoms. For voxels whose contents merge in the deforming phantom, the doses calculated by ETM are exactly the same as an analytical solution, contrasting to the DIM which has an average 1.1% dose discrepancy in the beam direction with a maximum error of 24.9% found in the penumbra of a 6 MV beam. The DIM error observed persists even if voxel subdivision is used. The ETM is computationally efficient and will be useful for 4D dose addition and benchmarking alternative 4D dose addition algorithms. PMID:18841862
Free energy calculation of permeation through aquaporin-5
NASA Astrophysics Data System (ADS)
Bastien, David
The work of this paper continues upon the large area of research being done on aquaporins (AQPs). AQPs are proteins that take on the role of facilitating the transfer of substances, mainly water, across cell membranes. There are many different types of AQPs, with each of these highly selective proteins conducting only certain solutes, along with unique permeability rates. The permeation characteristics of aquaporins rely mostly on the residue hydrophobicity and steric restraints of the aromatic arginine (ar/R) region of the protein channel. The purpose of this paper is to analyze the structures of aquaporin-5 (AQP5) and aquaglycerolporin (Glpf), including a radius profile of the respective protein channels, and to compare them to permeation events using steered molecular dynamics (SMD) pulling simulations. Two in silico experiments are performed in order to achieve the free Energy landscape of a single water molecule permeating through the four channels of both Aqp5 and GlpF. The equilibrium free energy curves are calculated from the non-equilibrium, irreversible work measurements using the fluctuation-dissipation theorem (FDT) of Brownian dynamicis (BD). The free energy profiles are then compared and related to the structural profiles of AQP5 and GlpF. The change in free energy across the ar/R region in AQP5 is found to be reasonably larger than that of GlpF. The free energy profiles of AQP5 and GlpF agree with the diameter profile of the channels respectively. Furthermore, free energy calculations are computed for the permeation of Na+ and Cl- ions through the central pore of Aqp5, which provide some insight into the structural mechanisms of AQP5. The free energy barrier for ion transport through the central pore is found to be very large, peaking at around 11 Kcal/mol for chloride and 20 Kcal/mol for sodium.
A Calculation of Spatial Range of Colloidal Silicic Acid Deposited Downstream from the Alkali Front
NASA Astrophysics Data System (ADS)
Niibori, Yuichi; Iijima, Kazuki; Tamura, Naoyuki; Mimura, Hitoshi
A high alkali domain spreads out due to the use of cement materials for the construction of the repository of radioactive wastes. Sudden change of pH at this alkali front produces colloidal silicic acid (polymeric silicic acid) in addition to the deposition of supersaturated monomeric silicic acid onto the fracture surface of flow-pathway. The colloidal silicic acid also deposits with relatively small rate-constant in the co-presence of solid phase. Once the flow-path surface is covered with the amorphous silica, the surface seriously degrades the sorption behavior of radionuclides (RNs). Therefore, so far, the authors have examined the deposition rates of supersaturated silicic acid. This study summarized the deposition rate-constants defined by the first-order reaction equation under various conditions of co-presence of amorphous silica powder. Then, using the smallest rate-constant (1.0×10-12 m/s in the co-presence of calcium ions of 1 mM) and a simulation code, COLFRAC-MRL, the spatial range of colloidal silicic acid deposited downstream from the alkali front was estimated. The results suggested the clogging caused by the deposition of colloidal silicic acid in flow-path. The altered spatial range in the flow-path was limited to around 30 m in fracture and to several centimeters in rock matrix.
Atomic Layer Deposition of Bismuth Vanadates for Solar Energy Materials.
Stefik, Morgan
2016-07-01
The fabrication of porous nanocomposites is key to the advancement of energy conversion and storage devices that interface with electrolytes. Bismuth vanadate, BiVO4 , is a promising oxide for solar water splitting where the controlled fabrication of BiVO4 layers within porous, conducting scaffolds has remained a challenge. Here, the atomic layer deposition of bismuth vanadates is reported from BiPh3 , vanadium(V) oxytriisopropoxide, and water. The resulting films have tunable stoichiometry and may be crystallized to form the photoactive scheelite structure of BiVO4 . A selective etching process was used with vanadium-rich depositions to enable the synthesis of phase-pure BiVO4 after spinodal decomposition. BiVO4 thin films were measured for photoelectrochemical performance under AM 1.5 illumination. The average photocurrents were 1.17 mA cm(-2) at 1.23 V versus the reversible hydrogen electrode using a hole-scavenging sulfite electrolyte. The capability to deposit conformal bismuth vanadates will enable a new generation of nanocomposite architectures for solar water splitting. PMID:27246652
NASA Astrophysics Data System (ADS)
Luhmann, J. G.; Kozyra, J. U.
1991-04-01
The fluxes and energy spectra of picked-up planetary O(+) ions incident on the dayside atmospheres of Venus and Mars are calculated. Maps of precipitating ion number flux and energy flux are presented which show the asymmetrical distribution of dayside energy deposition expected from this source. Although the associated heating of the atmosphere and ionosphere is found to be negligible compared to that from the usual sources, backscattered or sputtered neutral oxygen atoms are produced at energies which exceed that needed for escape from the gravitational fields of both planets. These neutral 'winds', driven by pickup ion precipitation, represent a possibly significant loss of atmospheric constituents over the age of the solar system.
Characteristic properties of the Casimir free energy for metal films deposited on metallic plates
NASA Astrophysics Data System (ADS)
Klimchitskaya, G. L.; Mostepanenko, V. M.
2016-04-01
The Casimir free energy and pressure of thin metal films deposited on metallic plates are considered using the Lifshitz theory and the Drude and plasma model approaches to the role of conduction electrons. The bound electrons are taken into account by using the complete optical data of film and plate metals. It is shown that for films of several tens of nanometers thickness the Casimir free energy and pressure calculated using these approaches differ by hundreds and thousands percent and can be easily discriminated experimentally. According to our results, the free energy of a metal film does not vanish in the limiting case of ideal metal if the Drude model approach is used in contradiction with the fact that the fluctuating field cannot penetrate in its interior. Numerical computations of the Casimir free energy and pressure of Ag and Au films deposited on Cu and Al plates have been performed using both theoretical approaches. It is shown that the free energy of a film can be both negative and positive depending on the metals used. For a Au film on a Ag plate and vice versa the Casimir energy of a film changes its sign with increasing film thickness. Applications of the obtained results for resolving the Casimir puzzle and the problem of stability of thin films are discussed.
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.
Hot-Jupiter Inflation due to Deep Energy Deposition
NASA Astrophysics Data System (ADS)
Ginzburg, Sivan; Sari, Re'em
2015-04-01
Some extrasolar giant planets in close orbits—“hot Jupiters”—exhibit larger radii than that of a passively cooling planet. The extreme irradiation {{L}eq} these hot Jupiters receive from their close in stars creates a thick isothermal layer in their envelopes, which slows down their convective cooling, allowing them to retain their inflated size for longer. This is still insufficient to explain the observed sizes of the most inflated planets. Some models invoke an additional power source, deposited deep in the planet's envelope. Here, we present an analytical model for the cooling of such irradiated and internally heated gas giants. We show that a power source {{L}dep}, deposited at an optical depth {{τ }dep}, creates an exterior convective region, between optical depths {{L}eq}/{{L}dep} and {{τ }dep}, beyond which a thicker isothermal layer exists, which in extreme cases may extend to the center of the planet. This convective layer, which occurs only for {{L}dep}{{τ }dep}\\gt {{L}eq}, further delays the cooling of the planet. Such a planet is equivalent to a planet irradiated with {{L}eq}{{(1+{{L}dep}{{τ }dep}/{{L}eq})}β }, where β ≈ 0.35 is an effective power-law index describing the radiative energy density as a function of the optical depth for a convective planet U\\propto {{τ }β }. Our simple analytical model reproduces the main trends found in previous numerical works and provides an intuitive understanding. We derive scaling laws for the cooling rate of the planet, its central temperature, and radius. These scaling laws can be used to estimate the effects of tidal or Ohmic dissipation, wind shocks, or any other mechanism involving energy deposition on the sizes of hot Jupiters.
Fossil fuel energy resources of Ethiopia: Oil shale deposits
NASA Astrophysics Data System (ADS)
Wolela, Ahmed
2006-10-01
The energy crisis affects all countries in the world. Considering the price scenarios, many countries in Africa have begun to explore various energy resources. Ethiopia is one of the countries that depend upon imported petroleum products. To overcome this problem, geological studies suggest a significant occurrence of oil shale deposits in Ethiopia. The Inter-Trappean oil shale-bearing sediments are widely distributed on the South-Western Plateau of Ethiopia in the Delbi-Moye, Lalo-Sapo, Sola, Gojeb-Chida and Yayu Basins. The oil shale-bearing sediments were deposited in fluviatile and lacustrine environments. The oil shales contain mixtures of algal, herbaceous and higher plant taxa. They are dominated by algal-derived liptinite with minor amounts of vitrinite and inertinite. The algal remains belong to Botryococcus and Pediastrum. Laboratory results confirm that the Ethiopian oil shales are dominated by long-chain aliphatic hydrocarbons and have a low sulphur content. Type-II and Type-I kerogen dominated the studied oil shales. Type-II and Type-I are good source rocks for oil and gas generation. Hydrogen index versus Tmax value plots indicated that most of the oil shale samples fall within the immature-early mature stage for hydrocarbon generation, consistent with the Ro values that range from 0.3% to 0.64%. Pyrolysis data of the oil shales sensu stricto indicate excellent source rocks with up to 61.2% TOC values. Calorific value ranges from 400 to 6165 cal/g. Palynological studies confirmed that the oil shale-bearing sediments of Ethiopia range from Eocene to Miocene in age. A total of about 253,000,000 ton of oil shale is registered in the country. Oil shale deposits in Ethiopia can be used for production of oil and gas.
Hot-electron energy deposition around unsupported laser targets
Eidmann, K.; Maaswinkel, A.; Sigel, R.; Witkowski, S.; Amiranoff, F.; Fabbro, R.; Hares, J.D.; Kilkenny, J.D.
1983-09-01
Free-falling spheres, released by a simple mechanism, are used as laser targets. Hot-electron energy transport upon one-sided irradiation with 300-ps iodine laser pulses (6 x 10/sup 15/ W cm/sup -2/) is studied by various methods, including x-ray pinhole photography and time-resolved shadowgraphy. Spatial energy deposition is consistent with hot-electron spreading in the presence of self-generated magnetic fields, as suggested by recent experiments and simulations. The insensitivity of the results to the presence of a supporting stalk is attributed to inductive decoupling of the target. Free-falling targets open the possibility of highly symmetric implosion experiments.
Energy deposition of corpuscular radiation in the middle atmosphere
NASA Technical Reports Server (NTRS)
Kudela, K.
1989-01-01
Main components of corpuscular radiation contributing to energy deposition (ED in eV/cu cm/s) in the atmosphere (10 to 100 km) are cosmic ray nuclei (CR - galactic and solar) and high energy electrons (HEE), mainly of magnetospheric origin. Galactic CR depending on solar cycle phase and latitude are dominant source of ED by corpuscular radiation below 50 to 60 km. Below 20 km secondaries must be assumed. More accurate treatment need assuming of individual HE solar flare particles, cut off rigidities in geomagnetic field and their changes during magnetospheric disturbances. Electrons E sub e greater than 30 keV of magnetospheric origin penetrating to atmosphere contribute to production rate below 100 km especially on night side. High temporal variability, local time dependence and complicated energy spectra lead to complicated structure of electron ED rate. Electrons of MeV energy found at geostationary orbit, pronouncing relation to solar and geomagnetic activity, cause maximum ED at 40 to 60 km. Monitoring the global distribution of ED by corpuscular radiation in middle atmosphere need continuing low altitude satellite measurements of both HEE and x ray BS from atmosphere as well as measurements of energy spectra and charge composition of HE solar flare particles.
Goshe, Lisa R; Snover, Melissa L; Hohn, Aleta A; Balazs, George H
2016-05-01
Somatic growth rate data for wild sea turtles can provide insight into life-stage durations, time to maturation, and total lifespan. When appropriately validated, the technique of skeletochronology allows prior growth rates of sea turtles to be calculated with considerably less time and labor than required by mark--recapture studies. We applied skeletochronology to 10 dead, stranded green turtles Chelonia mydas that had previously been measured, tagged, and injected with OTC (oxytetracycline) during mark-recapture studies in Hawaii for validating skeletochronological analysis. We tested the validity of back-calculating carapace lengths (CLs) from diameters of LAGs (lines of arrested growth), which mark the outer boundaries of individual skeletal growth increments. This validation was achieved by comparing CLs estimated from measurements of the LAG proposed to have been deposited closest to the time of tagging to actual CLs measured at the time of tagging. Measureable OTC-mark diameters in five turtles also allowed us to investigate the time of year when LAGs are deposited. We found no significant difference between CLs measured at tagging and those estimated through skeletochronology, which supports calculation of somatic growth rates by taking the difference between CLs estimated from successive LAG diameters in humerus bones for this species. Back-calculated CLs associated with the OTC mark and growth mark deposited closest to tagging indicated that annual LAGs are deposited in the spring. The results of this validation study increase confidence in utilization of skeletochronology to rapidly obtain accurate age and growth data for green turtles. PMID:27096079
Holtz, M.H.; Major, R.P. )
1994-03-01
The complex interplay between depositional facies and diagenesis in carbonate rocks presents numerous problems for calculating petrophysical properties from wireline logs. If carbonate reservoirs are divided into flow units of similar depositional and diagenetic textures, empirical equations that apply specifically to that geologically identified flow unit can be developed to accurately measure porosity and water saturation. In Guadalupian and Leonardian reservoirs, carbonate mudstones deposited in subtidal marine settings are predominantly dolomite, although they contain some shale. The shale in these rocks can be detected with gamma-ray logs and empirical equations for calculation of porosity from log must include a gamma-ray component to compensate for the presence of shale. Because porosity in these rocks is dominantly intercrystalline, capillary pressure characteristics are predictable and saturations can be calculated with the Archie equation. Subtidal carbonate packstones and grainstones are composed of dolomite, anhydrite, and gypsum. The matrix acoustic transit times of these three minerals are similar, and acoustic logs are the best tool for measuring porosity. Neutron logs are the least accurate porosity tools if gypsum is present. Photo-electric density logs can distinguish gypsum from anhydrite. Because porosity in these rocks is dominantly interparticle and/or moldic, dual porosity cementation exponent corrections are needed to calculate saturations with the Archie equation, and capillary pressure saturation relationships are variable. Carbonates deposited in tidal-flat environments are generally composed of dolomite, sulfate minerals, and quartz silt, requiring a full suite of open-hole logs to make reliable porosity measurements. Diagenesis influences reservoir mineralogy and pore types. A common style of burial diagenesis in Guadalupian and Leonardian reservoirs is hydration of anhydrite to gypsum and leaching of sulfate cement and dolomite matrix.
Variational calculations of the HT{sup +} rovibrational energies
Bekbaev, A. K.; Korobov, V. I.; Dineykhan, M.
2011-04-15
In this Brief Report, we use the exponential explicitly correlated variational basis set of the type exp(-{alpha}{sub n}R-{beta}{sub n}r{sub 1}-{gamma}{sub n}r{sub 2}) to calculate systematically the nonrelativistic bound-state energies for the hydrogen molecular ion HT{sup +}. We perform calculations for the states of the total orbital angular momentum L=0 and 1 with the complete set of vibrational quantum numbers v= 0-23, as well as for the states of L= 2-5 and v= 0-5. The E1 dipole transition moments, which are of importance for the planning of spectroscopic laser experiments, have been obtained as well.
Prediction of Protein Solubility from Calculation of Transfer Free Energy
Tjong, Harianto; Zhou, Huan-Xiang
2008-01-01
Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water. To account for the effects of pH, the protonation states of titratable side chains were sampled by running constant-pH molecular dynamics simulations. Conformations were then selected for calculations of the electrostatic solvation energy: once for the condensed phase, and once for the solution phase. The average transfer free energy from the condensed phase to the solution phase was found to predict reasonably well the variations in solubility of ribonuclease Sa and insulin with pH. This treatment of electrostatic contributions combined with a similar approach for nonelectrostatic contributions led to a quantitative rationalization of the effects of point mutations on the solubility of ribonuclease Sa. This study provides valuable insights into the physical basis of protein solubility. PMID:18515380
SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
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
Exploiting the Properties of Aquaporin to Calculate Free Energy
NASA Astrophysics Data System (ADS)
Espejel, Hugo; Chen, Liao
2010-03-01
Aquaporins' (AQPs) main purpose is to facilitate the transfer of water molecules through a molecular membrane. We can calculate the free energy of the AQP system when water permeates through it. This is performed using the Visual Molecular Dynamics (VMD) and the Nanoscale Molecular Dynamics (NAMD) programs. In our first set of experiments, AQP is submerged in a body of water, in which case a water molecule near AQP is pulled through the protein. The data is then used to calculate the free energy using two different equations: the Jarzynski equality and the fluctuation-dissipation theorem. The values from both equations are then compared to examine their accuracy. The second set of experiments has the same set up, but now AQP is embedded in a lipid bilayer. We found that both equations give values that are much smaller than kT. This verifies that AQP is a channel for water molecules because the pulling of water gives constant values of free energy. We also found that the water molecules' negative poles were all pointing towards the center of the AQP channel. This means that the process of proton transport in AQP is overwhelmingly difficult.
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.
Parquet decomposition calculations of the electronic self-energy
NASA Astrophysics Data System (ADS)
Gunnarsson, O.; Schäfer, T.; LeBlanc, J. P. F.; Merino, J.; Sangiovanni, G.; Rohringer, G.; Toschi, A.
2016-06-01
The parquet decomposition of the self-energy into classes of diagrams, those associated with specific scattering processes, can be exploited for different scopes. In this work, the parquet decomposition is used to unravel the underlying physics of nonperturbative numerical calculations. We show the specific example of dynamical mean field theory and its cluster extensions [dynamical cluster approximation (DCA)] applied to the Hubbard model at half-filling and with hole doping: These techniques allow for a simultaneous determination of two-particle vertex functions and self-energies and, hence, for an essentially "exact" parquet decomposition at the single-site or at the cluster level. Our calculations show that the self-energies in the underdoped regime are dominated by spin-scattering processes, consistent with the conclusions obtained by means of the fluctuation diagnostics approach [O. Gunnarsson et al., Phys. Rev. Lett. 114, 236402 (2015), 10.1103/PhysRevLett.114.236402]. However, differently from the latter approach, the parquet procedure displays important changes with increasing interaction: Even for relatively moderate couplings, well before the Mott transition, singularities appear in different terms, with the notable exception of the predominant spin channel. We explain precisely how these singularities, which partly limit the utility of the parquet decomposition and, more generally, of parquet-based algorithms, are never found in the fluctuation diagnostics procedure. Finally, by a more refined analysis, we link the occurrence of the parquet singularities in our calculations to a progressive suppression of charge fluctuations and the formation of a resonance valence bond state, which are typical hallmarks of a pseudogap state in DCA.
Investigation of Multipole Electrostatics in Hydration Free Energy Calculations
Shi, Yue; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu
2010-01-01
Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio (BAR) method. We have compared two approaches to derive the atomic multipoles from quantum mechanical (QM) calculations: one directly from the new distributed multipole analysis (DMA) and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-ccpVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the hydration free energy calculation. PMID:20925089
Empirically corrected HEAT method for calculating atomization energies
Brand, Holmann V
2008-01-01
We describe how to increase the accuracy ofthe most recent variants ofthe HEAT method for calculating atomization energies of molecules by means ofextremely simple empirical corrections that depend on stoichiometry and the number ofunpaired electrons in the molecule. Our corrections reduce the deviation from experiment for all the HEAT variants. In particular, our corrections reduce the average absolute deviation and the root-mean-square deviation ofthe 456-QP variant to 0.18 and 0.23 kJoule/mol (i.e., 0.04 and 0.05 kcallmol), respectively.
Multiple scattering calculations of relativistic electron energy loss spectra
NASA Astrophysics Data System (ADS)
Jorissen, K.; Rehr, J. J.; Verbeeck, J.
2010-04-01
A generalization of the real-space Green’s-function approach is presented for ab initio calculations of relativistic electron energy loss spectra (EELS) which are particularly important in anisotropic materials. The approach incorporates relativistic effects in terms of the transition tensor within the dipole-selection rule. In particular, the method accounts for relativistic corrections to the magic angle in orientation resolved EELS experiments. The approach is validated by a study of the graphite CK edge, for which we present an accurate magic angle measurement consistent with the predicted value.
Analysis of uncertainties in CRAC2 calculations: wet deposition and plume rise
Ward, R.C.; Kocher, D.C.; Hicks, B.B.; Hosker, R.P. Jr.; Ku, J.Y.; Rao, K.S.
1984-01-01
We have studied the sensitivity of results from the CRAC2 computer code, which predicts health impacts from a reactor-accident scenario, to uncertainties in selected meteorological models and parameters. The sources of uncertainty examined include the models for plume rise and wet deposition and the meteorological bin-sampling procedure. An alternative plume-rise model usually had little effect on predicted health impacts. In an alternative wet-deposition model, the scavenging rate depends only on storm type, rather than on rainfall rate and atmospheric stability class as in the CRAC2 model. Use of the alternative wet-deposition model in meteorological bin-sampling runs decreased predicted mean early injuries by as much as a factor of 2 to 3 and, for large release heights and sensible heat rates, decreased mean early fatalities by nearly an order of magnitude. The bin-sampling procedure in CRAC2 was expanded by dividing each rain bin into four bins that depend on rainfall rate. Use of the modified bin structure in conjunction with the CRAC2 wet-deposition model changed all predicted health impacts by less than a factor of 2. 9 references.
ATMOSPHERIC DEPOSITION OF TOXIC METALS TO LAKE MICHIGAN: PRELIMINARY ANNUAL MODEL CALCULATIONS
Concern is growing for the environmental water quality of the Great Lakes. tmospheric deposition of toxic substances is recognized as a major pathway of contaminants to the water medium. o estimate the annual atmospheric loadings of five toxic metals -- arsenic (As), cadmium (Cd)...
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.
Model for analytical calculation of nuclear photoabsorption at intermediate energies
NASA Astrophysics Data System (ADS)
Hütt, M.-Th.; Milstein, A. I.; Schumacher, M.
1997-02-01
The universal curve {σ}/{A} of nuclear photoabsorption is investigated within a Fermi gas model of nuclear matter. An energy range from pion threshold up to 400 MeV is considered. The interactions between nucleon, pion, Δ-isobar and photon are considered in the non-relativistic approximation with corrections of the order {1}/{M} taken into account with respect to proton mass. Analytical expressions are obtained, in which the influence of nuclear correlations and two-nucleon contributions is studied explicitly. The contributions of real and virtual pions are found to be sufficient to obtain agreement with experimental data in this energy range. An extension of the model calculation to nucleon knock-out reactions is discussed.
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
Calculated photoelectron pitch angle and energy spectra. [in upper atmosphere
NASA Technical Reports Server (NTRS)
Mantas, G. P.; Bowhill, S. A.
1974-01-01
Calculations of the steady-state photoelectron energy and angular distribution in the altitude region between 120 and 1000 km are presented. The distribution is found to be isotropic at all altitudes below 250 km, while above this altitude anisotropies in both pitch angle and energy are found. The isotropy found in the angular distribution below 250 km implies that photoelectron transport below 250 km is insignificant, while the angular anisotropy found above this altitude implies a net photoelectron current in the upward direction. The energy anisotropy above 500 km arises from the selective backscattering of the low energy photoelectron population of the upward flux component by Coulomb collisions with the ambient ions. The total photoelectron flux attains its maximum value between about 40 and 70 km above the altitude at which the photoelectron production rate is maximum. The displacement of the maximum of the equilibrium flux is attributed to an increasing (with altitude) photoelectron lifetime. Photoelectrons at altitudes above that where the flux is maximum are on the average more energetic than those below that altitude.
Enhancement of fast electron energy deposition by external magnetic fields
NASA Astrophysics Data System (ADS)
Honrubia, J. J.; Murakami, M.; Mima, K.; Johzaki, T.; Sunahara, A.; Nagatomo, H.; Fujioka, S.; Shiraga, H.; Azechi, H.
2016-03-01
Recently, generation of external magnetic fields of a few kT has been reported [Fujioka et al. Scientific Reports 2013 3 1170]. These fields can be used in fast ignition to mitigate the large fast electron divergence. In this summary, two fast ignition applications are briefly outlined. The first one deals with electron guiding by external B-fields applied at the end of the shell implosion of a re-entrant cone target. Preliminary results show that the B-field strength at the time of peak ρR may be sufficiently high for fast electron guiding. The second application deals with guiding of fast electrons in magnetized wires surrounded by plasma. Results show a significant enhancement of electron energy deposition at the end of the wire, which is particularly important for low-Z wires.
Hypersonic Flow Control Using Upstream Focused Energy Deposition
NASA Technical Reports Server (NTRS)
Riggins David W.; Nelson, H. F.
1999-01-01
A numerical study of centerline and off-centerline power deposition at a point upstream of a two-dimensional blunt body at Mach 6.5 at 30 km altitude are presented. The full Navier-Stokes equations are used. Wave drag, lift, and pitching moment are presented as a function of amount of power absorbed in the flow and absorption point location. It is shown that wave drag is considerably reduced. Modifications to the pressure distribution in the flow field due to the injected energy create lift and a pitching moment when the injection is off-centerline. This flow control concept may lead to effective ways to improve the performance and to stabilize and control hypersonic vehicles.
Magnetic field effects on the energy deposition spectra of MV photon radiation.
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%. PMID:19088391
Jia, Sayyed Bijan; Hadizadeh, Mohammad Hadi; Mowlavi, Ali Asghar; Loushab, Mahdy Ebrahimi
2014-01-01
Aim Evaluation of energy deposition of protons in human brain and calculation of the secondary neutrons and photons produced by protons in proton therapy. Background Radiation therapy is one of the main methods of treating localized cancer tumors. The use of high energy proton beam in radiotherapy was proposed almost 60 years ago. In recent years, there has been a revival of interest in this subject in the context of radiation therapy. High energy protons suffer little angular deflection and have a well-defined penetration range, with a sharp increase in the energy loss at the end of their trajectories, namely the Bragg peak. Materials and methods A slab head phantom was used for the purpose of simulating proton therapy in brain tissue. In this study simulation was carried out using the Monte Carlo MCNPX code. Results By using mono energetic proton pencil beams, energy depositions in tissues, especially inside the brain, as well as estimating the neutron and photon production as a result of proton interactions in the body, together with their energy spectra, were calculated or obtained. The amount of energy escaped from the head by secondary neutrons and photons was determined. Conclusions It was found that for high energy proton beams the amount of escaped energy by neutrons is almost 10 times larger than that by photons. We estimated that at 110 MeV beam energy, the overall proton energy “leaked” from the head by secondary photons and neutrons to be around 1%. PMID:25337410
Modelling heavy-ion energy deposition in extended media
NASA Astrophysics Data System (ADS)
Mishustin, I.; Pshenichnov, I.; Greiner, W.
2010-10-01
We present recent developments of the Monte Carlo model for heavy-ion therapy (MCHIT), which is currently based on the Geant4 toolkit of version 9.2. The major advancement of the model concerns the modelling of violent fragmentation reactions by means of the Fermi break-up model, which is used to simulate decays of hot fragments created after the first stage of nucleus-nucleus collisions. By means of MCHIT we study the dose distributions from therapeutic beams of carbon nuclei in tissue-like materials, like water and PMMA. The contributions to the total dose from primary beam nuclei and from charged secondary fragments produced in nuclear fragmentation reactions are calculated. The build-up of secondary fragments along the beam axis is calculated and compared with available experimental data. Finally, we demonstrate the impact of violent multifragment decays on energy distributions of secondary neutrons produced by carbon nuclei in water.
Scattering Theory Calculations of Casimir Energies at High Curvature
NASA Astrophysics Data System (ADS)
Graham, Noah; Emig, Thorsten; Forrow, Aden; Jaffe, Robert; Kardar, Mehran; Maghrebi, Mohammad; Rahi, Jamal; Shpunt, Alex
2013-03-01
Scattering theory provides a powerful tool for capturing the response of an object to electromagnetic charge and field fluctuations. Techniques based on scattering theory have made possible a wide range of new calculations of Casimir energies. In this approach, the Casimir interaction energy for a collection of objects can be expressed in terms of the scattering T-matrices for each object individually, combined with universal translation matrices describing the objects' relative positions and orientations. These translation matrices are derived from an expansion of the free Green's function in an appropriate coordinate system, independent of the details of the objects themselves. This method proves particularly valuable for geometries involving high curvature, such as edges and tips. I will describe this approach in general terms and then give results from several problems to which it has been applied successfully. I will also discuss new developments in scattering theory that have been motivated by these problems. I would like to request that this abstract be part of a session on Casimir physics. Supported by the National Science Foundation, the US Department of Energy, the Defense Advanced Research Projects Agency, and the Deutsche Forschungsgemeinschaft
Energy deposition and non-equilibrium infared radiation of energetic auroral electrons
NASA Astrophysics Data System (ADS)
Wu, Yadong; Gao, Bo; Zhu, Guangsheng; Li, Ziguang
2016-07-01
Infrared radiation caused by energetic auroral electrons plays an important role in the thermospheric hear budget, and may be seen as background by infrared surveillance sensors. The auroral electron deposition leads to the ionization, excitation, and dissociation of neutral species(N2,O2,and O), and initiates a series of chemical reaction in the upper atmosphere, finally causes the optical emission of infared excited emitters. In this study, the whole progress from the initial auroral electrons energy deposition to the final infrared emissions has been modeled, which including space plasma, atmospheric physical chemistry, and radiative transfer. The initial atmosphere parameters before auroral disturbing are given by MSIS00 model. The primary electron flux at the top of atmosphere is given by a statistical fitting with the sum of three distribution terms, a power law, a Maxwellian and a Guassian. A semi-emprical model is used in the calculation of energy depositon of single primary electron. The total integral ion pairs production rate is obtained after combining with the initial primary electron flux. The production rate and flux of secondary electrons are modeled with a continuous slow down approximation, using different excitation, ionization, dissociation cross sections of N2, O2, and O to electrons. The photochemical reactions with auroral disturbance is analysed, and its calculation model is established. A "three-step" calculation method is created to obtain number densities of eleven species in the hight between 90-160 km, which containing N2+, O2+, O+, O2+(a4Π), O+(2D), O+(2P), N2(A3Σ), N(2D), N(4S), NO+, and N+. Number densities of different vibraional levels of NO and NO+ are got with steady state assumption, considering 1-12 vibrational levels of NO and 1-14 vibrational levels of NO+. The infared emissions and the spectral lines of the two radiating bodies are calculated with a fuzzy model of spectral band.
Technology Transfer Automated Retrieval System (TEKTRAN)
A series of studies were conducted using dual energy X-ray absorptiometry (DXA) to measure energy and protein deposition in pigs. In an initial validation study DXA was compared directly with slaughter analysis as a method for measuring body composition and energy deposition in pigs. Mean values fo...
