Energy deposition calculated by PHITS code in Pb spallation target
NASA Astrophysics Data System (ADS)
Yu, Quanzhi
2016-01-01
Energy deposition in a Pb spallation target irradiated by high energetic protons was calculated by PHITS2.52 code. The validation of the energy deposition and neutron production calculated by PHITS code was performed. Results show good agreements between the simulation results and the experimental data. Detailed comparison shows that for the total energy deposition, PHITS simulation result was about 15% overestimation than that of the experimental data. For the energy deposition along the length of the Pb target, the discrepancy mainly presented at the front part of the Pb target. Calculation indicates that most of the energy deposition comes from the ionizations of the primary protons and the produced secondary particles. With the event generator mode of PHITS, the deposit energy distribution for the particles and the light nulclei is presented for the first time. It indicates that the primary protons with energy more than 100 MeV are the most contributors to the total energy deposition. The energy depositions peaking at 10 MeV and 0.1 MeV, are mainly caused by the electrons, pions, d, t, 3He and also α particles during the cascade process and the evaporation process, respectively. The energy deposition density caused by different proton beam profiles are also calculated and compared. Such calculation and analyses are much helpful for better understanding the physical mechanism of energy deposition in the spallation target, and greatly useful for the thermal hydraulic design of the spallation target.
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)
NASA Astrophysics Data System (ADS)
Li, Sui-xian; Chen, Haiyang; Sun, Min; Cheng, Zaijun
2009-11-01
Aimed at improving the calculation accuracy when calculating the energy deposition of electrons traveling in solids, a method we call optimal subdivision number searching algorithm is proposed. When treating the energy deposition of electrons traveling in solids, large calculation errors are found, we are conscious of that it is the result of dividing and summing when calculating the integral. Based on the results of former research, we propose a further subdividing and summing method. For β particles with the energy in the entire spectrum span, the energy data is set only to be the integral multiple of keV, and the subdivision number is set to be from 1 to 30, then the energy deposition calculation error collections are obtained. Searching for the minimum error in the collections, we can obtain the corresponding energy and subdivision number pairs, as well as the optimal subdivision number. The method is carried out in four kinds of solid materials, Al, Si, Ni and Au to calculate energy deposition. The result shows that the calculation error is reduced by one order with the improved algorithm.
Mowlavi, Ali Asghar; Fornasie, Maria Rosa; de Denaro, Mario
2011-01-01
In this study, the MCNPX code has been used to simulate a proton therapy in thyroid gland, in order to calculate the proton energy deposition in the target region. As well as, we have calculated the photon and neutron production spectra due to proton interactions with the tissue. We have considered all the layers of tissue, from the skin to the thyroid gland, and an incident high energy pencil proton beam. The results of the simulation show that the best proton energy interval, to cover completely the thyroid tissue, is from 42 to 54 MeV, assuming that the thyroid gland has a 14 mm thickness and is located 11.2mm under the skin surface. The most percentage of deposited energy (78%) is related to the 54 MeV proton energy beam. Total photon and neutron production are linear and polynomial second order functions of the proton energy, respectively.
Strain and Cohesive Energy of TiN Deposit on Al(001) Surface: Density Functional Calculation
NASA Astrophysics Data System (ADS)
Ren, Yuan; Liu, Xuejie
2016-07-01
To apply the high hardness of TiN film to soft and hard multilayer composite sheets, we constructed a new type of composite structural material with ultra-high strength. The strain of crystal and cohesive energy between the atoms in the eight structures of N atom, Ti atom, 2N2Ti island and TiN rock salt deposited on the Al(001) surface were calculated with the first-principle ultra-soft pseudopotential approach of the plane wave based on the density functional theory. The calculations of the cohesive energy showed that N atoms could be deposited in the face-centered-cubic vacancy position of the Al(001) surface and results in a cubic structure AlN surface. The TiN film could be deposited on the interface of β-AlN. The calculations of the strains showed that the strain in the TiN film deposited on the Al(001) surface was less than that in the 2N2Ti island deposited on the Al(001) surface. The diffusion behavior of interface atom N was investigated by a nudged elastic band method. Diffusion energy calculation showed that the N atom hardly diffused to the substrate Al layer.
Modeling reaction pathways of low energy particle deposition on thiophene via ab initio calculations
NASA Astrophysics Data System (ADS)
Crenshaw, Jasmine D.; Phillpot, Simon R.; Iordanova, Nedialka; Sinnott, Susan B.
2011-07-01
Chemical reactions of thiophene with organic molecules are of interest to modify thermally deposited coatings of conductive polymers. Here, energy barriers for reactions involving thiophene and small hydrocarbon radicals are identified. Enthalpies of formation involving reactants are also calculated using the B3LYP, BMK, and B98 hybrid functionals within the G AUSSIAN03 program. Experimental values, G3, and CBS-QB3 calculations are used as standards, due to their accurate thermochemistry parameters. The BMK functional is found to perform best for the selected organic molecules. These results provide insights into the reactivity of several polymerization and deposition processes.
Monte Carlo calculations of energy deposition distributions of electrons below 20 keV in protein.
Tan, Zhenyu; Liu, Wei
2014-05-01
The distributions of energy depositions of electrons in semi-infinite bulk protein and the radial dose distributions of point-isotropic mono-energetic electron sources [i.e., the so-called dose point kernel (DPK)] in protein have been systematically calculated in the energy range below 20 keV, based on Monte Carlo methods. The ranges of electrons have been evaluated by extrapolating two calculated distributions, respectively, and the evaluated ranges of electrons are compared with the electron mean path length in protein which has been calculated by using electron inelastic cross sections described in this work in the continuous-slowing-down approximation. It has been found that for a given energy, the electron mean path length is smaller than the electron range evaluated from DPK, but it is large compared to the electron range obtained from the energy deposition distributions of electrons in semi-infinite bulk protein. The energy dependences of the extrapolated electron ranges based on the two investigated distributions are given, respectively, in a power-law form. In addition, the DPK in protein has also been compared with that in liquid water. An evident difference between the two DPKs is observed. The calculations presented in this work may be useful in studies of radiation effects on proteins.
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.
The calculation of proportional counter energy-deposition spectra from experimental data.
NASA Technical Reports Server (NTRS)
Steigerwalt, J. E.; Baily, N. A.
1973-01-01
The experimental approach considered requires the measurement of energy-absorption distributions for a set of pathlengths which define a biological volume. A suitable folding procedure is necessary to produce composite energy-absorption distributions. The investigation is concerned with the quality of the prediction of energy-deposition distributions, taking into account distributions measured with a proportional counter.
Monte Carlo calculations of the energy deposited in biological samples and shielding materials
NASA Astrophysics Data System (ADS)
Akar Tarim, U.; Gurler, O.; Ozmutlu, E. N.; Yalcin, S.
2014-03-01
The energy deposited by gamma radiation from the Cs-137 isotope into body tissues (bone and muscle), tissue-like medium (water), and radiation shielding materials (concrete, lead, and water), which is of interest for radiation dosimetry, was obtained using a simple Monte Carlo algorithm. The algorithm also provides a realistic picture of the distribution of backscattered photons from the target and the distribution of photons scattered forward after several scatterings in the scatterer, which is useful in studying radiation shielding. The presented method in this work constitutes an attempt to evaluate the amount of energy absorbed by body tissues and shielding materials.
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)
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
NASA Astrophysics Data System (ADS)
Péron, A.; Malouch, F.; Zoia, A.; Diop, C. M.
2014-06-01
Nuclear heating evaluation by Monte-Carlo simulation requires coupled neutron-photon calculation so as to take into account the contribution of secondary photons. Nuclear data are essential for a good calculation of neutron and photon energy deposition and for secondary photon generation. However, a number of isotopes of the most common nuclear data libraries happen to be affected by energy and/or momentum conservation errors concerning the photon production or inaccurate thresholds for photon emission sections. In this paper, we perform a comprehensive survey of the three evaluations JEFF3.1.1, JEFF3.2T2 (beta version) and ENDF/B-VII.1, over 142 isotopes. The aim of this survey is, on the one hand, to check the existence of photon production data by neutron reaction and, on the other hand, to verify the consistency of these data using the kinematic limits method recently implemented in the TRIPOLI-4 Monte-Carlo code, developed by CEA (Saclay center). Then, the impact of these inconsistencies affecting energy deposition scores has been estimated for two materials using a specific nuclear heating calculation scheme in the context of the OSIRIS Material Testing Reactor (CEA/Saclay).
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.
Huang, J; Followill, D; Howell, R; Liu, X; Mirkovic, D; Stingo, F; Kry, S
2015-06-15
Purpose: To investigate two strategies for reducing dose calculation errors near metal implants: use of CT metal artifact reduction methods and implementation of metal-based energy deposition kernels in the convolution/superposition (C/S) method. Methods: Radiochromic film was used to measure the dose upstream and downstream of titanium and Cerrobend implants. To assess the dosimetric impact of metal artifact reduction methods, dose calculations were performed using baseline, uncorrected images and metal artifact reduction Methods: Philips O-MAR, GE’s monochromatic gemstone spectral imaging (GSI) using dual-energy CT, and GSI imaging with metal artifact reduction software applied (MARs).To assess the impact of metal kernels, titanium and silver kernels were implemented into a commercial collapsed cone C/S algorithm. Results: The CT artifact reduction methods were more successful for titanium than Cerrobend. Interestingly, for beams traversing the metal implant, we found that errors in the dimensions of the metal in the CT images were more important for dose calculation accuracy than reduction of imaging artifacts. The MARs algorithm caused a distortion in the shape of the titanium implant that substantially worsened the calculation accuracy. In comparison to water kernel dose calculations, metal kernels resulted in better modeling of the increased backscatter dose at the upstream interface but decreased accuracy directly downstream of the metal. We also found that the success of metal kernels was dependent on dose grid size, with smaller calculation voxels giving better accuracy. Conclusion: Our study yielded mixed results, with neither the metal artifact reduction methods nor the metal kernels being globally effective at improving dose calculation accuracy. However, some successes were observed. The MARs algorithm decreased errors downstream of Cerrobend by a factor of two, and metal kernels resulted in more accurate backscatter dose upstream of metals. Thus
Landfill Gas Energy Benefits Calculator
This page contains the LFG Energy Benefits Calculator to estimate direct, avoided, and total greenhouse gas reductions, as well as environmental and energy benefits, for a landfill gas energy project.
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
Calculating The Resistivity Of A Deposited Film
NASA Technical Reports Server (NTRS)
Oberle, Lawrence G.; Fralick, Gustave C.
1990-01-01
Iterative procedure computes resistivity from measurements by four-probe method. Computer program and technique developed to aid in solution of class of problems in which measurements of electrical resistivity needed for substance deposited on substrate of higher resistivity than deposited layer.
Calorimetric sensors for energy deposition measurements
Langenbrunner, J.; Cooper, R.; Morgan, G.
1998-12-31
A calorimetric sensor with several novel design features has been developed. These sensors will provide an accurate sampling of thermal power density and energy deposition from proton beams incident on target components of accelerator-based systems, such as the Accelerator Production of Tritium Project (APT) and the Spallation Neutron Source (SNS). A small, solid slug (volume = 0.347 cc) of target material is suspended by kevlar fibers and surrounded by an adiabatic enclosure in an insulating vacuum canister of stainless steel construction. The slug is in thermal contact with a low-mass, calibrated, 100-k{Omega} thermistor. Power deposition caused by the passage of radiation through the slug is calculated from the rate of temperature rise of the slug. The authors have chosen slugs composed of Pb, Al, and LiAl.
Wang, L; Jette, D
1999-08-01
The transport of the secondary electrons resulting from high-energy photon interactions is essential to energy redistribution and deposition. In order to develop an accurate dose-calculation algorithm for high-energy photons, which can predict the dose distribution in inhomogeneous media and at the beam edges, we have investigated the feasibility of applying electron transport theory [Jette, Med. Phys. 15, 123 (1988)] to photon dose calculation. In particular, the transport of and energy deposition by Compton electron and electrons and positrons resulting from pair production were studied. The primary photons are treated as the source of the secondary electrons and positrons, which are transported through the irradiated medium using Gaussian multiple-scattering theory [Jette, Med. Phys. 15, 123 (1988)]. The initial angular and kinetic energy distribution(s) of the secondary electrons (and positrons) emanating from the photon interactions are incorporated into the transport. Due to different mechanisms of creation and cross-section functions, the transport of and the energy deposition by the electrons released in these two processes are studied and modeled separately based on first principles. In this article, we focus on determining the dose distribution for an individual interaction site. We define the Compton dose deposition kernel (CDK) or the pair-production dose deposition kernel (PDK) as the dose distribution relative to the point of interaction, per unit interaction density, for a monoenergetic photon beam in an infinite homogeneous medium of unit density. The validity of this analytic modeling of dose deposition was evaluated through EGS4 Monte Carlo simulation. Quantitative agreement between these two calculations of the dose distribution and the average energy deposited per interaction was achieved. Our results demonstrate the applicability of the electron dose-calculation method to photon dose calculation.
Note: the influence of exploding foil shape on energy deposition.
Zeng, Qingxuan; Lv, Junjun; Li, Mingyu
2013-06-01
The main influence factors of exploding bridge foil were studied in order to improve energy utilization of the explosion foil initiator. "Square" and "curving" shaped bridge foils were fabricated using magnetron sputtering and chemical etching techniques, and the key dimension of the bridge foil was measured using surface profiler. Commercial software MATLAB was employed to calculate the burst current, burst voltage, and energy deposition. Simulation results were in good agreement with experiment data. In this study, the energy deposition ratio of "square" shaped bridge is between 45%-50%, while the value of "curving" shaped bridge is between 55%-75%.
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.
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.
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.
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.
The calculation of band gap energy in zinc oxide films
NASA Astrophysics Data System (ADS)
Arif, Ali; Belahssen, Okba; Gareh, Salim; Benramache, Said
2015-01-01
We investigated the optical properties of undoped zinc oxide thin films as the n-type semiconductor; the thin films were deposited at different precursor molarities by ultrasonic spray and spray pyrolysis techniques. The thin films were deposited at different substrate temperatures ranging between 200 and 500 °C. In this paper, we present a new approach to control the optical gap energy of ZnO thin films by concentration of the ZnO solution and substrate temperatures from experimental data, which were published in international journals. The model proposed to calculate the band gap energy with the Urbach energy was investigated. The relation between the experimental data and theoretical calculation suggests that the band gap energies are predominantly estimated by the Urbach energies, film transparency, and concentration of the ZnO solution and substrate temperatures. The measurements by these proposal models are in qualitative agreements with the experimental data; the correlation coefficient values were varied in the range 0.96-0.99999, indicating high quality representation of data based on Equation (2), so that the relative errors of all calculation are smaller than 4%. Thus, one can suppose that the undoped ZnO thin films are chemically purer and have many fewer defects and less disorder owing to an almost complete chemical decomposition and contained higher optical band gap energy.
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.
Energy and mass balance calculations for incinerators
Lee, C.C.; Huffman, G.L.
1998-01-01
Calculation of energy and mass balance within an incinerator is a very important part of designing and/or evaluating the incineration process. This article describes a simple computer model used to calculate an energy and mass balance for a rotary kiln incinerator. The main purpose of the model is to assist US Environmental Protection Agency (EPA) permit writers in evaluating the adequacy of the data submitted by applicants seeking incinerator permits. The calculation is based on the assumption that a thermodynamic equilibrium condition exits within the combustion chamber. Key parameters that the model can calculate include theoretical combustion air, excess air needed for actual combustion cases, flue gas flow rate, and exit temperature.
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.
Monte Carlo algorithm for free energy calculation.
Bi, Sheng; Tong, Ning-Hua
2015-07-01
We propose a Monte Carlo algorithm for the free energy calculation based on configuration space sampling. An upward or downward temperature scan can be used to produce F(T). We implement this algorithm for the Ising model on a square lattice and triangular lattice. Comparison with the exact free energy shows an excellent agreement. We analyze the properties of this algorithm and compare it with the Wang-Landau algorithm, which samples in energy space. This method is applicable to general classical statistical models. The possibility of extending it to quantum systems is discussed.
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).
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…
Kusuda, T
1980-10-31
The TC 4.7 simplified energy calculation method is a bin method used by the REAP procedure of the Carrier Corporation, except for the load estimating calculations. The simplified procedure was compared with hourly simulation procedures for an office building in Washington, DC. The comparison studied the extent as well as the reasons for agreement and discrepancies due to these two different types of annual energy analysis (bin method and hourly simulation methods). Results of the parallel calculations are discussed and the major reasons of discrepancies between the hourly simulation technique and the simplified TC 4.7 method are identified. Data resulting from the calculation methods are tabulated. (MCW)
Energy deposition rates by charged particles. [in upper atmosphere
NASA Technical Reports Server (NTRS)
Torkar, K. M.; Urban, A.; Bjordal, J.; Lundblad, J. A.; Soraas, F.; Smith, L. G.; Dumbs, A.; Grandal, B.; Ulwick, J. C.; Vancour, R. P.
1985-01-01
A summary of measurements of the precipitation of electrons and positive ions (in the keV-MeV range) detected aboard eight rockets launched within the Energy Budget Campaign from Northern Scandinavia is given, together with corresponding satellite data. In some cases strong temporal variations of the downgoing integral fluxes were observed. The fluxes provide the background for the calculated ion production rates and altitude profiles of the energy deposition into the atmosphere at different levels of geomagnetic disturbance and cosmic noise absorption. The derived ion production rates by eneretic particles are compared to other night-time ionisation sources.
Perturbation energy as an alternative to the total energy calculations
NASA Astrophysics Data System (ADS)
Kutepov, Andrey; Antropov, Vladimir; van Schilfgaarde, Mark; Antonov, Victor
2014-03-01
We analyze different approaches to determine the energy from a perturbation using modern electronic structure methods. We compare the energy of perturbation from standard perturbation theory with what is obtained directly in self consistent band structure methods. The method is applied for studies such perturbations as internal magnetic field and spin orbital coupling in solids. This method is further compared with integration over the coupling constant. Numerical tests have been performed for magnetic Fe and Gd systems using the local density approximation. The main advantage of present scheme is its usefulness in methods for strongly correlated electronic systems studies where total energy calculations are not always possible. Specific calculations are performed using self consistent quasiparticle GW and LDA+U calculations for MnBi where the right value of magnetic moment and sign/value of magnetic anisotropy as a function of temperature have been obtained. This research is supported in part by the Critical Materials Institute, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy through the Ames Laboraory.
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.
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
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.
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.
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.
Laser energy deposition in crossing shock interaction
NASA Astrophysics Data System (ADS)
Yan, H.; Knight, D.; Elliott, G.
A combined computational and experimental study was performed to investigate the effect of a single laser energy pulse on the transition from a Mach Reflection (MR) to a Regular Reflection (RR) in the Dual Solution Domain (DSD). The freestream Mach number is 3.45 and two oblique shock waves are formed by two symmetric 22° wedges. These conditions correspond to a point midway within the DSD wherein either an MR or an RR is possible. A steady MR was first obtained experimentally and numerically, then a single laser pulse was deposited above the horizontal center plane. The experiment showed that the Mach stem height decreased to 30% of its original height due to the interaction with the thermal spot generated by the laser pulse and then returned to its original height by 300μs. That the Mach stem returned to its original height was most likely due to freestream turbulence in the wind tunnel. The numerical simulation successfully predicted the reverse transition from a stable MR to a stable RR and the stable RR persisted across the span. This study showed the capability of a laser energy pulse to control the reverse transition of MR → RR within the Dual Solution Domain.
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
Influence of deposited energy on shock wave induced by underwater pulsed current discharge
NASA Astrophysics Data System (ADS)
Li, Xian-Dong; Liu, Yi; Liu, Si-Wei; Li, Zhi-Yuan; Zhou, Gu-Yue; Li, Hua; Lin, Fu-Chang; Pan, Yuan
2016-10-01
In this paper, an integrated experimental system is established to study the influence of deposited energy on the intensity of the shock wave induced by underwater pulse discharge. Considering the time varying behavior of the arc, the calculation methods of the deposited energy into the plasma channel and the average arc resistance are proposed and presented. The effect of the breakdown process on the deposited energy and the shock wave is analyzed. It can be concluded that the shock wave intensity can be improved by depositing more energy in the first half oscillation period and increasing the arc resistance. It is also found that the energy deposition and the shock wave intensity are significantly influenced by the breakdown time delay and the shape of the initial plasma channel.
CHP Energy and Emissions Savings Calculator
Download the CHP Emissions Calculator, a tool that calculates the difference between the anticipated carbon dioxide, methane, nitrous oxide, sulfur dioxide, and nitrogen oxide emissions from a CHP system to those of a separate heat and power system.
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
Energy and momentum deposited into a QCD medium by a jet shower.
Qin, G-Y; Majumder, A; Song, H; Heinz, U
2009-10-09
For a hard parton moving through a dense QCD medium, we compute self-consistently the energy loss and the fraction deposited into the medium due to showering and rescattering of the shower, assuming weak coupling between probe and medium. The same transport coefficients thus determine both the energy loss and its deposition into the medium. This allows a parameter free calculation of the latter once the former are computed or measured. We compute them for a weakly interacting medium. Assuming a short thermalization time for the deposited energy, we determine the medium's hydrodynamical response and obtain a conical pattern that is strongly enhanced by showering.
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.
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.
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)
Ionizing Energy Depositions After Fast Neutron Interactions in Silicon
Bergmann, Benedikt; Pospisil, Stanislav; Caicedo, Ivan; ...
2016-06-01
In our study we present the ionizing energy depositions in a 300 μm thick silicon layer after fast neutron impact. With the Time-of-Flight (ToF) technique, the ionizing energy deposition spectra of recoil silicons and secondary charged particles were assigned to (quasi-)monoenergetic neutron energies in the range from 180 keV to hundreds of MeV. We also show and interpret representative measured energy spectra. By separating the ionizing energy losses of the recoil silicon from energy depositions by products of nuclear reactions, the competition of ionizing (IEL) and non-ionizing energy losses (NIEL) of a recoil silicon within the silicon lattice was investigated.more » Furthermore, the data give supplementary information to the results of a previous measurement and are compared with different theoretical predictions.« less
Ionizing Energy Depositions After Fast Neutron Interactions in Silicon
Bergmann, Benedikt; Pospisil, Stanislav; Caicedo, Ivan; Kierstead, James; Takai, Helio; Frojdh, Erik
2016-06-01
In our study we present the ionizing energy depositions in a 300 μm thick silicon layer after fast neutron impact. With the Time-of-Flight (ToF) technique, the ionizing energy deposition spectra of recoil silicons and secondary charged particles were assigned to (quasi-)monoenergetic neutron energies in the range from 180 keV to hundreds of MeV. We also show and interpret representative measured energy spectra. By separating the ionizing energy losses of the recoil silicon from energy depositions by products of nuclear reactions, the competition of ionizing (IEL) and non-ionizing energy losses (NIEL) of a recoil silicon within the silicon lattice was investigated. Furthermore, the data give supplementary information to the results of a previous measurement and are compared with different theoretical predictions.
Edge energies : atomistic calculations of a continuum quantity.
Hamilton, John C.
2005-06-01
Controlling the properties of self-assembled nanostructures requires controlling their shape. Size-dependent shape transitions, frequently observed at nanolength scales, are commonly attributed to edge energy effects. To rigorously test such theories against experiment, quantitative atomistic calculations of edge energies are essential, yet none exist. I describe a fundamental ambiguity in the atomistic definition of edge energies, propose a definition based on equimolar dividing surfaces, and present an atomistic calculation of edge energies for Pd clusters.
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.