Absorbed dose calculations to blood and blood vessels for internally deposited radionuclides
Akabani, G. ); Poston, J.W. . Dept. of Nuclear Engineering)
1991-05-01
At present, absorbed dose calculations for radionuclides in the human circulatory system used relatively simple models and are restricted in their applications. To determine absorbed doses to the blood and to the surface of the blood vessel wall, EGS4 Monte Carlo calculations were performed. Absorbed doses were calculated for the blood and the blood vessel wall (lumen) for different blood vessels sizes. The radionuclides chosen for this study were those commonly used in nuclear medicine. No diffusion of the radionuclide into the blood vessel was assumed nor cross fire between vessel was assumed. Results are useful in assessing the dose in blood and blood vessel walls for different nuclear medicine procedures. 6 refs., 6 figs., 5 tabs.
Absorbed dose calculations to blood and blood vessels for internally deposited radionuclides
Akabani, G.; Poston, J.W. Sr. )
1991-05-01
At present, absorbed dose calculations for radionuclides in the human circulatory system used relatively simple models and are restricted in their applications. To determine absorbed doses to the blood and to the surface of the blood vessel wall, EGS4 Monte Carlo calculations were performed. Absorbed doses were calculated for the blood and the blood vessel wall (lumen) for different blood vessels sizes. The radionuclides chosen for this study were those commonly used in nuclear medicine. No penetration of the radionuclide into the blood vessel was assumed nor was cross fire between the vessel assumed. The results are useful in assessing the dose to blood and blood vessel walls for different nuclear medicine procedures.
3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.
Sergiievskyi, Volodymyr P; Fedorov, Maxim V
2012-06-12
In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarking of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good
Don W. Miller; Andrew Kauffmann; Eric Kreidler; Dongxu Li; Hanying Liu; Daniel Mills; Thomas D. Radcliff; Joseph Talnagi
2001-12-31
A comprehensive description of the accomplishments of the DOE grant titled, ''Local Measurement of Fuel Energy Deposition and Heat Transfer Environment During Fuel Lifetime using Controlled Calorimetry''.
Valence calculations of lanthanide anion binding energies: a comprehensive study
NASA Astrophysics Data System (ADS)
O'Malley, Steven M.; Beck, Donald R.
2009-05-01
We have applied a methodology of universal jls restrictions on the 4f^n subgroup of relativistic configuration-interaction calculations of progressively more complex lanthanide anionsootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 77, 012505 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 78, 012510 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A, in press.. Our completed study of the row predicts bound 6p attachments to all lanthanide ground state configurations except Yb, additional 6p attachments to excited opposite parity configurations in Tb and Lu, and 6s attachments to excited open-6s thresholds in La, Ce, Pr, and Gd. In total we predict more than 100 bound states for the lanthanide anions, and we hope this comprehensive study encourages further experimentalootnotetexte.g. V. T. Davis et al., Nucl. Instrum. Methods Phys. Res. B 241, 118 (2005).^,ootnotetexte.g. C. W. Walter et al., Phys. Rev. A 76, 052702 (2007). interest in these anions. Such measurements will be useful in ``fine tuning'' these ab initio binding energies to account for missing core-valence correlation and the approximations that were necessary in these complex calculations.
Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.
Morishita, Tetsuya; Itoh, Satoru G; Okumura, Hisashi; Mikami, Masuhiro
2012-06-01
A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule. PMID:23005238
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.
Tan, Zhenyu; Xia, Yueyuan; Liu, Xiangdong; Zhao, Mingwen; Zhang, Liming
2009-04-01
A new calculation of the stopping powers (SP) and inelastic mean free paths (IMFP) for electrons in toluene at energies below 10 keV has been presented. The calculation is based on the dielectric model and on an empirical evaluation approach of optical energy loss function (OELF). The reliability for the evaluated OELFs of several hydrocarbons with available experimental optical data has been systematically checked. For toluene, using the empirical OELF, the evaluated mean ionization potential, is compared with that given by Bragg's rule, and the calculated SP at 10 keV is also compared with the Bethe-Bloch prediction. The present results for SP and IMFP provide an alternative basic data for the study on the energy deposition of low-energy electrons transport through toluene, and also show that the method used in this work may be a good one for evaluating the SP and IMFP for hydrocarbons. PMID:19138526
Energy deposition and radiation quality of radon and radon daughters. Final report
Karam, L.R.; Caswell, R.S.
1996-09-09
This program was aimed at creating a quantitative physical description, at the micrometer and nanometer levels, of the physical interactions of the alpha particles from radon and its daughters with cells at risk in the bronchial epithelium. The authors calculated alpha-particle energy spectra incident upon the cells and also energy deposition spectra in micrometer- and nanometer-sized sites as a function of cell depth, site size, airway diameter, activities of {sup 218}Po and {sup 214}Po, and other parameters. These data are now being applied, using biophysical models of radiation effects, to predict cell killing, mutations, and cell transformation. The model predictions are then compared to experimental biophysical, biochemical, and biological information. These studies contribute to a detailed understanding of the mechanisms of the biological effectiveness of the radiations emitted by radon and its progeny.
Vapor-deposited porous films for energy conversion
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.
Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye
2016-02-01
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197
INDIVIDUALISED CALCULATION OF TISSUE IMPARTED ENERGY IN BREAST TOMOSYNTHESIS.
Geeraert, N; Klausz, R; Muller, S; Bloch, I; Bosmans, H
2016-06-01
The imparted energy to the glandular tissue in the breast (glandular imparted energy, GIE) is proposed for an improved assessment of the individual radiation-induced risk resulting from X-ray breast imaging. GIE is computed from an estimation of the quantity and localisation of glandular tissue in the breast. After a digital breast tomosynthesis (DBT) acquisition, the volumetric glandular content (volumetric breast density, VBD) is computed from the central X-ray projection. The glandular tissue distribution is determined by labelling the DBT voxels to ensure the conservation of the VBD. Finally, the GIE is calculated by Monte Carlo computation on the resulting tissue-labelled DBT volume. For verification, the method was applied to 10 breast-shaped digital phantoms made of different glandular spheres in an adipose background, and to a digital anthropomorphic phantom. Results were compared to direct GIE computations on the phantoms considered as 'ground-truth'. The major limitations in accuracy are those of DBT, in particular the limited z-resolution. However, for most phantoms, the results can be considered as acceptable. PMID:27127209
Handford, C.R. )
1990-08-01
Subaqueous deposits of aragonite, gypsum, and halite are accumulating in shallow solar salt ponds constructed in the Pekelmeer, a sea-level salina on Bonaire, Netherlands Antilles. Several halite facies are deposited in the crystallizer ponds in response to difference in water depth and wave energy. Cumulate halite, which originates as floating rafts, is present only along the protected, upwind margins of ponds where low-energy conditions foster their formation and preservation. Cornet crystals with peculiar mushroom- and mortarboard-shaped caps precipitate in centimetre-deep brine sheets within a couple of metres of the upwind or low-energy margins. Downwind from these margins, cornet and chevron halite precipitate on the pond floors in water depths ranging from a few centimetres to {approximately} 60 cm. Halite pisoids with radial-concentric structure are precipitated in the swash zone along downwind high-energy shorelines where they form pebbly beaches. This study suggests that primary halite facies are energy and/or depth dependent and that some primary features, if preserved in ancient halite deposits, can be used to infer physical energy conditions, subenvironments such as low- to high-energy shorelines, and extremely shallow water depths in ancient evaporite basins.
Deposition of dopant impurities and pulsed energy drive-in
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.
Deposition of dopant impurities and pulsed energy drive-in
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
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.
Energy deposition via magnetoplasmadynamic acceleration: II. modeling and performance predictions
NASA Astrophysics Data System (ADS)
Mikellides, P. G.; England, B.; Gilland, J. H.
2009-02-01
A time-dependent, two-dimensional, axisymmetric magnetohydrodynamics code is employed to model, validate and extend the experimentally-limited performance characteristics of a gigawatt-level plasma source that utilized magnetoplasmadynamic (MPD) acceleration for gas energy deposition. Accurate modeling required an upgrade of the code's circuit routines to properly capture the pulse-forming-network current waveform which also serves as the primary variable for validation. Comparisons with experimentally deduced current waveforms were in good agreement for all power levels. The simulations also produced values for the plasma voltage which were compared with the measured voltage across the electrodes. The trend agreement was encouraging while the magnitude of the discrepancy is approximately constant and interpreted as a representation of the electrode fall voltage. Force computations captured the expected electromagnetic acceleration trends and serve as further verification. They also allow examination of the device as a very high power MPD thruster operating at power levels in excess of 180 MW. The computations offer insights into the plasma's characteristics at different power levels through two-dimensional distributions of pertinent parameters and identify design guidelines for effective stagnation temperature values as a function of the mass-flow rate.
Identification of HIV Inhibitors Guided by Free Energy Perturbation Calculations
Acevedo, Orlando; Ambrose, Zandrea; Flaherty, Patrick T.; Aamer, Hadega; Jain, Prashi; Sambasivarao, Somisetti V.
2013-01-01
Free energy perturbation (FEP) theory coupled to molecular dynamics (MD) or Monte Carlo (MC) statistical mechanics offers a theoretically precise method for determining the free energy differences of related biological inhibitors. Traditionally requiring extensive computational resources and expertise, it is only recently that its impact is being felt in drug discovery. A review of computer-aided anti-HIV efforts employing FEP calculations is provided here that describes early and recent successes in the design of human immunodeficiency virus type 1 (HIV-1) protease and non-nucleoside reverse transcriptase inhibitors. In addition, our ongoing work developing and optimizing leads for small molecule inhibitors of cyclophilin A (CypA) is highlighted as an update on the current capabilities of the field. CypA has been shown to aid HIV-1 replication by catalyzing the cis/trans isomerization of a conserved Gly-Pro motif in the N-terminal domain of HIV-1 capsid (CA) protein. In the absence of a functional CypA, e.g., by the addition of an inhibitor such as cyclosporine A (CsA), HIV-1 has reduced infectivity. Our simulations of acylurea-based and 1-indanylketone-based CypA inhibitors have determined that their nanomolar and micromolar binding affinities, respectively, are tied to their ability to stabilize Arg55 and Asn102. A structurally novel 1-(2,6-dichlorobenzamido) indole core was proposed to maximize these interactions. FEP-guided optimization, experimental synthesis, and biological testing of lead compounds for toxicity and inhibition of wild-type HIV-1 and CA mutants have demonstrated a dose-dependent inhibition of HIV-1 infection in two cell lines. While the inhibition is modest compared to CsA, the results are encouraging. PMID:22316150
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.
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2011 CFR
2011-01-01
... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2014 CFR
2014-01-01
... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2013 CFR
2013-01-01
... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2012 CFR
2012-01-01
... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2010 CFR
2010-01-01
... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
Huang, Jessie Y.; Howell, Rebecca M.; Mirkovic, Dragan; Followill, David S.; Kry, Stephen F.; Eklund, David; Childress, Nathan L.
2013-12-15
Purpose: Several simplifications used in clinical implementations of the convolution/superposition (C/S) method, specifically, density scaling of water kernels for heterogeneous media and use of a single polyenergetic kernel, lead to dose calculation inaccuracies. Although these weaknesses of the C/S method are known, it is not well known which of these simplifications has the largest effect on dose calculation accuracy in clinical situations. The purpose of this study was to generate and characterize high-resolution, polyenergetic, and material-specific energy deposition kernels (EDKs), as well as to investigate the dosimetric impact of implementing spatially variant polyenergetic and material-specific kernels in a collapsed cone C/S algorithm.Methods: High-resolution, monoenergetic water EDKs and various material-specific EDKs were simulated using the EGSnrc Monte Carlo code. Polyenergetic kernels, reflecting the primary spectrum of a clinical 6 MV photon beam at different locations in a water phantom, were calculated for different depths, field sizes, and off-axis distances. To investigate the dosimetric impact of implementing spatially variant polyenergetic kernels, depth dose curves in water were calculated using two different implementations of the collapsed cone C/S method. The first method uses a single polyenergetic kernel, while the second method fully takes into account spectral changes in the convolution calculation. To investigate the dosimetric impact of implementing material-specific kernels, depth dose curves were calculated for a simplified titanium implant geometry using both a traditional C/S implementation that performs density scaling of water kernels and a novel implementation using material-specific kernels.Results: For our high-resolution kernels, we found good agreement with the Mackie et al. kernels, with some differences near the interaction site for low photon energies (<500 keV). For our spatially variant polyenergetic kernels, we found
Calculating activation energies for temperature compensation in circadian rhythms
NASA Astrophysics Data System (ADS)
Bodenstein, C.; Heiland, I.; Schuster, S.
2011-10-01
Many biological species possess a circadian clock, which helps them anticipate daily variations in the environment. In the absence of external stimuli, the rhythm persists autonomously with a period of approximately 24 h. However, single pulses of light, nutrients, chemicals or temperature can shift the clock phase. In the case of light- and temperature-cycles, this allows entrainment of the clock to cycles of exactly 24 h. Circadian clocks have the remarkable property of temperature compensation, that is, the period of the circadian rhythm remains relatively constant within a physiological range of temperatures. For several organisms, temperature-regulated processes within the circadian clock have been identified in recent years. However, how these processes contribute to temperature compensation is not fully understood. Here, we theoretically investigate temperature compensation in general oscillatory systems. It is known that every oscillator can be locally temperature compensated around a reference temperature, if reactions are appropriately balanced. A balancing is always possible if the control coefficient with respect to the oscillation period of at least one reaction in the oscillator network is positive. However, for global temperature compensation, the whole physiological temperature range is relevant. Here, we use an approach which leads to an optimization problem subject to the local balancing principle. We use this approach to analyse different circadian clock models proposed in the literature and calculate activation energies that lead to temperature compensation.
Path-breaking schemes for nonequilibrium free energy calculations
NASA Astrophysics Data System (ADS)
Chelli, Riccardo; Gellini, Cristina; Pietraperzia, Giangaetano; Giovannelli, Edoardo; Cardini, Gianni
2013-06-01
We propose a path-breaking route to the enhancement of unidirectional nonequilibrium simulations for the calculation of free energy differences via Jarzynski's equality [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)], 10.1103/PhysRevLett.78.2690. One of the most important limitations of unidirectional nonequilibrium simulations is the amount of realizations necessary to reach suitable convergence of the work exponential average featuring the Jarzynski's relationship. In this respect, a significant improvement of the performances could be obtained by finding a way of stopping trajectories with negligible contribution to the work exponential average, before their normal end. This is achieved using path-breaking schemes which are essentially based on periodic checks of the work dissipated during the pulling trajectories. Such schemes can be based either on breaking trajectories whose dissipated work exceeds a given threshold or on breaking trajectories with a probability increasing with the dissipated work. In both cases, the computer time needed to carry out a series of nonequilibrium trajectories is reduced up to a factor ranging from 2 to more than 10, at least for the processes under consideration in the present study. The efficiency depends on several aspects, such as the type of process, the number of check-points along the pathway and the pulling rate as well. The method is illustrated through radically different processes, i.e., the helix-coil transition of deca-alanine and the pulling of the distance between two methane molecules in water solution.
Calculation Of A Micro Discharge Energy Balance With PIC-MCC Method
Benstaali, W.; Belasri, A.; Hagelaar, G. J. M.; Boeuf, J. P.
2008-09-23
In this paper, we present a 1D Particle in Cell with Monte Carlo Collisions model, developed in order to calculate the energy balance in a micro-discharge, under conditions similar to those of a Plasma Display Panel (PDP) cell. The discharge takes place in a xenon-neon (10%-;90%) mixture at 560 torr and for a gap length of 100 {mu}m. The model is used to analyze in details the energy deposition during the discharge pulse. The results show the amount of energy dissipated by ions (collisions in the gas and on the cathode), by electrons (excitation of the different electronic states, ionization), and their variations with the applied voltage. This model will be used in the future to test the approximations of the fluid models which are generally used to optimize PDP operating conditions, and to check whether or not fluid models can correctly predict the trends in the variations of the energy balance with parameters such as voltage, pressure, gas mixture.
Gold deposited on a Ge(0 0 1) surface: DFT calculations.
Tsay, Shiow-Fon
2016-11-01
The atomic geometry, stability and electronic properties of self-organized Au induced nanowires on a Ge(0 0 1) surface are investigated based on the density-functional theory in the generalized gradient approximation and the stoichiometry of Au. According to the formation energy and the simulated STM image, the Ge atoms substituted by the Au atoms have been confirmed as occurring at a Au coverage lower than 0.25 Ml. The STM image with single and double dimer vacancies looks like the Au atoms have penetrated the subsurface. The energetically favorable dimer-row arrayed structures at 0.50 Ml and 0.75 Ml Au coverages have a 4 × 1, 4 × 2 or c(8 × 2) transition symmetry, which comprise a flat Au-Au homodimer row and an alternating various buckling phase Ge-Ge or Au-Ge dimer row. The c(8 × 2) zigzag-shaped protruding chains of shallow-groove STM images are highly consistent with the observations, but a long-range order dimer-row arrayed structure formation requires sufficient mobile energy to complete mass transport of the substituted Ge atoms in order to avoid the re-adsorption of these atoms; otherwise a deep-groove structure reconstruction is sequentially formed. A quasi-1D electron-like energy trough aligns in the direction perpendicular to the nanowire of the dimer-row arrayed structure in the c(8 × 2) phase on a 0.75 Ml Au/Ge(0 0 1) surface, which is contributed by the Au-Ge dimer rows and the subsurface Ge atoms below them. The bottom energy of the energy trough is consistent with angle-resolved photo-emission spectroscopy studies (Schäfer et al 2008 Phys. Rev. Lett. 101 236802, Meyer et al 2011 Phys. Rev. B 83 121411(R)). PMID:27603175
Evaluation of the mean energy deposit during the impact of charged particles on liquid water
NASA Astrophysics Data System (ADS)
Bernal, M. A.
2012-04-01
The DNA strand break yield due to the impact of ionizing particles on living beings is closely related to the number of inelastic events per unit absorbed dose produced by these particles. The higher this number, the higher the probability of causing DNA strand breaks per unit absorbed dose. In a previous work, it was found that the total number of events produced by primary particles and the secondary electrons is almost independent of the type and energy of the incident particle (or LET). This finding could be supported by a quasi-constant mean energy deposit by inelastic event (\\bar{\\varepsilon }). In this work, \\bar{\\varepsilon } was defined and determined for electrons and the non-negative charge states of hydrogen (H0, +) and helium (He0, +, 2 +) species impacting on liquid water. Ionization, excitation and charge transfer (up to two-electron transfers) processes have been included in present calculations. We found that, for liquid water, \\bar{\\varepsilon } is within 13.7 ± 4.1 eV, 14.2 ± 1.7 eV and 13.8 ± 1.4 eV for electrons, hydrogen and helium species, respectively, with impact energies changing over three orders of magnitude. Unlike the mean excitation energy, the mean energy deposit per inelastic event depends not only on the target molecule but also on the projectile features. However, this dependence is relatively weak. This fact supports the quasi-independent number of inelastic events per unit absorbed dose found previously when charged particles impact on matter.
Use of energy deposition spectrometer Liulin for individual monitoring of aircrew.
Ploc, O; Pachnerová Brabcová, K; Spurny, F; Malušek, A; Dachev, T
2011-03-01
Silicon energy deposition spectrometer Liulin was primarily developed for cosmic radiation monitoring onboard spacecrafts. Nowadays, Liulin type detectors are also used to characterise radiation field on board aircraft, at alpine observatories and behind the shielding of heavy ion accelerators. In this work, experiments and calibrations performed in these radiation fields are presented and the method developed for calculation of ambient dose equivalent H*(10) on board aircraft is described. Since 2001, a simple method employing the energy deposition spectra had been used to determine H*(10) on board aircraft but, in 2004, it became clear that the resulting values were strongly biased at locations close to Earth's equator. An improved method for the determination of H*(10) on board aircraft using the Liulin detector was developed. It took into account the composition of the radiation field via the ratio of absorbed doses D(low) and D(neut) reflecting the contributions from low-LET particles and neutrons, respectively. It resulted in much better agreement with the EPCARD computer code for all aircraft locations; relative differences were within 11 % for low-LET and 20 % for neutron components of H*(10). PMID:21186209
Caveat Emptor: Calculating All the Costs of Energy.
ERIC Educational Resources Information Center
Zinberg, Dorothy S.
This paper examines the energy problem. Specific topics discussed include the recent history of oil and gas consumption in the United States, conservation, coal, solar energy, and nuclear energy. While solutions to the energy problem differ, there is an urgent need for broad, public debate. Ultimately, the decisions made regarding energy will be…
NASA Astrophysics Data System (ADS)
Jia, Ye; Zeng, Ke; Wallace, Joshua S.; Gardella, Joseph A.; Singisetti, Uttam
2015-03-01
The energy band alignment between atomic layer deposited (ALD) SiO2 and β-Ga2O3 ( 2 ¯ 01 ) is calculated using x-ray photoelectron spectroscopy and electrical measurement of metal-oxide semiconductor capacitor structures. The valence band offset between SiO2 and Ga2O3 is found to be 0.43 eV. The bandgap of ALD SiO2 was determined to be 8.6 eV, which gives a large conduction band offset of 3.63 eV between SiO2 and Ga2O3. The large conduction band offset makes SiO2 an attractive gate dielectric for power devices.
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.
NASA Astrophysics Data System (ADS)
Zhang, Hui; Komori, Takuya; Zhang, Yulong; Yin, You; Hosaka, Sumio
2013-12-01
We proposed a model for calculating the resist profile in electron beam drawing. The model predicts the solubility rate on the basis of the energy deposition distribution (EDD) for the development of latent patterns in the resist. By unifying the exposure dose D (via experiments) and EDDs (via calculations), we roughly determined solubility rates for three-dimensional EDDs, and established the proposed model. The development simulation was achieved by the sequential calculation method for solubility rates based on EDD which was calculated by Monte Carlo simulation. By determining a suitable EDD region to achieve good patterning, we obtained a sharp nanodot pattern of the resist. This simulation results are in good agreement with the experimental results obtained using a combination of 2.3 wt % tetramethylammonium hydroxide (TMAH) and 4 wt % NaCl as the developer. The model was demonstrated to be useful for predicting resist profiles with different experimental solubility rates of developers.
Monte Carlo approach to the spatial deposition of energy by electrons in molecular hydrogen
NASA Technical Reports Server (NTRS)
Heaps, M. G.; Green, A. E. S.
1974-01-01
The Monte Carlo (MC) and continuous slowdown approximation (CSDA) approaches to the spatial deposition of energy by electrons are compared using the same detailed atomic cross section (DACS). It is found that the CSDA method overestimates the amount of energy that is deposited near the end of the path for electrons above a few hundred electron volts. The MC results are in approximate agreement with experimental data in such a way as to be relatively independent of the actual gas used. Our MC results are extended to obtain the three-dimensional deposition of energy by sub-keV electrons in molecular hydrogen.
Trypsin-Ligand Binding Free Energy Calculation with AMOEBA
Shi, Yue; Jiao, Dian; Schnieders, Michael J.; Ren, Pengyu
2010-01-01
The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was found to be the driving force for the binding. Structural analysis shows that the ligands form hydrogen bonds with residues and water molecules nearby in a competitive fashion. The dependence of binding free energy on molecular dipole moment and polarizability was also studied. While the binding free energy is independent on the dipole moment, it shows a negative correlation with the polarizability. PMID:19965178
NASA Astrophysics Data System (ADS)
Peeler, Christopher R.; Titt, Uwe
2012-06-01
In spot-scanning intensity-modulated proton therapy, numerous unmodulated proton beam spots are delivered over a target volume to produce a prescribed dose distribution. To accurately model field size-dependent output factors for beam spots, the energy deposition at positions radial to the central axis of the beam must be characterized. In this study, we determined the difference in the central axis dose for spot-scanned fields that results from secondary particle doses by investigating energy deposition radial to the proton beam central axis resulting from primary protons and secondary particles for mathematical point source and distributed source models. The largest difference in the central axis dose from secondary particles resulting from the use of a mathematical point source and a distributed source model was approximately 0.43%. Thus, we conclude that the central axis dose for a spot-scanned field is effectively independent of the source model used to calculate the secondary particle dose.
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer
NASA Astrophysics Data System (ADS)
Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.
2015-08-01
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm-1, only slightly below the 935 cm-1 value derived from experiment.
Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin
2013-01-24
A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. PMID:23268557
Cortes-Giraldo, M A; Carabe-Fernandez, A
2014-06-01
Purpose: To evaluate the differences in dose-averaged linear energy transfer (LETd) maps calculated in water by means of different strategies found in the literature in proton therapy Monte Carlo simulations and to compare their values with dose-mean lineal energy microdosimetry calculations. Methods: The Geant4 toolkit (version 9.6.2) was used. Dose and LETd maps in water were scored for primary protons with cylindrical voxels defined around the beam axis. Three LETd calculation methods were implemented. First, the LETd values were computed by calculating the unrestricted linear energy transfer (LET) associated to each single step weighted by the energy deposition (including delta-rays) along the step. Second, the LETd was obtained for each voxel by computing the LET along all the steps simulated for each proton track within the voxel, weighted by the energy deposition of those steps. Third, the LETd was scored as the quotient between the second momentum of the LET distribution, calculated per proton track, over the first momentum. These calculations were made with various voxel thicknesses (0.2 – 2.0 mm) for a 160 MeV proton beamlet and spread-out Bragg Peaks (SOBP). The dose-mean lineal energy was calculated in a uniformly-irradiated water sphere, 0.005 mm radius. Results: The value of the LETd changed systematically with the voxel thickness due to delta-ray emission and the enlargement of the LET distribution spread, especially at shallow depths. Differences of up to a factor 1.8 were found at the depth of maximum dose, leading to similar differences at the central and distal depths of the SOBPs. The third LETd calculation method gave better agreement with microdosimetry calculations around the Bragg Peak. Conclusion: Significant differences were found between LETd map Monte Carlo calculations due to both the calculation strategy and the voxel thickness used. This could have a significant impact in radiobiologically-optimized proton therapy treatments.
Subtleties in Energy Calculations in the Image Method
ERIC Educational Resources Information Center
Taddei, M. M.; Mendes, T. N. C.; Farina, C.
2009-01-01
In this pedagogical work, we point out a subtle mistake that can be made by undergraduate or graduate students in the computation of the electrostatic energy of a system containing charges and perfect conductors if they naively use the image method. Specifically, we show that naive expressions for the electrostatic energy for these systems…
NASA Astrophysics Data System (ADS)
Raine, M.; Gaillardin, M.; Paillet, P.; Duhamel, O.; Martinez, M.; Bernard, H.
2015-12-01
The dispersion of heavy ion deposited energy is explored in nanometric electronic devices. Experimental data are reported, in a large thin SOI diode and in a SOI FinFET device, showing larger distributions of collected charge in the nanometric volume device. Geant4 simulations are then presented, using two different modeling approaches. Both of them seem suitable to evaluate the dispersion of deposited energy induced by heavy ion beams in advanced electronic devices with nanometric dimensions.
NASA Technical Reports Server (NTRS)
Rees, M. H.; Lummerzheim, D.; Roble, R. G.; Winningham, J. D.; Craven, J. D.
1988-01-01
Auroral images obtained by the Spin Scan Auroral Imager (SAI) aboard the DE-1 satellite were used to derive auroral energy deposition rate, characteristic electron energy, and ionospheric parameters. The principles involved in the imaging technique and the physical mechanisms that underlie the relationship between the spectral images and the geophysical parameters are discussed together with the methodology for implementing such analyses. It is shown that images obtained with the SAI provide global parameters at 12-min temporal resolution; the spatial resolution is limited by the field of view of a pixel. The analysis of the 12-min images presented yielded a representation of ionospheric parameters that was better than can be obtained using empirical models based on local measurements averaged over long periods of time.
Yeh, Hsu-Chi; Phalen, R.F.; Chang, I.
1995-12-01
The National Council on Radiation Protection and Measurements (NCRP) in the United States and the International Commission on Radiological Protection (ICRP) have been independently reviewing and revising respiratory tract dosimetry models for inhaled radioactive aerosols. The newly proposed NCRP respiratory tract dosimetry model represents a significant change in philosophy from the old ICRP Task Group model. The proposed NCRP model describes respiratory tract deposition, clearance, and dosimetry for radioactive substances inhaled by workers and the general public and is expected to be published soon. In support of the NCRP proposed model, ITRI staff members have been developing computer software. Although this software is still incomplete, the deposition portion has been completed and can be used to calculate inhaled particle deposition within the respiratory tract for particle sizes as small as radon and radon progeny ({approximately} 1 nm) to particles larger than 100 {mu}m. Recently, ICRP published their new dosimetric model for the respiratory tract, ICRP66. Based on ICRP66, the National Radiological Protection Board of the UK developed PC-based software, LUDEP, for calculating particle deposition and internal doses. The purpose of this report is to compare the calculated respiratory tract deposition of particles using the NCRP/ITRI model and the ICRP66 model, under the same particle size distribution and breathing conditions. In summary, the general trends of the deposition curves for the two models were similar.
Engineering properties of superhard films with ion energy and post-deposition processing
Monteiro, Othon R.; Delplancke-Ogletree, Mari-Paule
2002-10-14
Recent developments in plasma synthesis of hard materials using energetic ions are described. Metal Plasma Immersion Ion Implantation and Deposition (MePIIID) has been used to prepare several hard films: from diamondlike carbon (DLC) to carbides, from nitrides to oxides. The energy of the depositing species is controlled to maximize adhesion as well as to change the physical and chemical properties of the films. Adhesion is promoted by the creation of a graded interface between the film and the substrate. The energy of the depositing ions is also used to modify and control the intrinsic stresses and the microstructure of the films. The deposition is carried out at room temperature, which is important for temperature sensitive substrates. A correlation between intrinsic stresses and the energetics of the deposition is presented for the case of DLC films, and means to reduce stress levels are discussed.