Park, H.; Budny, R.; McCune, D.; Taylor, G.; Zarnstorff, M.C. . Plasma Physics Lab.); Barnes, C.W. )
1991-12-01
The initial rate of rise of the central electron density during {approximately}100 keV deuterium neutral beam injection is found to agree well with calculations of the beam deposition rate. The best agreement is with beam deposition calculations using older tabulations of the atomic cross-sections; the effects of using new tabulations or including multi-step ionization processes appear to approximately cancel. The neutral-beam deposition profile is a strong function of both the magnitude and the shape of the target plasma density. Peaked heating profiles can be achieved at high target densities only from peaked target density profiles. 15 refs., 4 figs.
NASA Astrophysics Data System (ADS)
Kyser, David F.; Eib, Nicholas K.; Ritchie, Nicholas W. M.
2016-07-01
The absorbed energy density (eV/cm3) deposited by extreme ultraviolet (EUV) photons and electron beam (EB) high-keV electrons is proposed as a metric for characterizing the sensitivity of EUV resist films. Simulations of energy deposition are used to calculate the energy density as a function of the incident aerial flux (EUV: mJ/cm2, EB: μC/cm2). Monte Carlo calculations for electron exposure are utilized, and a Lambert-Beer model for EUV absorption. The ratio of electron flux to photon flux which results in equivalent energy density is calculated for a typical organic chemically amplified resist film and a typical inorganic metal-oxide film. This ratio can be used to screen EUV resist materials with EB measurements and accelerate advances in EUV resist systems.
Tests of MULTIMODE calculations of rovibrational energies of CH 4
NASA Astrophysics Data System (ADS)
Wu, Jiayan; Huang, Xinchuan; Carter, Stuart; Bowman, Joel M.
2006-08-01
We report variational calculations of rovibrational energies of CH 4 using the code MULTIMODE and an ab initio force field of Schwenke and Partridge. The systematic convergence of the energies with respect to the level of mode coupling is presented. Converged vibrational energies calculated using the five-mode representation of the potential for zero total angular momentum are compared with previous, benchmark calculations based on Radau coordinates using this force field for zero total angular momentum and for J = 1. Very good agreement with the previous benchmark calculations is found.
Asteroid fragmentation approaches for modeling atmospheric energy deposition
NASA Astrophysics Data System (ADS)
Register, Paul J.; Mathias, Donovan L.; Wheeler, Lorien F.
2017-03-01
During asteroid entry, energy is deposited in the atmosphere through thermal ablation and momentum-loss due to aerodynamic drag. Analytic models of asteroid entry and breakup physics are used to compute the energy deposition, which can then be compared against measured light curves and used to estimate ground damage due to airburst events. This work assesses and compares energy deposition results from four existing approaches to asteroid breakup modeling, and presents a new model that combines key elements of those approaches. The existing approaches considered include a liquid drop or "pancake" model where the object is treated as a single deforming body, and a set of discrete fragment models where the object breaks progressively into individual fragments. The new model incorporates both independent fragments and aggregate debris clouds to represent a broader range of fragmentation behaviors and reproduce more detailed light curve features. All five models are used to estimate the energy deposition rate versus altitude for the Chelyabinsk meteor impact, and results are compared with an observationally derived energy deposition curve. Comparisons show that four of the five approaches are able to match the overall observed energy deposition profile, but the features of the combined model are needed to better replicate both the primary and secondary peaks of the Chelyabinsk curve.
Density functional theory for comprehensive orbital energy calculations.
Nakata, Ayako; Tsuneda, Takao
2013-08-14
This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.
Calculation of the energy levels of lithium-like ions
NASA Astrophysics Data System (ADS)
Nadykto, B. A.
An attempt is made to develop a straightforward and sufficiently accurate method for calculating the energies of complex ion states. The method is based on Bohr's computational model and Sommerfeld's model in relativistic form (for circular orbits only). The method proposed here makes it possible to calculate excited ion states having different atomic and quantum numbers. A similar method can be used for calculating the energies of ion states with the number of electrons exceeding three.
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
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.
NASA Astrophysics Data System (ADS)
Shim, Do-Sik; Baek, Gyeong-Yun; Seo, Jin-Seon; Shin, Gwang-Yong; Kim, Kee-Poong; Lee, Ki-Yong
2016-12-01
Direct energy deposition is an additive manufacturing technique that involves the melting of metal powder with a high-powered laser beam and is used to build a variety of components. In laser-assisted metal deposition, the mechanical and metallurgical properties achieved are influenced by many factors. This paper addresses methods for selecting an appropriate layer thickness setting, which is an important parameter in layer-by-layer deposition manufacturing. A new procedure is proposed for determining the layer thickness setting for use in slicing of a part based on the single-layer height for a given depositing condition. This procedure was compared with a conventional method that uses an empirically determined layer thickness and with a feedback control method. The micro-hardness distribution, location of the melting pool, and microstructures of the deposited layers after deposition of a simple target shape were investigated for each procedure. The experimental results show that even though the feedback control method is the most effective method for obtaining the desired geometry, the deposited region was characterized by inhomogeneity of micro-hardness due to the time-variable depositing conditions involved. The largest dimensional error was associated with the conventional deposition procedure, which produced a rise in the melting zone due to over-deposition with respect to the slicing thickness, especially at the high laser power level considered. In contrast, the proposed procedure produced a stable melting zone position during deposition, which resulted in the deposited part having reasonable dimensional accuracy and uniform micro-hardness throughout the deposited region.
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.
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2010 CFR
2010-04-01
... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
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, 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...
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, 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...
Guidelines for the analysis of free energy calculations
NASA Astrophysics Data System (ADS)
Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.
2015-05-01
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, http://arxiv.org/abs/alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.
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.
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
Energy deposition model for I-125 photon radiation in water
NASA Astrophysics Data System (ADS)
Fuss, M. C.; Muñoz, A.; Oller, J. C.; Blanco, F.; Limão-Vieira, P.; Williart, A.; Huerga, C.; Téllez, M.; García, G.
2010-10-01
In this study, an electron-tracking Monte Carlo algorithm developed by us is combined with established photon transport models in order to simulate all primary and secondary particle interactions in water for incident photon radiation. As input parameters for secondary electron interactions, electron scattering cross sections by water molecules and experimental energy loss spectra are used. With this simulation, the resulting energy deposition can be modelled at the molecular level, yielding detailed information about localization and type of single collision events. The experimental emission spectrum of I-125 seeds, as used for radiotherapy of different tumours, was used for studying the energy deposition in water when irradiating with this radionuclide.
Calculation of astrophysical S factor at low energy levels
NASA Astrophysics Data System (ADS)
Andic, Halil Ibrahim; Ozer, Okan
2017-02-01
Nuclear reactions are very important for the structure, evolution, nucleosynthesis and various observational manifestations of main-sequence stars, white dwarfs and neutron stars. For astrophysical applications, one needs to know value of S-factor for many reactions at low energies. The experimental measurements of cross-sections at such low energies are essentially not easily available since the Coulomb barrier. Theoretical calculations are model dependent, so that nuclear physics uncertainties of calculated S-factor can be substantial. Using the supersymmetric quantum mechanics one can obtain the supersymmetric partner potential that can vary by several orders of magnitude in the energy range of a given reaction in the calculation of S factor. Since the determination of reaction rates requires accurate values of cross sections at very low energies, then in order to eliminate the main part of the energy dependence of these cross sections one makes use of the astrophysical S-factor in Taylor Expansion series about zero-energy.
EXCEDE Energy Deposition. Theory and Experiment Compared.
1980-11-30
1 -2 -1 -1 15 ergs cm sec ster (or 10 ergs CID sec ster at 391 1 A) . The calculated initensity (Figure 3-()), under the same viewingo Condi tions...t kli a s fo r 1 himn i fig filltfire IK\\CElE exper iment s ,itI i s v\\O I.. i mIo rt ant to0 bc able t1 dC 1 ISt i1 i,11i sli bet iSo.OlJI theSe rel
Energy deposition in the earth's atmosphere due to impact of solar activity-generated disturbances
NASA Technical Reports Server (NTRS)
Wu, S. T.; Kan, L. C.; Tandberg-Hanssen, E.; Dryer, M.
1979-01-01
Energy deposition in and dynamic responses of the terrestrial atmosphere to solar flare-generated shocks and other physical processes - such as particle precipitation and local heating - are investigated self-consistently in the context of hydrodynamics, the problem being treated as an initial boundary-value problem. It is extremely difficult to construct a general model for the line solar activity-magnetosphere-atmosphere; however, a limited model for this link is possible. The paper describes such a model, and presents some results on energy deposition into the earth's atmosphere due to solar activity-generated disturbances. Results from the present calculations are presented and discussed.
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.
Majid, Hussain; Alam, Khan; Madl, Pierre; Hofmann, Werner
2013-06-01
Ambient aerosol concentrations along the roadside of metropolitan cities of Pakistan were measured using a Grimm 1.109 dust monitor. Considering the high ambient aerosol concentrations, regional lung deposition of aerosol particles in the human respiratory tract was calculated to assess extent of exposure. Lung deposition was computed in terms of mass concentration and the associated surface area for 12 male traffic wardens using the latest version of the stochastic lung deposition code Inhalation, Deposition, and Exhalation of Aerosols in the Lung. The results have revealed 4 to 10 times higher concentrations than recommended by WHO guidelines. The deposition results derived from the model disclose that extrathoracic deposition is in the range of 22 to 28 % with total lung deposition ranging from 40 to 44 % for the scanned particle window of 0.25-10 μm. Considering an average 8-h shift per day and an average breathing rate of 1.3 m(3) h(-1), it is approximated that in a worker, up to 1.6 mg of inhalable particle mass can deposit per day.
Protein Thermostability Calculations Using Alchemical Free Energy Simulations
Seeliger, Daniel; de Groot, Bert L.
2010-01-01
Abstract Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design. PMID:20483340
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.
Spectrum of energy depositions in the Auger Water Cherenkov Detector
NASA Astrophysics Data System (ADS)
Salazar, Humberto
1999-08-01
The measured spectrum of energy depositions in a Water Cherenkov Detector (WCD) prototype for the Pierre Auger Observatory is presented. A WCD (area 10 m2 )is located in the Puebla University campus at a depth of 800 g/cm2 (2200 m above sea level). Differential and integral spectra in a wide energy deposition range (0.5 - 150 of vertical equivalent muons) are presented. The problem of the WCD "self calibration" procedure (by rate of the muon events) is discussed. The characteristic change of the slopes of the differential spectrum at the transition from single muon signals to EAS signals is also discussed. The measured energy deposition spectrum at extreme signals is used to estimate the linearity of the response of the WCD PMTs. Key words: Auger array, water Cherenkov detector, extensive air showers
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.
Energy deposition in discharge chamber of lightning protection multichamber system
NASA Astrophysics Data System (ADS)
Pinchuk, M. E.; Budin, A. V.; Kumkova, I. I.; Bogomaz, A. A.; Sivaev, A. D.; Chusov, A. N.; Zaynalov, R. I.
2016-11-01
The experimental data of energy deposition distribution along discharge chamber of lightning protection multichamber system in initial stage of discharge process aimed to model lightning current impulse up to 10 kA is presented. A multichamber system is a series connection of discharge chambers. According to our experiments the shock wave formation occurs during the breakdown phase between electrodes located at the bottom of discharge chamber. The consequent energy deposition during discharge development goes in the whole volume bounded by shock wave front.
Temporal and spatial characteristics of auroral energy deposition
NASA Astrophysics Data System (ADS)
Hampton, D. L.; Conde, M.
2015-12-01
Auroral electron precipitation forms a complex and dynamic energy input into the high-latitude ionosphere and thermopshere. Rapid changes in plasma density due to electron impact ionization create correspondingly rapid changes in conductivity which in turn change the magnitude and altitude profile of magnetospheric current closure in the E- and F-region. Modeling these changes in the ionosphere and their effects on the local or regional upper atmosphere requires detailed input over wide regions. In support of the AMISR PINOT campaign and several rocket campaigns (CASCADES-2, MICA, ASSP) we have developed and tested a method to determine the characteristics of auroral energy input using purely ground-based optical measurements in geometries away from magnetic zenith. Using the N2+ first negative emissions at 427.8 nm reproduces the total energy flux over a wide region, but alone does not indicate the altitude profile of this energy deposition. Using temperature maps of the E-region collected by a Scanning Doppler Imager (SDI) observing the auroral green-line emission is a proxy for the characteristic energy of the precipitating electrons. While in some cases the energy determination underestimates the average energy it still is a good proxy for understanding when the electron distribution changes. We examine two seasons worth of auroral observations and determine the spatial and temporal variability of auroral energy deposition in comparison to solar wind and geophysical activity parameters. We also compare the results with well-known empirical models of electron energy deposition and show that they underestimate the peak local energy deposition rates by as much as a factor of 30.
Large scale self energy calculations for ion-surface interactions
NASA Astrophysics Data System (ADS)
Kürpick, P.; Thumm, U.
1996-03-01
We present large scale non-perturbative self energy calculations for the interaction of an ion with a metal surface. Using both the simple jellium potential and more sophisticated ab initio potentials(P. J. Jennings, R. O. Jones and M. Weinert, Phys. Rev. B, 37), 6113 (1988)., we study the complex self energy matrix for various n-manifolds allowing for the calculation of diabatic and adiabatic non-perturbative level shifts and widths, and hybrid orbitals(P. Kürpick and U.Thumm, to be published.). Besides this self energy calculations a new adiabatic close--coupling calculation is being developed that will be applied to the interaction of ions in various charge states with metal surfaces.
A novel lattice energy calculation technique for simple inorganic crystals
NASA Astrophysics Data System (ADS)
Kaya, Cemal; Kaya, Savaş; Banerjee, Priyabrata
2017-01-01
In this pure theoretical study, a hitherto unexplored equation based on Shannon radii of the ions forming that crystal and chemical hardness of any crystal to calculate the lattice energies of simple inorganic ionic crystals has been presented. To prove the credibility of this equation, the results of the equation have been compared with experimental outcome obtained from Born-Fajans-Haber- cycle which is fundamentally enthalpy-based thermochemical cycle and prevalent theoretical approaches proposed for the calculation of lattice energies of ionic compounds. The results obtained and the comparisons made have demonstrated that the new equation is more useful compared to other theoretical approaches and allows to exceptionally accurate calculation of lattice energies of inorganic ionic crystals without doing any complex calculations.
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.
Towards a standardized setup for surface energy calculations
NASA Astrophysics Data System (ADS)
Kaminski, Jakub W.; Kratzer, Peter; Ratsch, Christian
2017-02-01
High-throughput design of new materials with desired electronic properties, based on screening of large collections of crystal structures organized in the from of libraries or databases require fast, widely applicable, consistent and unsupervised methods to calculate the property of interest. In this work we present an approach for the calculation of surface energies of two-dimensional periodic crystal lattices which meets all these requirements. For materials slabs which are terminated with two identical surfaces, the task of calculating the surface energy is trivial. More problematic are the cases where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed approach addresses this problem. It relies on appropriately chosen capping atoms, whose bonding energy contributions are used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surface energies with errors that are below 10%, and that are as low as 2% in many cases. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations.
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.
Effect of Embolization Material in the Calculation of Dose Deposition in Arteriovenous Malformations
NASA Astrophysics Data System (ADS)
De la Cruz, O. O. Galván; Lárraga-Gutiérrez, J. M.; Moreno-Jiménez, S.; Célis-López, M. A.
2010-12-01
In this work it is studied the impact of the incorporation of high Z materials (embolization material) in the dose calculation for stereotactic radiosurgery treatment for arteriovenous malformations. A statistical analysis is done to establish the variables that may impact in the dose calculation. To perform the comparison pencil beam (PB) and Monte Carlo (MC) calculation algorithms were used. The comparison between both dose calculations shows that PB overestimates the dose deposited. The statistical analysis, for the quantity of patients of the study (20), shows that the variable that may impact in the dose calculation is the volume of the high Z material in the arteriovenous malformation. Further studies have to be done to establish the clinical impact with the radiosurgery result.
Collapsed cone convolution of radiant energy for photon dose calculation in heterogeneous media.
Ahnesjö, A
1989-01-01
A method for photon beam dose calculations is described. The primary photon beam is raytraced through the patient, and the distribution of total radiant energy released into the patient is calculated. Polyenergetic energy deposition kernels are calculated from the spectrum of the beam, using a database of monoenergetic kernels. It is shown that the polyenergetic kernels can be analytically described with high precision by (A exp( -ar) + B exp( -br)/r2, where A, a, B, and b depend on the angle with respect to the impinging photons and the accelerating potential, and r is the radial distance. Numerical values of A, a, B, and b are derived and used to convolve energy deposition kernels with the total energy released per unit mass (TERMA) to yield dose distributions. The convolution is facilitated by the introduction of the collapsed cone approximation. In this approximation, all energy released into coaxial cones of equal solid angle, from volume elements on the cone axis, is rectilinearly transported, attenuated, and deposited in elements on the axis. Scaling of the kernels is implicitly done during the convolution procedure to fully account for inhomogeneities present in the irradiated volume. The number of computational operations needed to compute the dose with the method is proportional to the number of calculation points. The method is tested for five accelerating potentials; 4, 6, 10, 15, and 24 MV, and applied to two geometries; one is a stack of slabs of tissue media, and the other is a mediastinum-like phantom of cork and water. In these geometries, the EGS4 Monte Carlo system has been used to generate reference dose distributions with which the dose computed with the collapsed cone convolution method is compared. Generally, the agreement between the methods is excellent. Deviations are observed in situations of lateral charged particle disequilibrium in low density media, however, but the result is superior compared to that of the generalized Batho method.
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.
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.
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.
Removing the barrier to the calculation of activation energies
Mesele, Oluwaseun O.; Thompson, Ward H.
2016-10-06
Approaches for directly calculating the activation energy for a chemical reaction from a simulation at a single temperature are explored with applications to both classical and quantum systems. The activation energy is obtained from a time correlation function that can be evaluated from the same molecular dynamics trajectories or quantum dynamics used to evaluate the rate constant itself and thus requires essentially no extra computational work.
Perspective: Alchemical free energy calculations for drug discovery
NASA Astrophysics Data System (ADS)
Mobley, David L.; Klimovich, Pavel V.
2012-12-01
Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery.
Atomistic calculations of dislocation core energy in aluminium
Zhou, X. W.; Sills, R. B.; Ward, D. K.; ...
2017-02-16
A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin2β + B·cos2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less
Atomistic calculations of dislocation core energy in aluminium
NASA Astrophysics Data System (ADS)
Zhou, X. W.; Sills, R. B.; Ward, D. K.; Karnesky, R. A.
2017-02-01
A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy: Ec=A sin2β +B cos2β , and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. With our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.
Nikjoo, H; Uehara, S; Emfietzoglou, D; Pinsky, L
2011-02-01
Linear energy transfer (LET) is an average quantity, which cannot display the stochastics of the interactions of radiation tracks in the target volume. For this reason, microdosimetry distributions have been defined to overcome the LET shortcomings. In this paper, model calculations of frequency distributions for energy depositions in nanometre size targets, diameters 1-100 nm, and for a 1 μm diameter wall-less TEPC, for electrons, protons, alpha particles and carbon ions are reported. Frequency distributions for energy depositions in small-size targets with dimensions similar to those of biological molecules are useful for modelling and calculations of DNA damage. Monte Carlo track structure codes KURBUC and PITS99 were used to generate tracks of primary electrons 10 eV to 1 MeV, and ions 1 keV µm(-1) to 300 MeV µm(-1) energies. Distribution of absolute frequencies of energy depositions in volumes with diameters of 1-100 nm randomly positioned in unit density water irradiated with 1 Gy of the given radiation was obtained. Data are presented for frequency of energy depositions and microdosimetry quantities including mean lineal energy, dose mean lineal energy, frequency mean specific energy and dose mean specific energy. The modelling and calculations presented in this work are useful for characterisation of the quality of radiation beam in biophysical studies and in radiation therapy.
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.
The theoretical shape of sucrose crystals from energy calculations
NASA Astrophysics Data System (ADS)
Saska, Michael; Myerson, Allan S.
1983-05-01
The surface energies of individual crystallographic faces of crystalline sucrose were calculated using two forms of the 6-exp (Buckingham) potential. Hydrogen bond energies were calculated as a sum of O-H, O…H and O…O interactions where the Lippincott-Schroeder short-range potential was used for O-H and O…H pairs and the 6-exp potential for the non-bonded O…O interactions. Assuming that the surface energy equals half of the cohesive energy of the crystal, the attachment and surface energies of most of the faces found on as sucrose crystal were calculated. A computer program was written to draw the theoretical shape of crystals given the positions (central distances) of its faces. The resulting sucrose shapes are elongated along the c-axis. It is argued that the c-axis elongated habit is an intrinsic shape for vapor grown sucrose crystals (if realizable) and it is suggested that the usual shapes of solution grown sucrose crystals can be explained in terms of solvent (water) adsorption.
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.
Effects of internal gain assumptions in building energy calculations
NASA Astrophysics Data System (ADS)
Christensen, C.; Perkins, R.
The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations. Heating and cooling loads from simulations using the Department of Energy 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.
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.
Burigo, Lucas; Pshenichnov, Igor; Mishustin, Igor; Hilgers, Gerhard; Bleicher, Marcus
2016-05-21
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 (1)H, (4)He, (12)C and (16)O 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 (1)H, (2)H, (4)He, (6)Li, (7)Li, and (12)C 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.
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.
Calculated stacking-fault energies of elemental metals
NASA Astrophysics Data System (ADS)
Rosengaard, N. M.; Skriver, H. L.
1993-05-01
We have performed ab initio calculations of twin, intrinsic, and extrinsic face-centered-cubic stacking faults for all the 3d, 4d, and 5d transition metals by means of a Green's-function technique, based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The results are in excellent agreement with recent layer Korringa-Kohn-Rostoker Green's-function calculations where stacking-fault energies for Ni, Cu, Rh, Pd, Ag, Ir, and Au were found by means of the so-called force theorem. We find that the self-consistent fault energies for all the metals in the three transition series vary with atomic number essentially as the calculated structural energy differences between the face-centered-cubic and the hexagonal-close-packed phases. In addition we find that the simple relations between the different types of fault energies predicted by models based on the local atomic coordination are obeyed to a high degree of accuracy.
Surface energy balance calculations for small northern lakes
NASA Astrophysics Data System (ADS)
Binyamin, J.; Rouse, W. R.; Davies, J. A.; Oswald, C. J.; Schertzer, W. M.
2006-12-01
An energy balance model is used to determine diurnal surface energy balance components for three different sized high-latitude Canadian lakes in the Mackenzie River Basin (MRB) during the open water seasons of 2000, 2001, and 2002. Surface net radiation is derived from the component fluxes of the radiation balance. Turbulent heat fluxes are calculated using the aerodynamic method with input from local meteorological stations and experimentally derived drag coefficients. Lake heat storage, determined as a residual of the surface energy balance, is used together with measured water temperature profiles to calculate the daily mixing layer depth. The model uses readily available meteorological inputs for radiation calculations.Verification results for surface energy balance components show mean bias error (MBE) generally less than 5% of the mean measured daily fluxes and root mean square error (RMSE) less than 38%, which decreases to less than 16% for 10-day averaging periods. The model tends to overestimate net radiation by 7% and latent and sensible heat fluxes by about 4% and 1%, respectively, on average. Inferred slab layer depths indicate that the shallowest lake was isothermal while the deeper lakes showed temporal variations as expected.