Gruel, Gaëtan; Villagrasa, Carmen; Voisin, Pascale; Clairand, Isabelle; Benderitter, Marc; Bottollier-Depois, Jean-François; Barquinero, Joan Francesc
2016-01-01
Most studies that aim to understand the interactions between different types of photon radiation and cellular DNA assume homogeneous cell irradiation, with all cells receiving the same amount of energy. The level of DNA damage is therefore generally determined by averaging it over the entire population of exposed cells. However, evaluating the molecular consequences of a stochastic phenomenon such as energy deposition of ionizing radiation by measuring only an average effect may not be sufficient for understanding some aspects of the cellular response to this radiation. The variance among the cells associated with this average effect may also be important for the behaviour of irradiated tissue. In this study, we accurately estimated the distribution of the number of radiation-induced γH2AX foci (RIF) per cell nucleus in a large population of endothelial cells exposed to 3 macroscopic doses of gamma rays from 60Co. The number of RIF varied significantly and reproducibly from cell to cell, with its relative standard deviation ranging from 36% to 18% depending on the macroscopic dose delivered. Interestingly, this relative cell-to-cell variability increased as the dose decreased, contrary to the mean RIF count per cell. This result shows that the dose effect, in terms of the number of DNA lesions indicated by RIF is not as simple as a purely proportional relation in which relative SD is constant with dose. To analyse the origins of this observed variability, we calculated the spread of the specific energy distribution for the different target volumes and subvolumes in which RIF can be generated. Variances, standard deviations and relative standard deviations all changed similarly from dose to dose for biological and calculated microdosimetric values. This similarity is an important argument that supports the hypothesis of the conservation of the association between the number of RIF per nucleus and the specific energy per DNA molecule. This comparison allowed us to
Voisin, Pascale; Clairand, Isabelle; Benderitter, Marc; Bottollier-Depois, Jean-François; Barquinero, Joan Francesc
2016-01-01
Most studies that aim to understand the interactions between different types of photon radiation and cellular DNA assume homogeneous cell irradiation, with all cells receiving the same amount of energy. The level of DNA damage is therefore generally determined by averaging it over the entire population of exposed cells. However, evaluating the molecular consequences of a stochastic phenomenon such as energy deposition of ionizing radiation by measuring only an average effect may not be sufficient for understanding some aspects of the cellular response to this radiation. The variance among the cells associated with this average effect may also be important for the behaviour of irradiated tissue. In this study, we accurately estimated the distribution of the number of radiation-induced γH2AX foci (RIF) per cell nucleus in a large population of endothelial cells exposed to 3 macroscopic doses of gamma rays from 60Co. The number of RIF varied significantly and reproducibly from cell to cell, with its relative standard deviation ranging from 36% to 18% depending on the macroscopic dose delivered. Interestingly, this relative cell-to-cell variability increased as the dose decreased, contrary to the mean RIF count per cell. This result shows that the dose effect, in terms of the number of DNA lesions indicated by RIF is not as simple as a purely proportional relation in which relative SD is constant with dose. To analyse the origins of this observed variability, we calculated the spread of the specific energy distribution for the different target volumes and subvolumes in which RIF can be generated. Variances, standard deviations and relative standard deviations all changed similarly from dose to dose for biological and calculated microdosimetric values. This similarity is an important argument that supports the hypothesis of the conservation of the association between the number of RIF per nucleus and the specific energy per DNA molecule. This comparison allowed us to
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.
Laser energy deposition and its dynamic uniformity for direct-drive capsules
Xu, Yan; Wu, SiZhong; Zheng, WuDi
2015-04-15
The total laser energy deposition of multi-laser-beam irradiation is not only associated with the dynamic behavior of capsule but also the time-dependent angular distribution of the energy deposition of each beam around its axis. The dynamic behavior of laser energy deposition does not linearly respond to the dynamic behavior of laser irradiation. The laser energy deposition uniformity determines the symmetry of implosion. The dynamic behavior of laser energy deposition non-uniformity in OMEGA for laser with square beam shape intensity profile is investigated. In the case of smaller laser spot, the initial non-uniformity caused by laser beam overlap is very high. The shell asymmetry caused by the high initial laser irradiation non-uniformity is estimated by the extent of distortion of shock front which is not as severe as expected before the shock driven by main pulse arrives. This suggests that the large initial non-uniformity due to smaller laser spot is one of the elements that seed disturbance before the main pulse. The rms of laser energy deposition during the main pulse remains above 2%. Since the intensity of main driving pulse usually is several times higher than that of picket pulses, the non-uniformity in main pulse period may jeopardize the symmetrical implosion. When dynamic behavior of capsule is considered, the influence of beam pointing error, the target positioning error, and beam-to-beam power unbalance is quite different for the case of static capsule.
NASA Astrophysics Data System (ADS)
Correale, G.; Winkel, R.; Kotsonis, M.
2015-08-01
An experimental study aimed at the characterization of energy deposition of nanosecond Dielectric Barrier Discharge (ns-DBD) plasma actuators was carried out. Special attention was given on the effect of the thickness and material used for dielectric barrier. The selected materials for this study were polyimide film (Kapton), polyamide based nylon (PA2200), and silicone rubber. Schlieren measurements were carried out in quiescent air conditions in order to observe density gradients induced by energy deposited. Size of heated area was used to qualify the energy deposition coupled with electrical power measurements performed using the back-current shunt technique. Additionally, light intensity measurements showed a different nature of discharge based upon the material used for barrier, for a fixed thickness and frequency of discharge. Finally, a characterisation study was performed for the three tested materials. Dielectric constant, volume resistivity, and thermal conductivity were measured. Strong trends between the control parameters and the energy deposited into the fluid during the discharge were observed. Results indicate that efficiency of energy deposition mechanism relative to the thickness of the barrier strongly depends upon the material used for the dielectric barrier itself. In general, a high dielectric strength and a low volumetric resistivity are preferred for a barrier, together with a high heat capacitance and a low thermal conductivity coefficient in order to maximize the efficiency of the thermal energy deposition induced by an ns-DBD plasma actuator.
Oxyfluoroborate host glass for upconversion application: phonon energy calculation
NASA Astrophysics Data System (ADS)
Abdel-Baki, Manal; El-Diasty, Fouad
2016-04-01
Reducing the glass phonon energy is an essential procedure to achieve high efficient radiative upconversion process. The degree of covalence of chemical bonds is responsible for the high oscillator strength of intracenter transitions in rare-earth ions. So, conversion covalent to ionic glass character is proposed as a structure-sensitive criterion that controls the phonon energy of the glasses. A series of oxyfluoro aluminum-borate host glasses used for upconversion application is prepared by the conventional melt-quenching technique. Through lithium oxide substitution by lithium fluoride, the ionic-covalent property of Li+ ion successes to regulate the band gap energies of the studied glasses. Furthermore, a new method to determine the glass phonon energy is offered.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations. PMID:24697449
NASA Astrophysics Data System (ADS)
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-01
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
Stabilizing laser energy density on a target during pulsed laser deposition of thin films
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.
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. PMID:26931692
NASA Astrophysics Data System (ADS)
Horn, Paul R.; Head-Gordon, Martin
2016-02-01
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.
Energy levels of isoelectronic impurities by large scale LDA calculations
Li, Jingbo; Wang, Lin-Wang
2002-11-22
Isoelectronic impurity states are localized states induced by stoichiometric single atom substitution in bulk semiconductor. Photoluminescence spectra indicate deep impurity levels of 0.5 to 0.9eV above the top of valence band for systems like: GaN:As, GaN:P, CdS:Te, ZnS:Te. Previous calculations based on small supercells seemingly confirmed these experimental results. However, the current ab initio calculations based on thousand atom supercells indicate that the impurity levels of the above systems are actually much shallower(0.04 to 0.23 eV), and these impurity levels should be compared with photoluminescence excitation spectra, not photoluminescence spectra.
Biological characterization of low-energy ions with high-energy deposition on human cells.
Saha, Janapriya; Wilson, Paul; Thieberger, Peter; Lowenstein, Derek; Wang, Minli; Cucinotta, Francis A
2014-09-01
During space travel, astronauts are exposed to cosmic radiation that is comprised of high-energy nuclear particles. Cancer patients are also exposed to high-energy nuclear particles when treated with proton and carbon beams. Nuclear interactions from high-energy particles traversing shielding materials and tissue produce low-energy (<10 MeV/n) secondary particles of high-LET that contribute significantly to overall radiation exposures. Track structure theories suggest that high charge and energy (HZE) particles and low-energy secondary ions of similar LET will have distinct biological effects for cellular and tissue damage endpoints. We investigated the biological effects of low-energy ions of high LET utilizing the Tandem Van de Graaff accelerator at the Brookhaven National Laboratory (BNL), and compared these to experiments with HZE particles, that mimic the space environment produced at NASA Space Radiation Laboratory (NSRL) at BNL. Immunostaining for DNA damage response proteins was carried out after irradiation with 5.6 MeV/n boron (LET 205 keV/μm), 5.3 MeV/n silicon (LET 1241 keV/μm), 600 MeV/n Fe (LET 180 keV/μm) and 77 MeV/n oxygen (LET 58 keV/μm) particles. Low-energy ions caused more persistent DNA damage response (DDR) protein foci in irradiated human fibroblasts and esophageal epithelial cells compared to HZE particles. More detailed studies comparing boron ions to Fe particles, showed that boron-ion radiation resulted in a stronger G2 delay compared to Fe-particle exposure, and boron ions also showed an early recruitment of Rad51 at double-strand break (DSB) sites, which suggests a preference of homologous recombination for DSB repair in low-energy albeit high-LET particles. Our experiments suggest that the very high-energy radiation deposition by low-energy ions, representative of galactic cosmic radiation and solar particle event secondary radiation, generates massive but localized DNA damage leading to delayed DSB repair, and distinct cellular
A Variational Approach to Enhanced Sampling and Free Energy Calculations
NASA Astrophysics Data System (ADS)
Parrinello, Michele
2015-03-01
The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.
Variational Approach to Enhanced Sampling and Free Energy Calculations
NASA Astrophysics Data System (ADS)
Valsson, Omar; Parrinello, Michele
2014-08-01
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.
Point-by-point near-field optical energy deposition around plasmonic nanospheres in absorbing media.
Harrison, R K; Ben-Yakar, Adela
2015-08-01
Here we investigate the effects of absorbing media on plasmon-enhanced near-field optical energy deposition. We find that increasing absorption by the medium results in increased particle scattering at the expense of particle absorption, and that much of this increased particle scattering is absorbed by the medium close to the particle surface. We present an analytical method for evaluating the spatial distribution of near-field enhanced absorption surrounding plasmonic metal nanospheres in absorbing media using a new point-by-point method. We propose criteria to define relevant near-field boundaries and calculate the properties of the local absorption enhancement, which redistributes absorption to the near-field and decays asymptotically as a function of the distance from the particle to background levels. Using this method, we performed a large-scale parametric study to understand the effect of particle size and wavelength on the near-field absorption for gold nanoparticles in aqueous media and silicon, and identified conditions that are relevant to enhanced local infrared absorption in silicon. The presented approach provides insight into the local energy transfer around plasmonic nanoparticles for predicting near-field effects for advanced concepts in optical sensing, thin-film solar cells, nonlinear imaging, and photochemical applications. PMID:26367296
Advancing QCD-based calculations of energy loss
NASA Astrophysics Data System (ADS)
Tywoniuk, Konrad
2013-08-01
We give a brief overview of the basics and current developments of QCD-based calculations of radiative processes in medium. We put an emphasis on the underlying physics concepts and discuss the theoretical uncertainties inherently associated with the fundamental parameters to be extracted from data. An important area of development is the study of the single-gluon emission in medium. Moreover, establishing the correct physical picture of multi-gluon emissions is imperative for comparison with data. We will report on progress made in both directions and discuss perspectives for the future.
Turbulent energy exchange: Calculation and relevance for profile prediction
Candy, J.
2013-08-15
The anomalous heat production due to turbulence is neither routinely calculated in nonlinear gyrokinetic simulations nor routinely retained in profile prediction studies. In this work, we develop a symmetrized method to compute the exchange which dramatically reduces the intermittency in the time-dependent moment, thereby improving the accuracy of the time-average. We also examine the practical impact on transport-timescale simulations, and show that the exchange has only a minor impact on profile evolution for a well-studied DIII-D discharge.
Quantitation of absorbed or deposited materials on a substrate that measures energy deposition
Grant, Patrick G.; Bakajin, Olgica; Vogel, John S.; Bench, Graham
2005-01-18
This invention provides a system and method for measuring an energy differential that correlates to quantitative measurement of an amount mass of an applied localized material. Such a system and method remains compatible with other methods of analysis, such as, for example, quantitating the elemental or isotopic content, identifying the material, or using the material in biochemical analysis.
The Suppression of Energy Discretization Errors in Multigroup Transport Calculations
Larsen, Edward
2013-06-17
The Objective of this project is to develop, implement, and test new deterministric methods to solve, as efficiently as possible, multigroup neutron transport problems having an extremely large number of groups. Our approach was to (i) use the standard CMFD method to "coarsen" the space-angle grid, yielding a multigroup diffusion equation, and (ii) use a new multigrid-in-space-and-energy technique to efficiently solve the multigroup diffusion problem. The overall strategy of (i) how to coarsen the spatial an energy grids, and (ii) how to navigate through the various grids, has the goal of minimizing the overall computational effort. This approach yields not only the fine-grid solution, but also coarse-group flux-weighted cross sections that can be used for other related problems.
An artificial energy method for calculating flows with shocks
NASA Technical Reports Server (NTRS)
Rose, M. E.
1980-01-01
The artificial-viscosity method, first proposed by von Neumann and Richtmyer, introduces an artificial viscous pressure term in regions of compression such that an increase in entropy occurs in shock transition zones. The paper describes how dissipative flows can be induced by reducing the total energy available for adiabatic processes in shock zones. A class of inviscid fluid flows, called semiflows, is described in which the flows exhibit thermodynamic differences. Induced dissipative flows modify the pressure in regions of compression in a manner analogous to the artificial-viscosity method and for a gas, the effect is equivalent to suitably modifying the gas constant in the equation of state. By employing MacCormack's method and the usual non-adiabatic equations, numerical solutions of a Riemann problem are compared with the modified artificial energy method, showing that the dissipation effect predicted by the analytical formulation is reflected in the numerical method as well.
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.
Influence of the Presence of Tissue Expanders on Energy Deposition for Post-Mastectomy Radiotherapy
Trombetta, Débora M.; Cardoso, Simone C.; Facure, Alessandro; da Silva, Ademir X.; da Rosa, Luiz Antonio R.
2013-01-01
An increasing number of studies have shown that post-mastectomy radiotherapy presents benefits associated with the patients survival and a significant fraction of the treated patients makes use of tissue expanders for breast reconstruction. Some models of tissue expanders have a magnetic disk on their surface that constitutes heterogeneity in the radiation field, which can affect the dose distribution during the radiotherapy treatment. In this study, the influence of a metallic heterogeneity positioned in a breast tissue expander was evaluated by means of Monte Carlo simulations using the MCNPX code and using Eclipse treatment planning system. Deposited energy values were calculated in structures which have clinical importance for the treatment. Additionally, the effect in the absorbed energy due to backscattering and attenuation of the incident beam caused by the heterogeneity, as well as due to the expansion of the prosthesis, was evaluated in target structures for a 6 MV photon beam by simulations. The dose distributions for a breast treatment were calculated using a convolution/superposition algorithm from the Eclipse treatment planning system. When compared with the smallest breast expander volume, underdosage of 7% was found for the largest volume of breast implant, in the case of frontal irradiation of the chest wall, by Monte Carlo simulations. No significant changes were found in dose distributions for the presence of the heterogeneity during the treatment planning of irradiation with an opposed pair of beams. Even considering the limitation of the treatment planning system, the results obtained with its use confirm those ones found by Monte Carlo simulations for a tangent beam irradiation. The presence of a heterogeneity didńt alters the dose distributions on treatment structures. The underdosage of 7% observed with Monte Carlo simulations were found for irradiation at 0°, not used frequently in a clinical routine. PMID:23405149
Calculations of energy levels and lifetimes of low-lying states of barium and radium
Dzuba, V. A.; Ginges, J. S. M.
2006-03-15
We use the configuration-interaction method and many-body perturbation theory to perform accurate calculations of energy levels, transition amplitudes, and lifetimes of low-lying states of barium and radium. Calculations for radium are needed for the planning of measurements of parity- and time-invariance-violating effects which are strongly enhanced in this atom. Calculations for barium are used to control the accuracy of the calculations.
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.
Aradag, Selin
2013-01-01
In this study, the impact of laser energy deposition on pressure oscillations and relative sound pressure levels (SPL) in an open supersonic cavity flow is investigated. Laser energy with a magnitude of 100 mJ is deposited on the flow just above the cavity leading edge and up to 7 dB of reduction is obtained in the SPL values along the cavity back wall. Additionally, proper orthogonal decomposition (POD) method is applied to the x-velocity data obtained as a result of computational fluid dynamics simulations of the flow with laser energy deposition. Laser is numerically modeled using a spherically symmetric temperature distribution. By using the POD results, the effects of laser energy on the flow mechanism are presented. A one-dimensional POD methodology is applied to the surface pressure data to obtain critical locations for the placement of sensors for real time flow control applications. PMID:24363612
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.
Yilmaz, Ibrahim; Aradag, Selin
2013-01-01
In this study, the impact of laser energy deposition on pressure oscillations and relative sound pressure levels (SPL) in an open supersonic cavity flow is investigated. Laser energy with a magnitude of 100 mJ is deposited on the flow just above the cavity leading edge and up to 7 dB of reduction is obtained in the SPL values along the cavity back wall. Additionally, proper orthogonal decomposition (POD) method is applied to the x-velocity data obtained as a result of computational fluid dynamics simulations of the flow with laser energy deposition. Laser is numerically modeled using a spherically symmetric temperature distribution. By using the POD results, the effects of laser energy on the flow mechanism are presented. A one-dimensional POD methodology is applied to the surface pressure data to obtain critical locations for the placement of sensors for real time flow control applications. PMID:24363612
Experiment of Flow Control Using Laser Energy Deposition Around High Speed Propulsion System
NASA Astrophysics Data System (ADS)
Lee, HyoungJin; Jeung, InSeuck; Lee, SangHun; Kim, Seihwan
2011-11-01
An experimental investigation was conducted to examine the effect of a pulsed Nd:YAG laser energy deposition on the shock structures in supersonic/hypersonic flow and quiescent air. The effect of the laser energy and pressure in the blast wave generation were also investigated. As a result, the strength of plasma and blast wave becomes stronger as pressure or laser energy increase. And the breakdown threshold of air by laser energy deposition is 0.015 bar at 508 mJ laser energy, the blast wave threshold generation in air by laser energy deposition is 0.100 bar at same laser energy. As qualitative analysis, schlieren images are also obtained. After the series of experiments, the effect of laser energy deposition (LED) on high speed flow around the shock—shock interaction created by a wedge and blunt body. By LED, the structure of shock—shock interaction was collapsed momentary and the pressure of the stagnation point was fluctuated while interference of wave.
Free-energy calculation methods for collective phenomena in membranes
NASA Astrophysics Data System (ADS)
Smirnova, Yuliya G.; Fuhrmans, Marc; Barragan Vidal, Israel A.; Müller, Marcus
2015-09-01
Collective phenomena in membranes are those which involve the co-operative reorganization of many molecules. Examples of these are membrane fusion, pore formation, bending, adhesion or fission. The time and length scales, on which these processes occur, pose a challenge for atomistic simulations. Therefore, in order to solve the length scale problem it is popular to introduce a coarse-grained representation. To facilitate sampling of the relevant states additional computational techniques, which encourage the system to explore the free-energy landscape far from equilibrium and visit transition states, are needed. These computational techniques provide insights about the free-energy changes involved in collective transformations of membranes, yielding information about the rate limiting states, the transformation mechanism and the influence of architectural, compositional and interaction parameters. A common approach is to identify an order parameter (or reaction coordinate), which characterizes the pathway of membrane reorganization. However, no general strategy exists to define such an order parameter that can properly describe cooperative reorganizations in membranes. Recently developed methods can overcome this problem of the order-parameter choice and allow us to study collective phenomena in membranes. We will discuss such methods as thermodynamic integration, umbrella sampling, and the string method and results provided by their applications to particle-based simulations, particularly focusing on membrane fusion and pore formation.
Parallel implementation of electronic structure energy, gradient, and Hessian calculations.
Lotrich, V; Flocke, N; Ponton, M; Yau, A D; Perera, A; Deumens, E; Bartlett, R J
2008-05-21
ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort. PMID:18500853
Parallel implementation of electronic structure energy, gradient, and Hessian calculations
NASA Astrophysics Data System (ADS)
Lotrich, V.; Flocke, N.; Ponton, M.; Yau, A. D.; Perera, A.; Deumens, E.; Bartlett, R. J.
2008-05-01
ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.
Sparta, Manuel; Hansen, Mikkel B; Matito, Eduard; Toffoli, Daniele; Christiansen, Ove
2010-10-12
The availability of an accurate representation of the potential energy surface (PES) is an essential prerequisite in an anharmonic vibrational calculation. At the same time, the high dimensionality of the fully coupled PES and the adverse scaling properties with respect to the molecular size make the construction of an accurate PES a computationally demanding task. In the past few years, our group tested and developed a series of tools and techniques aimed at defining computationally efficient, black-box protocols for the construction of PESs for use in vibrational calculations. This includes the definition of an adaptive density-guided approach (ADGA) for the construction of PESs from an automatically generated set of evaluation points. Another separate aspect has been the exploration of the use of derivative information through modified Shepard (MS) interpolation/extrapolation procedures. With this article, we present an assembled machinery where these methods are embedded in an efficient way to provide both a general machinery as well as concrete computational protocols. In this framework we introduce and discuss the accuracy and computational efficiency of two methods, called ADGA[2gx3M] and ADGA[2hx3M], where the ADGA recipe is used (with MS interpolation) to automatically define modest sized grids for up to two-mode couplings, while MS extrapolation based on, respectively, gradients only and gradients and Hessians from the ADGA determined points provides access to sufficiently accurate three-mode couplings. The performance of the resulting potentials is investigated in vibrational coupled cluster (VCC) calculations. Three molecular systems serve as benchmarks: a trisubstituted methane (CHFClBr), methanimine (CH2NH), and oxazole (C3H3NO). Furthermore, methanimine and oxazole are addressed in accurate calculations aiming to reproduce experimental results. PMID:26616778
Effect of Low-Energy Ions on Plasma-Enhanced Deposition of Cubic Boron Nitride
NASA Astrophysics Data System (ADS)
Torigoe, M.; Fukui, S.; Teii, K.; Matsumoto, S.
2015-09-01
The effect of low-energy ions on deposition of cubic boron nitride (cBN) films in an inductively coupled plasma with the chemistry of fluorine is studied in terms of ion energy, ion flux, and ion to boron flux ratio onto the substrate. The ion energy and the ion to boron flux ratio are determined from the sheath potential and the ratio of incident ion flux to net deposited boron flux, respectively. For negative substrate biases where sp2-bonded BN phase only or no deposit is formed, both the ion energy and the ion to boron flux ratio are high. For positive substrate biases where cBN phase is formed, the ion energy and the ion to boron flux ratio are estimated in the range of a few eV to 35 eV and 100 to 130, respectively. The impact of negative ions is presumed to be negligible due to their low kinetic energy relative to the sheath potential over the substrate surface. The impact of positive ions with high ion to boron flux ratios is primarily responsible for reduction of the ion energy for cBN film deposition. Work supported in part by a Grant-in-Aid for Scientific Research (B), a Funding Program for Next Generation World-Leading Researchers, and an Industrial Technology Research Grant Program 2008.
Energy deposition dynamics of femtosecond pulses in water
Minardi, Stefano Pertsch, Thomas; Milián, Carles; Couairon, Arnaud; Majus, Donatas; Tamošauskas, Gintaras; Dubietis, Audrius; Gopal, Amrutha
2014-12-01
We exploit inverse Raman scattering and solvated electron absorption to perform a quantitative characterization of the energy loss and ionization dynamics in water with tightly focused near-infrared femtosecond pulses. A comparison between experimental data and numerical simulations suggests that the ionization energy of water is 8 eV, rather than the commonly used value of 6.5 eV. We also introduce an equation for the Raman gain valid for ultra-short pulses that validates our experimental procedure.
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.
Particle production and energy deposition studies for the neutrino factory target station
NASA Astrophysics Data System (ADS)
Back, John J.; Densham, Chris; Edgecock, Rob; Prior, Gersende
2013-02-01
We present FLUKA and MARS simulation studies of the pion production and energy deposition in the Neutrino Factory baseline target station, which consists of a 4 MW proton beam interacting with a liquid mercury jet target within a 20 T solenoidal magnetic field. We show that a substantial increase in the shielding is needed to protect the superconducting coils from too much energy deposition. Investigations reveal that it is possible to reduce the magnetic field in the solenoid capture system without adversely affecting the pion production efficiency. We show estimates of the amount of concrete shielding that will be required to protect the environment from the high radiation doses generated by the target station facility. We also present yield and energy deposition results for alternative targets: gallium liquid jet, tungsten powder jet, and solid tungsten bars.
Study on deposition rate and laser energy efficiency of Laser-Induction Hybrid Cladding
NASA Astrophysics Data System (ADS)
Wang, DengZhi; Hu, QianWu; Zheng, YinLan; Xie, Yong; Zeng, XiaoYan
2016-03-01
Laser-Induction Hybrid Cladding (LIHC) was introduced to prepare metal silicide based composite coatings, and influence of different factors such as laser type, laser power, laser scan speed and induction preheating temperature on the coating deposition rate and laser energy efficiency was studied systematically. Compared with conventional CO2 laser cladding, fiber laser-induction hybrid cladding improves the coating deposition rate and laser energy efficiency by 3.7 times. When a fiber laser with laser power of 4 kW was combined with an induction preheating temperature of 850 °C, the maximum coating deposition rate and maximum laser energy efficiency reaches 71 g/min and 64% respectively.
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.
Calculating kinetics parameters and reactivity changes with continuous-energy Monte Carlo
Kiedrowski, Brian C; Brown, Forrest B; Wilson, Paul
2009-01-01
The iterated fission probability interpretation of the adjoint flux forms the basis for a method to perform adjoint weighting of tally scores in continuous-energy Monte Carlo k-eigenvalue calculations. Applying this approach, adjoint-weighted tallies are developed for two applications: calculating point reactor kinetics parameters and estimating changes in reactivity from perturbations. Calculations are performed in the widely-used production code, MCNP, and the results of both applications are compared with discrete ordinates calculations, experimental measurements, and other Monte Carlo calculations.
Nikolai V. Mokhov et al.
2003-05-28
Beam-induced energy deposition in the LHC high luminosity interaction region components is one of the serious limits for the machine performance. The results of further optimization and comprehensive MARS14 calculations in the IP1 and IP5 inner and outer triplets are summarized for the updated lattice, calculation model, baseline pp-collision source term, and for realistic engineering constraints on the hardware design. It is shown that the optimized layout and absorbers would provide a sufficient reduction of peak power density and dynamic heat load in the superconducting components with an adequate safety margin. Accumulated dose and residual dose rates in and around the region components are also kept below the tolerable limits in the proposed design.
A Python tool to set up relative free energy calculations in GROMACS.
Klimovich, Pavel V; Mobley, David L
2015-11-01
Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations. PMID:26487189
Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.
2016-06-01
The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.
Modeling dose deposition and DNA damage due to low-energy β(-) emitters.
Alloni, D; Cutaia, C; Mariotti, L; Friedland, W; Ottolenghi, A
2014-09-01
One of the main issues of low-energy internal emitters concerns the very short ranges of the beta particles, versus the dimensions of the biological targets. Depending on the chemical form, the radionuclide may be more concentrated either in the cytoplasm or in the nucleus of the target cell. Consequently, since in most cases conventional dosimetry neglects this issue it may overestimate or underestimate the dose to the nucleus and hence the biological effects. To assess the magnitude of these deviations and to provide a realistic evaluation of the localized energy deposition by low-energy internal emitters, the biophysical track-structure code PARTRAC was used to calculate nuclear doses, DNA damage yields and fragmentation patterns for different localizations of radionuclides in human interphase fibroblasts. The nuclides considered in the simulations were tritium and nickel-63, which emit electrons with average energies of 5.7 (range in water of 0.42 μm) and 17 keV (range of 5 μm), respectively, covering both very short and medium ranges of beta-decay products. The simulation results showed that the largest deviations from the conventional dosimetry occur for inhomogeneously distributed short-range emitters. For uniformly distributed radionuclides selectively in the cytoplasm but excluded from the cell nucleus, the dose in the nucleus is 15% of the average dose in the cell in the case of tritium but 64% for nickel-63. Also, the numbers of double-strand breaks (DSBs) and the distributions of DNA fragments depend on subcellular localization of the radionuclides. In the low- and medium-dose regions investigated here, DSB numbers are proportional to the nuclear dose, with about 50 DSB/Gy for both studied nuclides. In addition, DSB numbers on specific chromosomes depend on the radionuclide localization in the cell as well, with chromosomes located more peripherally in the cell nucleus being more damaged by short-ranged emitters in cytoplasm compared with chromosomes
Morgan, D.O.; Robinson, A.T.; Allen, D.A.; Picton, D.J.; Thornton, D.A.; Shaw, S.E.
2011-07-01
This paper describes the development of a three-dimensional methodology for the assessment of neutron damage and nuclear energy deposition (or nuclear heating) throughout the graphite cores of the UK's Advanced Gas-cooled Reactors. Advances in the development of the Monte Carlo radiation transport code MCBEND have enabled the efficient production of detailed fully three-dimensional models that utilise three-dimensional source distributions obtained from Core Follow data supplied by the reactor physics code PANTHER. The calculational approach can be simplified to reduce both the requisite number of intensive radiation transport calculations, as well as the quantity of data output. These simplifications have been qualified by comparison with explicit calculations and they have been shown not to introduce significant systematic uncertainties. Simple calculational approaches are described that allow users of the data to address the effects on neutron damage and nuclear energy deposition predictions of the feedback resulting from the mutual dependencies of graphite weight loss and nuclear energy deposition. (authors)
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)
Ghosh, Soumya; Hammes-Schiffer, Sharon
2015-01-01
Electrochemical electron transfer reactions play an important role in energy conversion processes with many technological applications. Electrodes modified by self-assembled monolayers (SAMs) exhibit reduced double layer effects and are used in molecular electronics. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in the solute geometry and the environment. In this Letter, an approach for calculating the electrochemical reorganization energy for a redox molecule attached to or near a SAM modified electrode is presented. This integral equations formalism polarizable continuum model (IEF-PCM) approach accounts for the detailed electronic structure of the molecule, as well as the contributions from the electrode, SAM, and electronic and inertial solvent responses. The calculated total reorganization energies are in good agreement with experimental data for a series of metal complexes in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts. PMID:26263083
NASA Astrophysics Data System (ADS)
Wu, Zhe-Ying; Qi, Chong; Wyss, Ramon; Liu, Hong-Liang
2015-08-01
Background: The deviation between different model calculations that may occur when one goes toward regions where the masses are unknown is getting increased attention. This is related to the uncertainties of the different models which may have not been fully understood. Purpose: To explore in detail the effect of the isospin dependence of the spin-orbital force in the Woods-Saxon potential on global binding energy and deformation calculations. Method: The microscopic energies and nuclear deformations of about 1850 even-even nuclei are calculated systematically within the macroscopic-microscopic framework using three Woods-Saxon parametrizations, with different isospin dependencies, which were constructed mainly for nuclear spectroscopy calculations. Calculations are performed in the deformation space (β2,γ ,β4) . Both the monopole and doubly stretched quadrupole interactions are considered for the pairing channel. Results: The ground-state deformations obtained by the three calculations are quite similar to each other. Large differences are seen mainly in neutron-rich nuclei and in superheavy nuclei. Systematic calculations on the shape-coexisting second minima are also presented. As for the microscopic energies of the ground states, the results are also very close to each other. Only in a few cases the difference is larger than 2 MeV. The total binding energy is estimated by adding the macroscopic energy provided by the usual liquid drop model with its parameters fitted through the least square root and minimax criteria. Calculations are also compared with the results of other macroscopic-microscopic mass models. Conclusions: All the three calculations give similar values for the deformations, microscopic energies, and binding energies of most nuclei. One may expect to have a better understanding of the isospin dependence of the spin-orbital force with more data on proton- and neutron-rich nuclei.