Efficient free energy calculations of quantum systems through computer simulations
NASA Astrophysics Data System (ADS)
Antonelli, Alex; Ramirez, Rafael; Herrero, Carlos; Hernandez, Eduardo
2009-03-01
In general, the classical limit is assumed in computer simulation calculations of free energy. This approximation, however, is not justifiable for a class of systems in which quantum contributions for the free energy cannot be neglected. The inclusion of quantum effects is important for the determination of reliable phase diagrams of these systems. In this work, we present a new methodology to compute the free energy of many-body quantum systems [1]. This methodology results from the combination of the path integral formulation of statistical mechanics and efficient non-equilibrium methods to estimate free energy, namely, the adiabatic switching and reversible scaling methods. A quantum Einstein crystal is used as a model to show the accuracy and reliability the methodology. This new method is applied to the calculation of solid-liquid coexistence properties of neon. Our findings indicate that quantum contributions to properties such as, melting point, latent heat of fusion, entropy of fusion, and slope of melting line can be up to 10% of the calculated values using the classical approximation. [1] R. M. Ramirez, C. P. Herrero, A. Antonelli, and E. R. Hernández, Journal of Chemical Physics 129, 064110 (2008)
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.
A comparison of internal energy calculation methods for diatomic molecules
NASA Technical Reports Server (NTRS)
Liu, Yen; Shakib, Farzin; Vinokur, Marcel
1990-01-01
Various methods of calculating the internal energy of diatomic molecules are studied. An accurate and efficient method for computing the eigenvalues of the vibrational Schroedinger equation for an arbitrary potential is developed. The method is based on a finite-element discretization using the cubic Lobatto element. A combination of spectrum slicing and the Laguerre algorithm is used to solve for the eigenvalues. A simple method to compute the quasi-bound states is presented. For N2 molecules, all vibrational-rotational states of eleven available electronic potentials are computed, and summed to obtain the exact internal energy function with temperature. The total computation required 314 seconds of CPU-time on NASA's Cray 2 computer. Various approximate models are discussed and compared with the exact numerical simulation. It is shown that the splitting of the macroscopic internal energy into separate electronic, rotational, and vibrational energies is not justified at high temperatures.
Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria
Jorgensen, William L.; Thomas, Laura L.
2009-01-01
An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 – 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes. PMID:19936324
Energy deposition in the ionosphere derived from LEO satellite observations
NASA Astrophysics Data System (ADS)
Stolle, Claudia; Park, Jaeheung; Buchert, Stephan; Trulik, Vladimir; Bilitza, Dieter
2014-05-01
Ten years of successful operation of the multi-instrument CHAMP satellite mission at a unique orbit altitude of about 400 km revealed many interesting features of the coupling between the thermosphere and ionosphere. Different processes contribute to the deposition of solar and magnetospheric energy into the thermosphere. One important venue is heating through thermal electrons transferring energy by collisions with ions and neutrals. In the ionospheric F region thermal electrons are heated primarily through photoelectrons by local or non-local processes. At high latitudes soft precipitation and electromagnetic heating play a major role. The energy deposition can be quantified by a family of chemo-physical equations (Schunk and Nagy, 2009) that depend on plasma and neutral densities and temperatures. One important indicator for the energy transfer is the difference between electron and ion- and neutral- temperatures. Electron cooling leads to thermospheric heating and and we expect that this process leads to a local enhancement of mass density (air drag). Sizable electron cooling rates in the F region have been published from EISCAT radar observations in the ionospheric cusp. Based on CHAMP observation of electron density and temperature we estimate the energy deposit in the F-region through cooling of the thermal electron gas caused by elastic and inelastic processes. We find that a significant deposition is present during day at mid latitudes. At low latitudes the energy flux remains important until midnight. Observed heating rates depend on the satellite altitudes, but they are globally available from the CHAMP data. Missing observations in the CHAMP dataset, e.g., ion temperature, are derived from empirical models as IRI or MSIS. We investigate the global distribution of the electron cooling rate, we quantify the contributions of the different processes (equations) to the total energy transfer, e.g., depending on height, and we intend to compare our results
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
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.
Ab Initio Calculations for the Surface Energy of Silver Nanoclusters
NASA Astrophysics Data System (ADS)
Medasani, Bharat; Vasiliev, Igor; Park, Young Ho
2007-03-01
We apply first principles computational methods to study the surface energy and the surface stress of silver nanoparticles. The structures, energies and lattice contractions of spherical Ag nanoclusters are calculated in the framework of density functional theory combined with the generalized gradient approximation. Our calculations predict the surface energies of Ag nanoclusters to be in the range of 1-2 J/m^2. These values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m^2 derived from the Kelvin equation for free Ag nanoparticles. From the lattice contraction and the nearest neighbor interatomic distance, we estimate the surface stress of the silver nanoclusters to be in the the range of 1-1.45 N/m. This result suggests that a liquid droplet model can be employed to evaluate the surface energy and the surface stress of Ag nanoparticles. K. K. Nanda et al., Phys. Rev. Lett. 91, 106102 (2003).
Expected Energy Method for Electro-Optical SNR Calculations.
1984-02-02
r’AD-Ri39 984 EXPECTED ENERGY METHOD FOR ELECTPO-OPTICRL SNR i/i CALCULRTIONS(U) MASSRCHUSETTS INST OF TECH LEXINGTON LINCOLN LAB G J MAYER 82 FEB 84...ENERGY METHOD FOR ELECTRO-OPTICAL SNR CALCULATIONS * Ci. MA YER Group 9 TECHNICAL REPORT 634 2 FEBRUARY 1984 Approved for public release; distribution...analysis of image and sensor element configuration. This method allows the optimal pixel size to be selected to maximize the expected SNR for any point
Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.
Evenhuis, Christian R; Manthe, Uwe
2008-07-14
A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.
Effects of internal gain assumptions in building energy calculations
Christensen, C.; Perkins, R.
1981-01-01
The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results of this study indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.
Effects of internal gain assumptions in building energy calculations
NASA Astrophysics Data System (ADS)
Christensen, C.; Perkins, R.
1981-01-01
The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multifamily-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
2016-01-01
Binding selectivity is a requirement for the development of a safe drug, and it is a critical property for chemical probes used in preclinical target validation. Engineering selectivity adds considerable complexity to the rational design of new drugs, as it involves the optimization of multiple binding affinities. Computationally, the prediction of binding selectivity is a challenge, and generally applicable methodologies are still not available to the computational and medicinal chemistry communities. Absolute binding free energy calculations based on alchemical pathways provide a rigorous framework for affinity predictions and could thus offer a general approach to the problem. We evaluated the performance of free energy calculations based on molecular dynamics for the prediction of selectivity by estimating the affinity profile of three bromodomain inhibitors across multiple bromodomain families, and by comparing the results to isothermal titration calorimetry data. Two case studies were considered. In the first one, the affinities of two similar ligands for seven bromodomains were calculated and returned excellent agreement with experiment (mean unsigned error of 0.81 kcal/mol and Pearson correlation of 0.75). In this test case, we also show how the preferred binding orientation of a ligand for different proteins can be estimated via free energy calculations. In the second case, the affinities of a broad-spectrum inhibitor for 22 bromodomains were calculated and returned a more modest accuracy (mean unsigned error of 1.76 kcal/mol and Pearson correlation of 0.48); however, the reparametrization of a sulfonamide moiety improved the agreement with experiment. PMID:28009512
Calculating Free Energy Changes in Continuum Solvation Models
Ho, Junming; Ertem, Mehmed Z.
2016-02-27
We recently showed for a large dataset of pK_{a}s and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pK_{a} calculations, as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol^{-1} and 25 kJ mol^{-1} respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.
Calculating Free Energy Changes in Continuum Solvation Models
Ho, Junming; Ertem, Mehmed Z.
2016-02-27
We recently showed for a large dataset of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations,more » as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol-1 and 25 kJ mol-1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less
Quantum Monte Carlo calculations of the dimerization energy of borane.
Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele
2011-09-07
Accurate thermodynamic data are required to improve the performance of chemical hydrides that are potential hydrogen storage materials. Boron compounds are among the most interesting candidates. However, different experimental measurements of the borane dimerization energy resulted in a rather wide range (-34.3 to -39.1) ± 2 kcal/mol. Diffusion Monte Carlo (DMC) simulations usually recover more than 95% of the correlation energy, so energy differences rely less on error cancellation than other methods. DMC energies of BH(3), B(2)H(6), BH(3)CO, CO, and BH(2)(+) allowed us to predict the borane dimerization energy, both via the direct process and indirect processes such as the dissociation of BH(3)CO. Our D(e) = -43.12(8) kcal/mol, corrected for the zero point energy evaluated by considering the anharmonic contributions, results in a borane dimerization energy of -36.59(8) kcal/mol. The process via the dissociation of BH(3)CO gives -34.5(2) kcal/mol. Overall, our values suggest a slightly less D(e) than the most recent W4 estimate D(e) = -44.47 kcal/mol [A. Karton and J. M. L. Martin, J. Phys. Chem. A 111, 5936 (2007)]. Our results show that reliable thermochemical data for boranes can be predicted by fixed node (FN)-DMC calculations.
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 perturbation calculations on glucosidase-inhibitor complexes.
Ruiza, F M; Grigera, J Raúl
2005-09-01
Free energy perturbation studies have been performed on Glucoamylase II (471) from Aspergillus awamori var. X100 complexed with three different inhibitors: (+)lentiginosine, (+)(1S,2S,7R,8aS) 1,2,7-trihydroxyindolizidine, (+)(1S,2S,7S,8aS) 1,2,7-trihydroxyindolizidine and the inactive compound (+)(1S,7R,8aS)-1,7-dihydroxyindolizidine. Molecular dynamic simulations were carried out using a recently developed procedure for fast Free Energy Perturbation calculations. In this procedure only a sphere of 1.8 nm around the central atom of the inhibitor is considered in the calculations. Crystallographic restraints are applied over this reduced system using a generated electron density map. The obtained values for the free energy differences agree with experimental data showing the importance of fast calculations in drug design even when the crystallographic structure of the complex is not available. As the method uses only the crystallographic structure of the receptor, it is possible to test the possible efficiency of even still not synthesised ligands, making the pre-selection of compounds much easy and faster.
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.
Distinctive features of kinetics of plasma at high specific energy deposition
NASA Astrophysics Data System (ADS)
Lepikhin, Nikita; Popov, Nikolay; Starikovskaia, Svetlana
2016-09-01
A nanosecond capillary discharge in pure nitrogen at moderate pressures is used as an experimental tool for plasma kinetics studies at conditions of high specific deposited energy up to 1 eV/molecule. Experimental observations based on electrical (back current shunts, capacitive probe) and spectroscopic measurements (quenching rates; translational, rotational and vibrational temperature measurements) demonstrate that high specific deposited energy, at electric fields of 200-300 Td, can significantly change gas kinetics in the discharge and in the afterglow. The numerical calculations in 1D axially symmetric geometry using experimental data as input parameters show that changes in the plasma kinetics are caused by extremely high excitation degree: up to 10% of molecular nitrogen is electronically excited at present conditions. Distinctive features of kinetics of plasma at high specific energy deposition as well as details of the experimental technique and numerical calculations will be present. The work was partially supported by French National Agency, ANR (PLASMAFLAME Project, 2011 BS09 025 01), AOARD AFOSR, FA2386-13-1-4064 grant (Program Officer Prof. Chiping Li), LabEx Plas@Par and Linked International Laboratory LIA KaPPA (France-Russia).
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
CO dimer: new potential energy surface and rovibrational calculations.
Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker
2013-08-15
The spectrum of CO dimer was investigated by solving the rovibrational Schrödinger equation on a new potential energy surface constructed from coupled-cluster ab initio points. The Schrödinger equation was solved with a Lanczos algorithm. Several 4D (rigid monomer) global ab initio potential energy surfaces (PESs) were made using a previously reported interpolating moving least-squares (IMLS) fitting procedure specialized to describe the interaction of two linear fragments. The potential has two nonpolar minima giving rise to a complicated set of energy level stacks, which are very sensitive to the shapes and relative depths of the two wells. Although the CO dimer has defied previous attempts at an accurate purely ab initio description our best surface yields results in good agreement with experiment. Root-mean-square (rms) fitting errors of less than 0.1 cm(-1) were obtained for each of the fits using 2226 ab initio data at different levels. This allowed direct assessment of the quality of various levels of ab initio theory for prediction of spectra. Our tests indicate that standard CCSD(T) is slow to converge the interaction energy even when sextuple zeta bases as large as ACV6Z are used. The explicitly correlated CCSD(T)-F12b method was found to recover significantly more correlation energy (from singles and doubles) at the CBS limit. Correlation of the core-electrons was found to be important for this system. The best PES was obtained by extrapolation of calculations at the CCSD(T)(AE)-F12b/CVnZ-F12 (n = 3,4) levels. The calculated energy levels were compared to 105 J ≤ 10 levels from experiment. The rms error for 68 levels with J ≤ 6 is only 0.29 cm(-1). The calculated energy levels were assigned stack labels using several tools. New stacks were found. One of them, stack y1, has an energy lower than many previously known stacks and may be observable.
Free energy calculations: an efficient adaptive biasing potential method.
Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul
2010-05-06
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.
Dirac Calculations for Proton Inelastic Scattering at Intermediate Energies
NASA Astrophysics Data System (ADS)
El-Nohy, N. A.; El-Hammamy, M. N.; Aly, N. E.; Abdel-Moneim, A. M.; Hamza, A. F.
2016-12-01
Relativistic proton inelastic scattering from different targets (16O, 24Mg, 28Si, 40Ca, 54Fe, 58Ni, 90Zr, 154Sm, 176Yb, and 208Pb) at intermediate energies is analyzed in the framework of phenomenological optical potentials based on the Dirac formalism. Parameters of the Dirac phenomenological potential with Woods Saxon (WS) shape are obtained. The first order vibrational collective model with one phonon is used to calculate the transition optical potentials to the first low-lying excited state (2+) of the investigated target nuclei. Also, the variation of deformation length ( δ) with energy and mass number is studied. It is noticed that the deformation length increases slightly with energy at intermediate range.
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.
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.
Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.
Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G
2013-11-07
A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into
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.
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.
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
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 development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.
Calculation of Dose Deposition in 3D Voxels by Heavy Ions and Simulation of gamma-H2AX Experiments
NASA Technical Reports Server (NTRS)
Plante, I.; Ponomarev, A. L.; Wang, M.; Cucinotta, F. A.
2011-01-01
The biological response to high-LET radiation is different from low-LET radiation due to several factors, notably difference in energy deposition and formation of radiolytic species. Of particular importance in radiobiology is the formation of double-strand breaks (DSB), which can be detected by -H2AX foci experiments. These experiments has revealed important differences in the spatial distribution of DSB induced by low- and high-LET radiations [1,2]. To simulate -H2AX experiments, models based on amorphous track with radial dose are often combined with random walk chromosome models [3,4]. In this work, a new approach using the Monte-Carlo track structure code RITRACKS [5] and chromosome models have been used to simulate DSB formation. At first, RITRACKS have been used to simulate the irradiation of a cubic volume of 5 m by 1) 450 1H+ ions of 300 MeV (LET 0.3 keV/ m) and 2) by 1 56Fe26+ ion of 1 GeV/amu (LET 150 keV/ m). All energy deposition events are recorded to calculate dose in voxels of 20 m. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. Many differences are found in the spatial distribution of dose voxels for the 56Fe26+ ion. The track structure can be distinguished, and voxels with very high dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and indicate clustered energy deposition, which may be responsible for complex DSB. In the second step, assuming that DSB will be found only in voxels where energy is deposited by the radiation, the intersection points between voxels with dose > 0 and simulated chromosomes were obtained. The spatial distribution of the intersection points is similar to -H2AX foci experiments. These preliminary results suggest that combining stochastic track structure and chromosome models could be a good approach to understand radiation-induced DSB and chromosome aberrations.
Atomic Layer Deposition of Bismuth Vanadates for Solar Energy Materials.
Stefik, Morgan
2016-07-07
The fabrication of porous nanocomposites is key to the advancement of energy conversion and storage devices that interface with electrolytes. Bismuth vanadate, BiVO4 , is a promising oxide for solar water splitting where the controlled fabrication of BiVO4 layers within porous, conducting scaffolds has remained a challenge. Here, the atomic layer deposition of bismuth vanadates is reported from BiPh3 , vanadium(V) oxytriisopropoxide, and water. The resulting films have tunable stoichiometry and may be crystallized to form the photoactive scheelite structure of BiVO4 . A selective etching process was used with vanadium-rich depositions to enable the synthesis of phase-pure BiVO4 after spinodal decomposition. BiVO4 thin films were measured for photoelectrochemical performance under AM 1.5 illumination. The average photocurrents were 1.17 mA cm(-2) at 1.23 V versus the reversible hydrogen electrode using a hole-scavenging sulfite electrolyte. The capability to deposit conformal bismuth vanadates will enable a new generation of nanocomposite architectures for solar water splitting.
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.
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.
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.
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.
Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye
2016-02-09
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D.
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
Energy deposition rates by charged particles measured during the energy budget campaign
NASA Technical Reports Server (NTRS)
Urban, A.; Torkar, K. M.; Bjordal, J.; Lundblad, J. A.; Soraas, F.; Grandal, B.; Smith, L. G.; Ulwick, J. C.; Vancour, R. P.
1982-01-01
Measurements of the precipitation of electrons and positive ions (in the keV to MeV range) detected aboard eight rockets launched from Northern Scandinavia are reported together with corresponding satellite data. The downgoing integral fluxes indicate the temporal fluctuations during each flight. Height profiles of the energy deposition into the atmosphere at different levels of geomagnetic disturbance are given.
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.
Mahdavi, M; Koohrokhi, T
2012-01-01
The energy loss and penetration of multi-megelectronvolt protons into a uniform deuterium-tritium (DT) plasma has been calculated. The effects of nuclear elastic scattering and Coulomb interactions are treated from a unified point of view. In general, multiple scattering enhances the proton linear-energy transfer along the initial proton direction, thus the energy deposition increases near the end of its range. The net effect of multiple scattering is to reduce the penetration from 1.20 to 1.02 g cm-2 for 12 MeV protons in a ρ=500 g cm-3 plasma at T=5 keV. These results should have relevance to proton fast ignition, specifically to energy deposition calculations that critically assess quantitative ignition requirements.
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.
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.
Energy deposition in low-power coaxial plasma thrusters
NASA Technical Reports Server (NTRS)
Myers, R. M.; Kelly, A. J.; Jahn, R. G.
1991-01-01
An experimental examination of energy deposition in self-field, coaxial plasma thrusters revealed that the thrust efficiency ranged from 2-9 percent and that the dominant losses resulted from electrode heating and propellant ionization. Sensible enthalpy and radiative losses were negligible. Thruster specific impulse increased with current, ranging from 550-1750 seconds. Spectroscopic studies of the plume plasma showed that the electron temperature ranged from 0.5-2.5 eV and that the dominant species were singly and doubly ionized argon. Attempts to raise thruster efficiency by increasing the chamber pressure resulted in reduced electrode losses and lowered I(sp), but the thrust efficiency decreased because of a current redistribution that lowered the thrust beyond expectations.
Free-energy calculation of structure-H hydrates
NASA Astrophysics Data System (ADS)
Okano, Yamato; Yasuoka, Kenji
2006-01-01
A molecular-dynamics (MD) simulation of structure-H hydrates was performed under constant pressure and temperature with 6120 TIP4P water molecules, 900 OPLS-UA methane molecules, and 180 large molecular guest substance (LMGS) molecules. The LMGS molecules were represented in the form of a one-site Lennard-Jones (LJ) model using the LJ parameters σ and ɛ. In order to clarify the thermodynamic stability of structure-H hydrates, we calculated the free-energy difference, changing on the σ and ɛ only of the LMGS molecules. In this simulation, stable crystals of structure-H hydrates and a minimum value of ΔG were obtained at σ ˜6.2Å and large values of ɛ. All simulations were performed using the special-purpose computer hardware MDGRAPE-2.
Parallel Calculation of CCSDT and Mk-MRCCSDT Energies.
Prochnow, Eric; Harding, Michael E; Gauss, Jürgen
2010-08-10
A scheme for the parallel calculation of energies at the coupled-cluster singles, doubles, and triples (CCSDT) level of theory, several approximate iterative CCSDT schemes (CCSDT-1a, CCSDT-1b, CCSDT-2, CCSDT-3, and CC3), and for the state-specific multireference coupled-cluster ansatz suggested by Mukherjee with a full treatment of triple excitations (Mk-MRCCSDT) is presented. The proposed scheme is based on the adaptation of a highly efficient serial coupled-cluster code leading to a communication-minimized implementation by parallelizing the time-determining steps. The parallel algorithm is tailored for affordable cluster architectures connected by standard communication networks such as Gigabit Ethernet. In this way, CCSDT and Mk-MRCCSDT computations become feasible even for larger molecular systems and basis sets. An analysis of the time-determining steps for CCSDT and Mk-MRCCSDT, namely the computation of the triple-excitation amplitudes and their individual contributions, is carried out. Benchmark calculations are presented for the N2O, ozone, and benzene molecules, proving that the parallelization of these steps is sufficient to obtain an efficient parallel scheme. A first application to the case of 2,6-pyridyne using a triple-ζ quality basis (222 basis functions) is presented demonstrating the efficiency of the current implementation.
White, C.W.; Aziz, M.J.
1985-10-01
The fundamentals of energy deposition, heat flow, and rapid solidification during energy deposition from lasers and electron beams is reviewed. Emphasis is placed on the deposition of energy from pulsed sources (10 to 100 ns pulse duration time) in order to achieve high heating and cooling rates (10/sup 8/ to 10/sup 10/ /sup 0/C/s) in the near surface region. The response of both metals and semiconductors to pulsed energy deposition is considered. Guidelines are presented for the choice of energy source, wavelength, and pulse duration time.
Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid.
Saouane, Sofiane; Buth, Gernot; Fabbiani, Francesca P A
2013-11-01
The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by the PIXEL method brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure, PIXEL lattice energy calculations confirm the predominance of the Coulombic term (-379.1 kJ mol(-1)) ahead of the polarization (-141.4 kJ mol(-1)), dispersion (-133.7 kJ mol(-1)) and repulsion (266.3 kJ mol(-1)) contributions.
Effects of energy spectrum on dose distribution calculations for high energy electron beams.
Toutaoui, Abdelkader; Khelassi-Toutaoui, Nadia; Brahimi, Zakia; Chami, Ahmed Chafik
2009-01-01
In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities.
Effects of energy spectrum on dose distribution calculations for high energy electron beams
Toutaoui, Abdelkader; Khelassi-Toutaoui, Nadia; Brahimi, Zakia; Chami, Ahmed Chafik
2009-01-01
In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities. PMID:20126560
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.
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
Energy deposition study of low-energy cosmic radiation at sea level
NASA Astrophysics Data System (ADS)
Wijesinghe, Pushpa
In this dissertation work, a computer simulation model based on the Geant4 simulation package has been designed and developed to study the energy deposition and track structures of cosmic muons and their secondary electrons in tissue-like materials. The particle interactions in a cubic water volume were first simulated. To analyze the energy deposition and tracks in small structures, with the intention of studying the energy localization in nanometric structures such as DNA, the chamber was sliced in three dimentions. Validation studies have been performed by comparing the results with experimental, theoretical, and other simulation results to test the accuracy of the simulation model. A human body phantom in sea-level muon environment was modeled to measure the yearly dose to a human from cosmic muons. The yearly dose in this phantom is about 22 millirems. This is close to the accepted value for the yearly dose from cosmic radiation at sea level. Shielding cosmic muons with a concrete slab from 0 to 2 meters increased the dose received by the body. This dissertation presents an extensive study on the interactions of secondary electrons created by muons in water. Index words. Radiation Dosimetry Simulation, Track Structures, Sea-Level muon Flux, Energy Deposition
Control of MR to RR Transition by Pulsed Energy Deposition
NASA Astrophysics Data System (ADS)
Yan, Hong; Adelgren, Russell; Elliott, Gregory; Knight, Doyle
2003-11-01
This paper presents a study of the effect of a single laser energy pulse on the transition from a Mach Reflection (MR) to a Regular Reflection (RR) in the Dual Solution Domain (DSD). The freestream Mach number is 3.45 and two oblique shock waves are formed by two symmetric 22 degree wedges. These conditions correspond to a point midway within the DSD. A steady MR was first obtained experimentally and numerically, then a single laser pulse was deposited above the horizontal center plane. For the steady MR, the simulation showed the variation of Mach stem height along the span due to side effects. The predicted spanwise averaged Mach stem height was 1.96 mm within 2 percent of the experimental value of 2 mm. The experiment showed that the Mach stem height decreased to 30 percent of its original height due to the interaction with the laser spot and then returned to its original height by 300 microsec. That the Mach stem returned to its original height was most likely due to freestream turbulence in the wind tunnel. The numerical simulation successfully predicted the reverse transition from a stable MR to a stable RR and the stable RR persisted across the span. This study showed the capability of a laser energy pulse to control the reverse transition of MR -> RR within the Dual Solution Domain.