Wind Energy Finance (WEF): An Online Calculator for Economic Analysis of Wind Projects
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.
NASA Astrophysics Data System (ADS)
Ratsch, Christian; Kaminski, Jakub
In this talk we will present a new approach for the calculation of surface energies of periodic crystal. For non-polar materials slabs (which are terminated by two identical surfaces) the task of calculating the surface energy is trivial. But it is more problematic for polar systems where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed new approach addresses this problem. It relies on carefully chosen capping atoms and the assumptions that their bond energy contributions can be used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surfaces energies with errors as low as 2%. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations. Our approach is suitable for high-throughput screening of new material interfaces, as accurate calculations of surface energies can be performed in an unsupervised algorithm. A New Approach for Surface Energy Calculations Applicable to High-throughput Design of New Interfaces.
Variational calculation of highly excited rovibrational energy levels of H2O2.
Polyansky, Oleg L; Kozin, Igor N; Ovsyannikov, Roman I; Małyszek, Paweł; Koput, Jacek; Tennyson, Jonathan; Yurchenko, Sergei N
2013-08-15
Results are presented for highly accurate ab initio variational calculation of the rotation-vibration energy levels of H2O2 in its electronic ground state. These results use a recently computed potential energy surface and the variational nuclear-motion programs WARV4, which uses an exact kinetic energy operator, and TROVE, which uses a numerical expansion for the kinetic energy. The TROVE calculations are performed for levels with high values of rotational excitation, J up to 35. The purely ab initio calculations of the rovibrational energy levels reproduce the observed levels with a standard deviation of about 1 cm(-1), similar to that of the J = 0 calculation, because the discrepancy between theory and experiment for rotational energies within a given vibrational state is substantially determined by the error in the vibrational band origin. Minor adjustments are made to the ab initio equilibrium geometry and to the height of the torsional barrier. Using these and correcting the band origins using the error in J = 0 states lowers the standard deviation of the observed-calculated energies to only 0.002 cm(-1) for levels up to J = 10 and 0.02 cm(-1) for all experimentally known energy levels, which extend up to J = 35. PMID:23611762
Shi, Zongqian; Wang, Kun; Shi, Yuanjie; Wu, Jian; Han, Ruoyu
2015-12-28
Experimental investigations on the electrical explosion of aluminum wire using negative polarity current in vacuum are presented. Current pulses with rise rates of 40 A/ns, 80 A/ns, and 120 A/ns are generated for investigating the influence of current rise rate on energy deposition. Experimental results show a significant increase of energy deposition into the wire before the voltage breakdown with the increase of current rise rate. The influence of wire dimension on energy deposition is investigated as well. Decreasing the wire length allows more energy to be deposited into the wire. The energy deposition of a 0.5 cm-long wire explosion is ∼2.5 times higher than the energy deposition of a 2 cm-long wire explosion. The dependence of the energy deposition on wire diameter demonstrates a maximum energy deposition of 2.7 eV/atom with a diameter of ∼18 μm. Substantial increase in energy deposition is observed in the electrical explosion of aluminum wire with polyimide coating. A laser probe is applied to construct the shadowgraphy, schlieren, and interferometry diagnostics. The morphology and expansion trajectory of exploding products are analyzed based on the shadowgram. The interference phase shift is reconstructed from the interferogram. Parallel dual wires are exploded to estimate the expansion velocity of the plasma shell.
NASA Astrophysics Data System (ADS)
Shi, Zongqian; Wang, Kun; Shi, Yuanjie; Wu, Jian; Han, Ruoyu
2015-12-01
Experimental investigations on the electrical explosion of aluminum wire using negative polarity current in vacuum are presented. Current pulses with rise rates of 40 A/ns, 80 A/ns, and 120 A/ns are generated for investigating the influence of current rise rate on energy deposition. Experimental results show a significant increase of energy deposition into the wire before the voltage breakdown with the increase of current rise rate. The influence of wire dimension on energy deposition is investigated as well. Decreasing the wire length allows more energy to be deposited into the wire. The energy deposition of a 0.5 cm-long wire explosion is ˜2.5 times higher than the energy deposition of a 2 cm-long wire explosion. The dependence of the energy deposition on wire diameter demonstrates a maximum energy deposition of 2.7 eV/atom with a diameter of ˜18 μm. Substantial increase in energy deposition is observed in the electrical explosion of aluminum wire with polyimide coating. A laser probe is applied to construct the shadowgraphy, schlieren, and interferometry diagnostics. The morphology and expansion trajectory of exploding products are analyzed based on the shadowgram. The interference phase shift is reconstructed from the interferogram. Parallel dual wires are exploded to estimate the expansion velocity of the plasma shell.
T. Downar
2009-03-31
The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system.
METHODOLOGICAL NOTES: Energy density calculations for ball-lightning-like luminous silicon balls
NASA Astrophysics Data System (ADS)
Paiva, Gerson S.; Ferreira, Joacy V.; Bastos, Cristiano C.; dos Santos, Marcus V.; Pavão, Antonio C.
2010-05-01
The energy density of a luminous silicon ball [Phys. Rev. Lett. 98 048501 (2007)] is calculated for a model with a metal core surrounded by an atmosphere of silicon oxides. Experimental data combined with the molecular orbital calculations of the oxidation enthalpy lead to a mean energy density of 3.9 MJ m-3, which is within the range of estimates from other ball lightning models. This result provides good evidence to support the silicon-based model.
Strong shock generation by fast electron energy deposition
Fox, T. E.; Pasley, J.; Robinson, A. P. L.
2013-12-15
It has been suggested that fast electrons may play a beneficial role in the formation of the ignitor shock in shock ignition owing to the high areal density of the fuel at the time of the ignitor pulse. In this paper, we extend previous studies which have focused on monoenergetic electron sources to populations with extended energy distributions. In good agreement with analytic scalings, we show that strong shocks can be produced with peak pressures of a few hundred Mbar to over 1 Gbar using fast electron intensities of 1–10 PW/cm{sup 2} in a uniform deuterium-tritium plasma at 10 g/cm{sup 3}. However, the length required for shock formation increases with fast electron temperature. As this shock formation distance becomes comparable to the target size, the shock is not able to fully develop, and this implies a limit on the ability of fast electrons to aid shock formation.
Nighttime auroral energy deposition in the middle atmosphere
NASA Technical Reports Server (NTRS)
Goldberg, R. A.; Jackman, C. H.; Barcus, J. R.; Soraas, F.
1984-01-01
Ionospheric rocket sounding data for eight nighttime auroral events are used to characterize relativistic electron showers and their effects on atmospheric ozone. The rockets were launched from the Poker Flat Research Range in Alaska and from Andoya, Norway over the period 1976-82. Energetic fluxes were always detected but were of insufficient magnitude to produce significant changes in stratospheric ozone. However, middle atmospheric energy sources were found to be dominated by relativistic electrons and X-ray bremmstrahlung, the latter from 40-55 km and the former from 55-60 km altitudes. The ionizing radiation is concluded to be a significant factor in mesospheric ion conductivity, mobility, electric field structure and analytical models for the ion-neutral chemistry.
George, K.; Schweizer, T.
2008-01-01
This report details the methodology used by DOE to calculate levelized cost of wind energy and demonstrates the variation in COE estimates due to different financing assumptions independent of wind generation technology.
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
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer
Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.
2015-08-28
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be{sub 2} is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be{sub 2} from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be{sub 2}, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm{sup −1}, only slightly below the 935 cm{sup −1} value derived from experiment.
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer.
Deible, Michael J; Kessler, Melody; Gasperich, Kevin E; Jordan, Kenneth D
2015-08-28
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm(-1), only slightly below the 935 cm(-1) value derived from experiment. PMID:26328827
NASA Astrophysics Data System (ADS)
Taur, Vidya S.; Joshi, Rajesh A.; Sharma, Ramphal
2013-02-01
In the present manuscript we report about synthesis of nanostructured CdS/Cu2S thin films by economically viable soft chemical route and effect of post deposition treatments such as annealing in air and swift heavy ion irradiation on solar energy conversion efficiency of the heterojunction device. These as grown, annealed and irradiated thin films are characterized for structural, morphological, optical and I-V properties. X-ray diffraction pattern (XRD) represents structural as well as crystallite modifications, atomic force microscopy (AFM) shows improvement in surface appearance of the materials. The solar energy conversion efficiency calculated from I-V exhibited increase in conversion efficiency i. e. 0.09, 0.24 and 0.48 % for as grown, annealed and SHI irradiated thin films.
Chemical vapour deposition of thermochromic vanadium dioxide thin films for energy efficient glazing
Warwick, Michael E.A.; Binions, Russell
2014-06-01
Vanadium dioxide is a thermochromic material that undergoes a semiconductor to metal transitions at a critical temperature of 68 °C. This phase change from a low temperature monoclinic structure to a higher temperature rutile structure is accompanied by a marked change in infrared reflectivity and change in resistivity. This ability to have a temperature-modulated film that can limit solar heat gain makes vanadium dioxide an ideal candidate for thermochromic energy efficient glazing. In this review we detail the current challenges to such glazing becoming a commercial reality and describe the key chemical vapour deposition technologies being employed in the latest research. - Graphical abstract: Schematic demonstration of the effect of thermochromic glazing on solar radiation (red arrow represents IR radiation, black arrow represents all other solar radiation). - Highlights: • Vanadium dioxide thin films for energy efficient glazing. • Reviews chemical vapour deposition techniques. • Latest results for thin film deposition for vanadium dioxide.
Phenomenological calculation of nuclear binding energy and density with Yukawa-potentials
NASA Astrophysics Data System (ADS)
Scheid, W.
2016-01-01
In this paper, we study a phenomenological collective model for the calculation of the nuclear density and ground state binding energy of nuclei. The proton density is assumed proportional to the nuclear density. The total binding energy of the nuclear matter consists of the binding energy of infinite nuclear matter, of two Yukawa-potentials, of the Coulomb-energy and of the symmetry-energy. The parameters of the Yukawa-potential are fitted with the Bethe-Weizsäcker (BW) mass formula. The resulting binding energies and nuclear densities agree quite satisfying with known nuclear values.
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. PMID:17081554
Heterogeneous Shock Energy Deposition in Shock Wave Consolidation of Metal Powders.
NASA Astrophysics Data System (ADS)
Mutz, Andrew Howard
Shock wave consolidation of powder is a high deformation rate process in which a shock wave generated by an explosive or a colliding projectile rapidly densifies and bonds together the powder particles into a solid compact. The deposition of the shock energy during this process is highly inhomogeneous on the powder particle scale. Evidence of the extent and pattern of the energy deposition was provided by recovery experiments performed using a crystalline metallic glass forming alloy, and analyzed using a heat flow model. The energy deposited during the shock wave passage was best modeled as deposited partly into the particle bulk and partly onto particle surfaces. To investigate this inhomogeneity, and the powder parameters which influence it, a propellant driven gas gun was designed, built and utilized. The planarity of the shock waves produced using the targets designed for the gun was established. Powder - powder thermocouples were impacted with powders of varying sizes to establish the effect of particle size on energy deposition. Small particles in contact with large ones were inferred to absorb the greater fraction of shock energy. Hardened and unhardened steel powder was shocked to investigate the effect of particle hardness on energy distribution. The recovered compacts were not measurably affected by the initial hardness. Compaction experiments were performed on a Ni based super-alloy and on a SiC reinforced Ti matrix composite to test some of the practical applications of the process and the target designs developed. Superior tensile properties were observed in the shock consolidated and heat treated Ni based 718 alloy. The SiC reinforced composite was recovered in the intended net shape with no macro-cracks in the compact body, but with fractured SiC particles.
Wang, Y Y; Grygiel, C; Dufour, C; Sun, J R; Wang, Z G; Zhao, Y T; Xiao, G Q; Cheng, R; Zhou, X M; Ren, J R; Liu, S D; Lei, Y; Sun, Y B; Ritter, R; Gruber, E; Cassimi, A; Monnet, I; Bouffard, S; Aumayr, F; Toulemonde, M
2014-01-01
Modification of surface and bulk properties of solids by irradiation with ion beams is a widely used technique with many applications in material science. In this study, we show that nano-hillocks on CaF2 crystal surfaces can be formed by individual impact of medium energy (3 and 5 MeV) highly charged ions (Xe(22+) to Xe(30+)) as well as swift (kinetic energies between 12 and 58 MeV) heavy xenon ions. For very slow highly charged ions the appearance of hillocks is known to be linked to a threshold in potential energy (Ep) while for swift heavy ions a minimum electronic energy loss per unit length (Se) is necessary. With our results we bridge the gap between these two extreme cases and demonstrate, that with increasing energy deposition via Se the Ep-threshold for hillock production can be lowered substantially. Surprisingly, both mechanisms of energy deposition in the target surface seem to contribute in an additive way, which can be visualized in a phase diagram. We show that the inelastic thermal spike model, originally developed to describe such material modifications for swift heavy ions, can be extended to the case where both kinetic and potential energies are deposited into the surface. PMID:25034006
NASA Astrophysics Data System (ADS)
Paredes Marino, Joali; Morgavi, Daniele; Di Vito, Mauro; de Vita, Sandro; Sansivero, Fabio; Perugini, Diego
2016-04-01
Fractal fragmentation theory has been applied to characterize the particle size distribution of pyroclastic deposits generated by volcanic explosions. Recent works have demonstrated that fractal dimension on grain size distributions can be used as a proxy for estimating the energy associated with volcanic eruptions. In this work we seek to establish a preliminary analytical protocol that can be applied to better characterize volcanic fall deposits and derive the potential energy for fragmentation that was stored in the magma prior/during an explosive eruption. The methodology is based on two different techniques for determining the grain-size distribution of the pyroclastic samples: 1) dry manual sieving (particles larger than 297μm), and 2) automatic grain size analysis via a CamSizer-P4®device, the latter measure the distribution of projected area, obtaining a cumulative distribution based on volume fraction for particles up to 30mm. Size distribution data have been analyzed by applying the fractal fragmentation theory estimating the value of Df, i.e. the fractal dimension of fragmentation. In order to test our protocol we studied the Cretaio eruption, Ischia island, Italy. Results indicate that size distributions of pyroclastic fall deposits follow a fractal law, indicating that the fragmentation process of these deposits reflects a scale-invariant fragmentation mechanism. Matching the results from manual and automated techniques allows us to obtain a value of the "fragmentation energy" from the explosive eruptive events that generate the Cretaio deposits. We highlight the importance of these results, based on fractal statistics, as an additional volcanological tool for addressing volcanic risk based on the analyses of grain size distributions of natural pyroclastic deposits. Keywords: eruptive energy, fractal dimension of fragmentation, pyroclastic fallout.
Measurements of the energy deposit of inclined muon bundles in the CWD NEVOD
NASA Astrophysics Data System (ADS)
Kokoulin, R. P.; Bogdanov, A. G.; Dushkin, L. I.; Khokhlov, S. S.; Khomyakov, V. A.; Kindin, V. V.; Kovylyaeva, E. A.; Mannocchi, G.; Petrukhin, A. A.; Saavedra, O.; Shutenko, V. V.; Trinchero, G.; Yashin, I. I.
2015-08-01
First results of investigations of the energy deposits of inclined muon bundles in the ground-based Cherenkov water detector NEVOD are presented. As a measure of the muon bundle energy deposit, the total number of photoelectrons detected by PMTs of the Cherenkov calorimeter is used. For each event, the local muon density at the observation point and the muon bundle arrival direction are estimated from the data of the coordinate-tracking detector DECOR. Registration of the bundles in a wide range of zenith angles allows to explore the interval of primary particle energies from ∼ 1016 to ∼ 1018 eV. Measurement results are compared with CORSIKA based simulations of EAS muon component. It is found that the mean energy of muons detected in the bundles rapidly increases with the zenith angle and reaches about 500 GeV near the horizon.
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.
PERTURB: A program for calculating vibrational energies by generalized algebraic quantization
NASA Astrophysics Data System (ADS)
Fried, Laurence E.; Ezra, Gregory S.
1988-09-01
We describe PERTURB, a special purpose algebraic manipulation program which calculates vibrational eigenvalues in coupled oscillator systems. PERTURB implements the method of generalized algebraic quantization (AQ), in which Van Vleck perturbation theory is formulated in a mock phase space. The phase space formulation enables quantum and classical perturbation theory to be treated on the same footing, and allows the systematic calculation of corrections to classical perturbation results in powers of h̷. Generalized AQ is a powerful and efficient technique for calculating semiclassical vibrational energy levels. In many cases, including just the first correction to classical perturbation theory yields highly accurate energies.
Continuous-energy eigenvalue sensitivity coefficient calculations in TSUNAMI-3D
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)
Development of a SCALE Tool for Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
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 SCALE Tool for Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
NASA Astrophysics Data System (ADS)
Perfetti, Christopher M.; Rearden, Bradley T.
2014-06-01
Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several criticality safety problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and low memory requirements, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations.
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.
Effect of forage energy intake and supplementation on marbling deposition in growing beef cattle.
Technology Transfer Automated Retrieval System (TEKTRAN)
Glucose is the primary carbon source for fatty acid synthesis in intramuscular fat, whereas, acetate is primarily utilized by subcutaneous fat. Our objective was to examine the effect of forage energy intake and type of fermentation on marbling deposition by stocker cattle grazing dormant native ra...
Interferometric technique for determining the energy deposition in gas-flow nuclear-pumped lasers
Pikulev, A A
2001-06-30
An interference technique is developed for determining the energy deposition in gas-flow lasers pumped by uranium fission fragments. It is shown that four types of interference patterns may be formed. Algorithms are presented for determining the type of interference and for enumerating the maxima in interference pattern. (lasers, active media)
Technology Transfer Automated Retrieval System (TEKTRAN)
A study was conducted to examine the effects of controlled intake, dietary protein (CP) level, and ractopamine supplementation on growth, body composition, and the efficiency of energy and protein deposition in pigs during uninterrupted or compensatory growth from 60 to 100 kg. Seven groups of pigs ...
Simple energy-calculation method for solar industrial-process-heat steam systems
NASA Astrophysics Data System (ADS)
Gee, R. C.
1983-01-01
Designing a solar industrial process heat (IPH) system, sizing its components and predicting its annual energy delivery requires a method for calculating solar system performance. A calculation method that is accurate, easy to use, accounts for the impact of all important system parameters, and does not require use of a computer is described. Only simple graphs and a hand calculator are required to predict annual collector field performance and annual system losses. The energy calculation method is applicable to a variety of solar system configurations. The calculation method applied only to parabolic trough steam generation systems that do not employ thermal storage is described. Both flash tank and unfired boiler steam systems are covered.
Simple energy-calculation method for solar industrial-process-heat steam systems
Gee, R.
1983-01-01
Designing a solar industrial-process heat (IPH) system, sizing its components and predicting its annual energy delivery requires a method for calculating solar system performance. A calculation method that is accurate, easy to use, accounts for the impact of all important system parameters, and does not require use of a computer is described. Only simple graphs and a hand calculator are required to predict annual collector field performance and annual system losses. The energy-calculation method is applicable to a variety of solar-system configurations. The calculation method applied only to parabolic-trough steam-generation systems that do not employ thermal storage is described. Both flash tank and unfired-boiler steam systems are covered.
NASA Astrophysics Data System (ADS)
Montgomery, Jason
2007-12-01
Scattering resonances play a key role in many chemical processes, including unimolecular and bimolecular reactions and photodissociation. A significant theoretical emphasis over the past several decades has been placed on accurate resonance calculations for polyatomic systems. In spite of such efforts, a quantum treatment of molecular systems which exhibit a high density of states and strong coordinate coupling near dissociation remains a formidable task. The research described herein employs improved quantum mechanical methods to calculate a representation of nuclear motion, both bound and unbound, which is used subsequently to calculate accurate resonance energies and lifetimes for two triatomic systems: the neon trimer and ozone. Specifically, theory and results are given regarding the construction of an optimal, L2 eigenbasis using techniques such as the discrete variable representation, the energy selected basis (ESB) method, and iterative diagonalization methods. A new energy selection method is also developed and implemented for the neon trimer. Subsequent resonance calculations are described which make use of the artificial boundary inhomogeneity (ABI) method, adapted to work with the above mentioned ESB and hyperspherical coordinates. The ABI method is used to calculate a set of linearly independent wavefunctions (LIWs) at a given energy for the representation of the scattering wavefunction. Resonance parameters are obtained by imposing scattering boundary conditions on a linear combination of LIWs and solving for the S-matrix, S, its energy derivative, dS/dE, and the Smith lifetime matrix, Q. When available, comparisons are made with previously reported calculations.
Meson self-energies calculated by the relativistic particle-hole-antiparticle representation
Nakano, M.; Noda, N.; Mitsumori, T.; Koide, K.; Kouno, H.; Hasegawa, A.; Liu, L.
1997-12-01
A new formulation of meson self-energies is introduced for {sigma},{omega},{pi},{rho},{delta}, and {eta} mesons on the basis of the particle-hole-antiparticle representation. We have studied the difference between the meson self-energy (MSE) of this representation and the MSE of the traditional density-Feynman (DF) representation. It is shown that the new formulation describes exactly the physical processes such as particle-hole excitations or particle-antiparticle excitations, and that, on the other hand, the meson self-energy based on the DF representation includes unphysical components. By numerical calculations, the meson self-energies describing the particle-hole excitations are shown to be close to each other for most of the meson self-energy in low momentum (R{lt}500 MeV) and low energy (R{sub 0}{lt}200 MeV). This fact implies that former calculations using the low momentum and low-energy part do not change greatly. The density part of the density-Feynman representation has been shown to have a resonant structure around the energy of particle-antiparticle excitation, which causes a large difference between the two representations in the meson spectrum calculations. Our investigation concludes that the former calculations based on the density-Feynman representation are not invalidated in many cases, but the particle-hole-antiparticle representation is more appropriate to treat exactly the physical processes. {copyright} {ital 1997} {ital The American Physical Society}
Augustine, R.L.; Lahanas, K.M.; Cole, F.
1992-11-01
An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.
Augustine, R.L.; Lahanas, K.M.; Cole, F.
1992-01-01
An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.
ERIC Educational Resources Information Center
Barbiric, Dora; Tribe, Lorena; Soriano, Rosario
2015-01-01
In this laboratory, students calculated the nutritional value of common foods to assess the energy content needed to answer an everyday life application; for example, how many kilometers can an average person run with the energy provided by 100 g (3.5 oz) of beef? The optimized geometries and the formation enthalpies of the nutritional components…
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...
Yang, W.; Wu, H.; Cao, L.
2012-07-01
More and more MOX fuels are used in all over the world in the past several decades. Compared with UO{sub 2} fuel, it contains some new features. For example, the neutron spectrum is harder and more resonance interference effects within the resonance energy range are introduced because of more resonant nuclides contained in the MOX fuel. In this paper, the wavelets scaling function expansion method is applied to study the resonance behavior of plutonium isotopes within MOX fuel. Wavelets scaling function expansion continuous-energy self-shielding method is developed recently. It has been validated and verified by comparison to Monte Carlo calculations. In this method, the continuous-energy cross-sections are utilized within resonance energy, which means that it's capable to solve problems with serious resonance interference effects without iteration calculations. Therefore, this method adapts to treat the MOX fuel resonance calculation problem natively. Furthermore, plutonium isotopes have fierce oscillations of total cross-section within thermal energy range, especially for {sup 240}Pu and {sup 242}Pu. To take thermal resonance effect of plutonium isotopes into consideration the wavelet scaling function expansion continuous-energy resonance calculation code WAVERESON is enhanced by applying the free gas scattering kernel to obtain the continuous-energy scattering source within thermal energy range (2.1 eV to 4.0 eV) contrasting against the resonance energy range in which the elastic scattering kernel is utilized. Finally, all of the calculation results of WAVERESON are compared with MCNP calculation. (authors)
CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals.
Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav
2016-02-14
A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol(-1) on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems. PMID:26874495
CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals
NASA Astrophysics Data System (ADS)
Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav
2016-02-01
A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol-1 on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.
Complete calculation of electroweak corrections for polarized Møller scattering at high energies
NASA Astrophysics Data System (ADS)
Zykunov, V. A.
2009-09-01
A complete calculation of electroweak radiative corrections to observables of polarized Møller scattering at high energies was performed. This calculation took explicitly into account contributions caused by hard bremsstrahlung. A FORTRAN code that permitted including radiative corrections to high-energy Møller scattering under arbitrary electron-detection conditions was written. It was shown that the electroweak corrections caused by hard bremsstrahlung were rather strongly dependent on the choice of experimental cuts and changed substantially the polarization asymmetry in the region of high energies and over a broad interval of scattering angles.
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)
McKechnie, Scott; Booth, George H.; Cohen, Aron J.; Cole, Jacqueline M.
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.
McKechnie, Scott; Booth, George H; Cohen, Aron J; Cole, Jacqueline M
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared. PMID:26001454
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.
Li, Z.; Pan, Y.K.; Tao, F.M.
1996-01-15
Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.
NASA Astrophysics Data System (ADS)
Li, Ming; Kapusta, Joseph I.
2016-08-01
We generalize calculations of the energy-momentum tensor for classical gluon fields in the boost-invariant McLerran-Venugopalan model using the small-τ power series expansion method. Results to all orders for the energy density and pressures are given in the leading Q2 approximation and with the inclusion of estimated running coupling effects. The energy density and transverse pressure decrease monotonically with time while the longitudinal pressure starts from a negative value and increases towards zero.
NASA Astrophysics Data System (ADS)
Tamba, T.; Pham, H. S.; Shoda, T.; Iwakawa, A.; Sasoh, A.
2015-09-01
Modulation of shock foot oscillation due to energy deposition by repetitive laser pulses in shock wave-boundary layer interaction over an axisymmetric nose-cylinder-flare model in Mach 1.92 flow was experimentally studied. From a series of 256 schlieren images, density oscillation spectra at each pixel were obtained. When laser pulses of approximately 7 mJ were deposited with a repetition frequency, fe, of 30 kHz or lower, the flare shock oscillation had a peak spectrum equivalent to the value of fe. However, with fe of 40 kHz-60 kHz, it experienced frequency modulation down to lower than 20 kHz.
Monte Carlo calculation of the energy response characteristics of a RadFET radiation detector
NASA Astrophysics Data System (ADS)
Belicev, P.; Spasic Jokic, V.; Mayer, S.; Milosevic, M.; Ilic, R.; Pesic, M.
2010-07-01
The Metal -Oxide Semiconductor Field-Effect-Transistor (MOSFET, RadFET) is frequently used as a sensor of ionizing radiation in nuclear-medicine, diagnostic-radiology, radiotherapy quality-assurance and in the nuclear and space industries. We focused our investigations on calculating the energy response of a p-type RadFET to low-energy photons in range from 12 keV to 2 MeV and on understanding the influence of uncertainties in the composition and geometry of the device in calculating the energy response function. All results were normalized to unit air kerma incident on the RadFET for incident photon energy of 1.1 MeV. The calculations of the energy response characteristics of a RadFET radiation detector were performed via Monte Carlo simulations using the MCNPX code and for a limited number of incident photon energies the FOTELP code was also used for the sake of comparison. The geometry of the RadFET was modeled as a simple stack of appropriate materials. Our goal was to obtain results with statistical uncertainties better than 1% (fulfilled in MCNPX calculations for all incident energies which resulted in simulations with 1 - 2×109 histories.
Ghosh, Soumya; Hammes-Schiffer, Sharon
2015-01-02
Electrochemical electron transfer reactions play an important role in energy conversion processes with many technological applications. Electrodes modified by self-assembled monolayers (SAMs) are useful because the double layer effects are reduced. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in solute geometry and solvent configuration. In this Letter, an approach for calculating the electrochemical solvent reorganization energy for a redox molecule attached to or near a SAM modified electrode is presented. This integral equations formalism polarizable continuum model (IEF-PCM) approach accounts for the detailed electronic structure of the molecule, as well as the contributions from the electrode, SAM, and electronic and inertial solvent responses. The calculated total reorganization energies are in good agreement with experimental data for a series of metal complex in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.
Method for controlling energy density for reliable pulsed laser deposition of thin films
Dowden, P. C. E-mail: qxjia@lanl.gov; Bi, Z.; Jia, Q. X. E-mail: qxjia@lanl.gov
2014-02-15
We have established a methodology to stabilize the laser energy density on a target surface in pulsed laser deposition of thin films. To control the focused laser spot on a target, we have imaged a defined aperture in the beamline (so called image-focus) instead of focusing the beam on a target based on a simple “lens-focus.” To control the laser energy density on a target, we have introduced a continuously variable attenuator between the output of the laser and the imaged aperture to manipulate the energy to a desired level by running the laser in a “constant voltage” mode to eliminate changes in the lasers’ beam dimensions. This methodology leads to much better controllability/reproducibility for reliable pulsed laser deposition of high performance electronic thin films.
Calculation of the characteristics of clinical high-energy photon beams with EGS5-MPI
NASA Astrophysics Data System (ADS)
Shimizu, M.; Morishita, Y.; Kato, M.; Kurosawa, T.; Tanaka, T.; Takata, N.; Saito, N.
2014-03-01
A graphite calorimeter has been developed as a Japanese primary standard of absorbed dose to water in the high-energy photon beams from a clinical linac. To obtain conversion factors for the graphite calorimeter, the beam characteristics of the high-energy photon beams from the clinical linac at National Metrology Institute of Japan were calculated with the EGS5 Monte Carlo simulation code. To run the EGS5 code on High Performance Computing machines that have more than 1000 CPU cores, we developed the EGS5 parallelisation package "EGS5-MPI" by implementing a message-passing interface. We calculated the photon energy spectra, which are in good agreement with those previously calculated by D. Sheikh-Bagheri and D. W. O. Rogers (Med. Phys. 29 3). We also estimated the percentage-depth-dose distributions of photon beams from the linac using the calculated photon energy spectra. These calculated percentage-depth-dose distributions were compared with our measured distributions and were found they are in good agreement as well. We will calculate conversion factors for the graphite calorimeter using our results.
Bigildeev, E.A.; Lappa, A.V.
1994-09-01
The ionization method for determination of the energy deposited in sensitive sites of irradiated objects is usually used with the assumption that deposited energy is directly proportional to the number of ionization in a site. This assumption fails in two cases important for nanometer-sized sites: (1) when the fluctuation characteristics of deposited energy such as higher moments, probability distributions, etc. are determined instead of the mean value; (2) when the radiation field in a site is spatially non-uniform. In this paper both cases are investigated. Exact formulae connecting energy and ionization quantities (moments, cumulants, probability distributions) are established as well as practical procedures to obtain energy quantities from those of ionization. The validity of the direct proportionality principle is analyzed and approximate methods to correct it are propose. Some microdosimetric results are presented. The solution of these problems required that we refine some known notions and introduce new terms. In particular, in the paper the necessity of distinguishing two distinct types of events and correspondingly two sets of microdosimetric quantities is noted; new radiation parameters such as the fluctuation W value and non-equivalence factor for the events are defined and investigated numerically. 12 refs., 5 figs.
AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.
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. PMID:27214306
Measuring the energy flux at the substrate position during magnetron sputter deposition processes
Cormier, P.-A.; Thomann, A.-L.; Dussart, R.; Semmar, N.; Mathias, J.; Balhamri, A.; Snyders, R.; Konstantinidis, S.
2013-01-07
In this work, the energetic conditions at the substrate were investigated in dc magnetron sputtering (DCMS), pulsed dc magnetron sputtering (pDCMS), and high power impulse magnetron sputtering (HiPIMS) discharges by means of an energy flux diagnostic based on a thermopile sensor, the probe being set at the substrate position. Measurements were performed in front of a titanium target for a highly unbalanced magnetic field configuration. The average power was always kept to 400 W and the probe was at the floating potential. Variation of the energy flux against the pulse peak power in HiPIMS was first investigated. It was demonstrated that the energy per deposited titanium atom is the highest for short pulses (5 {mu}s) high pulse peak power (39 kW), as in this case, the ion production is efficient and the deposition rate is reduced by self-sputtering. As the argon pressure is increased, the energy deposition is reduced as the probability of scattering in the gas phase is increased. In the case of the HiPIMS discharge run at moderate peak power density (10 kW), the energy per deposited atom was found to be lower than the one measured for DCMS and pDCMS discharges. In these conditions, the HiPIMS discharge could be characterized as soft and close to a pulsed DCMS discharge run at very low duty cycle. For the sake of comparison, measurements were also carried out in DCMS mode with a balanced magnetron cathode, in the same working conditions of pressure and power. The energy flux at the substrate is significantly increased as the discharge is generated in an unbalanced field.
NASA Astrophysics Data System (ADS)
Shi, Zongqian; Shi, Yuanjie; Wang, Kun; Jia, Shenli
2016-03-01
This paper presents the experimental results of the electrical explosion of copper wires in vacuum using negative nanosecond-pulsed current with magnitude of 1-2 kA. The 20 μm-diameter copper wires with different lengths are exploded with three different current rates. A laser probe is applied to construct the shadowgraphy and interferometry diagnostics to investigate the distribution and morphology of the exploding product. The interference phase shift is reconstructed from the interferogram, by which the atomic density distribution is calculated. Experimental results show that there exist two voltage breakdown modes depending on the amount of the specific energy deposition. For the strong-shunting mode, shunting breakdown occurs, leading to the short-circuit-like current waveform. For the weak-shunting mode with less specific energy deposition, the plasma generated during the voltage breakdown is not enough to form a conductive plasma channel, resulting in overdamped declining current waveform. The influence of the wire length and current rate on the characteristics of the exploding wires is also analyzed.
NASA Astrophysics Data System (ADS)
Keerthisinghe, D.; Dassanayake, B. S.; Wickramarachchi, S. J.; Stolterfoht, N.; Tanis, J. A.
2013-12-01
The charge deposition dependence and energy loss in the transmission of electrons through insulating polyethylene terephthalate (PET) were studied for incident energies of 500 and 800 eV. Charge evolution at the sample tilt angles ψ = 0.0° and -1.7° was investigated. After an initial quiescent period transmission was observed and found to reach equilibrium rather quickly. Inelastic behavior of the transmitted electrons was observed during the initial transmission as well as after reaching equilibrium for ψ = -1.7° for both incident energies.
NASA Astrophysics Data System (ADS)
Li, Yongxiu; Zhang, Saiqun; Zhang, John Z. H.; He, Xiao
2016-05-01
Accurate description of the conformational energies of the amino acids is essential for molecular dynamics simulation of protein structures. In this study, we compute the relative energies at 51 conformations for a trialanine tetrapeptide at different levels of theory. The computed energies at various theoretical levels, including the semiempirical DFTB method, HF, DFT, MP2 and CCSD(T), are compared with each other. The calculated energies from density-fitting local CCSD(T)/CBS (complete basis set) calculations are taken as the benchmark. The accuracy of the theoretical methods is highly dependent on the electronic correlation and dispersion corrections as well as the size of the basis sets. The involvement of the empirical dispersion energies in HF and DFT methods consistently improves their performance. Considering both the accuracy and computational efficiency, the Minnesota density functional M06-L-D and M06-2X-D are efficient and accurate for modeling of trialanine structures.
Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.
Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S
2016-03-01
We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. PMID:26958888
Deposition of carbonate mud beds within high-energy subtidal sand Dunes, Bahamas
Dill, R.F.; Steinen, R.P.
1988-01-01
Laminated, carbonate mud beds are being deposited in the interisland channels of the Exuma Cays in the Bahamas. They are associated with stromatolites and interbedded with ooid sands that form large migrating subtidal dunes on flood tidal deltas and bars. Currents up to 3 knots sweep in and out of the 4-8 m deep channels 3 hours out of every 6 hours, creating a high-energy bank margin environment not usually considered to be the site of mud-sized particle deposition. Mud deposits reach thicknesses of 1 m and have individual beds 2-5 cm thick. When exposed to flowing seawater, bed surfaces become encrusted with carbonate cement and algal mats. The white interior of mud beds between the crusts appears homogeneous, is soft, and has the consistency of ''tooth paste.'' Loose uncemented ooid sand is found above and below the mud beds, showing that both are occupying the same depositional environment. Rip-up clasts of the crusted mud beds, formed by scour of underlying sands, are carried throughout the channels and accumulate as a lag deposit within the troughs of migrating dunes. Some clasts are colonized by algal mats that trap ooid and skeletal sands forming stromatolite structures that can grow up to 2 m high.
Assessing Locations of Energy Transfer/Deposit in the Ionosphere-Thermosphere System
NASA Astrophysics Data System (ADS)
Tu, J.; Song, P.
2014-12-01
It has long been believed that most of energy transferred from the magnetosphere and deposited in the ionosphere-thermosphere system occurs in the auroral zone, the region of strong field-aligned current density. Recent observations of the Poynting flux to the ionosphere and theoretical investigations of the magnetosphere-ionosphere coupling show that the strongest energy transfer may be in the polar cap proper where the plasma flow speed is high and not where the flow reverses. This implies that the field-aligned current is not the primary agent of the energy transfer into the ionosphere-thermosphere system and that other physical progresses are at play. Recent simulation studies using an inductive-dynamic approach (including self-consistent solutions of Faraday's law and retaining inertia terms in the ion momentum equations) on the magnetosphere-ionosphere-thermosphere coupling indicate that the energy transfer is through Alfven waves propagating to the ionosphere/thermosphere and the energy deposition is via the frictional heating caused by relative motion between ions and neutrals. In this study we assess the locations of the energy transfer and deposition by employing a self-consistent inductive-dynamic ionosphere-thermosphere model. In a 2-D numerical simulation (dawn-dusk meridian plane), we solve the continuity, momentum, and energy equations for multiple species of ions and neutrals including photochemistry and Maxwell's equations. By simulating responses of the ionosphere-thermosphere system to enhanced magnetosphere convection, we show that the strongest energy transfer occurs in the polar cap proper instead of the auroral zone.
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.
Perfetti, Christopher M; Martin, William R; Rearden, Bradley T; Williams, Mark L
2012-01-01
Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the SHIFT Monte Carlo code within the Scale code package. The methods were used for several simple test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods.
Santoro, R.T.; Alsmiller, R.G. Jr.; Barnes, J.M.; Chapman, G.T.
1980-08-01
Integral experiments that measure the transport of approx. 14 MeV D-T neutrons through laminated slabs of proposed fusion reactor shield materials have been carried out. Measured and calculated neutron and gamma ray energy spectra are compared as a function of the thickness and composition of stainless steel type 304, borated polyethylene, and Hevimet (a tungsten alloy), and as a function of detector position behind these materials. The measured data were obtained using a NE-213 liquid scintillator using pulse-shape discrimination methods to resolve neutron and gamma ray pulse height data and spectral unfolding methods to convert these data to energy spectra. The calculated data were obtained using two-dimensional discrete ordinates radiation transport methods in a complex calculational network that takes into account the energy-angle dependence of the D-T neutrons and the nonphysical anomalies of the S/sub n/ method.
NASA Astrophysics Data System (ADS)
Vessally, Esmail; Aryana, Soma
2016-01-01
The purpose of this research is to study the solar energy storage in norbornadiene ( 1)/quadricyclane ( 2) system by four direct attachments of substituents at two carbon atoms on both sides of the double bonds C2=C3 and C5=C6 in 1 X and 2 X; calculating the relative energies at B3LYP/6-311++G** level of theory. The solar energy storage of four electron donating substituents, (push-push effect), X (X =-NH2,-OH) and four electron withdrawing substituents, (pull-pull effect) X (X =-CO2H,-CONH2,-NO2 and CN) were examined. The solar absorption bands were calculated for 1 X. The DFT calculations reveal that the bands were shifted to the visible spectrum region when the electron withdrawing substituents were used rather than the electron donating substituents.
NASA Technical Reports Server (NTRS)
Armstrong, T. W.; Alsmiller, R. G., Jr.; Chandler, K. C.
1972-01-01
Results obtained using a recently developed calculational method for determining the nucleon-meson cascade induced in thick materials by high-energy nucleons and charged pions are presented. The calculational method uses the intranuclear-cascade-evaporation model to treat nonelastic collisions by particles with energies approximately or smaller than GeV and an extrapolation model at higher energies. The following configurations are considered: (1) 19.2-GeV/c protons incident on iron; (2) 30.3-GeV/c protons incident on iron; (3) solar and galactic protons incident on the moon, and (4) galactic protons incident on tissue. For the first three configurations, experimental results are available and comparisons between the experimental and calculated results are given.
Infrared Spectra and Calculated Binding Energies of γ-BUTYROLACTONE Dimers and Trimers
NASA Astrophysics Data System (ADS)
Willis, Eric; Baumann, Chris
2014-06-01
Infrared spectra for matrix-isolated γ-butyrolactone and γ-butyrolactone-d_6 were obtained. The carbonyl stretching mode occurs at 1803 cm-1 for the monomer species, 1786 cm-1 for the dimer species, and 1774 cm-1 for the trimer species (1797, 1789 and 1770 cm-1 for the deuterated isotopomer.) Vibrational frequencies calculated using density functional theory are in agreement with the experimental values. Density functional theory was used to calculate the structures and binding energies of γ-butyrolactone dimers and trimers. Binding energies of 55-58 kJ mol-1 are predicted for the dimer structures. Optimized geometries for stacked and ring trimer structures have been calculated, with predicted binding energies of up to 68 kJ mol-1.
Influence of emitter temperature on the energy deposition in a low-pressure plasma
NASA Astrophysics Data System (ADS)
Levko, Dmitry; Raja, Laxminarayan L.
2016-03-01
The influence of emitter temperature on the energy deposition into low-pressure plasma is studied by the self-consistent one-dimensional Particle-in-Cell Monte Carlo Collisions model. Depending on the emitter temperature, different modes of discharge operation are obtained. The mode type depends on the plasma frequency and does not depend on the ratio between the densities of beam and plasma electrons. Namely, plasma is stable when the plasma frequency is small. For this plasma, the energy transfer from emitted electrons to plasma electrons is inefficient. The increase in the plasma frequency results first in the excitation of two-stream electron instability. However, since the thermal velocity of plasma electrons is smaller than the electrostatic wave velocity, the resonant wave-particle interaction is inefficient for the energy deposition into the plasma. Further increase in the plasma frequency leads to the distortion of beam of emitted electrons. Then, the electrostatic wave generated due to two-stream instability decays into multiple slower waves. Phase velocities of these waves are comparable with the thermal velocity of plasma electrons which makes possible the resonant wave-particle interaction. This results in the efficient energy deposition from emitted electrons into the plasma.
NASA Astrophysics Data System (ADS)
Garcia, Gustavo
2011-10-01
Many radiation applications require detailed energy deposition maps in reduced volumes, typically at the nanoscale. In addition, information about the type of interaction processes taking place in these reduced areas is usually needed. In order to achieve this level of description, single particle tracks, both for primary radiation and secondary generated species, should be simulated upon reasonable physical descriptions of the interaction processes in terms of cross sections and energy loss. In this study we present a Low Energy Particle Track Simulation (LEPTS) Monte Carlo code which is based on experimental and theoretical cross section data we have previously derived as well as on the observed energy loss distribution functions. This model will be applied to the irradiation of atomic (Ar) and molecular (SF6) gases with high energy electrons, positrons and photons by simulating single particle tracks until their final thermalization in the medium. Special attention will be paid to the low energy secondary electrons generated along the tracks. Detailed energy deposition pictures and local radiation effects will be derived from the simulated track structure and compared with direct observations in simple experiments. Acknowledgement to the Spanish Ministry of Science and Innovation (Project FIS2009-10245).
Ab initio calculations on collisions of low energy electrons with polyatomic molecules
Rescigno, T.N.
1991-08-01
The Kohn variational method is one of simplest, and oldest, techniques for performing scattering calculations. Nevertheless, a number of formal problems, as well as practical difficulties associated with the computation of certain required matrix elements, delayed its application to electron--molecule scattering problems for many years. This paper will describe the recent theoretical and computational developments that have made the complex'' Kohn variational method a practical tool for carrying out calculations of low energy electron--molecule scattering. Recent calculations on a number of target molecules will also be summarized. 41 refs., 7 figs.
Efficient calculation of potential energy surfaces for the generation of vibrational wave functions
NASA Astrophysics Data System (ADS)
Rauhut, Guntram
2004-11-01
An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations—within the computation of the potential—on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan).
Efficient calculation of potential energy surfaces for the generation of vibrational wave functions.
Rauhut, Guntram
2004-11-15
An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations--within the computation of the potential--on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan). PMID:15538851
NASA Technical Reports Server (NTRS)
Brown, R. L.; Laufer, A. H.
1981-01-01
Activation energies are calculated by the bond-energy-bond-order (BEBO) and the bond-strength-bond-length (BSBL) methods for the reactions of C2H radicals with H2, CH4, and C2H6 and for the reactions of CN radicals with H2 and CH4. The BSBL technique accurately predicts the activation energies for these reactions while the BEBO method yields energies averaging 9 kcal higher than those observed. A possible reason for the disagreement is considered.
Model potential calculation of the thermal donor energy spectrum in silicon
NASA Astrophysics Data System (ADS)
Chen, C. S.; Schroder, D. K.
1988-06-01
The two-parameter model potential originally proposed by Ning and Sah [Phys. Rev. B 4, 3468 (1971)] for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schröter, and Bourret [J. Appl. Phys. 56, 1670 (1984)].
Model potential calculation of the thermal donor energy spectrum in silicon
Chen, C.S.; Schroder, D.K.
1988-06-15
The two-parameter model potential originally proposed by Ning and Sah (Phys. Rev. B 4, 3468 (1971)) for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schroeter, and Bourret (J. Appl. Phys. 56, 1670 (1984)).
Calculation of the Relative Change in Binding Free Energy of a Protein-Inhibitor Complex
NASA Astrophysics Data System (ADS)
Bash, Paul A.; Singh, U. Chandra; Brown, Frank K.; Langridge, Robert; Kollman, Peter A.
1987-01-01
By means of a thermodynamic perturbation method implemented with molecular dynamics, the relative free energy of binding was calculated for the enzyme thermolysin complexed with a pair of phosphonamidate and phosphonate ester inhibitors. The calculated difference in free energy of binding was 4.21 ± 0.54 kilocalories per mole. This compares well with the experimental value of 4.1 kilocalories per mole. The method is general and can be used to determine a change or ``mutation'' in any system that can be suitably represented. It is likely to prove useful for protein and drug design.
Calculation of energy barriers for magnetic vortices in sub-100 nm dots
NASA Astrophysics Data System (ADS)
Lapa, Pavel; King, Andrew; Roshchin, Igor V.
2012-10-01
In a magnetic vortex, the magnetization is curling in plane everywhere except the ``core,'' where it is out of plane. Interest in switching of magnetic vortices in nanodots is stimulated by their potential application for magnetic memories and nano-oscillators. By combining analytical and micromagnetic techniques, we calculated energy barriers for vortex switching in 20 nm-thick iron dots as a function of applied in-plane field and dot diameter. Using analytical formula for magnetization distribution in the vortex,footnotetextN. A. Usov and S. E. Peschany, J. Magn. Magn. Mater. 118, 290 (1992). we performed micromagnetic calculations of the dot energy for different vortex core positions. In contrast to the ``rigid body approximation,'' the core size and core shape in our calculations were varied to achieve the energy minimum for every core displacement. The energy barriers required for vortex nucleation and annihilation were calculated as a function of magnetic field. By comparing these barriers to the thermal energy kBT we obtained the temperature dependences of the vortex nucleation and annihilation fields in good agreement with the experiment.footnotetextR. K. Dumas et al., Appl. Phys. Lett. 91, 202501 (2007).
1-D Van der Waals Foams Heated by Ion Beam Energy Deposition
Zylstra, A. B.; Barnard, J. J.; More, R. M.
2009-12-23
One dimensional simulations of various initial average density aluminum foams (modeled as slabs of solid metal separated by low density regions) heated by volumetric energy deposition are conducted with a Lagrangian hydrodynamics code using a van der Waals equation of tate (EOS). The resulting behavior is studied to facilitate the design of future warm dense matter (WDM) experiments at LBNL. In the simulations the energy deposition ranges from 10 to 30 kJ/g and from 0.075 to 4.0 ns total pulse length, resulting in temperatures from approximately 1 o 4 eV. We study peak pressures and temperatures in the foams, expansion velocity, and the phase evolution. Five relevant time scales in the problem are identified. Additionally, we present a method for characterizing the level of inhomogeneity in a foam target as it is heated and the time it takes for a foam to homogenize.
1-D Van der Waals Foams Heated by Ion Beam Energy Deposition
Zylstra, A; Barnard, J J; More, R M
2010-03-19
One dimensional simulations of various initial average density aluminum foams (modeled as slabs of solid metal separated by low density regions) heated by volumetric energy deposition are conducted with a Lagrangian hydrodynamics code using a van der Waals equation of state (EOS). The resulting behavior is studied to facilitate the design of future warm dense matter (WDM) experiments at LBNL. In the simulations the energy deposition ranges from 10 to 30 kJ/g and from 0.075 to 4.0 ns total pulse length, resulting in temperatures from approximately 1 to 4 eV. We study peak pressures and temperatures in the foams, expansion velocity, and the phase evolution. Five relevant time scales in the problem are identified. Additionally, we present a method for characterizing the level of inhomogeneity in a foam target as it is heated and the time it takes for a foam to homogenize.
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.
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. PMID:25807150
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 achieved 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.
Wang, Jiyao; Deng, Yuqing; Roux, Benoît
2006-01-01
The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining
Phenomenological Rashba model for calculating the electron energy spectrum on a cylinder
NASA Astrophysics Data System (ADS)
Savinskiĭ, S. S.; Belosludtsev, A. V.
2007-05-01
The energy spectrum of an electron on the surface of a cylinder is calculated using the Pauli equation with an additional term that takes into account the spin-orbit interaction. This term is taken in the approximation of a phenomenological Rashba model, which provides exact expressions for the wave functions and the electron energy spectrum on the cylinder surface in a static magnetic field.
Variational calculation of energy levels for metastable states of antiprotonic helium
NASA Astrophysics Data System (ADS)
Hu, Mu-Hong; Yao, Si-Meng; Wang, Yi; Li, Wang; Gu, Ying-Ying; Zhong, Zhen-Xiang
2016-06-01
We apply the variational method in Hylleraas coordinates to solve the energy eigenvalue problem for antiprotonic helium molecular systems including p bar 3 He+ and p bar 4 He+. The numerical accuracy on the nonrelativistic energies is shown to reach 10-17, thus the precision of our results is only limited by the width of the metastable states. Expectation values of the Dirac delta operators for these states are also calculated.
Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics
NASA Astrophysics Data System (ADS)
Donev, Aleksandar; Stillinger, Frank H.; Torquato, Salvatore
2007-07-01
We present a new event-driven molecular dynamics (MD) algorithm for measuring the free energy of nearly jammed packings of spherical and non-spherical hard particles. This Bounding Cell Molecular Dynamics (BCMD) algorithm exactly calculates the free-energy of a single-occupancy cell (SOC) model in which each particle is restricted to a neighborhood of its initial position using a hard-wall bounding cell. Our MD algorithm generalizes previous ones in the literature by enabling us to study non-spherical particles as well as to measure the free-energy change during continuous irreversible transformations. Moreover, we make connections to the well-studied problem of computing the volume of convex bodies in high dimensions using random walks. We test and verify the numerical accuracy of the method by comparing against rigorous asymptotic results for the free energy of jammed and isostatic disordered packings of both hard spheres and ellipsoids, for which the free energy can be calculated directly as the volume of a high-dimensional simplex. We also compare our results to previously published Monte Carlo results for hard-sphere crystals near melting and jamming and find excellent agreement. We have successfully used the BCMD algorithm to determine the configurational and free-volume contributions to the free energy of glassy states of binary hard disks [A. Donev, F.H. Stillinger, S. Torquato, Do binary hard disks exhibit an ideal glass transition? Phys. Rev. Lett. 96 (22) (2006) 225502]. The algorithm can also be used to determine phases with locally- or globally-minimal free energy, to calculate the free-energy cost of point and extended crystal defects, or to calculate the elastic moduli of glassy or crystalline solids, among other potential applications.
Simulation of submarine gas hydrate deposits as a sustainable energy source and CO2 storage
NASA Astrophysics Data System (ADS)
Janicki, G.; Hennig, T.; Schlüter, S.; Deerberg, G.
2012-04-01
Being aware that conventionally exploitable natural gas resources are limited, research concentrates on the development of new technologies for the extraction of methane from gas hydrate deposits in subsea sediments. The quantity of methane stored in hydrate form is considered to be a promising means to overcome future shortages in energy resources. In combination with storing carbon dioxide (CO2) as hydrates in the deposits chances for sustainable energy supply systems are given. The combustion of hydrate-based natural gas can contribute to the energy supply, but the coupled CO2 emissions cause climate change effects. At present, the possible options to capture and subsequently store CO2 (CCS-Technology) become of particular interest. To develop a sustainable hydrate-based energy supply system, the production of natural gas from hydrate deposits has to be coupled with the storage of CO2. Hence, the simultaneous storage of CO2 in hydrate deposits has to be developed. Decomposition of methane hydrate in combination with CO2 sequestration appears to be promising because CO2 hydrate is stable within a wider range of pressure and temperature than methane hydrate. As methane hydrate provides structural integrity and stability in its natural formation, incorporating CO2 hydrate as substitute for methane hydrate will help to preserve the natural sediments' stability. Regarding the technological implementation, many problems have to be overcome. Especially heat and mass transfer in the deposits are limiting factors causing very long process times. Within the scope of the German research project »SUGAR«, different technological approaches are evaluated and compared by means of dynamic system simulations and analysis. Detailed mathematical models for the most relevant chemical and physical effects are developed. The basic mechanisms of gas hydrate formation/dissociation and heat and mass transport in porous media are considered and implemented into simulation programs like
Unloading Versus Driven Processes Derived from Auroral Energy Deposition and Polar Cap Size
NASA Technical Reports Server (NTRS)
Brittnacher, M. J.; Parks, G. K.; Fillingim, M. O.; Elsen, R.; Chua, D.; Germany, G. A.; Spann, J. F., Jr.
1998-01-01
The intensity of far ultraviolet auroral emissions at all local times during the three substorm phases has been monitored by the Ultraviolet Imager (UVI) on the Polar spacecraft for many substorms. Changes in the energy flux and characteristic energy of the precipitating electrons can be derived from these observations by modeling of the spectral emission processes. The global and local energy deposition is a new parameter that can be used in substorm studies since it provides a measure of energy transfer from the tail to the ionosphere due to precipitating electrons at a time resolution of three minutes. The polar cap area and area of auroral emissions can also be determined at high time resolution during substorms from the UVI images. An example of a substorm that appears to be driven by solar wind dynamic pressure alone will be presented. The polar cap area and other parameters do not indicate a growth phase prior to substorm onset. In another example, the slow growth phase followed by a very rapid increase in energy deposition during the expansion phase will be shown. This substorm was preceded by a southward IMF orientation. In these two examples, the role the solar wind in determining polar cap area is discussed. The time development of the area of auroral emissions is also discussed in relation to substorm phase and energy deposition. If the auroral emissions occur on closed field lines then the area of auroral emissions may provide an indication of changes in the thickness of the plasma sheet during each substorm phase.
Hong, Tianzhen; Buhl, Fred; Haves, Philip
2008-03-28
California has been using DOE-2 as the main building energy analysis tool in the development of building energy efficiency standards (Title 24) and the code compliance calculations. However, DOE-2.1E is a mature program that is no longer supported by LBNL on contract to the USDOE, or by any other public or private entity. With no more significant updates in the modeling capabilities of DOE-2.1E during recent years, DOE-2.1E lacks the ability to model, with the necessary accuracy, a number of building technologies that have the potential to reduce significantly the energy consumption of buildings in California. DOE-2's legacy software code makes it difficult and time consuming to add new or enhance existing modeling features in DOE-2. Therefore the USDOE proposed to develop a new tool, EnergyPlus, which is intended to replace DOE-2 as the next generation building simulation tool. EnergyPlus inherited most of the useful features from DOE-2 and BLAST, and more significantly added new modeling capabilities far beyond DOE-2, BLAST, and other simulations tools currently available. With California's net zero energy goals for new residential buildings in 2020 and for new commercial buildings in 2030, California needs to evaluate and promote currently available best practice and emerging technologies to significantly reduce energy use of buildings for space cooling and heating, ventilating, refrigerating, lighting, and water heating. The California Energy Commission (CEC) needs to adopt a new building energy simulation program for developing and maintaining future versions of Title 24. Therefore, EnergyPlus became a good candidate to CEC for its use in developing and complying with future Title 24 upgrades. In 2004, the Pacific Gas and Electric Company contracted with ArchitecturalEnergy Corporation (AEC), Taylor Engineering, and GARD Analytics to evaluate EnergyPlus in its ability to model those energy efficiency measures specified in both the residential and
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.
NASA Astrophysics Data System (ADS)
Limandri, Silvina; de Vera, Pablo; Fadanelli, Raul C.; Nagamine, Luiz C. C. M.; Mello, Alexandre; Garcia-Molina, Rafael; Behar, Moni; Abril, Isabel
2014-02-01
Ion-beam cancer therapy is a promising technique to treat deep-seated tumors; however, for an accurate treatment planning, the energy deposition by the ions must be well known both in soft and hard human tissues. Although the energy loss of ions in water and other organic and biological materials is fairly well known, scarce information is available for the hard tissues (i.e., bone), for which the current stopping power information relies on the application of simple additivity rules to atomic data. Especially, more knowledge is needed for the main constituent of human bone, calcium hydroxyapatite (HAp), which constitutes 58% of its mass composition. In this work the energy loss of H and He ion beams in HAp films has been obtained experimentally. The experiments have been performed using the Rutherford backscattering technique in an energy range of 450-2000 keV for H and 400-5000 keV for He ions. These measurements are used as a benchmark for theoretical calculations (stopping power and mean excitation energy) based on the dielectric formalism together with the MELF-GOS (Mermin energy loss function-generalized oscillator strength) method to describe the electronic excitation spectrum of HAp. The stopping power calculations are in good agreement with the experiments. Even though these experimental data are obtained for low projectile energies compared with the ones used in hadron therapy, they validate the mean excitation energy obtained theoretically, which is the fundamental quantity to accurately assess energy deposition and depth-dose curves of ion beams at clinically relevant high energies. The effect of the mean excitation energy choice on the depth-dose profile is discussed on the basis of detailed simulations. Finally, implications of the present work on the energy loss of charged particles in human cortical bone are remarked.
Front end energy deposition and collimation studies for IDS-NF
Rogers, C.; Neuffer, D.; Snopok, P.; /IIT, Chicago /Fermilab
2011-03-01
The function of the Neutrino Factory front end is to reduce the energy spread and size of the muon beam to a manageable level that will allow reasonable throughput to subsequent system components. Since the Neutrino Factory is a tertiary machine (protons to pions to muons), there is an issue of large background from the pion-producing target. The implications of energy deposition in the front end lattice for the Neutrino Factory are addressed. Several approaches to mitigating the effect are proposed and discussed, including proton absorbers, chicanes, beam collimation, and shielding.
Energy deposition of heavy ions in the regime of strong beam-plasma correlations.
Gericke, D O; Schlanges, M
2003-03-01
The energy loss of highly charged ions in dense plasmas is investigated. The applied model includes strong beam-plasma correlation via a quantum T-matrix treatment of the cross sections. Dynamic screening effects are modeled by using a Debye-like potential with a velocity dependent screening length that guarantees the known low and high beam velocity limits. It is shown that this phenomenological model is in good agreement with simulation data up to very high beam-plasma coupling. An analysis of the stopping process shows considerably longer ranges and a less localized energy deposition if strong coupling is treated properly. PMID:12689203
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
NASA Astrophysics Data System (ADS)
Amharrak, H.; Reynard-Carette, C.; Lyoussi, A.; Carette, M.; Brun, J.; De Vita, C.; Fourmentel, D.; Villard, J.-F.
2015-11-01
The nuclear heating measurements in Material Testing Reactors (MTRs) are crucial for the study of nuclear materials and fuels under irradiation. The reference measurements of this nuclear heating are especially performed by a differential calorimeter including a graphite sample material and two calorimetric cells. Then these measurements are used for other experimental conditions in order to predict the nuclear heating and thermal conditions induced in the irradiation devices. This paper will present simulations with MCNP5 Monte-Carlo transport code (using ENDF/B-VI nuclear data library) to evaluate the nuclear heating inside the calorimeter during irradiation campaigns of the CARMEN-1P mock-up inside OSIRIS reactor periphery (MTR based on Saclay, France). The whole complete geometry of the sensor has been considered. The calculation method corresponds to a calculation in two steps. Consequently, we used as an input source in the model, the neutron and photon spectra calculated in various experimental locations tested during the irradiation campaign (H9, H10, H11, D9). After a description of the differential calorimeter sensor, the MCNP5 model used for the calculations of nuclear heating inside the calorimeter elements is introduced by two quantities: KERMA and energy deposition rate per mass unit. The Charged Particle Equilibrium (CPE) inside the calorimeter elements is studied. The contribution of prompt gamma and neutron is determined. A comparison between this total nuclear heating calculation and the experimental results in a graphite sample will be made. Then parametric studies performed on the influence of the various calorimeter components on the nuclear heating are presented and discussed. The studies of the influence of the nature of materials, the sensor jacket, the source type and the comparison of the results obtained for the two calorimetric cells leads to some proposals for the sensor improvement.