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%.
NASA Astrophysics Data System (ADS)
Wu, Xiao-Zhi; Wang, Rui; Wang, Shao-Feng; Wei, Qun-Yi
2010-08-01
The ab initio calculations have been used to study the generalized-stacking-fault energy (GSFE) surfaces and surface energies for the closed-packed (1 1 1) plane in FCC metals Cu, Ag, Au, Ni, Al, Rh, Ir, Pd, Pt, and Pb. The GSFE curves along <112> (1 1 1) direction and <110> (1 1 1) direction, and surface energies have been calculated from first principles. Based on the translational symmetry of the GSFE surfaces, the fitted expressions have been obtained from the Fourier series. Our results of the GSFEs and surface energies agree better with experimental results. The metals Al, Pd, and Pt have low γ/γI value, so full dislocation will be observed easily; while Cu, Ag, Au, and Ni have large γ/γI value, so it is preferred to create partial dislocation. From the calculations of surface energies, it is confirmed that the VIII column elements Ni, Rh, Ir, Pd, and Pt have higher surface energies than other metals.
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.
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''.
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…
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.
On the calculation of absolute macromolecular binding free energies
Luo, Hengbin; Sharp, Kim
2002-01-01
The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B → AB with an association constant KAB is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of KAB is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior. PMID:12149474
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.
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.
Energy deposition of quasi-two temperature relativistic electrons in fast-shock ignition scenario
NASA Astrophysics Data System (ADS)
Ghasemi, Seyed Abolfazl; Farahbod, Amir Hossein
2016-10-01
Previous calculations from Solodov et al. (2008) indicate that classical stopping and scattering dominate electrons energy deposition and transport when the electrons reach the dense plasma in FSI inertial confinement fusion concept [1]. Our calculations show that, by using quasi- two temperature electrons energy distribution function [2] in comparison with exponential [3] or monoenergetic distribution function and also increasing fast electrons energy to about 7 MeV, the ratio of beam blooming to straggling definitely decreases. Our analytical analysis shows that for fuel mass more than 1 mg and for fast ignitor wavelength λif > 0.53 μ m, straggling and beam blooming increases. Meanwhile, by reducing fast ignitor wavelength from 0.53 to 0.35 micron, and for fuel mass about 2 mg, electron penetration into the dense fuel slightly increases. Therefore, reduction of scattering (blooming and straggling) of electrons and enhancement of electron penetration into the dense fuel, can be obtained in relativistic regime with high energy fast electrons of the order of 5 Mev and more. Such derivations can be used in theoretical studies of the ignition conditions and PIC simulations of the electron transport in fast ignition scenario.
Beres, D.A.; Hull, A.P.
1991-12-01
DEPDOSE is an interactive, menu driven, microcomputer based program designed to rapidly calculate committed dose from radionuclides deposited on the ground. The program is designed to require little or no computer expertise on the part of the user. The program consisting of a dose calculation section and a library maintenance section. These selections are available to the user from the main menu. The dose calculation section provides the user with the ability to calculate committed doses, determine the decay time needed to reach a particular dose, cross compare deposition data from separate locations, and approximate a committed dose based on a measured exposure rate. The library maintenance section allows the user to review and update dose modifier data as well as to build and maintain libraries of radionuclide data, dose conversion factors, and default deposition data. The program is structured to provide the user easy access for reviewing data prior to running the calculation. Deposition data can either be entered by the user or imported from other databases. Results can either be displayed on the screen or sent to the printer.
Takahashi, Takahiro; Fukui, Noriyuki; Arakawa, Masamoto; Funatsu, Kimito; Ema, Yoshinori
2011-09-01
We have developed an automatic modeling system for calculation processes of the simulator to reproduce experimental results of chemical vapor deposition (CVD), in order to decrease the calculation cost of the simulator. Replacing the simulator by the mathematical models proposed by the system will contribute towards decreasing the calculation costs for predicting the experimental results. The system consists of a mobile agent and two software resources in computer networks, that is, generalized modeling software and a simulator reproducing cross-sections of the deposited films on the substrates with the micrometer- or nanometer-sized trenches. The mobile agent autonomously creates appropriate models by moving to and then operating the software resources. The models are calculated by partial least squares regression (PLS), quadratic PLS (QPLS) and error back propagation (BP) methods using artificial neural networks (ANN) and expresses by mathematical formulas to reproduce the calculated results of the simulator. The models show good reproducibility and predictability both for uniformity and filling properties of the films calculated by the simulator. The models using the BP method yield the best performance. The filling property data are more suitable to modeling than film uniformity.
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.
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, 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.
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.
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.
Menezes, Elizabete Wenzel de; Grande, Fernanda; Giuntini, Eliana Bistriche; Lopes, Tássia do Vale Cardoso; Dan, Milana Cara Tanasov; Prado, Samira Bernardino Ramos do; Franco, Bernadette Dora Gombossy de Melo; Charrondière, U Ruth; Lajolo, Franco Maria
2016-02-15
Dietary fiber (DF) contributes to the energy value of foods and including it in the calculation of total food energy has been recommended for food composition databases. The present study aimed to investigate the impact of including energy provided by the DF fermentation in the calculation of food energy. Total energy values of 1753 foods from the Brazilian Food Composition Database were calculated with or without the inclusion of DF energy. The energy values were compared, through the use of percentage difference (D%), in individual foods and in daily menus. Appreciable energy D% (⩾10) was observed in 321 foods, mainly in the group of vegetables, legumes and fruits. However, in the Brazilian typical menus containing foods from all groups, only D%<3 was observed. In mixed diets, the DF energy may cause slight variations in total energy; on the other hand, there is appreciable energy D% for certain foods, when individually considered.
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.
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…
Comparison of Calibration of Sensors Used for the Quantification of Nuclear Energy Rate Deposition
Brun, J.; Reynard-Carette, C.; Tarchalski, M.; Pytel, K.; Lyoussi, A.; Fourmentel, D.; Villard, J.F.; Jagielski, J.
2015-07-01
This present work deals with a collaborative program called GAMMA-MAJOR 'Development and qualification of a deterministic scheme for the evaluation of GAMMA heating in MTR reactors with exploitation as example MARIA reactor and Jules Horowitz Reactor' between the National Centre for Nuclear Research of Poland, the French Atomic Energy and Alternative Energies Commission and Aix Marseille University. One of main objectives of this program is to optimize the nuclear heating quantification thanks to calculation validated from experimental measurements of radiation energy deposition carried out in irradiation reactors. The quantification of the nuclear heating is a key data especially for the thermal, mechanical design and sizing of irradiation experimental devices in specific irradiated conditions and locations. The determination of this data is usually performed by differential calorimeters and gamma thermometers such as used in the experimental multi-sensors device called CARMEN 'Calorimetric en Reacteur et Mesures des Emissions Nucleaires'. In the framework of the GAMMA-MAJOR program a new calorimeter was designed for the nuclear energy deposition quantification. It corresponds to a single-cell calorimeter and it is called KAROLINA. This calorimeter was recently tested during an irradiation campaign inside MARIA reactor in Poland. This new single-cell calorimeter differs from previous CALMOS or CARMEN type differential calorimeters according to three main points: its geometry, its preliminary out-of-pile calibration, and its in-pile measurement method. The differential calorimeter, which is made of two identical cells containing heaters, has a calibration method based on the use of steady thermal states reached by simulating the nuclear energy deposition into the calorimeter sample by Joule effect; whereas the single-cell calorimeter, which has no heater, is calibrated by using the transient thermal response of the sensor (heating and cooling steps). The paper will
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.
Free energy calculation from umbrella sampling using Bayesian inference
NASA Astrophysics Data System (ADS)
Bernstein, Noam; Stecher, Thomas; Csányi, Gábor
2013-03-01
Using simulations to obtain information about the free energy of a system far from its free energy minima requires biased sampling, for example using a series of harmonic umbrella confining potentials to scan over a range of collective variable values. One fundamental distinction between existing methods that use this approach is in what quantities are measured and how they are used: histograms of the system's probability distribution in WHAM, or gradients of the potential of mean force for umbrella integration (UI) and the single-sweep radial basis function (RBF) approach. Here we present a method that reconstructs the free energy from umbrella sampling data using Bayesian inference that effectively uses all available information from multiple umbrella windows. We show that for a single collective variable, our method can use histograms, gradients, or both, to match or outperform WHAM and UI in the accuracy of free energy for a given amount of total simulation time. In higher dimensions, our method can effectively use gradient information to reconstruct the multidimensional free energy surface. We test our method for the alanine polypeptide model system, and show that it is more accurate than a RBF reconstruction for sparse data, and more stable for abundant data.
Implications for High Energy Blazar Spectra from Intergalactic Absorption Calculations
NASA Technical Reports Server (NTRS)
Stecker, F
2008-01-01
Given a knowledge of the density spectra intergalactic low energy photons as a function of redshift, one can derive the intrinsic gamma-ray spectra and luminosities of blazars over a range of redshifts and look for possible trends in blazar evolution. Stecker, Baring & Summerlin have found some evidence hinting that TeV blazars with harder spectra have higher intrinsic TeV gamma-ray luminosities and indicating that there may be a correlation of spectral hardness and luminosity with redshift. Further work along these lines, treating recent observations of the blazers lES02291+200 and 3C279 in the TeV and sub-TeV energy ranges, has recently been explored by Stecker & Scully. GLAST will observe and investigate many blazars in the GeV energy range and will be sensitive to blazers at higher redshifts. I examine the implications high redshift gamma-ray absorption for both theoretical and observational blazer studies.
Accelerating atomistic calculations of quantum energy eigenstates on graphic cards
NASA Astrophysics Data System (ADS)
Rodrigues, Walter; Pecchia, A.; Lopez, M.; Auf der Maur, M.; Di Carlo, A.
2014-10-01
Electronic properties of nanoscale materials require the calculation of eigenvalues and eigenvectors of large matrices. This bottleneck can be overcome by parallel computing techniques or the introduction of faster algorithms. In this paper we report a custom implementation of the Lanczos algorithm with simple restart, optimized for graphical processing units (GPUs). The whole algorithm has been developed using CUDA and runs entirely on the GPU, with a specialized implementation that spares memory and reduces at most machine-to-device data transfers. Furthermore parallel distribution over several GPUs has been attained using the standard message passing interface (MPI). Benchmark calculations performed on a GaN/AlGaN wurtzite quantum dot with up to 600,000 atoms are presented. The empirical tight-binding (ETB) model with an sp3d5s∗+spin-orbit parametrization has been used to build the system Hamiltonian (H).
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.
Verification Of Energy Balance In The Ansys V5.4 Thermal Calculations
H. Marr; M.J. Anderson
2001-02-08
The objective of this calculation is to verify the energy balance of the thermal calculations analyzed by ANSYS Version (V) 5.4 solver (see Section 4). The scope of this calculation is limited to calculating the energy balance of a two-dimensional repository thermal representation using the temperatures obtained from ANSYS V5.4. The procedure, AP-3.124, Calculations (Ref. 3), and the Technical Work Plan for: Waste Package Design Description for LA (Ref. 2) are used to develop this calculation. The associated activity is the development of engineering evaluations to support the Licensing Application design activities.
Potential Energy Calculations for Collinear Cluster Tripartition Fission Events
NASA Astrophysics Data System (ADS)
Unzhakova, A. V.; Pashkevich, V. V.; Pyatkov, Y. V.
2014-09-01
Strutinsky shell correction calculations were performed to describe the recent experimental results on collinear ternary fission. Collinear Cluster Tripartion fission events were studied experimentally in neutron induced fission of 235U, where the missing mass in the detected binary decay was suggested to characterize fission event as a collinear tripartition; and in spontaneous fission of 252Cf, where the direct detection of the three fission fragments has been used to confirm the existence of the Collinear Cluster Tripartition channel with a probability of 4.7×10-3 relative to the binary fission events.
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.
The role of Energy Deposition in the Epitaxial Layer in Triggering SEGR in Power MOSFETs
NASA Technical Reports Server (NTRS)
Selva, L.; Swift, G.; Taylor, W.; Edmonds, L.
1999-01-01
In these SEGR experiments, three identical-oxide MOSFET types were irradiated with six ions of significantly different ranges. Results show the prime importance of the total energy deposited in the epitaxial layer.
Relativistic Calculations and Measurements of Energies, Auger Rates, and Lifetimes.
1982-12-01
Research and Industry, Denton, Texas, 8-10 November 1982. 7. B. Crasemann: "Efectos Relativ’sticos y de QED Sobre las Transiciones Rayos - X y Auger Entre...INNER-SHELL IONIZATION BY PROTONS X -RAY EMISSION BREIT INTERACTION AUGER TRANSITIONS DIRAC-HARTREE-SLATER COMPUTATIONS SYNCHROTRON RADIATION RESONANT...computations, including relativistic and quantum- electrodynamic effects, of atomic energy levels and of x -ray and Auger transitions in atoms with one or
Peeler, Christopher R; Titt, Uwe
2012-06-21
In spot-scanning intensity-modulated proton therapy, numerous unmodulated proton beam spots are delivered over a target volume to produce a prescribed dose distribution. To accurately model field size-dependent output factors for beam spots, the energy deposition at positions radial to the central axis of the beam must be characterized. In this study, we determined the difference in the central axis dose for spot-scanned fields that results from secondary particle doses by investigating energy deposition radial to the proton beam central axis resulting from primary protons and secondary particles for mathematical point source and distributed source models. The largest difference in the central axis dose from secondary particles resulting from the use of a mathematical point source and a distributed source model was approximately 0.43%. Thus, we conclude that the central axis dose for a spot-scanned field is effectively independent of the source model used to calculate the secondary particle dose.
Computational efficiences for calculating rare earth f^n energies
NASA Astrophysics Data System (ADS)
Beck, Donald R.
2009-05-01
RecentlyootnotetextD. R. Beck and E. J. Domeier, Can. J. Phys. Walter Johnson issue, Jan. 2009., we have used new computational strategies to obtain wavefunctions and energies for Gd IV 4f^7 and 4f^65d levels. Here we extend one of these techniques to allow efficent inclusion of 4f^2 pair correlation effects using radial pair energies obtained from much simpler calculationsootnotetexte.g. K. Jankowski et al., Int. J. Quant. Chem. XXVII, 665 (1985). and angular factors which can be simply computedootnotetextD. R. Beck and C. A. Nicolaides, Excited States in Quantum Chemistry, C. A. Nicolaides and D. R. Beck (editors), D. Reidel (1978), p. 105ff.. This is a re-vitalization of an older ideaootnotetextI. Oksuz and O. Sinanoglu, Phys. Rev. 181, 54 (1969).. We display relationships between angular factors involving the exchange of holes and electrons (e.g. f^6 vs f^8, f^13d vs fd^9). We apply the results to Tb IV and Gd IV, whose spectra is largely unknown, but which may play a role in MRI medicine as endohedral metallofullerenes (e.g. Gd3N-C80ootnotetextM. C. Qian and S. N. Khanna, J. Appl. Phys. 101, 09E105 (2007).). Pr III results are in good agreement (910 cm-1) with experiment. Pu I 5f^2 radial pair energies are also presented.
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton
2013-08-15
Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.
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.
Laser energy deposition and its dynamic uniformity for direct-drive capsules
NASA Astrophysics Data System (ADS)
Xu, Yan; Wu, SiZhong; Zheng, WuDi
2015-04-01
The total laser energy deposition of multi-laser-beam irradiation is not only associated with the dynamic behavior of capsule but also the time-dependent angular distribution of the energy deposition of each beam around its axis. The dynamic behavior of laser energy deposition does not linearly respond to the dynamic behavior of laser irradiation. The laser energy deposition uniformity determines the symmetry of implosion. The dynamic behavior of laser energy deposition non-uniformity in OMEGA for laser with square beam shape intensity profile is investigated. In the case of smaller laser spot, the initial non-uniformity caused by laser beam overlap is very high. The shell asymmetry caused by the high initial laser irradiation non-uniformity is estimated by the extent of distortion of shock front which is not as severe as expected before the shock driven by main pulse arrives. This suggests that the large initial non-uniformity due to smaller laser spot is one of the elements that seed disturbance before the main pulse. The rms of laser energy deposition during the main pulse remains above 2%. Since the intensity of main driving pulse usually is several times higher than that of picket pulses, the non-uniformity in main pulse period may jeopardize the symmetrical implosion. When dynamic behavior of capsule is considered, the influence of beam pointing error, the target positioning error, and beam-to-beam power unbalance is quite different for the case of static capsule.
Fluorocarbon thin-film deposition on polymer surfaces from low-energy polyatomic ion beams
NASA Astrophysics Data System (ADS)
Wijesundara, Muthu Bandage Jayathilaka
Low energy polyatomic ion deposition is attractive for selective surface modification of advanced materials. Surface modification by fluorocarbon (FC) thin film deposition is widely used for many technological applications. Thus, polymer surface modification by FC thin film deposition was carried out using mass-separated low energy FC ion beams. X-ray photoelectron spectroscopy, atomic force microscopy and air/water contact angles were employed to examine how the FC film chemistry, morphology, and long term stability depend on incident ion structure, kinetic energy, and fluence. Molecular dynamics simulations were performed to support experimental data. 25--100 eV CF3+ and C3F 5+ ion deposition on polystyrene (PS) surface was examined. CF3+ and C3F5+ each formed a distribution of different FC functional groups on PS in amounts dependent upon the incident ion energy, structure, and fluence. Both ions deposited mostly intact upon the surface at 25 eV. The total fluorine and fluorinated carbon content were increased with ion energy. The fluorination efficiency was higher for the larger ion. The simulations revealed that the fragmentation behavior depends on the incident ion structure and its energy. The simulations also confirmed that FC ions only penetrated a few angstroms into the surface. The compositional changes of 25--100 eV CF3+ and C3F5+ ion-modified PS surfaces were examined after being exposed to atmosphere for four and eight weeks. The FC films oxidized in atmospheric conditions. Oxygen incorporation into the ion-modified surfaces increased with ion energy due to higher surface bond breakage and active site formation at high collision energy. Overall, the aging process of these ion-deposited films appeared similar to that of plasma-deposited films. Mass-selected 50 eV C3F5+ ion deposition was employed to create chemical gradient thin films on polymethylmethacrylate (PMMA) by variation of the ion fluence across the substrate surface. The surface chemistry
Enzymatic minimum free energy path calculations using swarms of trajectories.
Sanchez-Martinez, Melchor; Field, Martin; Crehuet, Ramon
2015-01-22
The development of approaches for simulating rare events in complex molecular systems is a central concern in chemical physics. In recent work, Roux and co-workers proposed a novel, swarms of trajectories (SoT) method for determining the transition paths of such events. It consists of the dynamical refinement on the system's free energy surface of a putative transition path that is parametrized in terms of a set of collective variables (CVs) that are identified as being important for the transition. In this work, we have implemented the SoT method and used it to investigate the catalytic mechanisms of two enzymatic reactions using hybrid QM/MM potentials. Our aim has been to test the performance of SoT for enzyme systems and to devise robust simulation protocols that can be employed in future studies of this type. We identify the conditions under which converged results can be obtained using inertial and Brownian dynamical evolutions of the CVs, show that the inclusion of several CVs can give significant additional insight into the mechanisms of the reactions, and show that the use of minimum energy paths as starting guesses can greatly accelerate path refinement.
Engineering Properties of Superhard Films with Ion Energy and Post-Deposition Processing
Monteiro, Othon R.; Delplancke-Ogletree, Marie-Paule
2003-08-26
Recent developments in plasma synthesis of hard materials using energetic ions are described. Metal Plasma Immersion Ion Implantation and Deposition (MePIIID) has been used to prepare several hard films: from diamondlike carbon (DLC) to carbides, from nitrides to oxides. The energy of the depositing species is controlled to maximize adhesion as well as to change the physical and chemical properties of the films. Adhesion is promoted by the creation of a graded interface between the film and the substrate. The energy of the depositing ions is also used to modify and control the intrinsic stresses and the microstructure of the films. The deposition is carried out at room temperature, which is important for temperature sensitive substrates. A correlation between intrinsic stresses and the energetics of the deposition is presented for the case of DLC films, and means to reduce stress levels are discussed.
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.
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.
A surface hopping algorithm for nonadiabatic minimum energy path calculations.
Schapiro, Igor; Roca-Sanjuán, Daniel; Lindh, Roland; Olivucci, Massimo
2015-02-15
The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.
NASA Astrophysics Data System (ADS)
Zhang, Dawei
2017-03-01
Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.
Zhang, Dawei
2017-01-01
Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems. PMID:28300179
Glushkov, Alexander V.; Gurnitskaya, E.P.; Loboda, A.V.
2005-10-26
Advanced quantum approach to calculation of spectra for superheavy ions with an account of relativistic, correlation, nuclear, radiative effects is developed and based on the gauge invariant quantum electrodynamics (QED) perturbation theory (PT). The Lamb shift polarization part is calculated in the Ueling approximation, self-energy part is defined within a new non-PT procedure of Ivanov-Ivanova. Calculation results for energy levels, hyperfine structure parameters of some heavy elements ions are presented.
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.
Radial dose distributions from protons of therapeutic energies calculated with Geant4-DNA.
Wang, He; Vassiliev, Oleg N
2014-07-21
Models based on the amorphous track structure approximation have been successful in predicting the biological effects of heavy charged particles. Development of such models remains an active area of research that includes applications to hadrontherapy. In such models, the radial distribution of the dose deposited by delta electrons and directly by the particle is the main characteristic of track structure. We calculated these distributions with Geant4-DNA Monte Carlo code for protons in the energy range from 10 to 100 MeV. These results were approximated by a simple formula that combines the well-known inverse square distance dependence with two factors that eliminate the divergence of the radial dose integral at both small and large distances. A clear physical interpretation is given to the asymptotic behaviour of the radial dose distribution resulting from these two factors. The proposed formula agrees with the Monte Carlo data within 10% for radial distances of up to 10 μm, which corresponds to a dose range covering over eight orders of magnitude. Differences between our results and those of previously published analytical models are discussed.
Radial dose distributions from protons of therapeutic energies calculated with Geant4-DNA
NASA Astrophysics Data System (ADS)
Wang, He; Vassiliev, Oleg N.
2014-07-01
Models based on the amorphous track structure approximation have been successful in predicting the biological effects of heavy charged particles. Development of such models remains an active area of research that includes applications to hadrontherapy. In such models, the radial distribution of the dose deposited by delta electrons and directly by the particle is the main characteristic of track structure. We calculated these distributions with Geant4-DNA Monte Carlo code for protons in the energy range from 10 to 100 MeV. These results were approximated by a simple formula that combines the well-known inverse square distance dependence with two factors that eliminate the divergence of the radial dose integral at both small and large distances. A clear physical interpretation is given to the asymptotic behaviour of the radial dose distribution resulting from these two factors. The proposed formula agrees with the Monte Carlo data within 10% for radial distances of up to 10 μm, which corresponds to a dose range covering over eight orders of magnitude. Differences between our results and those of previously published analytical models are discussed.