NASA Astrophysics Data System (ADS)
Zhong, Zhaopeng
In the past twenty 20 years considerable progress has been made in developing new methods for solving the multi-dimensional transport problem. However the effort devoted to the resonance self-shielding calculation has lagged, and much less progress has been made in enhancing resonance-shielding techniques for generating problem-dependent multi-group cross sections (XS) for the multi-dimensional transport calculations. In several applications, the error introduced by self-shielding methods exceeds that due to uncertainties in the basic nuclear data, and often they can be the limiting factor on the accuracy of the final results. This work is to improve the accuracy of the resonance self-shielding calculation by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. A new method has been developed, it can calculate the continuous-energy neutron fluxes for the whole two-dimensional domain, which can be utilized as weighting function to process the self-shielded multi-group cross sections for reactor analysis and criticality calculations, and during this process, the two-dimensional heterogeneous effect in the resonance self-shielding calculation can be fully included. A new code, GEMINEWTRN (Group and Energy-Pointwise Methodology Implemented in NEWT for Resonance Neutronics) has been developed in the developing version of SCALE [1], it combines the energy pointwise (PW) capability of the CENTRM [2] with the two-dimensional discrete ordinates transport capability of lattice physics code NEWT [14]. Considering the large number of energy points in the resonance region (typically more than 30,000), the computational burden and memory requirement for GEMINEWTRN is tremendously large, some efforts have been performed to improve the computational efficiency, parallel computation has been implemented into GEMINEWTRN, which can save the computation and memory requirement a lot; some energy points reducing
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)
Microscopic calculations of nuclear and neutron matter, symmetry energy and neutron stars
Gandolfi, S.
2015-02-01
We present Quantum Monte Carlo calculations of the equation of state of neutron matter. The equation of state is directly related to the symmetry energy and determines the mass and radius of neutron stars, providing then a connection between terrestrial experiments and astronomical observations. As a result, we also show preliminary results of the equation of state of nuclear matter.
Calculation of the vacuum condensates of the trace of the energy-momentum tensor
Ksenzov, V. G.
2008-04-15
It is shown that a modification of the effective potential proposed by A.A. Migdal and Shifman makes it possible to calculate the vacuum condensates of the trace of the energy-momentum tensor in massless theories in various spacetime dimensions.
ERIC Educational Resources Information Center
Vargas, Francisco M.
2014-01-01
The temperature dependence of the Gibbs energy and important quantities such as Henry's law constants, activity coefficients, and chemical equilibrium constants is usually calculated by using the Gibbs-Helmholtz equation. Although, this is a well-known approach and traditionally covered as part of any physical chemistry course, the required…
Calculations of the heights, periods, profile parameters, and energy spectra of wind waves
NASA Technical Reports Server (NTRS)
Korneva, L. A.
1975-01-01
Sea wave behavior calculations require the precalculation of wave elements as well as consideration of the spectral functions of ocean wave formation. The spectrum of the random wave process is largely determined by the distribution of energy in the actual wind waves observed on the surface of the sea as expressed in statistical and spectral characteristics of the sea swell.
NASA Astrophysics Data System (ADS)
Endo, Kazunaka
2016-02-01
In the Auger electron spectra (AES) simulations, we define theoretical modified kinetic energies of AES in the density functional theory (DFT) calculations. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. This method is applied to simulate Auger electron spectra (AES) of 2nd periodic atom (Li, Be, B, C, N, O, F)-involving substances (LiF, beryllium, boron, graphite, GaN, SiO2, PTFE) by deMon DFT calculations using the model molecules of the unit cell. Experimental KVV (valence band electrons can fill K-shell core holes or be emitted during KVV-type transitions) AES of the (Li, O) atoms in the substances agree considerably well with simulation of AES obtained with the maximum kinetic energies of the atoms, while, for AES of LiF, and PTFE substance, the experimental F KVV AES is almost in accordance with the spectra from the transitionstate kinetic energy calculations.
Hyperspherical hidden crossing calculation of Ps formation in low-energy e+-Na collisions
NASA Astrophysics Data System (ADS)
Ward, S. J.; Shertzer, J.
2011-05-01
The hyperspherical hidden crossing method (HHCM) can provide important insight into scattering processes. Previously, we have used the HHCM to calculate the Ps(1s)-formation cross section in low-energy e+-H and e+-Li collisions. Here we apply the HHCM to low-energy e+-Na collisions. We use the Peach model potential and treat e+e-Na+ as an effective three-body system. We calculate the Ps(1s)-formation cross sections for 0 <= L <= 3 and compare our results with a hyperspherical close-coupling calculation. The HHCM provides an explanation for the small S-wave Ps(1s)-formation cross section. The S-wave Stückelberg phase is close to π for the three collision systems due to destructive interference between the two amplitudes that correspond to different paths leading to Ps(1s) formation.
NASA Astrophysics Data System (ADS)
Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo
2015-05-01
We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.
Automated calculation of surface energy fluxes with high-frequency lake buoy data
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.
On calculating the energy characteristics of a metal film with a dielectric coating
NASA Astrophysics Data System (ADS)
Babich, A. V.
2014-02-01
A method for calculating the characteristics of a metal film in a dielectric surroundings is suggested. The most interesting case of asymmetric metal-dielectric sandwiches, in which the dielectrics on both sides of the film are different, is considered in the context of the Kohn-Sham modified method. The spectrum, the electron work function, and the surface energy of polycrystalline and single-crystal films placed into passive insulators are calculated for the first time. In general, the dielectric surroundings leads to a negative change in the electron work function and the surface energy. In addition to size-effect-related changes, the shift of the work function is determined by the arithmetic mean of the dielectric constants of the surrounding media. Calculations have been performed for Na, Al, and Pb.
Chakraborty, Arindam; Truhlar, Donald G; Bowman, Joel M; Carter, Stuart
2004-08-01
The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. PMID:15260761
Calculation of energy levels and transition amplitudes for barium and radium.
Dzuba, V. A.; Flambaum, V. V.; Physics; Univ. of New South Wales
2007-01-01
The radium atom is a promising system for studying parity and time invariance violating weak interactions. However, available experimental spectroscopic data for radium are insufficient for designing an optimal experimental setup. We calculate the energy levels and transition amplitudes for radium states of significant interest. Forty states corresponding to all possible configurations consisting of the 7s, 7p and 6d single-electron states as well as the states of the 7s8s, 7s8p and 7s7d configurations have been calculated. The energies of ten of these states corresponding to the 6d{sup 2}, 7s8s, 7p{sup 2} and 6d7p configurations are not known from experiment. Calculations for barium are used to control the accuracy.
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
X-ray Attenuation and Absorption Calculations.
Energy Science and Technology Software Center (ESTSC)
1988-02-25
This point-source, polychromatic, discrete energy X-ray transport and energy deposition code system calculates first-order spectral estimates of X-ray energy transmission through slab materials and the associated spectrum of energy absorbed by the material.
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2015-03-07
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB{sub 4} molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q){sup −2} type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH{sub 4} molecule is demonstrated.
NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2015-03-01
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)-2 type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.
Calculated Energy Levels, Oscillator Strengths and Lifetimes in Al-like Argon
NASA Astrophysics Data System (ADS)
Gupta, G. P.; Msezane, A. Z.
Excitation energies, oscillator strengths and transition probabilities for electric-dipole-allowed and inter-combination transitions among the 25 LS levels belonging to the (1s22s22p6)3s23p, 3s3p2, 3s23d, 3p3, 3s3p3d, 3s24s, 3s24p, 3s24d, 3s24f and 3s3p4s configurations of Ar VI are calculated using extensive configuration-interaction (CI) wave functions. From our transition probabilities we have also calculated the radiative lifetimes of doublet and quartet states of Ar VI. Our results are compared with other available theoretical calculations and the experimental data. To assess the importance of relativistic effects on our calculated values, we have also carried out calculations in the intermediate-coupling scheme. These effects are incorporated through the Breit-Pauli approximation via spin-orbit, spin-other-orbit, spin-spin, Darwin and mass correction terms. Small adjustments to the diagonal elements of the Hamiltonian matrices have been made so that the energy splittings are as close as possible to the experimental values. The energy splitting of 54 fine-structure levels, the oscillator strengths and transition probabilities for some strong dipole-allowed and intercombination transitions and the lifetimes of some fine-structure levels are presented and compared with available experimental and other theoretical values. Our lifetime for the 3s3p(1Po)3d(2Po) level calculated in intermediate-coupling scheme, while differing significantly from our LS value, shows excellent agreement with the experimental result of Pinnington et al. In this calculation we also predict new data for several levels where no other theoretical and experimental results are available.
NASA Astrophysics Data System (ADS)
Garcia-Alonso, Diana; Parco, Maria; Stokes, Joseph; Looney, Lisa
2012-01-01
Thermal spraying is widely employed to deposit hydroxyapatite (HA) and HA-based biocomposites on hip and dental implants. For thick HA coatings (>150 μm), problems are generally associated with the build-up of residual stresses and lack of control of coating crystallinity. HA/polymer composite coatings are especially interesting to improve the pure HA coatings' mechanical properties. For instance, the polymer may help in releasing the residual stresses in the thick HA coatings. In addition, the selection of a bioresorbable polymer may enhance the coatings' biological behavior. However, there are major challenges associated with spraying ceramic and polymeric materials together because of their very different thermal properties. In this study, pure HA and HA/poly-ɛ-caprolactone (PCL) thick coatings were deposited without significant thermal degradation by low-energy plasma spraying (LEPS). PCL has never been processed by thermal spraying, and its processing is a major achievement of this study. The influence of selected process parameters on microstructure, composition, and mechanical properties of HA and HA/PCL coatings was studied using statistical design of experiments (DOE). The HA deposition rate was significantly increased by the addition of PCL. The average porosity of biocomposite coatings was slightly increased, while retaining or even improving in some cases their fracture toughness and microhardness. Surface roughness of biocomposites was enhanced compared with HA pure coatings. Cell culture experiments showed that murine osteoblast-like cells attach and proliferate well on HA/PCL biocomposite deposits.
NASA Astrophysics Data System (ADS)
Sahoo, Somanand; Saxena, Alok K.; Kaushik, Trilok C.; Gupta, Satish C.
2015-12-01
The process of electrical explosion of metal conductors has been used to produce nano particles under normal atmospheric conditions. The impact of average rate of energy deposition, overheat factor on size distribution of particles and expansion characteristics of plasma generated from exploding conductors have been experimentally investigated. The particle size was characterized by TEM and XRD while expansion rate was measured using streak photography.The geometric mean diameter of size distribution was found to be influenced by rate of energy deposition in the conductors. It is observed that higher the rate of energy deposition, higher will be the expansion velocity, and smaller will be the size of particles formed.
A method for calculating strain energy release rate based on beam theory
NASA Technical Reports Server (NTRS)
Sun, C. T.; Pandey, R. K.
1993-01-01
The Timoshenko beam theory was used to model cracked beams and to calculate the total strain energy release rate. The root rotation of the beam segments at the crack tip were estimated based on an approximate 2D elasticity solution. By including the strain energy released due to the root rotations of the beams during crack extension, the strain energy release rate obtained using beam theory agrees very well with the 2D finite element solution. Numerical examples were given for various beam geometries and loading conditions. Comparisons with existing beam models were also given.
Similarity criteria in calculations of the energy characteristics of a cw oxygen - iodine laser
NASA Astrophysics Data System (ADS)
Mezhenin, A. V.; Azyazov, V. N.
2012-12-01
The calculated and experimental data on the energy efficiency of a cw oxygen - iodine laser (OIL) are analysed based on two similarity criteria, namely, on the ratio of the residence time of the gas mixture in the resonator to the characteristic time of extraction of the energy stored in singlet oxygen td and on the gain-to-loss ratio Π. It is shown that the simplified two-level laser model satisfactorily predicts the output characteristics of OILs with a stable resonator at τd <= 7. Efficient energy extraction from the OIL active medium is achieved in the case of τd = 5 - 7, Π = 4 - 8.
Similarity criteria in calculations of the energy characteristics of a cw oxygen - iodine laser
Mezhenin, A V; Azyazov, V N
2012-12-31
The calculated and experimental data on the energy efficiency of a cw oxygen - iodine laser (OIL) are analysed based on two similarity criteria, namely, on the ratio of the residence time of the gas mixture in the resonator to the characteristic time of extraction of the energy stored in singlet oxygen td and on the gain-to-loss ratio {Pi}. It is shown that the simplified two-level laser model satisfactorily predicts the output characteristics of OILs with a stable resonator at {tau}{sub d} {<=} 7. Efficient energy extraction from the OIL active medium is achieved in the case of {tau}{sub d} = 5 - 7, {Pi} = 4 - 8. (lasers)
Calculating splittings between energy levels of different symmetry using path-integral methods.
Mátyus, Edit; Althorpe, Stuart C
2016-03-21
It is well known that path-integral methods can be used to calculate the energy splitting between the ground and the first excited state. Here we show that this approach can be generalized to give the splitting patterns between all the lowest energy levels from different symmetry blocks that lie below the first-excited totally symmetric state. We demonstrate this property numerically for some two-dimensional models. The approach is likely to be useful for computing rovibrational energy levels and tunnelling splittings in floppy molecules and gas-phase clusters. PMID:27004864
NASA Technical Reports Server (NTRS)
Howell, L. W.
1985-01-01
An APL program which numerically evaluates the probability density function (PDF) for the energy deposited in a thin absorber by a charged particle is proposed, with application to the construction, pointing, and control of spacecraft. With this program, the PDF of the restricted energy loss distribution of Watts (1973) is derived, and Vavilov's (1957) distribution is obtained by proper parameter selection. The method is demonstrated with the example of the effect of charged particle induced radiation on the Hubble Space Telescope (HST) pointing accuracy. A Monte Carlo study simulates the photon noise caused by charged particles passing through the photomultiplier tube window, and the stochastic variation of energy loss is introduced into the simulation by generating random energy losses from a power law distribution. The program eliminates annoying loop procedures, and model parameter sensitivity can be studied using the graphical output.
NASA Astrophysics Data System (ADS)
Whitney, K. G.; Chang, C. S.
2008-07-01
Analyses of the resonant multiphoton ionization of atoms require knowledge of ac Stark energy shifts and of multiphoton, bound-to-bound state, transition amplitudes. In this paper, we consider the three-photon photoionization of hydrogen atoms at frequencies that are at and surrounding the two-photon 1s to 2s resonance. AC energy shift sums of both the 1s and 2s states are calculated as a function of the laser frequency along with two-photon 1s → 2s resonant transition amplitude sums. These quantities are calculated using an extended version of a method, which has often been employed in a variety of ways, of calculating these sums by expressing them in terms of solutions to a variety of differential equations that are derived from the different sums being evaluated. We demonstrate how exact solutions are obtained to these differential equations, which lead to exact evaluations of the corresponding sums. A variety of different cases are analysed, some involving analytic continuation, some involving real number analysis and some involving complex number analysis. A dc Stark sum calculation of the 2s state is carried out to illustrate the case where analytic continuation, pole isolation and pole subtraction are required and where the calculation can be carried out analytically; the 2s state, ac Stark shift sum calculations involve a case where no analytic continuation is required, but where the solution to the differential equation produces complex numbers owing to the finite photoionization lifetime of the 2s state. Results from these calculations are then used to calculate three-photon ionization probabilities of relevance to an analysis of the multiphoton ionization data published by Kyrala and Nichols (1991 Phys. Rev. A 44, R1450).
A highly efficient hybrid method for calculating the hydration free energy of a protein.
Oshima, Hiraku; Kinoshita, Masahiro
2016-03-30
We develop a new method for calculating the hydration free energy (HFE) of a protein with any net charge. The polar part of the energetic component in the HFE is expressed as a linear combination of four geometric measures (GMs) of the protein structure and the generalized Born (GB) energy plus a constant. The other constituents in the HFE are expressed as linear combinations of the four GMs. The coefficients (including the constant) in the linear combinations are determined using the three-dimensional reference interaction site model (3D-RISM) theory applied to sufficiently many protein structures. Once the coefficients are determined, the HFE and its constituents of any other protein structure are obtained simply by calculating the four GMs and GB energy. Our method and the 3D-RISM theory give perfectly correlated results. Nevertheless, the computation time required in our method is over four orders of magnitude shorter. PMID:26576506
Efficient ab initio free energy calculations by classically assisted trajectory sampling
NASA Astrophysics Data System (ADS)
Wilson, Hugh F.
2015-12-01
A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.
Learning Approach on the Ground State Energy Calculation of Helium Atom
Shah, Syed Naseem Hussain
2010-07-28
This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function.The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.
Learning Approach on the Ground State Energy Calculation of Helium Atom
NASA Astrophysics Data System (ADS)
Shah, Syed Naseem Hussain
2010-07-01
This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function. The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.
Long-range correlation energy calculated from coupled atomic response functions
Ambrosetti, Alberto; Reilly, Anthony M.; Tkatchenko, Alexandre; DiStasio, Robert A.
2014-05-14
An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy.
Brenner, C. M.; Robinson, A. P. L.; Markey, K.; Scott, R. H. H.; Lancaster, K. L.; Musgrave, I. O.; Spindloe, C.; Winstone, T.; Wyatt, D.; Neely, D.; Gray, R. J.; McKenna, P.; Rosinski, M.; Badziak, J.; Wolowski, J.; Deppert, O.; Batani, D.; Davies, J. R.; Hassan, S. M.; Tatarakis, M.; and others
2014-02-24
An all-optical approach to laser-proton acceleration enhancement is investigated using the simplest of target designs to demonstrate application-relevant levels of energy conversion efficiency between laser and protons. Controlled deposition of laser energy, in the form of a double-pulse temporal envelope, is investigated in combination with thin foil targets in which recirculation of laser-accelerated electrons can lead to optimal conditions for coupling laser drive energy into the proton beam. This approach is shown to deliver a substantial enhancement in the coupling of laser energy to 5–30 MeV protons, compared to single pulse irradiation, reaching a record high 15% conversion efficiency with a temporal separation of 1 ps between the two pulses and a 5 μm-thick Au foil. A 1D simulation code is used to support and explain the origin of the observation of an optimum pulse separation of ∼1 ps.
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
Rezaee, Mohammad Hunting, Darel J.; Sanche, Léon
2014-07-15
be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.
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.
Low-energy deposition of high-strength Al(0) alloys from an ECR plasma
Barbour, J.C.; Follstaedt, D.M.; Knapp, J.A.; Myers, S.M.; Marshall, D.A.; Lad, R.J.
1995-12-31
Low-energy deposition of Al(O) alloys from an electron cyclotron resonance (ECR) plasma offers a scaleable method for the synthesis of thick, high-strength Al layers. This work compares alloy layers formed by an ECR-0{sub 2} plasma in conjunction with Al evaporation to 0-implanted Al (ion energies 25-200 keV); and it examines the effects of volume fraction of A1{sub 2}0{sub 3} phase and deposition temperature on the yield stress of the material. TEM showed the Al(O) alloys contain a dense dispersion of small {gamma}-Al{sub 2}0{sub 3} precipitates ({approximately}l nm) in a fine-grain (10-100 nm) fcc Al matrix when deposited at a temperature of {approximately}100C, similar to the microstructure for gigapascal-strength 0-implanted Al. Nanoindentation gave hardnesses for ECR films from 1.1 to 3.2 GPa, and finite-element modeling gave yield stresses up to 1.3 {plus_minus} 0.2 GPa with an elastic modulus of 66 GPa {plus_minus} 6 GPa (similar to pure bulk Al). The yield stress of a polycrystalline pure Al layer was only 0.19 {plus_minus} 0.02 GPa, which was increased to 0.87 {plus_minus} 0.15 GPa by implantation with 5 at. % 0.
Enhancement of X-ray Energy Deposition via Heavy Element Sensitization in Biological Environments
NASA Astrophysics Data System (ADS)
Lim, Sara; Pradhan, Anil; Nahar, Sultana; Barth, Rolf
2015-05-01
Energy (dose) deposition by low vs. high energy x-rays (LEX & HEX), approximately E ~ 100 keV and E > 1 MeV respectively, was studied in biological matter sensitized with heavy elements (high-Z or HZ) to improve radiation therapy of cancer. Computations and simulations show that LEX interact favorably with HZ sensitizers by depositing more dose than HEX. LEX photons effectively photoionize deep inner electronic shells and release cell-killing Auger electrons near malignant cells embedded with HZ atoms. HEX photons predominantly Compton scatter with little interaction, even with HZ elements. Monte Carlo simulations show that in comparison to unsensitized tissue, LEX irradiation of HZ-sensitized models resulted in up to a factor of 2 increase in dose deposition relative to HEX. To validate the studies, in vitro experiments were performed using 2 distinct cancer cell types treated with Pt-based sensitizers, then irradiated with a LEX 160 KV x-ray source and a HEX 6 MV LINAC employed in radiation therapy. The experiments support numerical simulations, and demonstrate several factors lower survival of HZ-sensitized cells irradiated with LEX compared with HEX.
Lin, Bin; Wong, Ka-Yiu; Hu, Char; Kokubo, Hironori; Pettitt, B. Montgomery
2011-01-01
Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy. PMID:21765968
Lin, Bin; Wong, Ka-Yiu; Hu, Char Y.; Kokubo, Hironori; Pettitt, Bernard M.
2011-07-07
Although detailed atomic models may be applied for a full description of solvation, simpler phenomenologicalmodels are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.
NASA Technical Reports Server (NTRS)
Marshall, C. J.; Ladbury, R.; Marshall, P. W.; Reed, R. A.; Howe, C.; Weller, B.; Mendenhall, M.; Waczynski, A.; Jordan, T. M.; Fodness, B.
2006-01-01
This paper presents a combined Monte Carlo and analytic approach to the calculation of the pixel-to-pixel distribution of proton-induced damage in a HgCdTe sensor array and compares the results to measured dark current distributions after damage by 63 MeV protons. The moments of the Coulombic, nuclear elastic and nuclear inelastic damage distribution were extracted from Monte Carlo simulations and combined to form a damage distribution using the analytic techniques first described in [I]. The calculations show that the high energy recoils from the nuclear inelastic reactions (calculated using the Monte Car10 code MCNPX [2]) produce a pronounced skewing of the damage energy distribution. The nuclear elastic component (also calculated using the MCNPX) has a negligible effect on the shape of the damage distribution. The Coulombic contribution was calculated using MRED [3,4], a Geant4 [4,5] application. The comparison with the dark current distribution strongly suggests that mechanisms which are not linearly correlated with nonionizing damage produced according to collision kinematics are responsible for the observed dark current increases. This has important implications for the process of predicting the on-orbit dark current response of the HgCdTe sensor array.
NASA Astrophysics Data System (ADS)
de Jong, Maarten; Qi, Liang; Olmsted, David L.; van de Walle, Axel; Asta, Mark
2016-03-01
A method is described for calculating the energetics of planar defects in alloys based on the special-quasirandom-structure (SQS) approach. We examine the accuracy of the approach employing atomistic calculations based on a classical embedded-atom-method (EAM) interatomic potential for hexagonal close packed (hcp) alloys, for which benchmark results can be obtained by direct configurational averaging. The results of these calculations demonstrate that the SQS-based approach can be employed to derive the concentration dependence of the energies of twin boundaries, unstable stacking faults, and surfaces to within an accuracy of approximately 10%. The SQS considered in this study contain up to 72 atoms and hence are small enough to be considered in first-principles density-functional-theory (DFT) based calculations. The application of the SQS-based approach in direct DFT-based calculations is demonstrated in a study of the concentration dependence of interfacial energies for {11 2 ¯1 } twins in hcp Ti-Al alloys.
Energy Loss Calculations for Target Thickness Determinations using SRIM and Excel
NASA Astrophysics Data System (ADS)
Pawlak, A. S.; Greene, J. P.
2011-10-01
The thickness of a thin target foil can be determined by measuring the energy loss of alpha particles that travel through it. In the Target Laboratory of the Physics Division at Argonne National Laboratory (ANL), this is accomplished by measuring the energy loss of the 5812 keV alpha particles emitted by a 2 49 Cf source using a silicon detector set-up. The energy loss is translated into the target foil thickness using the stopping power for 4He in the target material obtained from the stopping/range tables provided by SRIM. This calculation has until recently been carried out using a program developed for this purpose, ``ENELOSS.'' This program uses the stopping/range tables from the original work published by Ziegler. Additionally, due to its design, ENELOSS is unable to easily accommodate targets made from compounds. In order to perform theses measurements using the most recent SRIM data, and to better calculate the thickness of compound targets, we have developed a ``Thickness Calculation'' spreadsheet using Microsoft Excel. This spreadsheet approach is not limited to elemental targets and employs stopping/range tables from the most recent edition of SRIM available on the web. The calculations obtained allow for more accurate target thicknesses and automates the process conveniently for repetitive measurements. This work was supported by the U.S. DoE, Nuclear Physics Division, under Contract No. W-31-109-Eng-38.
Excitation energy deposition in {sup 209}Bi({alpha},{alpha}{sup {prime}}) reactions at 240 MeV
Fabris, D.; Lunardon, M.; Nebbia, G.; Viesti, G.; Fioretto, E.; Napoli, D.R.; Prete, G.; Natowitz, J.B.; Wada, R.; Gonthier, P.; Majka, Z.; Alfarro, R.; Zhao, Y.; Mdeiwayeh, N.; Ho, T.
1998-08-01
The energy deposition associated with inelastic {alpha} particle scattering on {sup 209}Bi at 240 MeV has been determined using the TAMU neutron ball. A comparison of the reconstructed average excitation energies with the beam energy losses demonstrates that only part of the missing beam energy is usually deposited as thermal excitation in the target nucleus. Requiring an additional coincidence with a light charged particle or fission fragment leads to selection of a significant higher average excitation energy. {copyright} {ital 1998} {ital The American Physical Society}
NASA Astrophysics Data System (ADS)
Pavlyuchko, A. I.; Yurchenko, S. N.; Tennyson, Jonathan
2015-07-01
A procedure for calculation of rotational-vibrational states of medium-sized molecules is presented. It combines the advantages of variational calculations and perturbation theory. The vibrational problem is solved by diagonalising a Hamiltonian matrix, which is partitioned into two sub-blocks. The first, smaller sub-block includes matrix elements with the largest contribution to the energy levels targeted in the calculations. The second, larger sub-block comprises those basis states which have little effect on these energy levels. Numerical perturbation theory, implemented as a Jacobi rotation, is used to compute the contributions from the matrix elements of the second sub-block. Only the first sub-block needs to be stored in memory and diagonalised. Calculations of the vibrational-rotational energy levels also employ a partitioning of the Hamiltonian matrix into sub-blocks, each of which corresponds either to a single vibrational state or a set of resonating vibrational states, with all associated rotational levels. Physically, this partitioning is efficient when the Coriolis coupling between different vibrational states is small. Numerical perturbation theory is used to include the cross-contributions from different vibrational states. Separate individual sub-blocks are then diagonalised, replacing the diagonalisation of a large Hamiltonian matrix with a number of small matrix diagonalisations. Numerical examples show that the proposed hybrid variational-perturbation method greatly speeds up the variational procedure without significant loss of precision for both vibrational-rotational energy levels and transition intensities. The hybrid scheme can be used for accurate nuclear motion calculations on molecules with up to 15 atoms on currently available computers.
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
NASA Astrophysics Data System (ADS)
Ramsay, Donald J.; Walker, Philip J.; Dadswell, Nicola G.; May, James; Piper, James A.; Wacher, Christine
1990-06-01
Laser angioplasty continues to attract interest as a potential method for treating atherosclerotic arterial disease. Current efforts are aimed at finding the most effective combination of laser and delivery system. High energy pulsed ultraviolet or infrared lasers demonstrate good photoablative properties but there remain practical difficulties with the optical fibre delivery. Continuous wave lasers are widely used in conjunction with "hot-tip" fibres for thermal ablation but their direct (optical) ablation efficiency is low, causing significant surrounding thermal damage in soft tissue. While considerable attention has been directed previously at the ablative effects for different laser wavelengths, little systematic study has been made of the efficacy for different temporal rates of energy deposition. We have compared the efficacy for tissue ablation in cadaveric human aorta of three different laser systems with similar wavelengths in the visible (green) but different temporal rates of energy deposition. The laser sources were the continuous wave argon ion laser (514.5 nm), the high pulse energy, frequency doubled Nd:YAG laser (532 nm) and the copper vapour laser. The copper vapour laser is a high repetition rate, high average power, pulsed laser emitting in the green (511 nm) and yellow (578 nm) which has temporal characteristics intermediate between those of the Nd:YAG laser and the argon ion laser, and has the potential to be effective both for direct optical ablation and hot-tip thermal ablation.
Perfetti, C.; Martin, W.; Rearden, B.; Williams, M.
2012-07-01
Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the Shift Monte Carlo code within the SCALE code package. The methods were used for two small-scale test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods. (authors)
An Exact Calculation of Electron-Ion Energy Splitting in a Hot Plasma
Singleton, Robert L
2012-09-10
In this brief report, I summarize the rather involved recent work of Brown, Preston, and Singleton (BPS). In Refs. [2] and [3], BPS calculate the energy partition into ions and electrons as a charged particle traverses a non-equilibrium two-temperature plasma. These results are exact to leading and next-to-leading order in the plasma coupling g, and are therefore extremely accurate in a weakly coupled plasma. The new BPS calculations are compared with the more standard work of Fraley et al. [12]. The results differ substantially at higher temperature when T{sub I} {ne} T{sub e}.
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.
Calculation of quasiparticle energy spectrum of silicon using the correlated Hartree-Fock method
NASA Astrophysics Data System (ADS)
Ishihara, Takamitsu; Yamagami, Hiroshi; Matsuzawa, Kazuya; Yasuhara, Hiroshi
1999-06-01
We present quasiparticle energy spectrum calculations of silicon using the correlated Hartree-Fock method proposed by Yasuhara and Takada [Phys. Rev. B 43, 7200 (1991)], in which the information on the effective mass of an electron liquid is included in the form of a nonlocal spin-parallel potential in addition to a local potential. The calculated band gaps of silicon are much improved, compared with the local density approximation values. The minimum indirect band gap is evaluated to be 1.37 eV.
Rashev, Svetoslav; Moule, David C
2015-04-01
In this work we present a full 6D quartic potential energy surface (PES) for S0 thiophosgene in curvilinear symmetrized bond-angle coordinates. The PES was refined starting from an ab initio field derived from acc-pVTZ basis set with CCSD(T) corrections for electron correlation. In the present calculations we used our variational method that was recently tested on formaldehyde and some of its isotopomers, along with additional improvements. The lower experimentally known vibrational levels for 35Cl2CS were reproduced quite well in the calculations, which can be regarded as a test for the feasibility of the obtained quartic PES. PMID:25615683
Feasibility of a wavelet expansion method to treat energy in cell calculations
Van Rooijen, W. F. G.
2012-07-01
This paper discusses the application of the Discrete Wavelet Transform (DWT) for the functional expansion of the energy variable in a cell calculation. The motivation of the work is the desire to obtain a self-shielding methodology in which the treatment of the energy variable in a given material region can be automatically adapted to the complexity of the cross section in that region. Unfortunately, the work presented in this paper shows that it is generally not possible to obtain the desired adaptivity. The most fundamental reason is that in a multi-region system, the energy dependence of the flux in a given material region is a function of the energy dependent cross sections and sources in all material regions through which the neutrons have crossed before entering into the present material. The complexity of the energy dependence of the cross section in a material region is thus not necessarily linked to the energy dependence of the flux in that region. If one sacrifices the objective of adaptivity, then an accurate method can be obtained using the DWT as a functional expansion. However, the resulting system of equations is more complicated than the direct solution of a hyper-fine group calculation. The conclusion is thus that the DWT approach is not very practical. (authors)
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.