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.
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.
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.
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.
Jin, Xinsheng; Zhang, John Z H; He, Xiao
2017-03-30
In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.
Gapsys, Vytautas; Seeliger, Daniel; de Groot, Bert L
2012-07-10
The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations.
Demireva, Maria; Williams, Evan R
2010-07-01
The internal energy deposited in both on- and off-resonance collisional activation in Fourier transform ion cyclotron resonance mass spectrometry is measured with ion nanocalorimetry and is used to obtain information about the dissociation energy and entropy of a protonated peptide. Activation of Na(+)(H(2)O)(30) results in sequential loss of water molecules, and the internal energy of the activated ion can be obtained from the abundances of the product ions. Information about internal energy deposition in on-resonance collisional activation of protonated peptides is inferred from dissociation data obtained under identical conditions for hydrated ions that have similar m/z and degrees-of-freedom. From experimental internal energy deposition curves and Rice-Ramsperger-Kassel-Marcus (RRKM) theory, dissociation data as a function of collision energy for protonated leucine enkephalin, which has a comparable m/z and degrees-of-freedom as Na(+)(H(2)O)(30), are modeled. The threshold dissociation energies and entropies are correlated for data acquired at a single time point, resulting in a relatively wide range of threshold dissociation energies (1.1 to 1.7 eV) that can fit these data. However, this range of values could be significantly reduced by fitting data acquired at different dissociation times. By measuring the internal energy of an activated ion, the number of fitting parameters necessary to obtain information about the dissociation parameters by modeling these data is reduced and could result in improved accuracy for such methods.
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.
Neuhauser, Daniel; Rabani, Eran; Baer, Roi
2013-04-04
A fast method is developed for calculating the random phase approximation (RPA) correlation energy for density functional theory. The correlation energy is given by a trace over a projected RPA response matrix, and the trace is taken by a stochastic approach using random perturbation vectors. For a fixed statistical error in the total energy per electron, the method scales, at most, quadratically with the system size; however, in practice, due to self-averaging, it requires less statistical sampling as the system grows, and the performance is close to linear scaling. We demonstrate the method by calculating the RPA correlation energy for cadmium selenide and silicon nanocrystals with over 1500 electrons. We find that the RPA correlation energies per electron are largely independent of the nanocrystal size. In addition, we show that a correlated sampling technique enables calculation of the energy difference between two slightly distorted configurations with scaling and a statistical error similar to that of the total energy per electron.
Mechanisms of ignition by transient energy deposition: Regimes of combustion wave propagation
NASA Astrophysics Data System (ADS)
Kiverin, A. D.; Kassoy, D. R.; Ivanov, M. F.; Liberman, M. A.
2013-03-01
Regimes of chemical reaction wave propagating in reactive gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied depending on the characteristics of a transient thermal energy deposition localized in a finite volume of reactive gas. Different regimes of the reaction wave propagation are initiated depending on the amount of deposited thermal energy, power of the source, and the size of the hot spot. The main parameters which define regimes of the combustion waves facilitated by the transient deposition of thermal energy are acoustic time scale, duration of the energy deposition, ignition time scale, and size of the hot spot. The interplay between these parameters specifies the role of gasdynamical processes, the formation and steepness of the temperature gradient, and speed of the spontaneous wave. The obtained results show how ignition of one or another combustion regime depends on the value of energy, rate of the energy deposition, and size of the hot spot, which is important for the practical use and for risk assessment.
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.
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.
On the role of energy deposition in triggering SEGR in power MOSFETs
Selva, L.E.; Swift, G.M.; Taylor, W.A.; Edmonds, L.D.
1999-12-01
Single event gate rupture (SEGR) was studied using three types of power MOSFET devices with ions having incident linear energy transfers (LETs) in silicon from 26 to 82 MeV{center{underscore}dot}cm{sup 2}/mg. Results are: (1) consistent with Wrobel's oxide breakdown for V{sub DS} = 0 volts (for both normal incidence and angle); and (2) when V{sub GS} = 0 volts, energy deposited near the Si/SiO{sub 2} interface is more important than the energy deposited deeper in the epi.
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil
2013-01-28
Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.charmm-gui.org/input/gbinding ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil
2013-01-01
Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly web interface, CHARMM-GUI Ligand Binder (http://www.charmm-gui.org/input/gbinding), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently setup the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three non-polar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). CHARMM-GUI Ligand Binder provides a convenient and reliable way to setup the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems. PMID:23205773
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.
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.
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.
Efficiency of free-energy calculations of spin lattices by spectral quantum algorithms
Master, Cyrus P.; Yamaguchi, Fumiko; Yamamoto, Yoshihisa
2003-03-01
Ensemble quantum algorithms are well suited to calculate estimates of the energy spectra for spin-lattice systems. Based on the phase estimation algorithm, these algorithms efficiently estimate discrete Fourier coefficients of the density of states. Their efficiency in calculating the free energy per spin of general spin lattices to bounded error is examined. We find that the number of Fourier components required to bound the error in the free energy due to the broadening of the density of states scales polynomially with the number of spins in the lattice. However, the precision with which the Fourier components must be calculated is found to be an exponential function of the system size.
NASA Astrophysics Data System (ADS)
Mamedov, Bahtiyar Akber; Copuroglu, Ebru
2017-02-01
By using the Löwdin-α function method, we have analytically calculated the two-center kinetic energy integrals over Slater type orbitals (STOs). The two-center kinetic energy integrals are presented in terms of the two-center overlap integrals. A new approach is applicable to accurate calculations of two-center kinetic energy integral over STOs for arbitrary values of scaling parameters and interatomic distances. Obtained results show that the proposed method is easy to apply to the real systems, and has better calculation CPU time with compared to the existing approximations.
Simoncini, David; Nakata, Hiroya; Ogata, Koji; Nakamura, Shinichiro; Zhang, Kam Yj
2015-02-01
Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.
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.
Photon Energy Deposition in Strong-Field Single Ionization of Multielectron Molecules.
Zhang, Wenbin; Li, Zhichao; Lu, Peifen; Gong, Xiaochun; Song, Qiying; Ji, Qinying; Lin, Kang; Ma, Junyang; He, Feng; Zeng, Heping; Wu, Jian
2016-09-02
Molecules exposed to strong laser fields may coherently absorb multiple photons and deposit the energy into electrons and nuclei, triggering the succeeding dynamics as the primary stage of the light-molecule interaction. We experimentally explore the electron-nuclear sharing of the absorbed photon energy in above-threshold multiphoton single ionization of multielectron molecules. Using CO as a prototype, vibrational and orbital resolved electron-nuclear sharing of the photon energy is observed. Different from the simplest one- or two-electron systems, the participation of the multiple orbitals and the coupling of various electronic states in the strong-field ionization and dissociation processes alter the photon energy deposition dynamics of the multielectron molecule. The population of numerous vibrational states of the molecular cation as the energy reservoir in the ionization process plays an important role in photon energy sharing between the emitted electron and the nuclear fragments.
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.
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.
2015-08-24
wind density enhancement, followed by solar wind dynamic pressure pulses that trigger excess low- energy particle flux to the upper atmosphere; (2...state and input solar and auroral activity. Our results suggest that GLOWfast may be even more appropriate for low characteristic energy auroral...AFRL-AFOSR-VA-TR-2015-0247 Framework for Understanding Global Versus Local Energy Deposition into the Ionosphere and Thermosphere Joachim Raeder
[Calculation of energy losses in the participants of the skiing expedition to the North Pole].
Efremov, V V; Ushakov, A S; Khmelevskiĭ, Iu I
1983-01-01
During the expedition to the North Pole, the food consumption rates were calculated on a regular basis. The mean daily energy losses of the participants of the expedition, the energy losses during skiing with a rucksack across the drifting ice were estimated and the energy metabolism curve by days was built up. The body weight of the participants averaged 78 +/- 5 kg. This made it possible to perform an overall calculation per whole group. The total energy supply with food was appraised from the total amount of the food consumed during the expedition. The total body weight loss of the participants was 11.5 kg, the energy consumption being 100.000 kkal. The total (for 7 men) energy consumption during skiing without a rucksack was calculated according to the formula: [(2,770 kkal X 28.5 days)]+ +[(2,385 kkal X 35.5 days)]. It was thus found to be equal to 1.145.300 kkal. The total energy consumption during skiing with a rucksack was calculated according to the formula: (7 men X X 449 h) and was found to be equal to 1.883.200 kkal. The total energy consumption during the expedition amounted to 3.237.500 kkal. During the expedition, the daily energy deficiency per man was 1.300-1.500 kkal. This deficiency was compensated for during rest. The maintenance of such an energy supply pattern made it possible to preserve a high level of work fitness.
NASA Astrophysics Data System (ADS)
Wang, Y. Y.; Grygiel, C.; Dufour, C.; Sun, J. R.; Wang, Z. G.; Zhao, Y. T.; Xiao, G. Q.; Cheng, R.; Zhou, X. M.; Ren, J. R.; Liu, S. D.; Lei, Y.; Sun, Y. B.; Ritter, R.; Gruber, E.; Cassimi, A.; Monnet, I.; Bouffard, S.; Aumayr, F.; Toulemonde, M.
2014-07-01
Modification of surface and bulk properties of solids by irradiation with ion beams is a widely used technique with many applications in material science. In this study, we show that nano-hillocks on CaF2 crystal surfaces can be formed by individual impact of medium energy (3 and 5 MeV) highly charged ions (Xe22+ to Xe30+) as well as swift (kinetic energies between 12 and 58 MeV) heavy xenon ions. For very slow highly charged ions the appearance of hillocks is known to be linked to a threshold in potential energy (Ep) while for swift heavy ions a minimum electronic energy loss per unit length (Se) is necessary. With our results we bridge the gap between these two extreme cases and demonstrate, that with increasing energy deposition via Se the Ep-threshold for hillock production can be lowered substantially. Surprisingly, both mechanisms of energy deposition in the target surface seem to contribute in an additive way, which can be visualized in a phase diagram. We show that the inelastic thermal spike model, originally developed to describe such material modifications for swift heavy ions, can be extended to the case where both kinetic and potential energies are deposited into the surface.
Wang, Y Y; Grygiel, C; Dufour, C; Sun, J R; Wang, Z G; Zhao, Y T; Xiao, G Q; Cheng, R; Zhou, X M; Ren, J R; Liu, S D; Lei, Y; Sun, Y B; Ritter, R; Gruber, E; Cassimi, A; Monnet, I; Bouffard, S; Aumayr, F; Toulemonde, M
2014-07-18
Modification of surface and bulk properties of solids by irradiation with ion beams is a widely used technique with many applications in material science. In this study, we show that nano-hillocks on CaF2 crystal surfaces can be formed by individual impact of medium energy (3 and 5 MeV) highly charged ions (Xe(22+) to Xe(30+)) as well as swift (kinetic energies between 12 and 58 MeV) heavy xenon ions. For very slow highly charged ions the appearance of hillocks is known to be linked to a threshold in potential energy (Ep) while for swift heavy ions a minimum electronic energy loss per unit length (Se) is necessary. With our results we bridge the gap between these two extreme cases and demonstrate, that with increasing energy deposition via Se the Ep-threshold for hillock production can be lowered substantially. Surprisingly, both mechanisms of energy deposition in the target surface seem to contribute in an additive way, which can be visualized in a phase diagram. We show that the inelastic thermal spike model, originally developed to describe such material modifications for swift heavy ions, can be extended to the case where both kinetic and potential energies are deposited into the surface.
CAS SCF/CI calculations of potential energy surfaces of He 3+ and He 2+
NASA Astrophysics Data System (ADS)
Balasubramanian, K.; Liao, M. Z.; Lin, S. H.
1987-12-01
Complete active space MC SCF (CAS SCF) calculations followed by second-order configuration interaction (SOCI) calculations are carried out on the potential energy surfaces (bending surface, linear surfaces) of the 2Σ g+ ground state of He 3+. The potential minimum for the 2Σ g+ state occurs at a linear geometry with HeHe bond length of 1.248 Å. The binding energy of He 3+ with respect to He + He + + He was calculated to be 2.47 eV at the SOCI level. The energy required to dissociate He 3+ ( 2Σ g+) into He 2+ ( 2Σ u+) and He( 1S) is calculated to be 0.14 eV. The same level of SOCI calculations of He 2+ yield a De value of 2.36 eV.
Gold deposited on a Ge(0 0 1) surface: DFT calculations
NASA Astrophysics Data System (ADS)
Tsay, Shiow-Fon
2016-11-01
The atomic geometry, stability and electronic properties of self-organized Au induced nanowires on a Ge(0 0 1) surface are investigated based on the density-functional theory in the generalized gradient approximation and the stoichiometry of Au. According to the formation energy and the simulated STM image, the Ge atoms substituted by the Au atoms have been confirmed as occurring at a Au coverage lower than 0.25 Ml. The STM image with single and double dimer vacancies looks like the Au atoms have penetrated the subsurface. The energetically favorable dimer-row arrayed structures at 0.50 Ml and 0.75 Ml Au coverages have a 4 × 1, 4 × 2 or c(8 × 2) transition symmetry, which comprise a flat Au-Au homodimer row and an alternating various buckling phase Ge-Ge or Au-Ge dimer row. The c(8 × 2) zigzag-shaped protruding chains of shallow-groove STM images are highly consistent with the observations, but a long-range order dimer-row arrayed structure formation requires sufficient mobile energy to complete mass transport of the substituted Ge atoms in order to avoid the re-adsorption of these atoms; otherwise a deep-groove structure reconstruction is sequentially formed. A quasi-1D electron-like energy trough aligns in the direction perpendicular to the nanowire of the dimer-row arrayed structure in the c(8 × 2) phase on a 0.75 Ml Au/Ge(0 0 1) surface, which is contributed by the Au-Ge dimer rows and the subsurface Ge atoms below them. The bottom energy of the energy trough is consistent with angle-resolved photo-emission spectroscopy studies (Schäfer et al 2008 Phys. Rev. Lett. 101 236802, Meyer et al 2011 Phys. Rev. B 83 121411(R)).
On the Surface Free Energy of PVC/EVA Polymer Blends: Comparison of Different Calculation Methods.
Michalski; Hardy; Saramago
1998-12-01
The surface free energy of polymeric films of polyvinylchloride (PVC) + poly(ethylene-co-vinylacetate) (EVA) blends was calculated using the van Oss treatment (Lifshitz and electron donor-electron acceptor components of surface free energy) and the Owens-Wendt treatment (dispersive and nondispersive components of surface free energy). Surface free energy results were found to be greatly dependent on the calculation method and on the number of standard liquids used for contact angle measurements. The nondispersive/donor-acceptor surface free energy component and the total surface free energy of polymeric films were always higher when the van Oss treatment was used compared to the Owens-Wendt treatment. Conversely, both methods led to similar apolar/Lifshitz components. All the calculation methods were in good agreement for the surface free energy of PVC; however, a discrepancy between the methods arose as EVA content in the blends increased. It seems that there is not yet a definite solution for the calculation of solid surface free energy. Further developments of existing models are needed in order to gain consistency when calculating this important physicochemical quantity. Copyright 1998 Academic Press.
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.
Effect of Mach number on the efficiency of microwave energy deposition in supersonic flow
NASA Astrophysics Data System (ADS)
Lashkov, V. A.; Karpenko, A. G.; Khoronzhuk, R. S.; Mashek, I. Ch.
2016-05-01
The article is devoted to experimental and numerical studies of the efficiency of microwave energy deposition into a supersonic flow around the blunt cylinder at different Mach numbers. Identical conditions for energy deposition have been kept in the experiments, thus allowing to evaluate the pure effect of varying Mach number on the pressure drop. Euler equations are solved numerically to model the corresponding unsteady flow compressed gas. The results of numerical simulations are compared to the data obtained from the physical experiments. It is shown that the momentum, which the body receives during interaction of the gas domain modified by microwave discharge with a shock layer before the body, increases almost linearly with rising of Mach number and the efficiency of energy deposition also rises.
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.
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.
Void formation in amorphous germanium due to high electronic energy deposition
Gaertner, K.; Joehrens, J.; Steinbach, T.; Schnohr, C. S.; Wesch, W.; Ridgway, M. C.
2011-06-01
The effect of high electronic energy deposition in amorphous germanium has been studied experimentally by Au irradiation with ion energies of up to 185 MeV and different angles of incidence and by molecular dynamics computer simulations. In both cases, the energy deposition leads to void formation accompanied by strong swelling of the amorphous germanium. The simulation results prove that the formation of the voids is mainly based on a shock wave mechanism and the swelling is determined by the competing processes of the formation and growth of voids on the one hand and the shrinking and annihilation of voids on the other hand. In full agreement between experiment and simulation, the amount of the swelling is a linear function of the total energy deposited into electronic processes and there exists a threshold value of the electronic energy loss per ion and depth for swelling. A comparison of the threshold values obtained by the experiment and the simulation suggests that approximately 20% of the energy deposited into electronic processes is converted into atomic motion.
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.
Microscopic Calculation of Fission Fragment Energies for the 239Pu(nth,f) Reaction
Younes, W; Gogny, D
2011-10-03
We calculate the total kinetic and excitation energies of fragments produced in the thermal-induced fission of {sup 239}Pu. This result is a proof-of-principle demonstration for a microscopic approach to the calculation of fission-fragment observables for applied data needs. In addition, the calculations highlight the application of a fully quantum mechanical description of scission, and the importance of exploring scission configurations as a function of the moments of the fragments, rather than through global constraints on the moments of the fissioning nucleus. Using a static microscopic calculation of configurations at and near scission, we have identified fission fragments for the {sup 239}Pu (n{sub th}, f) reaction and extracted their total kinetic and excitation energies. Comparison with data shows very good overall agreement between theory and experiment. Beyond their success as a proof of principle, these calculations also highlight the importance of local constraints on the fragments themselves in microscopic calculations.
On the consequences of the energy imbalance for calculating surface conductance to water vapour
Wohlfahrt, Georg; Haslwanter, Alois; Hörtnagl, Lukas; Jasoni, Richard L.; Fenstermaker, Lynn F.; Arnone, John A.; Hammerle, Albin
2014-01-01
The Penman-Monteith combination equation, which is most frequently used to derive the surface conductance to water vapour (Gs), implicitly assumes the energy balance to be closed. Any energy imbalance (positive or negative) will thus affect the calculated Gs. Using eddy covariance energy flux data from a temperate grassland and a desert shrub ecosystem we explored five possible approaches of closing the energy imbalance and show that calculated Gs may differ considerably between these five approaches depending on the relative magnitudes of sensible and latent heat fluxes, and the magnitude and sign of the energy imbalance. Based on our limited understanding of the nature of the energy imbalance, we tend to favour an approach which preserves the Bowen-ratio and closes the energy balance on a larger time scale. PMID:24465070
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.
Kadmensky, S. G. Titova, L. V.; Pen'kov, N. V.
2006-08-15
In the framework of quantum-mechanical fission theory, the method of calculation for partial fission width amplitudes and asymptotic behavior of the fissile nucleus wave function with strong channel coupling taken into account has been suggested. The method allows one to solve the calculation problem of angular and energy distribution countation for binary and ternary fission.
A Template-Matching Method For Measuring Energy Depositions In TES Films
NASA Astrophysics Data System (ADS)
Shank, Benjamin; Yen, Jeffrey; Cabrera, Blas; Kreikebaum, John Mark; Moffatt, Robert; Redl, Peter; Young, Betty; Brink, Paul; Cherry, Matthew; Tomada, Astrid
2014-03-01
Transition edge sensors (TES) have a wide variety of applications in particle ∖astrophysics for detecting incoming particles with high energy resolution. In TES design, the need for sufficient heat capacity to avoid saturation limits the ultimate energy resolution. Building on the TES model developed for SuperCDMS by Yen et al. for tungsten TESs deposited next to aluminum collection fins, we outline a time-domain non-linear optimal filter method for reconstructing energy depositions in TES films. This allows us to operate devices into their saturation region while taking into account changing noise performance and loss of energy collection. We show how this method has improved our understanding of quasiparticle diffusion and energy collection in our superconducting sensors.
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.
Extended bulk defects induced by low-energy ions during partially ionized beam deposition
Lee, W.I.; Wong, J.; Borrego, J.M.; Lu, T.
1988-08-15
The study of possible defects generated by low-energy ions during partially ionized beam (PIB) depositions was performed. No defects were observed when acceleration voltage was set lower than 1 kV. Surprisingly, several deep levels were detected up to the depth of 4000 A in the 3-kV sample. However, these levels can be annealed out at a relatively low temperature of 400 /sup 0/C. It is concluded in this study that, by properly choosing the ion energy range, PIB deposition will not cause severe damage to the substrate and can be a viable technique for growing heterostructures.
Amorphization due to electronic energy deposition in defective strontium titanate
Xue, Haizhou; Zarkadoula, Eva; Liu, Peng; ...
2017-01-27
The synergistic interaction of electronic energy loss by ions with ion-induced defects created by elastic nuclear scattering processes has been investigated for single crystal SrTiO3. An initial pre-damaged defect state corresponding to a relative disorder level of 0.10–0.15 sensitizes the SrTiO3 to amorphous track formation along the ion path of 12 and 20 MeV Ti, 21 MeV Cl and 21 MeV Ni ions, where Ti, Cl and Ni ions otherwise do not produce amorphous or damage tracks in pristine SrTiO3. The electronic stopping power threshold for amorphous ion track formation is found to be 6.7 keV/nm for the pre-damaged defectmore » state studied in this work. Lastly, these results suggest the possibility of selectively producing nanometer scale, amorphous ion tracks in thin films of epitaxial SrTiO3.« less
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
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.
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)
Solar and internal gain adjustments in calculation of energy conservation savings
NASA Astrophysics Data System (ADS)
Christensen, C.; Wortman, D.
1983-07-01
Heating degree days are often used as a climatic measure in building energy calculations. To account for the effects of solar and internal gains, degree days at a lower base temperature are sometimes used, or the number of degree days is adjusted downward by a degree-day correction factor. A theoretical derivation which demonstrates that ASHRAE (American Society of Heating, Refrigerating, and Air-Conditioning Engineers) C sub d factors are not the appropriate correction factors for calculation of energy savings from envelope conservation measures is presented. The results of this derivation can be used to develop new correlation factors appropriate for savings calculations.
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…
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}
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...
Zero-point energy constraint in quasi-classical trajectory calculations.
Xie, Zhen; Bowman, Joel M
2006-04-27
A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.
Hiking down the energy landscape: progress toward the Kauzmann temperature via vapor deposition.
Kearns, Kenneth L; Swallen, Stephen F; Ediger, M D; Wu, Tian; Sun, Ye; Yu, Lian
2008-04-24
Physical vapor deposition was employed to prepare amorphous samples of indomethacin and 1,3,5-(tris)naphthylbenzene. By depositing onto substrates held somewhat below the glass transition temperature and varying the deposition rate from 15 to 0.2 nm/s, glasses with low enthalpies and exceptional kinetic stability were prepared. Glasses with fictive temperatures that are as much as 40 K lower than those prepared by cooling the liquid can be made by vapor deposition. As compared to an ordinary glass, the most stable vapor-deposited samples moved about 40% toward the bottom of the potential energy landscape for amorphous materials. These results support the hypothesis that enhanced surface mobility allows stable glass formation by vapor deposition. A comparison of the enthalpy content of vapor-deposited glasses with aged glasses was used to evaluate the difference between bulk and surface dynamics for indomethacin; the dynamics in the top few nanometers of the glass are about 7 orders of magnitude faster than those in the bulk at Tg - 20 K.