Potential energy surface and second virial coefficient of methane-water from ab initio calculations
NASA Astrophysics Data System (ADS)
Akin-Ojo, Omololu; Szalewicz, Krzysztof
2005-10-01
Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03kcal /mol at a geometry where H2O is the proton donor, HO -H⋯CH4, with the O-H-C angle of 165°, while the secondary minimum, with an energy of -0.72kcal/mol, has CH4 in the role of the proton donor (H3C -H⋯OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.
Chen, Z, J; Xiao, H. Y.; Zu, Xiaotao T.; Gao, Fei
2008-11-01
The electronic structures and defect formation energies for a series of stannate pyrochlores Ln2Sn2O7 *Ln=La, Pr, Nd, Sm, Gd, Tb, Ho, Er, Lu, and Y* have been investigated using the first-principles total energy calculations. The calculated results show that Ln-site cation ionic radius, x-O48f, lattice constant and the covalency of the *Sn–O48f* bond have a significant affect on the defect formation energies. The cation-antisite defect has the lowest formation energy, as compared with that of other defects, indicating that cation disorder causes local oxygen disordering. The present studies suggest that Lu2Sn2O7 is the most resistant to ion beam-induced amorphization. The electronic structure calculations reveal that Ln2Sn2O7 compounds have direct band gaps of 2.64– 2.95 eV at the * point in the Brillouin zone. © 2008 American Institute of Physics.
Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane
Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas
2014-04-28
Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.
NASA Astrophysics Data System (ADS)
Valipa, Mayur S.; Aydil, Eray S.; Maroudas, Dimitrios
2004-11-01
We report a direct, statistically significant calculation of the surface reactivity of the SiH 3 radical on hydrogenated amorphous silicon (a-Si:H) using molecular-dynamics simulations of repeated impingement of SiH 3 radicals on growth surfaces of smooth a-Si:H films over the temperature range 475-800 K. SiH 3 can either incorporate into the film by adsorbing onto a surface Si dangling bond or inserting into Si-Si bonds (sticking), or abstract surface H through Eley-Rideal (ER) or Langmuir-Hinshelwood (LH) pathways to produce SiH 4 gas, or react with another surface SiH 3 to desorb as Si 2H 6 (recombination), or leave the film by reflection or desorption. The overall surface reaction probability, β, includes both radical sticking and recombination. In agreement with experimental measurements, β is almost constant over the temperature range studied, as are the probabilities for sticking and recombination, s and γ, respectively; the calculated mean value of β is 0.47 ± 0.03. Energetic analysis of the various surface reactions shows that radical adsorption, radical insertion, and ER abstraction are barrierless processes, which explains the measured temperature independence of β. LH abstraction is activated, but competes with disilane formation, yielding a temperature-independent γ. Also, LH abstraction leads to H elimination from a-Si:H during growth and can partly explain the experimentally measured temperature dependence of the H content in the a-Si:H film.
Effect of energy deposited by cosmic-ray particles on interferometric gravitational wave detectors
NASA Astrophysics Data System (ADS)
Yamamoto, Kazuhiro; Hayakawa, Hideaki; Okada, Atsushi; Uchiyama, Takashi; Miyoki, Shinji; Ohashi, Masatake; Kuroda, Kazuaki; Kanda, Nobuyuki; Tatsumi, Daisuke; Tsunesada, Yoshiki
2008-07-01
We investigated the noise of interferometric gravitational wave detectors due to heat energy deposited by cosmic-ray particles. We derived a general formula that describes the response of a mirror against a cosmic-ray passage. We found that there are differences in the comic-ray responses (the dependence of temperature and cosmic-ray track position) in cases of interferometric and resonant gravitational wave detectors. The power spectral density of vibrations caused by low-energy secondary muons is 100 times smaller than the goal sensitivity of future second-generation interferometer projects, such as LCGT and Advanced LIGO. The arrival frequency of high-energy cosmic-ray muons that generate enough large showers inside mirrors of LCGT and Advanced LIGO is one per a millennium. We also discuss the probability of exotic-particle detection with interferometers.
Effect of energy deposited by cosmic-ray particles on interferometric gravitational wave detectors
Yamamoto, Kazuhiro; Hayakawa, Hideaki; Okada, Atsushi; Uchiyama, Takashi; Miyoki, Shinji; Ohashi, Masatake; Kuroda, Kazuaki; Kanda, Nobuyuki; Tatsumi, Daisuke; Tsunesada, Yoshiki
2008-07-15
We investigated the noise of interferometric gravitational wave detectors due to heat energy deposited by cosmic-ray particles. We derived a general formula that describes the response of a mirror against a cosmic-ray passage. We found that there are differences in the comic-ray responses (the dependence of temperature and cosmic-ray track position) in cases of interferometric and resonant gravitational wave detectors. The power spectral density of vibrations caused by low-energy secondary muons is 100 times smaller than the goal sensitivity of future second-generation interferometer projects, such as LCGT and Advanced LIGO. The arrival frequency of high-energy cosmic-ray muons that generate enough large showers inside mirrors of LCGT and Advanced LIGO is one per a millennium. We also discuss the probability of exotic-particle detection with interferometers.
NASA Astrophysics Data System (ADS)
Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Yang, Weitao
2009-04-01
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao
2009-04-28
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
Ho, T.; Rabitz, H.
1996-02-01
A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}
Buryak, Ilya; Vigasin, Andrey A.
2015-12-21
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
Bubin, Sergiy; Adamowicz, Ludwik
2014-01-14
Benchmark variational calculations are performed for the seven lowest 1s(2)2s np ((1)P), n = 2...8, states of the beryllium atom. The calculations explicitly include the effect of finite mass of (9)Be nucleus and account perturbatively for the mass-velocity, Darwin, and spin-spin relativistic corrections. The wave functions of the states are expanded in terms of all-electron explicitly correlated Gaussian functions. Basis sets of up to 12,500 optimized Gaussians are used. The maximum discrepancy between the calculated nonrelativistic and experimental energies of 1s(2)2s np ((1)P) →1s(2)2s(2) ((1)S) transition is about 12 cm(-1). The inclusion of the relativistic corrections reduces the discrepancy to bellow 0.8 cm(-1). PMID:24437871
NASA Astrophysics Data System (ADS)
Buryak, Ilya; Vigasin, Andrey A.
2015-12-01
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
GPU-based acceleration of free energy calculations in solid state physics
NASA Astrophysics Data System (ADS)
Januszewski, Michał; Ptok, Andrzej; Crivelli, Dawid; Gardas, Bartłomiej
2015-07-01
Obtaining a thermodynamically accurate phase diagram through numerical calculations is a computationally expensive problem that is crucially important to understanding the complex phenomena of solid state physics, such as superconductivity. In this work we show how this type of analysis can be significantly accelerated through the use of modern GPUs. We illustrate this with a concrete example of free energy calculation in multi-band iron-based superconductors, known to exhibit a superconducting state with oscillating order parameter (OP). Our approach can also be used for classical BCS-type superconductors. With a customized algorithm and compiler tuning we are able to achieve a 19×speedup compared to the CPU (119×compared to a single CPU core), reducing calculation time from minutes to mere seconds, enabling the analysis of larger systems and the elimination of finite size effects.
Dobos, A. P.
2012-05-01
This paper describes an improved algorithm for calculating the six parameters required by the California Energy Commission (CEC) photovoltaic (PV) Calculator module model. Rebate applications in California require results from the CEC PV model, and thus depend on an up-to-date database of module characteristics. Currently, adding new modules to the database requires calculating operational coefficients using a general purpose equation solver - a cumbersome process for the 300+ modules added on average every month. The combination of empirical regressions and heuristic methods presented herein achieve automated convergence for 99.87% of the 5487 modules in the CEC database and greatly enhance the accuracy and efficiency by which new modules can be characterized and approved for use. The added robustness also permits general purpose use of the CEC/6 parameter module model by modelers and system analysts when standard module specifications are known, even if the module does not exist in a preprocessed database.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-01-01
Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. PMID:26418190
Ceriotti, Michele; Manolopoulos, David E
2012-09-01
Light nuclei at room temperature and below exhibit a kinetic energy which significantly deviates from the predictions of classical statistical mechanics. This quantum kinetic energy is responsible for a wide variety of isotope effects of interest in fields ranging from chemistry to climatology. It also furnishes the second moment of the nuclear momentum distribution, which contains subtle information about the chemical environment and has recently become accessible to deep inelastic neutron scattering experiments. Here, we show how, by combining imaginary time path integral dynamics with a carefully designed generalized Langevin equation, it is possible to dramatically reduce the expense of computing the quantum kinetic energy. We also introduce a transient anisotropic Gaussian approximation to the nuclear momentum distribution which can be calculated with negligible additional effort. As an example, we evaluate the structural properties, the quantum kinetic energy, and the nuclear momentum distribution for a first-principles simulation of liquid water. PMID:23005275
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.
NASA Astrophysics Data System (ADS)
van de Bovenkamp, J.; van Mourik, T.; van Duijneveldt, F. B.
A multi-reference configuration interaction (MRCI) method is described, which is devised for the calculation of interaction energies of van der Waals complexes and applied to calculating the HeNe potential energy curve. The MRCI calculations make use of a generalized Poplecorrection in order to account for the lack of size consistency. The orbital space is partitioned into three subspaces: the first active space (AS1), which contains the strongly occupied orbitals; the second active space (AS2), which contains the main intra-correlating orbitals; and the external space (ES). It is shown that, to keep the error below 0.2K in the excitation scheme and the active orbital space it is sufficient to include only sigma-orbitals in AS2 and to use an excitation scheme (labelled Qq-MRCI) that encompasses only up to quadruply excited configurations. The final active orbital space (AS2) turned out to be 2s(He), 2psigma(He), 3s(Ne), 3psigma(Ne) and 3dsigma(Ne). Other MRCI variants, in which most or all quadruply excited configurations were deleted from the CI expansion (Qt- and Tt-MRCI), were found to be inadequate. Using the Qq-MRCI scheme together with a 197-orbital 'interaction optimized' basis set (IO197), the MRCI interaction energy at R = 5.7 a0 was calculated to be-21.12K. The corresponding values at the MP4 and CCSD(T) levels of theory are-20.06K and-20.99K, respectively, indicating that the MP4 method is inappropriate for highly accurate calculations on this system. Fitting the calculated data using a generalized Morse function, including an additional C6/R6 term to account for a correct long-range behaviour of the potential, the MRCI well depth was calculated to be-21.16K at Req = 5.73 a0. The MRCI and CCSD(T) potentials have the same quality and are found to be in good agreement with the HartreeFock dispersion (HFD-B) potential of Keil, M., Danielson, L. J., and Dunlop, P. J., 1991, J. Chem. Phys., 94, 296. It is concluded that, for basis IO197, the CCSD(T) method is
Calorimetric measurement of electron energy deposition in extended media. Theory vs experiment
Lockwood, G.J.; Ruggles, L.E.; Miller, G.H.; Halbleib, J.A.
1980-01-01
A new calorimetric technique has been developed for measuring electron energy deposition profiles in one dimension. The experimental procedures and theoretical analyses required in the application of the new method are reviewed. Extensive results are presented for electron energy deposition profiles in semi-infinite homogeneous and multilayer configurations. These data cover a range of elements from beryllium through uranium at source energies from 0.3 to 1.0 MeV (selected data at 0.5 and 0.1 MeV) and at incident angles from 0/sup 0/ to 60/sup 0/. In every case, the experimental profiles are compared with the predictions of a coupled electron/photon Monte Carlo transport code. Overall agreement between theory and experiment is very good. However, there appears to be a tendency for the theoretical profiles to be higher near the peaks and lower near the tails, especially in high-Z materials. There is also a discrepancy between theory and experiment in low-Z materials near high-Z/low-Z interfaces.
Calculation of positron binding energies using the generalized any particle propagator theory
Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés
2014-09-21
We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.
Calculated dipole moment and energy in collision of a hydrogen molecule and a hydrogen atom
NASA Technical Reports Server (NTRS)
Patch, R. W.
1973-01-01
Calculations were carried out using three Slater-type 1s orbitals in the orthogonalized valencebond theory of McWeeny. Each orbital exponent was optimized, the H2 internuclear distance was varied from 7.416 x 10 to the -11th power to 7.673 x 10 to the -11th power m (1.401 to 1.450 bohrs). The intermolecular distance was varied from 1 to 4 bohrs (0.5292 to 2.117 x 10 to the 10th power). Linear, scalene, and isosceles configurations were used. A weighted average of the interaction energies was taken for each intermolecular distance. Although energies are tabulated, the principal purpose was to calculate the electric dipole moment and its derivative with respect to H2 internuclear distance.
Calculating alpha Eigenvalues in a Continuous-Energy Infinite Medium with Monte Carlo
Betzler, Benjamin R.; Kiedrowski, Brian C.; Brown, Forrest B.; Martin, William R.
2012-09-04
The {alpha} eigenvalue has implications for time-dependent problems where the system is sub- or supercritical. We present methods and results from calculating the {alpha}-eigenvalue spectrum for a continuous-energy infinite medium with a simplified Monte Carlo transport code. We formulate the {alpha}-eigenvalue problem, detail the Monte Carlo code physics, and provide verification and results. We have a method for calculating the {alpha}-eigenvalue spectrum in a continuous-energy infinite-medium. The continuous-time Markov process described by the transition rate matrix provides a way of obtaining the {alpha}-eigenvalue spectrum and kinetic modes. These are useful for the approximation of the time dependence of the system.
NASA Astrophysics Data System (ADS)
Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas
2015-08-01
The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm-1, and a harmonic vibrational frequency of 20.5 cm-1. The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 103, C8 = 6.978 × 105, and C10 = 8.786 × 107 atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment.
S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence
sapirstein, J; Cheng, K T
2010-11-02
A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.
Microscopic calculation of interacting boson model parameters by potential-energy surface mapping
Bentley, I.; Frauendorf, S.
2011-06-15
A coherent state technique is used to generate an interacting boson model (IBM) Hamiltonian energy surface which is adjusted to match a mean-field energy surface. This technique allows the calculation of IBM Hamiltonian parameters, prediction of properties of low-lying collective states, as well as the generation of probability distributions of various shapes in the ground state of transitional nuclei, the last two of which are of astrophysical interest. The results for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium, and erbium nuclei are compared with experiment.
Calculation of free energies in fluid membranes subject to heterogeneous curvature fields
NASA Astrophysics Data System (ADS)
Agrawal, Neeraj J.; Radhakrishnan, Ravi
2009-07-01
We present a computational methodology for incorporating thermal effects and calculating relative free energies for elastic fluid membranes subject to spatially dependent intrinsic curvature fields using the method of thermodynamic integration. Based on a simple model for the intrinsic curvature imposed only in a localized region of the membrane, we employ thermodynamic integration to calculate the free-energy change as a function of increasing strength of the intrinsic curvature field and a thermodynamic cycle to compute free-energy changes for different sizes of the localized region. By explicitly computing the free-energy changes and by quantifying the loss of entropy accompanied with increasing membrane deformation, we show that the membrane stiffness increases with increasing intrinsic field, thereby, renormalizing the membrane bending rigidity. The second main conclusion of this work is that the entropy of the membrane decreases with increasing size of the localized region subject to the curvature field. Our results help to quantify the free-energy change when a planar membrane deforms under the influence of curvature-inducing proteins at a finite temperature.
Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation
Pan, Keyao; Deem, Michael W.
2011-01-01
Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody binding free energy (ΔΔG) induced by amino acid substitution at each position in epitope B of the H3N2 influenza hemagglutinin, the key target for antibody. A substitution with positive ΔΔG value decreases the antibody binding constant. On average an uncharged to charged amino acid substitution generates the highest ΔΔG values. Also on average, substitutions between small amino acids generate ΔΔG values near to zero. The 21 sites in epitope B have varying expected free energy differences for a random substitution. Historical amino acid substitutions in epitope B for the A/Aichi/2/1968 strain of influenza A show that most fixed and temporarily circulating substitutions generate positive ΔΔG values. We propose that the observed pattern of H3N2 virus evolution is affected by the free energy landscape, the mapping from the free energy landscape to virus fitness landscape, and random genetic drift of the virus. Monte Carlo simulations of virus evolution are presented to support this view. PMID:21691431
Calculations of binding energies and masses of heavy quarkonia using renormalon cancellation
NASA Astrophysics Data System (ADS)
Contreras, Carlos; Cvetič, Gorazd; Gaete, Patricio
2004-08-01
We use various methods of Borel integration to calculate the binding ground energies and masses of bb¯ and tt¯ quarkonia. The methods take into account the leading infrared renormalon structure of the (hard+)soft part of the binding energies E(s), and of the corresponding quark pole masses mq, where the contributions of these singularities in M(s)=2mq+E(s) cancel. Beforehand, we carry out the separation of the binding energy into its (hard+)soft and ultrasoft parts. The resummation formalisms are applied to expansions of mq and E(s) in terms of quantities which do not involve renormalon ambiguity, such as MS¯ mass mq and αs(μ). The renormalization scales μ are different in calculations of mq, E(s) and E(us). The mass mb is extracted, and the binding energies Ett¯ and the peak (resonance) energies Eres. for tt¯ production are obtained.
Cecchini, M; Krivov, S V; Spichty, M; Karplus, M
2009-07-23
Conformational free-energy differences are key quantities for understanding important phenomena in molecular biology that involve large structural changes of macromolecules. In this paper, an improved version of the confinement approach, which is based on earlier developments, is used to determine the free energy of individual molecular states by progressively restraining the corresponding molecular structures to pure harmonic basins, whose absolute free energy can be computed by normal-mode analysis. The method is used to calculate the free-energy difference between two conformational states of the alanine dipeptide in vacuo, and of the beta-hairpin from protein G with an implicit solvation model. In all cases, the confinement results are in excellent agreement with the ones obtained from converged equilibrium molecular dynamics simulations, which have a much larger computational cost. The systematic and statistical errors of the results are evaluated and the origin of the errors is identified. The sensitivity of the calculated free-energy differences to structure-based definitions of the molecular states is discussed. A variant of the method, which closes the thermodynamic cycle by a quasi-harmonic rather than harmonic analysis, is introduced. The latter is proposed for possible use with explicit solvent simulations. PMID:19552392
Jia, Ye; Zeng, Ke; Singisetti, Uttam; Wallace, Joshua S.; Gardella, Joseph A
2015-03-09
The energy band alignment between atomic layer deposited (ALD) SiO{sub 2} and β-Ga{sub 2}O{sub 3} (2{sup ¯}01) is calculated using x-ray photoelectron spectroscopy and electrical measurement of metal-oxide semiconductor capacitor structures. The valence band offset between SiO{sub 2} and Ga{sub 2}O{sub 3} is found to be 0.43 eV. The bandgap of ALD SiO{sub 2} was determined to be 8.6 eV, which gives a large conduction band offset of 3.63 eV between SiO{sub 2} and Ga{sub 2}O{sub 3}. The large conduction band offset makes SiO{sub 2} an attractive gate dielectric for power devices.
NASA Astrophysics Data System (ADS)
Sirois, A.
Uncertainties in the calculation of monthly, seasonal and annual precipitation-weighted-mean concentrations due to missing data are addressed. An algorithm is presented to estimate the effects of missing samples through the use of a simulation technique. Quantitative estimates of uncertainty due to missing data are given for monthly, seasonal and annual precipitation-weighted-mean sulphate and nitrate concentrations at six monitoring sites where daily precipitation samples were taken. It is found that the expected value of the precipitation-weighted-mean concentration estimator is biased if the percentage of missing samples (% MN), and the percentage (% MP) of the precipitation amount associated with the missing samples, are different. The absolute value of the bias becomes larger as the difference increases. The standard deviation of the estimator increases with increasing values of % MP. For a given value of % MP, its a minimum when % MN is equal to % MP, and increases with increasing differences between % MN and % MP. These results indicate that % MN of about 10%, which is not uncommon in precipitation networks data, gives an uncertainty of about 10, 5 and 2 % for monthly, seasonal and annual averaging periods, respectively. Procedures to estimate confidence intervals for the true values from observed precipitation-weighted-mean concentrations are presented.
USING TIME VARIANT VOLTAGE TO CALCULATE ENERGY CONSUMPTION AND POWER USE OF BUILDING SYSTEMS
Makhmalbaf, Atefe; Augenbroe , Godfried
2015-12-09
Buildings are the main consumers of electricity across the world. However, in the research and studies related to building performance assessment, the focus has been on evaluating the energy efficiency of buildings whereas the instantaneous power efficiency has been overlooked as an important aspect of total energy consumption. As a result, we never developed adequate models that capture both thermal and electrical characteristics (e.g., voltage) of building systems to assess the impact of variations in the power system and emerging technologies of the smart grid on buildings energy and power performance and vice versa. This paper argues that the power performance of buildings as a function of electrical parameters should be evaluated in addition to systems’ mechanical and thermal behavior. The main advantage of capturing electrical behavior of building load is to better understand instantaneous power consumption and more importantly to control it. Voltage is one of the electrical parameters that can be used to describe load. Hence, voltage dependent power models are constructed in this work and they are coupled with existing thermal energy models. Lack of models that describe electrical behavior of systems also adds to the uncertainty of energy consumption calculations carried out in building energy simulation tools such as EnergyPlus, a common building energy modeling and simulation tool. To integrate voltage-dependent power models with thermal models, the thermal cycle (operation mode) of each system was fed into the voltage-based electrical model. Energy consumption of systems used in this study were simulated using EnergyPlus. Simulated results were then compared with estimated and measured power data. The mean square error (MSE) between simulated, estimated, and measured values were calculated. Results indicate that estimated power has lower MSE when compared with measured data than simulated results. Results discussed in this paper will illustrate the
Bimodality emerges from transport model calculations of heavy ion collisions at intermediate energy
NASA Astrophysics Data System (ADS)
Mallik, S.; Das Gupta, S.; Chaudhuri, G.
2016-04-01
This work is a continuation of our effort [S. Mallik, S. Das Gupta, and G. Chaudhuri, Phys. Rev. C 91, 034616 (2015)], 10.1103/PhysRevC.91.034616 to examine if signatures of a phase transition can be extracted from transport model calculations of heavy ion collisions at intermediate energy. A signature of first-order phase transition is the appearance of a bimodal distribution in Pm(k ) in finite systems. Here Pm(k ) is the probability that the maximum of the multiplicity distribution occurs at mass number k . Using a well-known model for event generation [Botzmann-Uehling-Uhlenbeck (BUU) plus fluctuation], we study two cases of central collision: mass 40 on mass 40 and mass 120 on mass 120. Bimodality is seen in both the cases. The results are quite similar to those obtained in statistical model calculations. An intriguing feature is seen. We observe that at the energy where bimodality occurs, other phase-transition-like signatures appear. There are breaks in certain first-order derivatives. We then examine if such breaks appear in standard BUU calculations without fluctuations. They do. The implication is interesting. If first-order phase transition occurs, it may be possible to recognize that from ordinary BUU calculations. Probably the reason this has not been seen already is because this aspect was not investigated before.
Sharp, K A
1998-01-01
A description is given of a method to calculate the electron transfer reorganization energy (lambda) in proteins using the linear or nonlinear Poisson-Boltzmann (PB) equation. Finite difference solutions to the linear PB equation are then used to calculate lambda for intramolecular electron transfer reactions in the photosynthetic reaction center from Rhodopseudomonas viridis and the ruthenated heme proteins cytochrome c, myoglobin, and cytochrome b and for intermolecular electron transfer between two cytochrome c molecules. The overall agreement with experiment is good considering both the experimental and computational difficulties in estimating lambda. The calculations show that acceptor/donor separation and position of the cofactors with respect to the protein/solvent boundary are equally important and, along with the overall polarizability of the protein, are the major determinants of lambda. In agreement with previous studies, the calculations show that the protein provides a low reorganization environment for electron transfer. Agreement with experiment is best if the protein polarizability is modeled with a low (<8) average effective dielectric constant. The effect of buried waters on the reorganization energy of the photosynthetic reaction center was examined and found to make a contribution ranging from 0.05 eV to 0.27 eV, depending on the donor/acceptor pair. PMID:9512022
NASA Technical Reports Server (NTRS)
Popinceanu, N. G.; Kremmer, I.
1974-01-01
A mechano-acoustic model is reported for calculating acoustic energy radiated by a working gear. According to this model, a gear is an acoustic coublet formed of the two wheels. The wheel teeth generate cylindrical acoustic waves while the front surfaces of the teeth behave like vibrating pistons. Theoretical results are checked experimentally and good agreement is obtained with open gears. The experiments show that the air noise effect is negligible as compared with the structural noise transmitted to the gear box.
New algorithms for the Vavilov distribution calculation and the corresponding energy loss sampling
Chibani, O. |
1998-10-01
Two new algorithms for the fast calculation of the Vavilov distribution within the interval 0.01 {le} {kappa} {le} 10, where neither the Gaussian approximation nor the Landau distribution may be used, are presented. These algorithms are particularly convenient for the sampling of the corresponding random energy loss. A comparison with the exact Vavilov distribution for the case of protons traversing Al slabs is given.
Role of suprathermal electrons during nanosecond laser energy deposit in fused silica
Grua, P.; Hébert, D.; Lamaignère, L.; Rullier, J.-L.
2014-08-25
An accurate description of interaction between a nanosecond laser pulse and a wide band gap dielectric, such as fused silica, requires the understanding of energy deposit induced by temperature changes occurring in the material. In order to identify the fundamental processes involved in laser-matter interaction, we have used a 1D computational model that allows us to describe a wide set of physical mechanisms and intended for comparison with specially designed “1D experiments.” We have pointed out that suprathermal electrons are very likely implicated in heat conduction, and this assumption has allowed the model to reproduce the experiments.
Energy deposition in selected-mammalian cell for several-MeV single-proton beam
NASA Astrophysics Data System (ADS)
Ding, K.; Yu, Z.
2007-05-01
The phenomena resulting from interaction between ion beam and mammalian cell pose important problems for biological applications. Classic Bethe-Bloch theory utilizing attached V79 mammalian cell has been conducted in order to establish the stopping powers of the mammalian cell for several-MeV single-proton microbeam. Based on the biological structure of the mammalian cell, a physical model is proposed which presumes that the attached cell is simple MWM model. According to this model and Monte Carlo simulation, we studied the energy deposition and its ratio on the selected attached mammalian cell for MeV proton implantation.
Brambrink, E; Schlegel, T; Malka, G; Amthor, K U; Aléonard, M M; Claverie, G; Gerbaux, M; Gobet, F; Hannachi, F; Méot, V; Morel, P; Nicolai, P; Scheurer, J N; Tarisien, M; Tikhonchuk, V; Audebert, P
2007-06-01
We report on strong nonuniformities in target heating with intense, laser-produced proton beams. The observed inhomogeneity in energy deposition can strongly perturb equation of state (EOS) measurements with laser-accelerated ions which are planned in several laboratories. Interferometric measurements of the target expansion show different expansion velocities on the front and rear surfaces, indicating a strong difference in local temperature. The nonuniformity indicates at an additional heating mechanism, which seems to originate from electrons in the keV range. PMID:17677318
Energy deposition in parallel-plate plasma accelerators. Ph.D. Thesis
NASA Technical Reports Server (NTRS)
Dicapua, M. S.
1971-01-01
To appraise the ratio of energy deposition into kinetic and thermal modes in plasma accelerators, a parallel-plate plasma accelerator has been operated in the quasi-steady mode with current pulses in the range of 10 to 100 kilo-amperes (kA), durations of the order of one millisecond, and argon mass flows up to 100 grams/sec. From photographic observations, spectroscopic measurements of velocity and electron density, and pressure measurements with a fast-rise piezoelectric transducer it is found that, for currents between 50 and 90 kA, the accelerated argon plasma is supersonic with ion velocities of 5 to 6 kilometers/sec.
PIV analysis of the homogeneity of energy deposition during development of a plasma actuator channel
NASA Astrophysics Data System (ADS)
Glazyrin, F. N.; Znamenskaya, I. A.; Mursenkova, I. V.; Naumov, D. S.; Sysoev, N. N.
2016-01-01
Nonstationary velocity fields that arise during the development of flows behind shock (blast) waves initiated by pulsed surface sliding discharge in air at a pressure of (2-4) × 104 Pa have been experimentally studied by the particle image velocimetry (PIV) technique. Plasma sheets (nanosecond discharges slipping over a dielectric surface) were initiated on walls of a rectangular chamber. Spatial analysis of the shape of shock-wave fronts and the distribution of flow velocities behind these waves showed that the pulsed energy deposition is homogeneous along discharge channels of a plasma sheet, while the integral visible plasma glow intensity decreases in the direction of channel propagation.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
Dual-energy CT-based material extraction for tissue segmentation in Monte Carlo dose calculations
NASA Astrophysics Data System (ADS)
Bazalova, Magdalena; Carrier, Jean-François; Beaulieu, Luc; Verhaegen, Frank
2008-05-01
Monte Carlo (MC) dose calculations are performed on patient geometries derived from computed tomography (CT) images. For most available MC codes, the Hounsfield units (HU) in each voxel of a CT image have to be converted into mass density (ρ) and material type. This is typically done with a (HU; ρ) calibration curve which may lead to mis-assignment of media. In this work, an improved material segmentation using dual-energy CT-based material extraction is presented. For this purpose, the differences in extracted effective atomic numbers Z and the relative electron densities ρe of each voxel are used. Dual-energy CT material extraction based on parametrization of the linear attenuation coefficient for 17 tissue-equivalent inserts inside a solid water phantom was done. Scans of the phantom were acquired at 100 kVp and 140 kVp from which Z and ρe values of each insert were derived. The mean errors on Z and ρe extraction were 2.8% and 1.8%, respectively. Phantom dose calculations were performed for 250 kVp and 18 MV photon beams and an 18 MeV electron beam in the EGSnrc/DOSXYZnrc code. Two material assignments were used: the conventional (HU; ρ) and the novel (HU; ρ, Z) dual-energy CT tissue segmentation. The dose calculation errors using the conventional tissue segmentation were as high as 17% in a mis-assigned soft bone tissue-equivalent material for the 250 kVp photon beam. Similarly, the errors for the 18 MeV electron beam and the 18 MV photon beam were up to 6% and 3% in some mis-assigned media. The assignment of all tissue-equivalent inserts was accurate using the novel dual-energy CT material assignment. As a result, the dose calculation errors were below 1% in all beam arrangements. Comparable improvement in dose calculation accuracy is expected for human tissues. The dual-energy tissue segmentation offers a significantly higher accuracy compared to the conventional single-energy segmentation.
NASA Astrophysics Data System (ADS)
Nassar, Abdalla R.; Reutzel, Edward W.; Brown, Stephen W.; Morgan, John P.; Morgan, Jacob P.; Natale, Donald J.; Tutwiler, Rick L.; Feck, David P.; Banks, Jeffery C.
2016-04-01
Additive manufacturing of metal components through directed energy deposition or powder bed fusion is a complex undertaking, often involving hundreds or thousands of individual laser deposits. During processing, conditions may fluctuate, e.g. material feed rate, beam power, surrounding gas composition, local and global temperature, build geometry, etc., leading to unintended variations in final part geometry, microstructure and properties. To assess or control as-deposited quality, researchers have used a variety of methods, including those based on sensing of melt pool and plume emission characteristics, characteristics of powder application, and layer-wise imaging. Here, a summary of ongoing process monitoring activities at Penn State is provided, along with a discussion of recent advancements in the area of layer-wise image acquisition and analysis during powder bed fusion processing. Specifically, methods that enable direct comparisons of CAD model, build images, and 3D micro-tomographic scan data will be covered, along with thoughts on how such analyses can be related to overall process quality.
Ash deposit characterisation in a large-scale municipal waste-to-energy incineration plant.
Phongphiphat, Awassada; Ryu, Changkook; Finney, Karen N; Sharifi, Vida N; Swithenbank, Jim
2011-02-15
The deposition of ash - combustion residues - on superheaters and heat exchanger surfaces reduce their efficiency; this phenomenon was investigated for a large-scale waste-to-energy incineration facility. Over a period of six months, ash samples were collected from the plant, which included the bottom ash and deposits from the superheater, as well as flyash from the convective heat exchanger, the economiser and fabric filters. These were analysed for particle size, unburned carbon, elemental composition and surface morphology. Element partitioning was evident in the different combustion residues, as volatile metals, such as cadmium, antimony and arsenic, were found to be depleted in the bottom ash by the high combustion temperatures (1000+°C) and concentrated/enriched in the fabric filter ash (transferred by evaporation). Non-volatile elements by contrast were distributed equally in all locations (transported by particle entrainment). The heat exchanger deposits and fabric filter ash had elevated levels of alkali metals. 82% of flyash particles from the fabric filter were in the submicron range. PMID:21146293
Shalabi, Ahmad S; Assem, Mervat M; Soliman, Kamal A
2011-12-01
We have analyzed, by means of density functional theory calculations and the embedded cluster model, the adsorption and spin-state properties of Cr, Ni, Mo, and Pt deposited on a MgO crystal. We considered deposition at the Mg(2+) site of a defect-free surface and at Li(+) and Na(+) sites of impurity-containing surfaces. To avoid artificial polarization effects, clusters of moderate sizes with no border anions were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The interaction between a transition metal atom and a surface results from a competition between Hund's rule for the adsorbed atom and the formation of a chemical bond at the interface. We found that the adsorption energies of the metal atoms are significantly enhanced by the cation impurities, and the adsorption energies of the low-spin states of spin-quenched complexes are always more favorable than those of the high-spin states. Spin polarization effects tend to preserve the spin states of the adsorbed atoms relative to those of the isolated atoms. The metal-support interactions stabilize the low-spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. Spin quenching occurs for Cr and Mo complexes at the Mg(2+) site of the pure surface and at Li(+) and Na(+) sites of the impurity-containing surfaces. Variations of the spin-state properties of free metals and of the adsorption and spin-state properties of metal complexes are correlated with the energies of the frontier orbitals. The electrostatic potential energy curves provide further understanding of the nature of the examined properties. PMID:21369929
Weather data for simplified energy calculation methods. Volume IV. United States: WYEC data
Olsen, A.R.; Moreno, S.; Deringer, J.; Watson, C.R.
1984-08-01
The objective of this report is to provide a source of weather data for direct use with a number of simplified energy calculation methods available today. Complete weather data for a number of cities in the United States are provided for use in the following methods: degree hour, modified degree hour, bin, modified bin, and variable degree day. This report contains sets of weather data for 23 cities using Weather Year for Energy Calculations (WYEC) source weather data. Considerable overlap is present in cities (21) covered by both the TRY and WYEC data. The weather data at each city has been summarized in a number of ways to provide differing levels of detail necessary for alternative simplified energy calculation methods. Weather variables summarized include dry bulb and wet bulb temperature, percent relative humidity, humidity ratio, wind speed, percent possible sunshine, percent diffuse solar radiation, total solar radiation on horizontal and vertical surfaces, and solar heat gain through standard DSA glass. Monthly and annual summaries, in some cases by time of day, are available. These summaries are produced in a series of nine computer generated tables.
Use of SCALE Continuous-Energy Monte Carlo Tools for Eigenvalue Sensitivity Coefficient Calculations
Perfetti, Christopher M; Rearden, Bradley T
2013-01-01
The TSUNAMI code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, such as quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The CLUTCH and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE KENO framework to generate the capability for TSUNAMI-3D to perform eigenvalue sensitivity calculations in continuous-energy applications. This work explores the improvements in accuracy that can be gained in eigenvalue and eigenvalue sensitivity calculations through the use of the SCALE CE KENO and CE TSUNAMI continuous-energy Monte Carlo tools as compared to multigroup tools. The CE KENO and CE TSUNAMI tools were used to analyze two difficult models of critical benchmarks, and produced eigenvalue and eigenvalue sensitivity coefficient results that showed a marked improvement in accuracy. The CLUTCH sensitivity method in particular excelled in terms of efficiency and computational memory requirements.
NASA Astrophysics Data System (ADS)
Luna, D.; Alexander, P.; de la Torre, A.
2013-09-01
The application of the Global Positioning System (GPS) radio occultation (RO) method to the atmosphere enables the determination of height profiles of temperature, among other variables. From these measurements, gravity wave activity is usually quantified by calculating the potential energy through the integration of the ratio of perturbation and background temperatures between two given altitudes in each profile. The uncertainty in the estimation of wave activity depends on the systematic biases and random errors of the measured temperature, but also on additional factors like the selected vertical integration layer and the separation method between background and perturbation temperatures. In this study, the contributions of different parameters and variables to the uncertainty in the calculation of gravity wave potential energy in the lower stratosphere are investigated and quantified. In particular, a Monte Carlo method is used to evaluate the uncertainty that results from different GPS RO temperature error distributions. In addition, our analysis shows that RO data above 30 km height becomes dubious for gravity waves potential energy calculations.
NASA Technical Reports Server (NTRS)
Rosen, A.; Ellis, D. E.; Adachi, H.; Averill, F. W.
1976-01-01
A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.
Lundborg, Magnus; Lindahl, Erik
2015-01-22
Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized. PMID:25343332
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Thiel, Walter; Jensen, Per
2007-10-01
We present a new computational method with associated computer program TROVE (Theoretical ROVibrational Energies) to perform variational calculations of rovibrational energies for general polyatomic molecules of arbitrary structure in isolated electronic states. The (approximate) nuclear kinetic energy operator is represented as an expansion in terms of internal coordinates. The main feature of the computational scheme is a numerical construction of the kinetic energy operator, which is an integral part of the computation process. Thus the scheme is self-contained, i.e., it requires no analytical pre-derivation of the kinetic energy operator. It is also general, since it can be used in connection with any internal coordinates. The method represents an extension of our model for pyramidal XY 3 molecules reported previously [S.N. Yurchenko, M. Carvajal, P. Jensen, H. Lin, J.J. Zheng, W. Thiel, Mol. Phys. 103 (2005) 359]. Non-rigid molecules are treated in the Hougen-Bunker-Johns approach [J.T. Hougen, P.R. Bunker, J.W.C. Johns, J. Mol. Spectrosc. 34 (1970) 136]. In this case, the variational calculations employ a numerical finite basis representation for the large-amplitude motion using basis functions that are generated by Numerov-Cooley integration of the appropriate one-dimensional Schrödinger equation.
NASA Astrophysics Data System (ADS)
Sanchez-Parcerisa, D.; Cortés-Giraldo, M. A.; Dolney, D.; Kondrla, M.; Fager, M.; Carabe, A.
2016-02-01
In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm-1) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process.
Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
Kaus, Joseph W; McCammon, J Andrew
2015-05-21
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
Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
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
Star sub-pixel centroid calculation based on multi-step minimum energy difference method
NASA Astrophysics Data System (ADS)
Wang, Duo; Han, YanLi; Sun, Tengfei
2013-09-01
The star's centroid plays a vital role in celestial navigation, star images which be gotten during daytime, due to the strong sky background, have a low SNR, and the star objectives are nearly submerged in the background, takes a great trouble to the centroid localization. Traditional methods, such as a moment method, weighted centroid calculation method is simple but has a big error, especially in the condition of a low SNR. Gaussian method has a high positioning accuracy, but the computational complexity. Analysis of the energy distribution in star image, a location method for star target centroids based on multi-step minimum energy difference is proposed. This method uses the linear superposition to narrow the centroid area, in the certain narrow area uses a certain number of interpolation to pixels for the pixels' segmentation, and then using the symmetry of the stellar energy distribution, tentatively to get the centroid position: assume that the current pixel is the star centroid position, and then calculates and gets the difference of the sum of the energy which in the symmetric direction(in this paper we take the two directions of transverse and longitudinal) and the equal step length(which can be decided through different conditions, the paper takes 9 as the step length) of the current pixel, and obtain the centroid position in this direction when the minimum difference appears, and so do the other directions, then the validation comparison of simulated star images, and compare with several traditional methods, experiments shows that the positioning accuracy of the method up to 0.001 pixel, has good effect to calculate the centroid of low SNR conditions; at the same time, uses this method on a star map which got at the fixed observation site during daytime in near-infrared band, compare the results of the paper's method with the position messages which were known of the star, it shows that :the multi-step minimum energy difference method achieves a better
Baldacci, F; Mittone, A; Bravin, A; Coan, P; Delaire, F; Ferrero, C; Gasilov, S; Létang, J M; Sarrut, D; Smekens, F; Freud, N
2015-03-01
The track length estimator (TLE) method, an "on-the-fly" fluence tally in Monte Carlo (MC) simulations, recently implemented in GATE 6.2, is known as a powerful tool to accelerate dose calculations in the domain of low-energy X-ray irradiations using the kerma approximation. Overall efficiency gains of the TLE with respect to analogous MC were reported in the literature for regions of interest in various applications (photon beam radiation therapy, X-ray imaging). The behaviour of the TLE method in terms of statistical properties, dose deposition patterns, and computational efficiency compared to analogous MC simulations was investigated. The statistical properties of the dose deposition were first assessed. Derivations of the variance reduction factor of TLE versus analogous MC were carried out, starting from the expression of the dose estimate variance in the TLE and analogous MC schemes. Two test cases were chosen to benchmark the TLE performance in comparison with analogous MC: (i) a small animal irradiation under stereotactic synchrotron radiation therapy conditions and (ii) the irradiation of a human pelvis during a cone beam computed tomography acquisition. Dose distribution patterns and efficiency gain maps were analysed. The efficiency gain exhibits strong variations within a given irradiation case, depending on the geometrical (voxel size, ballistics) and physical (material and beam properties) parameters on the voxel scale. Typical values lie between 10 and 10(3), with lower levels in dense regions (bone) outside the irradiated channels (scattered dose only), and higher levels in soft tissues directly exposed to the beams. PMID:24973309
Monte Carlo dose calculation improvements for low energy electron beams using eMC.
Fix, Michael K; Frei, Daniel; Volken, Werner; Neuenschwander, Hans; Born, Ernst J; Manser, Peter
2010-08-21
The electron Monte Carlo (eMC) dose calculation algorithm in Eclipse (Varian Medical Systems) is based on the macro MC method and is able to predict dose distributions for high energy electron beams with high accuracy. However, there are limitations for low energy electron beams. This work aims to improve the accuracy of the dose calculation using eMC for 4 and 6 MeV electron beams of Varian linear accelerators. Improvements implemented into the eMC include (1) improved determination of the initial electron energy spectrum by increased resolution of mono-energetic depth dose curves used during beam configuration; (2) inclusion of all the scrapers of the applicator in the beam model; (3) reduction of the maximum size of the sphere to be selected within the macro MC transport when the energy of the incident electron is below certain thresholds. The impact of these changes in eMC is investigated by comparing calculated dose distributions for 4 and 6 MeV electron beams at source to surface distance (SSD) of 100 and 110 cm with applicators ranging from 6 x 6 to 25 x 25 cm(2) of a Varian Clinac 2300C/D with the corresponding measurements. Dose differences between calculated and measured absolute depth dose curves are reduced from 6% to less than 1.5% for both energies and all applicators considered at SSD of 100 cm. Using the original eMC implementation, absolute dose profiles at depths of 1 cm, d(max) and R50 in water lead to dose differences of up to 8% for applicators larger than 15 x 15 cm(2) at SSD 100 cm. Those differences are now reduced to less than 2% for all dose profiles investigated when the improved version of eMC is used. At SSD of 110 cm the dose difference for the original eMC version is even more pronounced and can be larger than 10%. Those differences are reduced to within 2% or 2 mm with the improved version of eMC. In this work several enhancements were made in the eMC algorithm leading to significant improvements in the accuracy of the dose
Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.
Boulougouris, Georgios C
2014-05-15
The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be
Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.
Giovan, Stefan M; Scharein, Robert G; Hanke, Andreas; Levene, Stephen D
2014-11-01
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases. PMID:25381542
Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations.
Zeller, Fabian; Zacharias, Martin
2014-06-27
Generalized Born (GB) implicit solvent models are widely used in molecular dynamics simulations to evaluate the interactions of biomolecular complexes. The continuum treatment of the solvent results in significant computational savings in comparison to an explicit solvent representation. It is, however, not clear how accurately the GB approach reproduces the absolute free energies of biomolecular binding. On the basis of induced dissociation by means of umbrella sampling simulations, the absolute binding free energies of small proline-rich peptide ligands and a protein receptor were calculated. Comparative simulations according to the same protocol were performed by employing an explicit solvent model and various GB-type implicit solvent models in combination with a nonpolar surface tension term. The peptide ligands differed in a key residue at the peptide-protein interface, including either a nonpolar, a neutral polar, a positively charged, or a negatively charged group. For the peptides with a neutral polar or nonpolar interface residue, very good agreement between the explicit solvent and GB implicit solvent results was found. Deviations in the main separation free energy contributions are smaller than 1 kcal/mol. In contrast, for peptides with a charged interface residue, significant deviations of 2-4 kcal/mol were observed. The results indicate that recent GB models can compete with explicit solvent representations in total binding free energy calculations as long as no charged residues are present at the binding interface. PMID:24941018
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
NASA Astrophysics Data System (ADS)
Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.
2014-11-01
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.
2014-11-07
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Recent advances in QM/MM free energy calculations using reference potentials☆
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
Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu
2015-01-28
We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
NASA Astrophysics Data System (ADS)
Mielke, Steven L.; Truhlar, Donald G.
2015-01-01
We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P-6) to O(P-12), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ˜1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
Douglas, Anna; Muralidharan, Nitin; Carter, Rachel; Share, Keith; Pint, Cary L
2016-04-14
Here we demonstrate the first on-chip silicon-integrated rechargeable transient power source based on atomic layer deposition (ALD) coating of vanadium oxide (VOx) into porous silicon. A stable specific capacitance above 20 F g(-1) is achieved until the device is triggered with alkaline solutions. Due to the rational design of the active VOx coating enabled by ALD, transience occurs through a rapid disabling step that occurs within seconds, followed by full dissolution of all active materials within 30 minutes of the initial trigger. This work demonstrates how engineered materials for energy storage can provide a basis for next-generation transient systems and highlights porous silicon as a versatile scaffold to integrate transient energy storage into transient electronics. PMID:26984120
Beam-induced energy deposition issues in the Very Large Hadron Collider
Nikolai V. Mokhov; Alexandr I. Drozhdin; G. William Foster
2001-06-26
Energy deposition issues are extremely important in the Very Large Hadron Collider (VLHC) with huge energy stored in its 20 TeV (Stage-1) and 87.5 TeV (Stage-2) beams. The status of the VLHC design on these topics, and possible solutions of the problems are discussed. Protective measures are determined based on the operational and accidental beam loss limits for the prompt radiation dose at the surface, residual radiation dose, ground water activation, accelerator components radiation damage and quench stability. The beam abort and beam collimation systems are designed to protect accelerator from accidental and operational beam losses, IP region quadrupoles from irradiation by the products of beam-beam collisions, and to reduce the accelerator-induced backgrounds in the detectors.
A program to calculate non-bonded interaction energy in biomolecular aggregates.
Sundaram, K; Prasad, C V
1982-02-01
This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416
S-model calculations for high-energy-electron-impact double ionization of helium
NASA Astrophysics Data System (ADS)
Gasaneo, G.; Mitnik, D. M.; Randazzo, J. M.; Ancarani, L. U.; Colavecchia, F. D.
2013-04-01
In this paper the double ionization of helium by high-energy electron impact is studied. The corresponding four-body Schrödinger equation is transformed into a set of driven equations containing successive orders in the projectile-target interaction. The transition amplitude obtained from the asymptotic limit of the first-order solution is shown to be equivalent to the familiar first Born approximation. The first-order driven equation is solved within a generalized Sturmian approach for an S-wave (e,3e) model process with high incident energy and small momentum transfer corresponding to published measurements. Two independent numerical implementations, one using spherical and the other hyperspherical coordinates, yield mutual agreement. From our ab initio solution, the transition amplitude is extracted, and single differential cross sections are calculated and could be taken as benchmark values to test other numerical methods in a previously unexplored energy domain.
Hansen, L.F.
1985-05-01
Neutron elastic and inelastic differential cross sections for targets between /sup 9/Be and /sup 239/Pu at energies, E > 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed. 17 refs.
Chen, Xiao-bo; Wang, Ce; Kang, Dong-guo; Sawanobori, Naruhito; Wang, Shui-feng; Li, Yong-liang; Wang, Ping
2010-08-01
The dynamics of all levels were calculated numerically in the present article for Er(0.5)Yb(3):FOV oxyfluoride nanophase vitroceramics. The population dynamical processes were analyzed carefully. It was found for the first time that traditional phonon-assisted energy transfer theory of rare earth ion energy transfer can not well explain the observed experimental calibrated results, as it does not take into account the difference between Stokes and anti-Stokes process. A coefficient, the improved factor of the intensity ratio of Stokes to anti-Stokes process in quantum Raman theory compared to classical Raman theory, was introduced for the first time to successfully describe the anti-Stokes energy transfer. The theoretical improvement results are coincident with experiments very well. This improvement is very significant and indispensable when the photonics of nanomaterials is probed. PMID:20939297
Variational calculations with explicit energy functionals for fermion systems at zero temperature
NASA Astrophysics Data System (ADS)
Takano, M.; Suzuki, T.; Sakumichi, N.
2016-03-01
The variational method with explicit energy functionals (EEFs) is applied to infinite neutron matter. Starting from the Argonne v8’ two-body potential and the repulsive part of the Urbana IX three-body potential, the energy per neutron is expressed explicitly with the spin-dependent central, tensor, and spin-orbit distribution functions. This EEF is constructed as an extension of the previously proposed one for the Argonne v6’ potential, including central and tensor forces. The Euler-Lagrange equations derived from this EEF are solved numerically. The obtained fully minimized energy with this EEF is in good agreement with that obtained from the auxiliary field diffusion Monte Carlo calculation.
NASA Astrophysics Data System (ADS)
Hansen, L. F.
Neutron elastic and inelastic differential cross sections for targets between (9)Be and (239)Pu at energies, E 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed.
First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces
Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.
2014-10-21
A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and themore » dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less
First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces
Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.
2014-10-21
A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.
Free energy calculations using dual-level Born-Oppenheimer molecular dynamics
NASA Astrophysics Data System (ADS)
Retegan, Marius; Martins-Costa, Marilia; Ruiz-López, Manuel F.
2010-08-01
We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.
Free Energies of Redox Half-Reactions from First-Principles Calculations.
Tazhigulov, Ruslan N; Bravaya, Ksenia B
2016-07-01
Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values. PMID:27295124
Monte Carlo charged-particle tracking and energy deposition on a Lagrangian mesh.
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. PMID:16383566
Buoyancy driven mixing of miscible fluids by volumetric energy deposition of microwaves.
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. PMID:24779141
Cremer, T.; Tatchyn, R.
1995-12-31
One of the more promising technologies for developing minimal-length insertion devices for linac-driven, single-pass Free Electron Lasers (FELs) operating in the x-ray range is based on the use of superconducting (SC) materials. In recent FEL simulations, for example, a bifilar helical SC device with a 2 cm period and 1.8 T field was found to require a 30 m saturation length for operation at 1.5{Angstrom} on a 15 GeV linac, more than 40% shorter than an alternative hybrid/permanent magnet (hybrid/PM) undulator. AT the same time, however, SC technology is known to present characteristic difficulties for insertion device design, both in engineering detail and in operation. Perhaps the most critical problem, as observed, e.g., by Madey and co-workers in their initial FEL experiments, was the frequent quenching induced by scattered electrons upstream of their (bifilar) device. Postulating that this quenching was precipitated by directly-scattered or bremsstrahlung-induced particle energy deposited into the SC material or into material contiguous with it, the importance of numerical and experimental characterizations of this phenomenon for linac-based, user-facility SC undulator design becomes evident. In this paper we discuss selected prior experimental results and report on initial EGS4 code studies of scattered and bremsstrahlung induced particle energy deposition into SC structures with geometries comparable to a small-bore bifilar helical undulator.
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.
Development and deposition of resilin in energy stores for locust jumping.
Burrows, Malcolm
2016-08-15
Locusts jump by using a catapult mechanism in which energy produced by slow contractions of the extensor tibiae muscles of the hind legs is stored in distortions of the exoskeleton, most notably (1) the two semi-lunar processes at each knee joint and (2) the tendons of the extensor muscles themselves. The energy is then suddenly released from these stores to power the rapid, propulsive movements of the hind legs. The reliance on the mechanical storage of energy is likely to impact on jumping because growth occurs by a series of five moults, at each of which the exoskeleton is replaced by a new one. All developmental stages (instars) nevertheless jump as a means of forward locomotion, or as an escape movement. Here, I show that in each instar, resilin is added to the semi-lunar processes and to the core of the extensor tendons so that their thickness increases. As the next moult approaches, a new exoskeleton forms within the old one, with resilin already present in the new semi-lunar processes. The old exoskeleton, the tendons and their resilin are discarded at moulting. The resilin of the semi-lunar processes and tendons of the new instar is initially thin, but a similar pattern of deposition results in an increase of their thickness. In adults, resilin continues to be deposited so that at 4 weeks old the thickness in the semi-lunar processes has increased fourfold. These changes in the energy stores accompany changes in jumping ability and performance during each moulting cycle. PMID:27259374
Model of enhanced energy deposition in a Z-pinch plasma
Velikovich, A. L.; Davis, J.; Thornhill, J. W.; Giuliani, J. L. Jr.; Rudakov, L. I.; Deeney, C.
2000-08-01
In numerous experiments, magnetic energy coupled to strongly radiating Z-pinch plasmas exceeds the thermalized kinetic energy, sometimes by a factor of 2-3. An analytical model describing this additional energy deposition based on the concept of macroscopic magnetohydrodynamic (MHD) turbulent pinch heating proposed by Rudakov and Sudan [Phys. Reports 283, 253 (1997)] is presented. The pinch plasma is modeled as a foam-like medium saturated with toroidal ''magnetic bubbles'' produced by the development of surface m=0 Rayleigh-Taylor and MHD instabilities. As the bubbles converge to the pinch axis, their magnetic energy is converted to thermal energy of the plasma through pdV work. Explicit formulas for the average dissipation rate of this process and the corresponding contribution to the resistance of the load, which compare favorably to the experimental data and simulation results, are presented. The possibility of using this enhanced (relative to Ohmic heating) dissipation mechanism to power novel plasma radiation sources and produce high K-shell yields using long current rise time machines is discussed. (c) 2000 American Institute of Physics.
Vanden-Eijnden, Eric; Venturoli, Maddalena
2009-05-21
An improved and simplified version of the finite temperature string (FTS) method [W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005)] is proposed. Like the original approach, the new method is a scheme to calculate the principal curves associated with the Boltzmann-Gibbs probability distribution of the system, i.e., the curves which are such that their intersection with the hyperplanes perpendicular to themselves coincides with the expected position of the system in these planes (where perpendicular is understood with respect to the appropriate metric). Unlike more standard paths such as the minimum energy path or the minimum free energy path, the location of the principal curve depends on global features of the energy or the free energy landscapes and thereby may remain appropriate in situations where the landscape is rough on the thermal energy scale and/or entropic effects related to the width of the reaction channels matter. Instead of using constrained sampling in hyperplanes as in the original FTS, the new method calculates the principal curve via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve. As shown here, this modification results in greater algorithmic simplicity. As a by-product, it also gives the free energy associated with the Voronoi tessellation. The new method can be applied both in the original Cartesian space of the system or in a set of collective variables. We illustrate FTS on test-case examples and apply it to the study of conformational transitions of the nitrogen regulatory protein C receiver domain using an elastic network model and to the isomerization of solvated alanine dipeptide. PMID:19466817
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. PMID:21693886
NASA Astrophysics Data System (ADS)
Domain, C.; Olsson, P.; Becquart, C. S.; Legris, A.; Guillemoles, J. F.
2008-02-01
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.
NASA Astrophysics Data System (ADS)
Mallick, Ritam; Bhattacharyya, Abhijit; Ghosh, Sanjay K.; Raha, Sibaji
2013-02-01
The estimate of the energy deposition rate (EDR) for neutrino pair annihilation has been carried out. The EDR for the neutrinos coming from the equatorial plane of a rotating neutron star is calculated along the rotation axis using the Cook-Shapiro-Teukolsky metric. The neutrino trajectories and hence the neutrinos emitted from the disk are affected by the redshift due to disk rotation and gravitation. The EDR is very sensitive to the value of the temperature and its variation along the disk. The rotation of the star has a negative effect on the EDR; it decreases with increase in rotational velocity.
Calculation of energy levels, {ital E}1 transition amplitudes, and parity violation in francium
Dzuba, V.A.; Flambaum, V.V.; Sushkov, O.P.
1995-05-01
Many-body perturbation theory in the screened Coulomb interaction was used to calculate energy levels, {ital E}1 trransition amplitudes, and the parity-nonconserving (PNC) {ital E}1 amplitude of the 7{ital s}-8{ital s} transition in francium. The method takes into account the core-polarization effect, the second-order correlations, and the three dominating sequences of higher-order correlation diagrams: screening of the electron-electron interaction, particle-hole interaction, and the iterations of the self-energy operator. The result for the PNC amplitude for {sup 223}Fr is {ital E}1(7{ital s}-8{ital s})=(1.59{plus_minus}{similar_to}1%){times}10{sup {minus}10}{ital iea}{sub {ital B}}({minus}{ital Q}{sub {ital W}}/{ital N}), where {ital Q}{sub {ital W}} is the weak charge of the nucleus, {ital N}=136 is the number of neutrons, {ital e}={vert_bar}{ital e}{vert_bar} is the elementary charge, and {ital a}{sub {ital B}} is the Bohr radius. Our prediction for the position of the 8{ital s} energy level of Fr, which has not been measured yet, is 13 110 cm{sup {minus}1} below the limit of the continuous spectrum. The accuracy of the calculations was controlled by comparison with available experimental data and analogous calculations for cesium. It is estimated to be {similar_to}0.1% for the energy levels and {similar_to}1% for the transition amplitudes.
NASA Astrophysics Data System (ADS)
Sharaf, J. M.; Saleh, H.
2015-05-01
The shielding properties of three different construction styles, and building materials, commonly used in Jordan, were evaluated using parameters such as attenuation coefficients, equivalent atomic number, penetration depth and energy buildup factor. Geometric progression (GP) method was used to calculate gamma-ray energy buildup factors of limestone, concrete, bricks, cement plaster and air for the energy range 0.05-3 MeV, and penetration depths up to 40 mfp. It has been observed that among the examined building materials, limestone offers highest value for equivalent atomic number and linear attenuation coefficient and the lowest values for penetration depth and energy buildup factor. The obtained buildup factors were used as basic data to establish the total equivalent energy buildup factors for three different multilayer construction styles using an iterative method. The three styles were then compared in terms of fractional transmission of photons at different incident photon energies. It is concluded that, in case of any nuclear accident, large multistory buildings with five layers exterior walls, style A, could effectively attenuate radiation more than small dwellings of any construction style.
Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes.
Miranda, Williams E; Noskov, Sergei Yu; Valiente, Pedro A
2015-09-28
In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The protocol, coined LIE-D, builds on the linear relationship between the empirical coefficient γ in the standard LIE scheme and the D parameter, introduced in our work. The D-parameter encompasses the balance (difference) between electrostatic (polar) and van der Waals (nonpolar) energies in protein–ligand complexes. Leave-one-out cross-validation showed that LIE-D reproduced accurately the absolute binding free energies for our training set of protein–ligand complexes (<|error|> = 0.92 kcal/mol, SDerror = 0.66 kcal/mol, R(2) = 0.90, QLOO(2) = 0.89, and sPRESS(LOO) = 1.28 kcal/mol). We also demonstrated LIE-D robustness by predicting accurately the binding free energies for three different protein–ligand systems outside the training data set, where the electrostatic and van der Waals interaction energies were calculated with different force fields. PMID:26180998
NASA Technical Reports Server (NTRS)
Spann, J. F., Jr.; Germany, G. A.; Parks, G. K.; Brittnacher, M. J.
1998-01-01
For several cases where the full auroral zone is imaged and transpolar structures exist, we compare the total energy input to the auroral oval with the total energy input in the polar cap. This comparison is made for cases where auroral intensification near local midnight is and is not observed. Temporal evolution of the energy balance between the energy deposited in the oval and polar cap can be used to understand the mechanism that triggers substorms.
Importance of light scattering properties of cloud particles on calculating the earth energy cycle
NASA Astrophysics Data System (ADS)
Letu, H.; Nakajima, T. Y.; Nagao, T. M.; Ishimoto, H.
2013-12-01
The Earth is an open system, and the energy cycle of the Earth is not always a certain amount. In other words, the energy cycle in the nature is imbalance. A better understanding of the earth energy cycle is very important to study global climate change. the IPCC-AR4 reported that the cloud in the atmosphere are still characterized by large uncertainties in the estimation of their effects on energy sysle of the Earth's atmosphere. There are two types of cloud in the atmosphere, which are Cirrus and warm water cloud. In order to strongly reflect visible wavelength from sun light, thick water cloud has the effect of cooling the earth surface. When Cirrus is compared to water cloud, temperature is almost lower. Thus, there is a feature that Cirrus is easy to absorb long-wave radiation than warm water cloud. However, in order to quantitatively evaluate the reflection and absorption characteristics of cloud on remote senssing application and energy cycle of the imbalance of nature, it is necessary to obtain the scattering properties of cloud particles. Since the shapes of the water cloud particle are close to spherical, scattering properties of the particles can be calculated accurately by the Mie theory. However, Cirrus particles have a complex shape, including hexagonal, plate, and other non- spherical shapes. Different from warm water cloud partical, it is required to use several different light scattering methods when calculating the light scattering properties of the non-spherical Cirrus cloud particals. Ishimoto et al. [2010, 2012] and Masuda et al. [2012] developed the Finite-Difference Time Domain method (FDTD) and Improved Geometrical-Optics Method (IGOM) for the solution of light scattering by non-spherical particles. Nakajima et al [1997,2009] developed the LIght Scattering solver for Arbitral Shape particle (Lisas)-Geometrical-Optics Method (GOM) and Surface Integral Equations Method of Müller-type (SIEMM) to calculate the light scattering properties for