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)
A universal method to calculate the surface energy density of spherical surfaces in crystals
NASA Astrophysics Data System (ADS)
Wang, Jian; Bian, Jianjun; Niu, Xinrui; Wang, Gangfeng
2017-02-01
Surface energy plays an important role in the mechanical performance of nanomaterials; however, determining the surface energy density of curved surfaces remains a challenge. In this paper, we conduct atomic simulations to calculate the surface energy density of spherical surfaces in various crystalline metals. It is found that the average surface energy density of spherical surfaces remains almost constant once its radius exceeds 5 nm. Then, using a geometrical analysis and the scaling law, we develop an analytical approach to estimate the surface energy density of spherical surfaces through that of planar surfaces. The theoretical prediction agrees well with the direct atomic simulations, and thus provides a simple and general method to calculate the surface energy density in crystals.
Caro, M A; Schulz, S; O'Reilly, E P
2013-01-16
We explore the calculation of the elastic properties of zinc-blende and wurtzite semiconductors using two different approaches: one based on stress and the other on total energy as a function of strain. The calculations are carried out within the framework of density functional theory in the local density approximation, with the plane wave-based package VASP. We use AlN as a test system, with some results also shown for selected other materials (C, Si, GaAs and GaN). Differences are found in convergence rate between the two methods, especially in low symmetry cases, where there is a much slower convergence for total energy calculations with respect to the number of plane waves and k points used. The stress method is observed to be more robust than the total energy method with respect to the residual error in the elastic constants calculated for different strain branches in the systems studied.
The Activation Energy Of Ignition Calculation For Materials Based On Plastics
NASA Astrophysics Data System (ADS)
Rantuch, Peter; Wachter, Igor; Martinka, Jozef; Kuracina, Marcel
2015-06-01
This article deals with the activation energy of ignition calculation of plastics. Two types of polyamide 6 and one type of polypropylene and polyurethane were selected as samples. The samples were tested under isothermal conditions at several temperatures while times to ignition were observed. From the obtained data, activation energy relating to the moment of ignition was calculated for each plastics. The values for individual plastics were different. The highest activation energies (129.5 kJ.mol-1 and 106.2 kJ.mol-1) were achieved by polyamides 6, while the lowest was determined for a sample of polyurethane.
The calculations of small molecular conformation energy differences by density functional method
NASA Astrophysics Data System (ADS)
Topol, I. A.; Burt, S. K.
1993-03-01
The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.
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.
Energy deposition through radiative processes in absorbers irradiated by electron beams
NASA Astrophysics Data System (ADS)
Tatsuo, Tabata; Pedro, Andreo; Kunihiko, Shinoda; Rinsuke, Ito
1994-09-01
The component of energy deposition due to radiative processes (bremsstrahlung component) in absorbers irradiated by electron beams has been computed together with the total energy deposition by using the ITS Monte Carlo system version 3.0. Plane-parallel electron beams with energies from 0.1 to 100 MeV have been assumed to be incident normally on the slab absorber, whose thickness is 2.5 times the continuous slowing-down approximation (csda) range of the incident electrons. Absorber materials considered are elemental solids with atomic numbers between 4 and 92 (Be, C, Al, Cu, Ag, Au and U). An analytic formula is given to express the depth profile of the bremsstrahlung component as a function of scaled depth (depth in units of the csda range), incident-electron energy and absorber atomic number. It is also applicable to compounds.
Energy Deposition and Shielding Study of the Front End for the Neutrino Factory
Snopok, Pavel; Neuffer, David; Rogers, Chris
2013-06-01
In the Neutrino Factory and Muon Collider muons are produced by firing high energy protons onto a target to produce pions. The pions decay to muons which are then accelerated. This method of pion production results in significant background from protons and electrons, which may result in heat deposition on superconducting materials and activation of the machine preventing manual handling. In this paper we discuss the design of a secondary particle handling system. The system comprises a solenoidal chicane that filters high momentum particles, followed by a proton absorber that reduces the energy of all particles, resulting in the rejection of low energy protons that pass through the solenoid chicane. We detail the design and optimization of the system and energy deposition and shielding analysis in MARS15.
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.
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.
NASA Astrophysics Data System (ADS)
Chen, Z. J.; Xiao, H. Y.; Zu, X. T.; Gao, F.
2008-11-01
The electronic structures and defect formation energies for a series of stannate pyrochlores Ln2Sn2O7 (Ln=La, Pr, Nd, Sm, Gd, Tb, Ho, Er, Lu, and Y) have been investigated using the first-principles total energy calculations. The calculated results show that Ln-site cation ionic radius, x-O48f, lattice constant and the covalency of the ⟨Sn-O48f⟩ bond have a significant affect on the defect formation energies. The cation-antisite defect has the lowest formation energy, as compared with that of other defects, indicating that cation disorder causes local oxygen disordering. The present studies suggest that Lu2Sn2O7 is the most resistant to ion beam-induced amorphization. The electronic structure calculations reveal that Ln2Sn2O7 compounds have direct band gaps of 2.64-2.95 eV at the Γ point in the Brillouin zone.
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.
Energy bandgap variation in oblique angle-deposited indium tin oxide
Kim, Kyurin; Kim, Hyunsoo; Cho, Jaehee; Park, Jun Hyuk; Kim, Jong Kyu; Fred Schubert, E.
2016-01-25
Indium tin oxide (ITO) thin films deposited using the oblique angle deposition (OAD) technique exhibit a strong correlation between structural and optical properties, especially the optical bandgap energy. The microstructural properties of ITO thin films are strongly influenced by the tilt angle used during the OAD process. When changing the tilt angle, the refractive index, porosity, and optical bandgap energy of ITO films also change due to the existence of a preferential growth direction at the interface between ITO and the substrate. Experiments reveal that the ITO film's optical bandgap varies from 3.98 eV (at normal incident deposition) to 3.87 eV (at a 60° tilt angle)
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.
NASA Astrophysics Data System (ADS)
Elliott, S. D.; Dey, G.; Maimaiti, Y.
2017-02-01
Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.
Elliott, S D; Dey, G; Maimaiti, Y
2017-02-07
Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.
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.
2016-01-01
Electrode materials play a decisive role in almost all electrochemical energy storage devices, determining their overall performance. Proper selection, design and fabrication of electrode materials have thus been regarded as one of the most critical steps in achieving high electrochemical energy storage performance. As an advanced nanotechnology for thin films and surfaces with conformal interfacial features and well controllable deposition thickness, atomic layer deposition (ALD) has been successfully developed for deposition and surface modification of electrode materials, where there are considerable issues of interfacial and surface chemistry at atomic and nanometer scale. In addition, ALD has shown great potential in construction of novel nanostructured active materials that otherwise can be hardly obtained by other processing techniques, such as those solution‐based processing and chemical vapor deposition (CVD) techniques. This review focuses on the recent development of ALD for the design and delivery of advanced electrode materials in electrochemical energy storage devices, where typical examples will be highlighted and analyzed, and the merits and challenges of ALD for applications in energy storage will also be discussed. PMID:27840793
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.
Guan, Cao; Wang, John
2016-10-01
Electrode materials play a decisive role in almost all electrochemical energy storage devices, determining their overall performance. Proper selection, design and fabrication of electrode materials have thus been regarded as one of the most critical steps in achieving high electrochemical energy storage performance. As an advanced nanotechnology for thin films and surfaces with conformal interfacial features and well controllable deposition thickness, atomic layer deposition (ALD) has been successfully developed for deposition and surface modification of electrode materials, where there are considerable issues of interfacial and surface chemistry at atomic and nanometer scale. In addition, ALD has shown great potential in construction of novel nanostructured active materials that otherwise can be hardly obtained by other processing techniques, such as those solution-based processing and chemical vapor deposition (CVD) techniques. This review focuses on the recent development of ALD for the design and delivery of advanced electrode materials in electrochemical energy storage devices, where typical examples will be highlighted and analyzed, and the merits and challenges of ALD for applications in energy storage will also be discussed.
Energy deposition in scintillation detectors and the triggers formation in the GAMMA-400 experiment
NASA Astrophysics Data System (ADS)
Arkhangelskaja, Irene; Yurkin, Yuri T.; Arkhangelsky, Andrey; Topchiev, Nikolay; Kheymits, Maxim; Chasovikov, Evgeniy; Galper, Arkady; Chistyakov, Pavel
In this paper, some details of the GAMMA-400 trigger system construction are presented. The comparison between relativistic electron, proton, and gamma-ray energy deposition is described and methods of on-board triggers and trigger markers formation for discrimination between each of other are proposed.
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.
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)
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
Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?
Fouda, Adam; Ryde, Ulf
2016-11-08
We have examined how the self-interaction error in density-functional theory (DFT) calculations affects energies calculated on large systems (600-1000 atoms) involving several charged groups. We employ 18 different quantum mechanical (QM) methods, including Hartree-Fock, as well as pure, hybrid, and range-separated DFT methods. They are used to calculate reaction and activation energies for three different protein models in vacuum, in a point-charge surrounding, or with a continuum-solvent model. We show that pure DFT functionals give rise to a significant delocalization of the charges in charged groups in the protein, typically by ∼0.1 e, as evidenced from the Mulliken charges. This has a clear effect on how the surroundings affect calculated reaction and activation energies, indicating that these methods should be avoided for DFT calculations on large systems. Fortunately, methods such as CAM-B3LYP, BHLYP, and M06-2X give results that agree within a few kilojoules per mole, especially when the calculations are performed in a point-charge surrounding. Therefore, we recommend these methods to estimate the effect of the surroundings with large QM systems (but other QM methods may be used to study the intrinsic reaction and activation energies).
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.
First-principle Calculations of Equation of State for Metals at High Energy Density
NASA Astrophysics Data System (ADS)
Minakov, Dmitry; Levashov, Pavel; Khishchenko, Konstantin
2012-02-01
In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and isentropic sound velocity behind the shock front for aluminum. Also we perform similar calculations for nickel and iron. We use the VASP code with ultrasoft and PAW pseudopotentials and GGA exchange-correlation functional. Up to 512 particles have been used in calculations. To calculate Hugoniots we solve the Hugoniot equation numerically. To obtain release isentropes, we use Zel'dovich's approach and integrate an ordinary differential equation for the temperature thus restoring all thermodynamic parameters. Isentropic sound velocity is calculated by differentiation of pressure along isentropes. The results of our calculations are in good agreement with experimental data at densities both higher and lower than the normal one. Thus, quantum molecular dynamics results can be effectively used for verification or calibration of semiempirical equations of state under conditions of lack of experimental information at high energy densities.
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)
Yang, Xue; Hassanein, Ahmed
2014-02-01
Tungsten surface binding energy is calculated using classical molecular dynamic simulations with three many-body potentials. We present the consistency in tungsten sputtering yield by beryllium bombardment between molecular dynamic LAMMPS code and binary collision approximation ITMC code using the new surface binding energy (11.75 eV). The commonly used heat of sublimation value (8.68 eV) could lead to overestimated sputtering yield results. The analysis of the sputtered tungsten angular distributions show that molecular dynamic accurately reproduced the [1 1 1] most prominent preferential ejection directions in bcc tungsten, while the distinct shapes by typical MC codes such as ITMC code is caused by the treatment of amorphous target. The ITMC calculated emitted tungsten energy profile matches the Thompson energy spectrum, while the molecular dynamic results generally follow the Falcone energy spectrum.
Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion
Ryham, Rolf J.; Klotz, Thomas S.; Yao, Lihan; Cohen, Fredric S.
2016-01-01
We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. PMID:26958888
Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.
Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S
2016-03-08
We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm.
Chen, Changjun
2016-03-31
The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.
NASA Astrophysics Data System (ADS)
Lobanov, Igor S.; Jónsson, Hannes; Uzdin, Valery M.
2016-11-01
The mechanism and activation energy for the annihilation of a magnetic skyrmion is studied by finding the minimum energy path for the transition in a system described by a Heisenberg-type Hamiltonian extended to include dipole-dipole, Dzyaloshinskii-Moriya, and anisotropy interactions so as to represent a Co monolayer on a Pt(111) surface. The annihilation mechanism involves isotropic shrinking of the skyrmion and slow increase of the energy until the transition state is reached after which the energy drops abruptly as the ferromagnetic final state forms. The maximum energy along the minimum energy path, which gives an estimate of the activation energy within the harmonic approximation of transition state theory, is found to be in excellent agreement with direct Langevin dynamics simulations at relatively high temperature carried out by Rohart et al. [Phys. Rev. B 93, 214412 (2016), 10.1103/PhysRevB.93.214412]. The dipole-dipole interaction, the computationally most demanding term in the Hamiltonian, is found to be important but its effect on the stability of the skyrmion and shape of the transition path can be mimicked accurately by reducing the anisotropy constant in the Hamiltonian.
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.
Kinetic-energy induced smoothening and delay of epitaxial breakdown in pulsed-laser deposition
Shin, Byungha; Aziz, Michael J.
2007-08-15
We have isolated the effect of kinetic energy of depositing species from the effect of flux pulsing during pulsed-laser deposition (PLD) on surface morphology evolution of Ge(001) homoepitaxy at low temperature (100 deg. C). Using a dual molecular beam epitaxy (MBE) PLD chamber, we compare morphology evolution from three different growth methods under identical experimental conditions except for the differing nature of the depositing flux: (a) PLD with average kinetic energy 300 eV (PLD-KE); (b) PLD with suppressed kinetic energy comparable to thermal evaporation energy (PLD-TH); and (c) MBE. The thicknesses at which epitaxial breakdown occurs are ranked in the order PLD-KE>MBE>PLD-TH; additionally, the surface is smoother in PLD-KE than in MBE. The surface roughness of the films grown by PLD-TH cannot be compared due to the early epitaxial breakdown. These results demonstrate convincingly that kinetic energy is more important than flux pulsing in the enhancement of epitaxial growth, i.e., the reduction in roughness and the delay of epitaxial breakdown.
Calculation of Liquid-Solid Interfacial Free Energy in Pb-Cu Binary Immiscible System
NASA Astrophysics Data System (ADS)
Li, Hong-shan; Zhou, Sheng-gang; Cao, Yong
2016-11-01
Based on the solid-liquid interfacial free energy theory of the complex Warren binary & pseudo-binary system and through the simplification of it by taking Pb-Cu binary system as an example, the physical model for it in binary immiscible system can be obtained. Next, its thermodynamic formula is derived to obtain a theoretical formula that only contains two parameters, and comparisons are made with regard to γSL calculated values and experimental values of MPE (multiphase equilibrium method) under several kinds of temperatures. As manifested in the outcomes, the improved physical model and theoretical formula will become not only easy to understand but also simple for calculation (the calculated value of γSL depends on two parameters, i.e. temperature and percentage composition of Cu atom). It can be treated as the foundation of application for the γSL calculation of liquid-solid interfacial free energy in other immiscible systems.
Robiche, J.; Rax, J.-M.; Bonnaud, G.; Gremillet, L.
2010-03-15
The collisional dynamics of a relativistic electron jet in a magnetized plasma are investigated within the framework of kinetic theory. The relativistic Fokker-Planck equation describing slowing down, pitch angle scattering, and cyclotron rotation is derived and solved. Based on the solution of this Fokker-Planck equation, an analytical formula for the root mean square spot size transverse to the magnetic field is derived and this result predicts a reduction in radial transport. Some comparisons with particle-in-cell simulation are made and confirm striking agreement between the theory and the simulation. For fast electron with 1 MeV typical kinetic energy interacting with a solid density hydrogen plasma, the energy deposition density in the transverse direction increases by a factor 2 for magnetic field of the order of 1 T. Along the magnetic field, the energy deposition profile is unaltered compared with the field-free case.
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.
Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy
NASA Astrophysics Data System (ADS)
Chen, Xi H.; Zhang, John Z. H.
2004-06-01
In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.
Lime-mud layers in high-energy tidal channels: a record of hurricane deposition
Shinn, E.A.; Steinen, R.P.; Dill, R.F.; Major, R.
1993-01-01
During or immediately following the transit of Hurricane Andrew (August 23-24, 1992) across the northern part of the Great Bahama Bank, thin laminated beds of carbonate mud were deposited in high-energy subtidal channels (4 m depth) through the ooid shoals of south Cat Cay and Joulters Cays. Thicker, more cohesive (and therefore older) mud beds and angular mud fragments associated with ooids from Joulters Cays have similar characteristics but lack fresh plant fragments. We infer that these older beds were similarly deposited and thus record the passage of previous hurricanes or tropical storms. -from Authors
1993-11-04
6. AUTHOR(S) P.P. Schmidt Indrani Bhattacharya- Kodali and Gregory Voth 7. PERFORMING ORGANIZATION NAME(S) AND AODRESS(ES) 8. PERIORMING ORGANIZATION...13. ABSTRACT (Maimum 200 words) The extended reference interaction site method (RISM) integral equation theory is applied to calculate the solvent...Integral Equation Calculation of Solvent Activation Free Energies for Electron and Proton Transfer Reactions Indrani Bhattacharya- Kodali and Gregory A. Voth
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.
Nikitin, A V; Rey, M; Tyuterev, Vl G
2015-03-07
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)(-2) type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.
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.
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.
DFT calculations of magnetic anisotropy energy of Ge(1-x)Mn(x)Te ferromagnetic semiconductor.
Łusakowski, A; Bogusławski, P; Story, T
2015-06-10
Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge(1-x)Mn(x)Te were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge(1-x)Mn(x)Te (1 1 1) thin layers.
DFT calculations of magnetic anisotropy energy of Ge1-xMnxTe ferromagnetic semiconductor
NASA Astrophysics Data System (ADS)
Łusakowski, A.; Bogusławski, P.; Story, T.
2015-06-01
Density functional theory (DFT) calculations of the energy of magnetic anisotropy for diluted ferromagnetic semiconductor Ge1-xMnxTe were performed using OpenMX package with fully relativistic pseudopotentials. The influence of hole concentration and magnetic ion neighbourhood on magnetic anisotropy energy is presented. Analysis of microscopic mechanism of magnetic anisotropy is provided, in particular the role of spin-orbit coupling, spin polarization and spatial changes of electron density are discussed. The calculations are in accordance with the experimental observation of perpendicular magnetic anisotropy in rhombohedral Ge1-xMnxTe (1 1 1) thin layers.
Accuracy and precision of free-energy calculations via molecular simulation
NASA Astrophysics Data System (ADS)
Lu, Nandou
A quantitative characterization of the methodologies of free-energy perturbation (FEP) calculations is presented, and optimal implementation of the methods for reliable and efficient calculation is addressed. Some common misunderstandings in the FEP calculations are corrected. The two opposite directions of FEP calculations are uniquely defined as generalized insertion and generalized deletion, according to the entropy change along the perturbation direction. These two calculations are not symmetric; they produce free-energy results differing systematically due to the different capability of each to sample the important phase-space in a finite-length simulation. The FEP calculation errors are quantified by characterizing the simulation sampling process with the help of probability density functions for the potential energy change. While the random error in the FEP calculation is analyzed with a probabilistic approach, the systematic error is characterized as the most-likely inaccuracy, which is modeled considering the poor sampling of low-probability energy distribution tails. Our analysis shows that the entropy difference between the perturbation systems plays a key role in determining the reliability of FEP results, and the perturbation should be carried out in the insertion direction in order to ensure a good sampling and thus a reliable calculation. Easy-to-use heuristics are developed to estimate the simulation errors, as well as the simulation length that ensures a certain accuracy level of the calculation. The fundamental understanding obtained is then applied to tackle the problem of multistage FEP optimization. We provide the first principle of optimal staging: For each substage FEP calculation, the higher entropy system should be used as the reference to govern the sampling, i.e., the calculation should be conducted in the generalized insertion direction for each stage of perturbation. To minimize the simulation error, intermediate states should be
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.
Calculating the rate of exothermic energy release for catalytic converter efficiency monitoring
Hepburn, J.S.; Meitzler, A.H.
1995-12-31
This paper reports on the development of a new methodology for OBD-II catalyst efficiency monitoring. Temperature measurements taken from the center of the catalyst substrate or near the exterior surface of the catalyst brick were used in conjunction with macroscopic energy balances to calculate the instantaneous rate of exothermic energy generation within the catalyst. The total calculated rate of exothermic energy release over the FTP test cycle was within 10% of the actual or theoretical value and provided a good indicator of catalyst light-off for a variety of aged catalytic converters. Normalization of the rate of exothermic energy release in the front section of the converter by the mass flow rate of air inducted through the engine was found to provide a simple yet practical means of monitoring the converter under both FTP and varying types of road driving.
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.
NASA Astrophysics Data System (ADS)
Li, Lei; Zhang, Yiteng
In the electromagnetic environment set by the MHD model (Ma et al.,2004), considering the dynamic feature of O+ ions, the spatial distributions and energy spectra of O+ ions impacting the atmosphere of Mars are calculated by tracing the trajectories of cold O+ ions launched from the sunlit hemisphere. The effects of the crustal fields on the spatial distribution of precipitating O+ ions are investigated by turning on or off the crustal fields. Global maps of precipitating O+ ion flux show that the crustal fields have no significant effect on the spatial distribution of lower energy precipitating ions(<100eV), while the distribution of higher energyprecipitating O+ ions (>100eV) is closely related with the distribution of the crustal fields. Most O+ ions originated in lower exosphere impact day side atmosphere before getting much energy since the electric field is weak there. O+ ions from higher source may impact the atmosphere with higher energy deposition, forming patchy precipitation regions both at dayside and nightside when the crustal fields are present. A precipitation belt formed by high energy O+ ions (around 1keV) is found near the midnight region, revealing that the crustal fields may change the electromagnetic environment near Mars significantly and result in the acceleration of precipitating O+ ions at the nightside. Together with the rotation of the planet, the consequences of the impacting of O+, including heating and sputtering of the atmosphere and ionosphere, should be much more complicated than expected.
Approximate method of free energy calculation for spin system with arbitrary connection matrix
NASA Astrophysics Data System (ADS)
Kryzhanovsky, Boris; Litinskii, Leonid
2015-01-01
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with long-range interaction, where large coordination number q ensures the correctness of the central limit theorem application. However, the method provides good results also for systems with short-range interaction when the number q is not so large.
NASA Astrophysics Data System (ADS)
Dapprich, S.; Pidun, U.; Ehlers, A. W.; Frenking, G.
1995-08-01
The metal-ligand bond dissociation energies (CO) nM-L are theoretically predicted at the HF, MP2 and CCSD(T) levels of theory using effective core potentials for the metals for M = Cr, Mo, W, Ni, Pd, Pt and for L = CO, NO +, CN -, NC -, CS, SiO, N 2. The bond energies at the HF level are too low and the MP2 values are too high, while the CCSD(T) results are in good agreement with experimental data. The bond energies at MP2 show the same trend as the CCSD(T) values and may therefore be used for the prediction of relative bond dissociation energies. The absolute values for the bond energies calculated at MP2 are significantly improved when they are corrected using the energies of isostructural reactions M(CO) n + L → M(CO) n-1 L + CO.
Laser energy density, structure and properties of pulsed-laser deposited zinc oxide films
NASA Astrophysics Data System (ADS)
Tsoutsouva, M. G.; Panagopoulos, C. N.; Kompitsas, M.
2011-05-01
Zinc oxide thin films were deposited on soda lime glass substrates by pulsed laser deposition in an oxygen-reactive atmosphere at 20 Pa and a constant substrate temperature at 300 °C. A pulsed KrF excimer laser, operated at 248 nm with pulse duration 10 ns, was used to ablate the ceramic zinc oxide target. The structure, the optical and electrical properties of the as-deposited films were studied in dependence of the laser energy density in the 1.2-2.8 J/cm 2 range, with the aid of X-ray Diffraction, Atomic Force Microscope, Transmission Spectroscopy techniques, and the Van der Pauw method, respectively. The results indicated that the structural and optical properties of the zinc oxide films were improved by increasing the laser energy density of the ablating laser. The surface roughness of the zinc oxide film increased with the decrease of laser energy density and both the optical bang gap and the electrical resistivity of the film were significantly affected by the laser energy density.
Measurement of Runaway Electron Plateau Final Loss Energy Deposition into Wall of DIII-D
NASA Astrophysics Data System (ADS)
Hollmann, E. M.; Bykov, I.; Moyer, R. A.; Rudakov, D. L.; Commaux, N.; Shiraki, D.; Lasnier, C.; Martin-Solis, R.; Cooper, C.; Eidietis, N.; Parks, P.; Paz-Soldan, C.
2016-10-01
Intentional runaway electron (RE) plateau-wall strikes with different initial impurity levels are used to study the effect of background plasma relativistic electron Z (as well as plasma resistivity for slow electrons) on RE-wall loss dynamics. RE wall loss time is found to be close to the avalanche time (meC/eE| |) 1 nλ √{ 3 (Z + 5) / π } , consistent with REs being lost by a series of MHD reconnection events, with timescale limited by current profile filling via avalanche. Local kinetic energy deposition is estimated with both hard x-ray emission and with infra-red imaging. At higher plasma impurity levels Z 10 , energy deposition appears to be consistent with power balance estimates, as long as collisional dissipation during the final loss event is included. At low impurity levels Z 1 , however, local energy deposition appears around 10 × less than expected, indicating that the energy dissipation at low Z is still poorly understood. Work supported by the US DOE under DE-FG02-07ER54917, DE-AC05-00OR22725, DE-AC52-07NA27344, DE-FC02-04ER54698.
NASA Astrophysics Data System (ADS)
Heath, Emily; Tessier, Frederic; Kawrakow, Iwan
2011-08-01
A new deformable geometry class for the VMC++ Monte Carlo code was implemented based on the voxel warping method. Alternative geometries which use tetrahedral sub-elements were implemented and efficiency improvements investigated. A new energy mapping method, based on calculating the volume overlap between deformed reference dose grid and the target dose grid, was also developed. Dose calculations using both the voxel warping and energy mapping methods were compared in simple phantoms as well as a patient geometry. The new deformed geometry implementation in VMC++ increased calculation times by approximately a factor of 6 compared to standard VMC++ calculations in rectilinear geometries. However, the tetrahedron-based geometries were found to improve computational efficiency, relative to the dodecahedron-based geometry, by a factor of 2. When an exact transformation between the reference and target geometries was provided, the voxel and energy warping methods produced identical results. However, when the transformation is not exact, there were discrepancies in the energy deposited on the target geometry which lead to significant differences in the dose calculated by the two methods. Preliminary investigations indicate that these energy differences may correlate with registration errors; however, further work is needed to determine the usefulness of this metric for quantifying registration accuracy.
Energy Deposition and Condition of the Metal Core in Exploding Wire Experiments
NASA Astrophysics Data System (ADS)
Sarkisov, G. S.; Rosenthal, S. E.; Struve, K. W.; McDaniel, D. H.; Waisman, E. M.; Sasorov, P. V.
2002-11-01
Measurements of the Joule energy deposition into exploding wire and its relation with condition of the expanding wire core are presented. Wires of nine different metals with diameters of 10-30 microns, have been exploded by fast 150A/ns and slow 20A/ns pulses, in vacuum and in air. It has been shown by interferometry and light emission that expanding wire core has different conditions. The substances with small atomization enthalpy (Ag, Al, Cu, Au) demonstrate full vaporization of the wire core. The refractory metals (Ti, Pt, Mo, W) demonstrates that core consists from vapor and small and hot microparticles. In this case we observe "firework effect" when large radiation from the wire exceed the energy deposition time in a three order of magnitude. For non-refractory metals radiation dropping fast in 100 ns time scale due to effective adiabatic cooling. It is possible if main part of the metal core was vaporized. The interferometrical investigation of the refraction coefficient of expanding metal core is proof this conclusion. It has been shown that energy deposition before surface breakdown dependent strongly from current rate, surface coatings, environment, wire diameter and radial electric field. The regime of wire explosion in vacuum without shunting plasma shell has been realized for fast exploding mode. In this case we observe anomaly high energy deposition in to the wire core exceeding regular value in almost 20 times. The experimental results for Al wire have been compared with ALEGRA 2D MHD simulations. *Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL8500.
A novel method for calculating relative free energy of similar molecules in two environments
NASA Astrophysics Data System (ADS)
Farhi, Asaf; Singh, Bipin
2017-03-01
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy, simple implementation, robustness and efficiency, which prevent the calculations from being automated and limit their use. Here we present an exact and complete decoupling analysis in which the partition functions of the compared systems decompose into the partition functions of the common and different subsystems. This decoupling analysis is applicable to submolecules with coupled degrees of freedom such as the methyl group and to any potential function (including the typical dihedral potentials), enabling to remove less terms in the transformation which results in a more efficient calculation. Then we show mathematically, in the context of partition function decoupling, that the two compared systems can be simulated separately, eliminating the need to design a composite system. We demonstrate the decoupling analysis and the separate transformations in a relative free energy calculation using MD simulations for a general force field and compare to another calculation and to experimental results. We present a unified soft-core technique that ensures the monotonicity of the numerically integrated function (analytical proof) which is important for the selection of intermediates. We show mathematically that in this soft-core technique the numerically integrated function can be non-steep only when we transform the systems separately, which can simplify the numerical integration. Finally, we show that when the systems have rugged energy landscape they can be equilibrated without introducing another sampling dimension which can also enable to use the simulation results for other free energy calculations.
Amharrak, H.; Reynard-Carette, C.; Carette, M.; Lemaire, M.; Vaglio-Gaudard, C.; Fourmentel, D.; Lyoussi, A.
2015-07-01
carried out. A preliminary analysis shows that the numerical results overestimate the measurements by about 20 %. A new approach has been developed in order to estimate the nuclear heating by two methods (energy deposition or KERMA) by considering the whole complete geometry of the sensor. This new approach will contribute to the interpretation of the irradiation campaign and will be useful to improve the out-of-pile calibration procedure of the sensor and its thermal response during irradiations. The aim of this paper is to present simulations made by using MCNP5 Monte-Carlo transport code (using ENDF/B-VI nuclear data library) for the nuclear heating inside the different parts of the calorimeter (head, rod and base). Calculations into two steps will be realized. We will use as an input source in the model new spectra (neutrons, prompt-photons and delayed-photons) calculated with the Monte Carlo code TRIPOLI-4{sup R} inside different experimental channels (water) located into the OSIRIS periphery and used during the CARMEN-1P irradiation campaign. We will consider Neutrons- Photons-Electrons and Photons-Electrons modes. We will begin by a brief description of the differential-calorimeter device geometry. Then the MCNP5 model used for the calculations of nuclear heating inside the calorimeter elements will be introduced. The energy deposition due to the prompt-gamma, delayed-gamma and neutrons, the neutron-activation of the device will be considered. The different components of the nuclear heating inside the different parts of the calorimeter will be detailed. Moreover, a comparison between KERMA and nuclear energy deposition estimations will be given. Finally, a comparison between this total nuclear heating Calculation and Experiment in graphite sample will be determined. (authors)
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
In-situ monitoring by reflective high energy electron diffraction during pulsed laser deposition
NASA Astrophysics Data System (ADS)
Blank, Dave H. A.; Rijnders, Guus J. H. M.; Koster, Gertjan; Rogalla, Horst
1999-01-01
Pulsed laser deposition (PLD) has developed during the past decade from a fast but limited preparation tool towards a competitive thin film deposition technique. One of the advantages above other techniques is the possibility of growth at relative high background pressure. There is a large freedom in choosing which kind of gas. Moreover, in a number of applications, the gaseous species in the background pressure are part of the elements to be grown, e.g., oxygen in the case of high Tc superconductors. However, the advantage of relative high pressures leads to restrictions of using standard diagnostics and monitoring of the film growth, e.g., reflective high energy electron diffraction (RHEED). Here, a PLD chamber including an in-situ RHEED system is presented, which makes it possible to monitor and study the growth at standard PLD parameters. Using a two-stages differential pumped, magnetically shielded, extension tube mounted at the electron gun side and a special designed phosphor screen including CCD camera, real time monitoring by observation of RHEED oscillations could be established at pressures up to 50 Pa. In this paper the latest results on applying this technique on SrTiO 3 and YBa 2Cu 3O 7 will be presented. Additional to the usual diagnostics performed with RHEED, another phenomena can be observed. The pulsed way of deposition, characteristic for PLD, leads to relaxations in the intensity of the diffracted pattern due to the mobility of the deposited material. These relaxation times give extra information about relaxation, crystallization, and nucleation of the deposited material. The presented technique leads to a better understanding of the growth during pulsed laser deposition and, because of the possibility to monitor the growth, will make PLD competitive with other deposition techniques.
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.
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.
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.
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2010 CFR
2010-01-01
... cost indexes? 591.220 Section 591.220 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS ALLOWANCES AND DIFFERENTIALS Cost-of-Living Allowance and Post Differential-Nonforeign Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a)...
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.
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.
ERIC Educational Resources Information Center
Bowen, J. Philip; Sorensen, Jennifer B.; Kirschner, Karl N.
2007-01-01
The analysis explains the basis set superposition error (BSSE) and fragment relaxation involved in calculating the interaction energies using various first principle theories. Interacting the correlated fragment and increasing the size of the basis set can help in decreasing the BSSE to a great extent.
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)
Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine.
Suzuki, Masayo; Kino, Katsuhito; Morikawa, Masayuki; Kobayashi, Takanobu; Komori, Rie; Miyazawa, Hiroshi
2012-06-01
DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H)-oxazolone (Oz), guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiro-imino-dihydantoin (Sp) are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.
The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.
ERIC Educational Resources Information Center
Castano, F.; And Others
1983-01-01
The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)
First-principles Calculations of Twin-boundary and Stacking-fault Energies in Magnesium
2010-01-01
The interfacial energies of twin boundaries and stacking faults in metal magnesium have been calculated using first-principles supercell approach...Four types of twin boundaries and two types of stacking faults are investigated, namely, those due to the mirror reflection, the mirror glide and the
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…
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
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.
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.
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.
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
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.
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.
NASA Astrophysics Data System (ADS)
Hu, Ching-Han; Chong, Delano P.
1996-11-01
Our recent procedure of the unrestricted generalized transition state (uGTS) model for density functional calculations of core-electron binding energies has been applied to seven carbonyl and nitrosyl inorganic complexes: Fe(CO) 5, Ni(CO) 4, Mn(CO) 4NO, Co(CO) 3NO, Fe(CO) 2(NO) 2, Mn(NO) 3CO and Cr(NO) 4. The exchange-correlation potential is based on a combined functional of Becke's exchange (B88) and Perdew's correlation (P86). The cc-pVTZ basis set was used for the calculation of neutral molecules, while for the partial cation created in the uGTS approach we scaled the cc-pVTZ basis set using a procedure based on Clementi and Raimondi's rules for atomic screening. The average absolute deviation of the calculated core-electron binding energy from experiment is 0.28 eV.
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.
Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.
Ellingson, Benjamin A; Geballe, Matthew T; Wlodek, Stanislaw; Bayly, Christopher I; Skillman, A Geoffrey; Nicholls, Anthony
2014-03-01
Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson-Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5-2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors.
Zhang, Yong; Voth, Gregory A.
2011-01-01
Free energy calculations are one of the most useful methods for the study of ion transport mechanisms through confined spaces such as protein ion channels. Their reliability depends on a correctly defined reaction coordinate (RC). A straight line is usually not a proper RC for such complicated processes so in this work a combined metadynamics/umbrella sampling (MTD/US) method is proposed. In the combined method, the ion transport pathway is first identified by the MTD method and then the free energy profile or potential of mean force (PMF) along the path is calculated using umbrella sampling. This combined method avoids the discontinuity problem often associated with normal umbrella sampling calculations that assume a straight line RC and it provides a more physically accurate PMF for such processes. The method is demonstrated for the proton transport process through the protein channel of aquaporin-1. PMID:25100923
High-energy cosmic-ray fluxes in the Earth atmosphere: Calculations vs experiments
NASA Astrophysics Data System (ADS)
Kochanov, A. A.; Sinegovskaya, T. S.; Sinegovsky, S. I.
2008-12-01
A new calculation of the atmospheric fluxes of cosmic-ray hadrons and muons in the energy range 10-105 GeV has been performed for the set of hadron production models, EPOS 1.6, QGSJET II-03, SIBYLL 2.1, and others that are of interest to cosmic-ray physicists. The fluxes of secondary cosmic rays at several levels in the atmosphere are computed using directly data of the ATIC-2, GAMMA experiments, and the model proposed recently by Zatsepin and Sokolskaya as well as the parameterization of the primary cosmic-ray spectrum by Gaisser and Honda. The calculated energy spectra of the hadrons and muon flux as a function of zenith angle are compared with measurements as well as other calculations. The effect of uncertainties both in the primary cosmic-ray flux and hadronic model predictions on the spectra of atmospheric hadrons and muons is considered.
NASA Astrophysics Data System (ADS)
Goldzak, Tamar; Gilary, Ido; Moiseyev, Nimrod
2012-05-01
We show here for a simple model system that the wavepacket dynamics in the interaction region can be described by a superposition of the non-Hermitian exponential divergent eigenfunctions of the physical Hamiltonian. We demonstrate how it is possible to obtain the complex eigenvalues and also the corresponding resonance eigenfunctions from the propagation of the wavepacket within the framework of the standard formalism of quantum mechanics. The general results demonstrated here for a simple model can lead to two different types of computational applications: (i) for systems where one can obtain the resonance energies and lifetimes as well as their corresponding eigenfunctions it is possible to study the evolution of the physical properties solely based on the initially populated resonance states without the need to propagate the wavepacket; (ii) for molecular systems where it is quite difficult to solve the non-Hermitian time-independent Schrödinger equation and obtain molecular resonance energies and functions. For this type of problem, the methods presented here enable one to evaluate the topology of complex potential energy surfaces from the wavepacket propagation and facilitate the study of the nuclear dynamics of ionizing molecular systems.
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.
2008-07-02
pp. 1344-1347 2 Kuga et al., “Novel Optical Trap of Atoms with a Doughnut Beam,” Physical Review Letters 78, (1997), pp. 4713-4716 3 Dotsenko et...other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a ...Technical Paper 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Energy Deposition into a Collisional Gas from
Brambrink, E.; Audebert, P.; Schlegel, T.; Malka, G.; Aleonard, M. M.; Claverie, G.; Gerbaux, M.; Gobet, F.; Hannachi, F.; Scheurer, J. N.; Tarisien, M.; Amthor, K. U.; Meot, V.; Morel, P.
2007-06-15
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.
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.
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.
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.
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.
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.
Calculation of Energy Diagram of Asymmetric Graded-Band-Gap Semiconductor Superlattices.
Monastyrskii, Liubomyr S; Sokolovskii, Bogdan S; Alekseichyk, Mariya P
2017-12-01
The paper theoretically investigates the peculiarities of energy diagram of asymmetric graded-band-gap superlattices with linear coordinate dependences of band gap and electron affinity. For calculating the energy diagram of asymmetric graded-band-gap superlattices, linearized Poisson's equation has been solved for the two layers forming a period of the superlattice. The obtained coordinate dependences of edges of the conduction and valence bands demonstrate substantial transformation of the shape of the energy diagram at changing the period of the lattice and the ratio of width of the adjacent layers. The most marked changes in the energy diagram take place when the period of lattice is comparable with the Debye screening length. In the case when the lattice period is much smaller that the Debye screening length, the energy diagram has the shape of a sawtooth-like pattern.
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.
Beres, D.A.; Hull, A.P.
1991-12-01
DEPDOSE is an interactive, menu driven, microcomputer based program designed to rapidly calculate committed dose from radionuclides deposited on the ground. The program is designed to require little or no computer expertise on the part of the user. The program consisting of a dose calculation section and a library maintenance section. These selections are available to the user from the main menu. The dose calculation section provides the user with the ability to calculate committed doses, determine the decay time needed to reach a particular dose, cross compare deposition data from separate locations, and approximate a committed dose based on a measured exposure rate. The library maintenance section allows the user to review and update dose modifier data as well as to build and maintain libraries of radionuclide data, dose conversion factors, and default deposition data. The program is structured to provide the user easy access for reviewing data prior to running the calculation. Deposition data can either be entered by the user or imported from other databases. Results can either be displayed on the screen or sent to the printer.
The simplest method for calculating energy output and Gurney velocity of explosives.
Keshavarz, Mohammad Hossein; Semnani, Abolfazl
2006-04-17
Two correlations are introduced for calculating Gurney velocity as a useful parameter for thermochemical estimation of explosive energy output. For CaHbNcOd explosives, only the chemical composition of high explosive as well as its condensed or estimated gas phase heat of formation, which later is calculated by group additivity rules, is needed for calculating Gurney velocity. The introduced simple correlations in the present work may be applied to any explosive that contains the elements of carbon, hydrogen, nitrogen and oxygen with no difficulties at any loading density. There is no need to use any assumed decomposition reaction in present work. Gurney velocity are calculated for different pure and explosive formulations and compared with measured Gurney velocity at specified loading density. The results show that the agreement is good for present method as compared to previous correlations.
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.
Lines of Energy Deposition for Supersonic/Hypersonic Temperature/ Drag-Reduction and Vehicle Control
2009-10-06
amount of energy to deposit along the cone axis in order to open up low-density cylindrical cores of various radii. The reason behind modeling the...for a 15° half- angle cone and up to 96% for a 45° half-angle cone . The energy retum ratio [thrust (power) saved]:[invested power] of this...addresses the r ~q .•-.~~,~.~ .• ~.~.~.~, ~.~.~. (a) X ·2 · $ ·4 ·3 ·~ · 1 0 I l 3 4 5 6 (c) X FIGURE 3: A low-density core streaming over the cone
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.
NASA Astrophysics Data System (ADS)
Lei, Yinkai; Gong, Yu; Duan, Zhiyao; Wang, Guofeng
2013-06-01
To acquire knowledge on the lattice and grain boundary diffusion processes in alumina, we have determined the activation energies of elementary O and Al diffusive jumps in the bulk crystal, Σ3(0001) grain boundaries, and Σ3(101¯0) grain boundaries of α-Al2O3 using the first-principles density functional theory method. Specifically, we calculated the activation energies for four elementary jumps of both O and Al lattice diffusion in alumina. It was predicted that the activation energy of O lattice diffusion varied from 3.58 to 5.03 eV, while the activation energy of Al lattice diffusion ranged from 1.80 to 3.17 eV. As compared with experimental measurements, the theoretical predictions of the activation energy for lattice diffusion were lower and thus implied that there might be other high-energy diffusive jumps in the experimental alumina samples. Moreover, our results suggested that the Al lattice diffusion was faster than the O lattice diffusion in alumina, in agreement with experiment observations. Furthermore, it was found from our calculations for α-Al2O3 that the activation energies of O and Al grain boundary diffusion in the high-energy Σ3(0001) grain boundaries were significantly lower than those of the lattice diffusion. In contrast, the activation energies of O and Al grain boundary diffusion in the low-energy Σ3(101¯0) grain boundaries could be even higher than those of the lattice diffusion.
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
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)
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)
Gallicchio, Emilio; Deng, Nanjie; He, Peng; Wickstrom, Lauren; Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Olson, Arthur J.; Levy, Ronald M.
2014-04-01
As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization.
Gallicchio, Emilio; Deng, Nanjie; He, Peng; Wickstrom, Lauren; Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Olson, Arthur J.; Levy, Ronald M.
2014-01-01
As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization. PMID:24504704
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.
Light absorption and excitation energy transfer calculations in primitive photosynthetic bacteria
NASA Astrophysics Data System (ADS)
Komatsu, Yu; Kayanuma, Megumi; Shoji, Mitsuo; Yabana, Kazuhiro; Shiraishi, Kenji; Umemura, Masayuki
2015-06-01
In photosynthetic organisms, light energy is converted into chemical energy through the light absorption and excitation energy transfer (EET) processes. These processes start in light-harvesting complexes, which contain special photosynthetic pigments. The exploration of unique mechanisms in light-harvesting complexes is directly related to studies, such as artificial photosynthesis or biosignatures in astrobiology. We examined, through ab initio calculations, the light absorption and EET processes using cluster models of light-harvesting complexes in purple bacteria (LH2). We evaluated absorption spectra and energy transfer rates using the LH2 monomer and dimer models to reproduce experimental results. After the calibration tests, a LH2 aggregation model, composed of 7 or 19 LH2s aligned in triangle lattice, was examined. We found that the light absorption is red shifted and the energy transfer becomes faster as the system size increases. We also found that EET is accelerated by exchanging the central pigments to lower energy excited pigments. As an astrobiological application, we calculated light absorptions efficiencies of the LH2 in different photoenvironments.
Baudin, Pablo; Bykov, Dmytro; Liakh, Dmitry I.; ...
2017-02-22
Here, the recently developed Local Framework for calculating Excitation energies (LoFEx) is extended to the coupled cluster singles and doubles (CCSD) model. In the new scheme, a standard CCSD excitation energy calculation is carried out within a reduced excitation orbital space (XOS), which is composed of localised molecular orbitals and natural transition orbitals determined from time-dependent Hartree–Fock theory. The presented algorithm uses a series of reduced second-order approximate coupled cluster singles and doubles (CC2) calculations to optimise the XOS in a black-box manner. This ensures that the requested CCSD excitation energies have been determined to a predefined accuracy compared tomore » a conventional CCSD calculation. We present numerical LoFEx-CCSD results for a set of medium-sized organic molecules, which illustrate the black-box nature of the approach and the computational savings obtained for transitions that are local compared to the size of the molecule. In fact, for such local transitions, the LoFEx-CCSD scheme can be applied to molecular systems where a conventional CCSD implementation is intractable.« less
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.
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies.
Fowler, Philip W; Jha, Shantenu; Coveney, Peter V
2005-08-15
The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differences using thermodynamic integration can be significantly reduced: potentially from weeks or months to days of wall-clock time. To be able to perform such accelerated calculations requires the ability to both run concurrently and control in realtime several parallel simulations on a computational Grid. We describe how the RealityGrid computational steering system, in conjunction with a scalable classical MD code, can be used to dramatically reduce the time to achieve a result. This is necessary to improve the adoption of this technique and further allows more detailed investigations into the accuracy and precision of thermodynamic integration. Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.
Kirby, B.; King, J.; Milligan, M.
2012-06-01
The anticipated increase in variable generation in the Western Interconnection over the next several years has raised concerns about how to maintain system balance, especially in smaller Balancing Authority Areas (BAAs). Given renewable portfolio standards in the West, it is possible that more than 50 gigawatts of wind capacity will be installed by 2020. Significant quantities of solar generation are likely to be added as well. The consequent increase in variability and uncertainty that must be managed by the conventional generation fleet and responsive loads has resulted in a proposal for an Energy Imbalance Market (EIM). This paper extends prior work to estimate the reserve requirements for regulation, spinning, and non-spinning reserves with and without the EIM. We also discuss alternative approaches to allocating reserve requirements and show that some apparently attractive allocation methods have undesired consequences.
Computational scheme for pH-dependent binding free energy calculation with explicit solvent.
Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R
2016-01-01
We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations.
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.
The influence of energy deposition parameters on laser plasma drag reduction
NASA Astrophysics Data System (ADS)
Dou, Zhiguo; Liu, Zhun; Yao, Honglin; Li, Xiuqian
2013-09-01
Laser plasma drag reduction is a new method to reduce the wave drag of hypersonic flight. The research of the laser plasma drag reduction performance is an important work. The purpose of this paper is investigating laser plasma drag reduction by numerical simulation to enhance the understanding of the drag reduction mechanism, get the drag reduction performance in different conditions, and provide references for laser plasma drag reduction experiment in the future. Based on summarizing correlative references systematically, through building the model of energy deposition and comparison the simulated results to the empirical formula and computation results to verify the program correctness, the influence of laser energy parameters to laser plasma drag reduction were simulated numerically for optimize the performance. The follow conclusions were got by numerical simulation: The computation program can well simulate the interacting of LSDW(laser supported detonation wave) to the bow shock in front of the blunt body. Results indicate that the blunt body drag could be decreased by injecting laser energy into the incoming hypersonic flow. The correctness of program was verified by compare result to the experiment and computation results. Blunt body drag will be greatly decreased with injected laser power increased, The bigger laser power is injected, the more drag decreases. There's an energy saturation value for each laser power level, the injecting laser power effectiveness values are never quite high for all laser power level. There is an optimized energy deposition location in upstream flow, this location is right ahead of the blunt body. When the distance from deposition location to the surface of blunt body is 5 times the blunt radius, blunt body drag decreased the most. This paper investigated the parameters which primary influence the performance of drag reduction. The numerical simulation data and obtained results are meaningful for laser plasma drag reduction
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.
FreeSolv: A database of experimental and calculated hydration free energies, with input files
Mobley, David L.; Guthrie, J. Peter
2014-01-01
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz. PMID:24928188
FreeSolv: a database of experimental and calculated hydration free energies, with input files.
Mobley, David L; Guthrie, J Peter
2014-07-01
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz .
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.
Calculation of excess interfacial entropy, stress and energy for solid-liquid interfaces
NASA Astrophysics Data System (ADS)
Laird, Brian B.; Davidchack, Ruslan L.; Asta, Mark; Yang, Yang
2009-03-01
The solid-liquid interfacial free energy, γsl, governs a number of important phenomena, e.g., crystal nucleation and growth, and wetting. For an equilibrium crystal-melt interface, γsl can be calculated via simulation using thermodynamic integration or capillary fluctuations [Phys. Chem. B 109, 17802 (2005)]. The calculation of γsl away from coexistence requires the temperature and strain dependence of γsl, which can be determined from the excess interfacial entropy, ηsl, and stress tensor, τsl. We determine ηsl and τsl for a system of Lennard-Jones particles and for particles with an inverse-power interaction [φ(r) = ɛ(σ/r)^n] for n = 6, 8 (fcc and bcc) and 12, 20 (fcc). We determine ηsl and τsl for the (100), (110) and (111) orientations. We calculate ηsl using two methods, both using the Gibbs dividing surface defined so that the excess interfacial particle number is zero. In the first, we calculate ηsl from the temperature dependence of γsl, τsl and the number density, ρ, along the coexistence curve. In the second, we calculate the excess interfacial energy, esl, and use the equation γsl= esl- T ηsl. The results agree within estimated errors. One surprising observation is that ηsl, esl and τsl are significantly more anisotropic than γsl.
Empirical free energy calculations: a blind test and further improvements to the method.
Novotny, J; Bruccoleri, R E; Davis, M; Sharp, K A
1997-05-02
Empirical Gibbs functions estimate free energies of non-covalent reactions (deltaG) from atomic coordinates of reaction products (e.g. antibody-antigen complexes). The function previously developed by us has four terms that quantify the effects of hydrophobic, electrostatic and entropy changes (conformational, association) upon complexation. The function was used to calculate delta deltaG of ten lysozyme mutants affecting the stability of the HyHEL-10 antibody-lysozyme complex. The mutants were computer-modeled from the X-ray structure of the wild-type, and free energy calculations produced a correlation coefficient of 0.5 with the experimental delta deltaG data (average absolute error +/-3 kcal). The following changes were then introduced into the Gibbs function: (1) the hydrophobic force was made proportional to the molecular surface, as calculated by the GEPOL93 algorithm, with the scaling constant of 70 cal/mol/A2; (2) calculation of the electrostatics of binding was carried out by the finite difference Poisson-Boltzmann algorithm, which employed uniform grid charging, dielectric boundary smoothing and charge anti-aliasing; and (3) side-chain conformational entropy was estimated from the CONGEN sampling of torsional degrees of freedom. In the new calculations, correlation with experimental data improved to 0.6 or 0.8 if a single outlying mutant, K96M, was neglected. Analysis of the errors remaining in our calculations indicated that molecular mechanics-based modeling of the mutants, rather than the form of our amended Gibbs function, was the main factor limiting the accuracy of the free energy estimates.
Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation.
Genheden, Samuel; Ryde, Ulf
2012-04-10
We have studied whether the efficiency of alchemical free-energy calculations with the Bennett acceptance ratio method of protein-ligand binding energies can be improved by simulating only part of the protein. To this end, we solvated the full protein in a spherical droplet with a radius of 46 Å, surrounded by a vacuum. Then, we systematically reduced the size of the droplet and at the same time ignored protein residues that were outside the droplet. Radii of 40-15 Å were tested. Ten inhibitors of the blood clotting factor Xa were studied, and the results were compared to an earlier study in which the protein was solvated in a periodic box, showing complete agreement between the two sets of calculations within statistical uncertainty. We then show that the simulated system can be truncated down to 15 Å, without changing the calculated affinities by more than 0.5 kJ/mol on average (maximum difference of 1.4 kJ/mol). Moreover, we show that reducing the number of intermediate states in the calculations from eleven to three gave deviations that, on average, were only 0.5 kJ/mol (maximum of 1.4 kJ/mol). Together, these results show that truncation is an appropriate way to improve the efficiency of free-energy calculations for small mutations that preserve the net charge of the ligand. In fact, each calculation of a relative binding affinity requires only six simulations, each of which takes ∼15 CPU h of computation on a single processor.
Calculation and modeling of the energy released in result of water freezing process (WFP)
NASA Astrophysics Data System (ADS)
Ghodsi Hassanabad, M.; Mehrbadi, A. Dehghani
Process of water freezing in different pressures has been studied with appropriate accuracy and freezing phenomenon has been tested in variety conditions. The effects of pressure on volume change in constant volume and constant pressure have also been reviewed. Calculation of these changes has been done by using the finite difference. Therefore, experimental model has been designed and built to validate these calculations and this experimental model has been studied the power of freezing water during the freezing process in different conditions. Finally, the results were used to design a machine that has an ability to control the power of freezing and turn it into a new clean energy. In this machine, some water is frozen due to temperature difference that is exerting between day and night and energy which is produced by this reaction consumes for creating electrical energy. The amount of extractable power from the temperature difference between day and night were calculated in different temperatures. As an overall result, the most energy extracted from freezing in one cubic meters water with a temperature below -22 °C during the night is 12.8 MJ, the equivalent of using 356 W for 10 h.
Potential energy surface and second virial coefficient of methane-water from ab initio calculations.
Akin-Ojo, Omololu; Szalewicz, Krzysztof
2005-10-01
Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03 kcal/mol at a geometry where H2O is the proton donor, HO-H...CH4, with the O-H-C angle of 165 degrees, while the secondary minimum, with an energy of -0.72 kcal/mol, has CH4 in the role of the proton donor (H3C-H...OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06 kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653 K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.
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.
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.
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}.
Multireference coupled-cluster calculation of the dissociation energy profile of triplet ketene
NASA Astrophysics Data System (ADS)
Ogihara, Yusuke; Yamamoto, Takeshi; Kato, Shigeki
2011-07-01
Triplet ketene exhibits a steplike structure in the experimentally observed photodissociation rates, but its mechanism is still unknown despite many theoretical efforts. Here we revisit this problem by calculating the potential energy profile of triplet ketene with the Adamowicz and Mukherjee multireference coupled-cluster (MRCC) theories. At the MRCCSD level, the imaginary frequency of the dissociation barrier is calculated to be about 300i cm-1, which is slightly smaller than the previous estimates but is still much greater than the expected maximum value for reproducing the observed steps (100i cm-1). This implies that other types of mechanisms (including nonadiabatic ones) may be more plausible for the observed steps.
Surface energy calculation - metals with 1 and 2 delocalized electrons per atom
NASA Astrophysics Data System (ADS)
Halas, S.; Durakiewicz, T.; Joyce, J. J.
2002-05-01
In this paper we calculate surface energy (SE) of monovalent, divalent and some trivalent metals. For these metals for which SE can be solely expressed by dimensionless Wigner-Seitz density parameter, rs, of delocalized electrons: SE=C 1r s-5+C 2r s-3.5-C 3r s-4, where constants C1, C2 and C3 have been calculated on the basis of Sommerfeld's free electron and surface plasma models. Excellent agreement with experimental data was obtained. On the basis of our model SE values for Fr and Ra have been predicted as well.
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.
First-principles calculations of free energies of unstable phases: the case of fcc W.
Ozolins, V
2009-02-13
Ab initio molecular dynamics simulations are used to solve the long-standing problem of calculating the free energies of unstable phases, such as fcc W. We find that fcc W is mechanically unstable with respect to long-wavelength shear at all temperatures considered (T>2500 K), while the short-wavelength phonon modes are anharmonically stabilized. The calculated fcc-bcc enthalpy and entropy differences at T=3500 K (308 meV and 0.74k_{B} per atom, respectively) agree well with the recent values derived from analysis of experimental data.
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.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-10-26
Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange.
Ceriotti, Michele; Manolopoulos, David E
2012-09-07
Light nuclei at room temperature and below exhibit a kinetic energy which significantly deviates from the predictions of classical statistical mechanics. This quantum kinetic energy is responsible for a wide variety of isotope effects of interest in fields ranging from chemistry to climatology. It also furnishes the second moment of the nuclear momentum distribution, which contains subtle information about the chemical environment and has recently become accessible to deep inelastic neutron scattering experiments. Here, we show how, by combining imaginary time path integral dynamics with a carefully designed generalized Langevin equation, it is possible to dramatically reduce the expense of computing the quantum kinetic energy. We also introduce a transient anisotropic Gaussian approximation to the nuclear momentum distribution which can be calculated with negligible additional effort. As an example, we evaluate the structural properties, the quantum kinetic energy, and the nuclear momentum distribution for a first-principles simulation of liquid water.
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
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.
NASA Astrophysics Data System (ADS)
Washiyama, K.; Bennaceur, K.; Avez, B.; Bender, M.; Heenen, P.-H.; Hellemans, V.
2012-11-01
Background: Symmetry restoration and configuration mixing in the spirit of the generator coordinate method based on energy density functionals have become widely used techniques in low-energy nuclear structure physics. Recently, it has been pointed out that these techniques are ill defined for standard Skyrme functionals, and a regularization procedure has been proposed to remove the resulting spuriosities from such calculations. This procedure imposes an integer power of the density for the density-dependent terms of the functional. At present, only dated parametrizations of the Skyrme interaction fulfill this condition.Purpose: To construct a set of parametrizations of the Skyrme energy density functional for multireference energy density functional calculations with regularization using the state-of-the-art fitting protocols.Method: The parametrizations were adjusted to reproduce ground-state properties of a selected set of doubly magic nuclei and properties of nuclear matter. Subsequently, these parameter sets were validated against properties of spherical and deformed nuclei.Results: Our parameter sets successfully reproduce the experimental binding energies and charge radii for a wide range of singly magic nuclei. Compared to the widely used SLy5 and to the SIII parametrization that has integer powers of the density, a significant improvement of the reproduction of the data is observed. Similarly, a good description of the deformation properties at A˜80 was obtained.Conclusions: We have constructed new Skyrme parametrizations with integer powers of the density and validated them against a broad set of experimental data for spherical and deformed nuclei. These parametrizations are tailor-made for regularized multireference energy density functional calculations and can be used to study correlations beyond the mean field in atomic nuclei.
Fogarty, Heather A; Ottosson, Henrik; Michl, Josef
2006-12-21
The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.
A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies.
Cave-Ayland, Christopher; Skylaris, Chris-Kriton; Essex, Jonathan W
2017-02-14
Hybrid free energy methods allow estimation of free energy differences at the quantum mechanics (QM) level with high efficiency by performing sampling at the classical mechanics (MM) level. Various approaches to allow the calculation of QM corrections to classical free energies have been proposed. The single step free energy perturbation approach starts with a classically generated ensemble, a subset of structures of which are postprocessed to obtain QM energies for use with the Zwanzig equation. This gives an estimate of the free energy difference associated with the change from an MM to a QM Hamiltonian. Owing to the poor numerical properties of the Zwanzig equation, however, recent developments have produced alternative methods which aim to provide access to the properties of the true QM ensemble. Here we propose an approach based on the resampling of MM structural ensembles and application of a Monte Carlo acceptance test which in principle, can generate the exact QM ensemble or intermediate ensembles between the MM and QM states. We carry out a detailed comparison against the Zwanzig equation and recently proposed non-Boltzmann methods. As a test system we use a set of small molecule hydration free energies for which hybrid free energy calculations are performed at the semiempirical Density Functional Tight Binding level. Equivalent ensembles at this level of theory have also been generated allowing the reverse QM to MM perturbations to be performed along with a detailed analysis of the results. Additionally, a previously published nucleotide base pair data set simulated at the QM level using ab initio molecular dynamics is also considered. We provide a strong rationale for the use of the Monte Carlo Resampling and non-Boltzmann approaches by showing that configuration space overlaps can be estimated which provide useful diagnostic information regarding the accuracy of these hybrid approaches.
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.
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
NASA Astrophysics Data System (ADS)
Kondo, Minoru; Kawamura, Junya; Terauchi, Nobuo
We are developing a new high performance traction motor for railway vehicle using interior permanent magnet synchronous motor (IPMSM) and expecting it can reduce energy consumption. To estimate the losses and energy consumption of IPMSM, a simple motor model is needed. In this paper, We propose a simple equivalent circuit and loss model for IPMSM, the constants of which can be obtained from several simple test results. The calculation results using them show that the total loss of the IPMSM becomes about 60% of that of the induction motor when used as a traction motor for a typical commuter train.
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.
Calculated self-energy contributions for an ns valence electron using the multiple-commutator method
NASA Astrophysics Data System (ADS)
Labzowsky, Leonti; Goidenko, Igor; Tokman, Maria; Pyykkö, Pekka
1999-04-01
The self-energy (SE) correction is evaluated for a single valence ns electron of heavy and superheavy atoms with n up to 8 and the nuclear charge Z up to 119. The recently developed approach based on the commutator expansion is employed. Various Dirac-Slater one-electron local potentials with extended nuclei are used. The Lamb shifts were calculated by adding the average values of the Uehling potential to the SE contributions. The results confirm the earlier estimates for the quantum electrodynamical effects on the valence energies of heavy and superheavy atoms.
First-principles calculations of the OH- adsorption energy on perovskite oxide
NASA Astrophysics Data System (ADS)
Ohzuku, Hideo; Ikeno, Hidekazu; Yamada, Ikuya; Yagi, Shunsuke
2016-08-01
The oxygen evolution reaction (OER) that occurs during water oxidation is of considerable importance as an essential energy conversion reaction for rechargeable metal-air batteries and direct solar water splitting. ABO3 perovskite oxides have been extensively studied because of their high catalytic OER activity. In the present study, the OH- adsorption process on the perovskite surface about different B site cations was investigated by the first-principles calculations. We concluded that the adsorption energy of SrFeO3 surface is larger than that of SrTiO3.
1979-06-01
TECHNICAL REPORT ARBRL-TR-02168 d’ A NEtJ INTFRNAL ENERGY CALCULATION FOR THE HELP CODE AND ITS IMPLICATIONS TO CONICAL SHAPED CHARGE SIMULATIONS...Energy Calculation for the HELP Code and Its Implications to Conical Shaped Cha Simulat.ions S. PERFORMING ORG. REPORT NUMBER 7- AUTHOIR,&) 8. CONTRACT...terms of the order of the truncation errrlr in the kinetic energy calculation . A corrcc- tion is given and qualitative the.-mal agreement is achieved, for
New Method for Calculating the Potential Energy of Deformed Nuclei within the Liquid-Drop Model
Kurmanov, R.S.; Kosenko, G.I.
2004-11-01
The method that we previously developed for going over from double volume integrals to double surface integrals in calculating the Coulomb energy of nuclei that have a sharp surface is generalized to the case of nuclei where the range of nuclear forces is finite and where the nuclear surface is diffuse. New formulas for calculating the Coulomb and the nuclear energy of deformed nuclei are obtained within this approach. For a spherically symmetric nucleus, in which case there is an analytic solution to the problem in question, the results are compared with those that are quoted in the literature, and it is shown that the respective results coincide identically. A differential formulation of the method developed previously by Krappe, Nix, and Sierk for going over from double volume integrals to double surface integrals is proposed here on the basis of the present approach.
Estimation of nitrogen ion energy calculated using distribution for nitrogen in Si implanted by PBII
NASA Astrophysics Data System (ADS)
Tanaka, T.; Watanabe, S.; Takagi, T.
2006-01-01
Plasma-based ion implantation (PBII) using N2 gas is examined as a sterilization technique for three-dimensional targets. The application of a pulsed negative voltage (5 μs pulse width, 300 pulses/s, -800 V to -13 kV) at an N2 gas pressure of 2.4 Pa is shown to reduce the number of Bacillus pumilus survivors by up to 105 times after just 5 min of exposure. The energy of nitrogen ions is calculated based on the depth profile of nitrogen concentration in Si implanted by PBII, and it is revealed that the actual nitrogen ion energy is much lower than that calculated based on the voltage applied during processing.
Caricato, Marco; Curutchet, Carles; Mennucci, Benedetta; Scalmani, Giovanni
2015-11-10
Quantum mechanical (QM) calculations of electronic couplings provide great insights for the study of resonance energy transfer (RET). However, most of these calculations rely on approximate QM methods due to the computational limitations imposed by the size of typical donor-acceptor systems. In this work, we present a novel implementation that allows computing electronic couplings at the coupled cluster singles and doubles (CCSD) level of theory. Solvent effects are also taken into account through the polarizable continuum model (PCM). As a test case, we use a dimer of indole, a common model system for tryptophan, which is routinely used as an intrinsic fluorophore in Förster resonance energy transfer studies. We consider two bright π → π* states, one of which has charge transfer character. Lastly, the results are compared with those obtained by applying TD-DFT in combination with one of the most popular density functionals, B3LYP.
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.
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.
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.
Calculation of positron binding energies using the generalized any particle propagator theory
NASA Astrophysics Data System (ADS)
Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés
2014-09-01
We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ˜0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.
Methods for calculating dietary energy density in a nationally representative sample.
Vernarelli, Jacqueline A; Mitchell, Diane C; Rolls, Barbara J; Hartman, Terryl J
2013-01-01
There has been a growing interest in examining dietary energy density (ED, kcal/g) as it relates to various health outcomes. Consuming a diet low in ED has been recommended in the 2010 Dietary Guidelines, as well as by other agencies, as a dietary approach for disease prevention. Translating this recommendation into practice; however, is difficult. Currently there is no standardized method for calculating dietary ED; as dietary ED can be calculated with foods alone, or with a combination of foods and beverages. Certain items may be defined as either a food or a beverage (e.g., meal replacement shakes) and require special attention. National survey data are an excellent resource for evaluating factors that are important to dietary ED calculation. The National Health and Nutrition Examination Survey (NHANES) nutrient and food database does not include an ED variable, thus researchers must independently calculate ED. The objective of this study was to provide information that will inform the selection of a standardized ED calculation method by comparing and contrasting methods for ED calculation. The present study evaluates all consumed items and defines foods and beverages based on both USDA food codes and how the item was consumed. Results are presented as mean EDs for the different calculation methods stratified by population demographics (e.g. age, sex). Using United State Department of Agriculture (USDA) food codes in the 2005-2008 NHANES, a standardized method for calculating dietary ED can be derived. This method can then be adapted by other researchers for consistency across studies.
Artem’ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.
2016-01-15
We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2–5 nm and for neutron energies 3 × 10{sup -7}–10{sup -3} eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.
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.
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.
NASA Astrophysics Data System (ADS)
Artem'ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.
2016-01-01
We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2-5 nm and for neutron energies 3 × 10-7-10-3 eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.
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.
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.
Luiz Guilherme M. de Macedo; de Jong, Wibe A.
2008-01-24
The electronic structure and spectroscopic properties (R_{e}, ω_{e}x_{e}, β_{e}, T_{e} ) of the ground state and the 22 lowest excited states of chlorine molecule were studied within a four component relativistic framework using the MOLFDIR program package. The potential energy curves of all possible 23 covalent states were calculated using relativistic complete open shell configuration interaction (COSCI) approach. In addition, four component multi-reference configuration interaction with singles and doubles excitations (MRCISD) calculations were performed in order to infer the effects due to dynamical correlation in vertical excitations. The calculated properties are in good agreement with the available experimental data.
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.
Pak, Alireza; Lesage, Denis; Gimbert, Yves; Vékey, Károly; Tabet, Jean-Claude
2008-04-01
The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values (
Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package
Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew
2013-01-01
Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license. PMID:24185531
NASA Astrophysics Data System (ADS)
Gouda, M. M.; Hamzawy, A.; Badawi, M. S.; El-Khatib, A. M.; Thabet, A. A.; Abbas, M. I.
2016-02-01
The full-energy peak efficiency of high-purity germanium well-type detector is extremely important to calculate the absolute activities of natural and artificial radionuclides for samples with low radioactivity. In this work, the efficiency transfer method in an integral form is proposed to calculate the full-energy peak efficiency and to correct the coincidence summing effect for a high-purity germanium well-type detector. This technique is based on the calculation of the ratio of the effective solid angles subtended by the well-type detector with cylindrical sources measured inside detector cavity and an axial point source measured out the detector cavity including the attenuation of the photon by the absorber system. This technique can be easily applied in establishing the efficiency calibration curves of well-type detectors. The calculated values of the efficiency are in good agreement with the experimental calibration data obtained with a mixed γ-ray standard source containing 60Co and 88Y.
Larriba, Carlos Hogan, Christopher J.
2013-10-15
The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas
Ab initio calculation of optical constants from visible to x-ray energies
NASA Astrophysics Data System (ADS)
Prange, M. P.; Rivas, G.; Ankudinov, A. L.; Rehr, J. J.
2004-03-01
We present a semi-automated approach for ab initio calculations of optical constants of materials from the visible to the hard x-ray energies. The approach is based on a generalization of the real space Green's formalism implemented in the FEFF8 spectroscopy code to include optical spectra. The method includes self-consistent potentials, core-hole and self-energy effects, inelastic losses and a full- or high order multiple-scattering. The procedure is based on calculations of the imaginary part of the dielectric function ɛ2 summed over all edges, from which other optical constants are derived using Kramers-Kronig transforms and analytical relations. These constants include the complex index of refraction, the real part of the dielectric function, and energy loss spectra. In contrast to standard atomic tables, the calculations include solid-state corrections, such as fine structure, Debye-Waller factors, lifetime broadening, etc. Typical results for several materials are presented and compared with experiment.
Total energy magnetic anisotropy calculations for free-standing transition-metal monolayers.
NASA Astrophysics Data System (ADS)
Shick, A. B.; Blügel, S.
1997-03-01
A self-consistent relativistic spin-polarized version of the full potential linearized augmented planewave (FLAPW) method (E. Wimmer, H. Krakauer, M. Weinert and A.J. Freeman, Phys. Rev. B 24), 864 (1981). is developed on the basis of a second variation treatment of the spin-orbit (SOC) interaction. The method is applied to the study of the magnetic anisotropy energy (MAE) of free-standing transition-metal monolayers (Fe, Rh, Ir). The total energy results are compared with different theoretical models used to calculate the MAE, e.g. those based on the "local force" theorem for SOC interaction or rotation of the magnetization direction. The anisotropy of the orbital magnetic moment is calculated to be in qualitative agreement with previous theoretical predictions. For Fe and Rh monolayers, the self-consistently determined MAE and the results based on the "local force" theorem are in good agreement, but the approaches fail to agree for the case of Ir. On the basis of self-consistent total energy calculations we show that an Ir monolayer shows a large in-plane magnetic anisotropy and a large anisotropy for the spin and orbital magnetic moments.
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.
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.
Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study
NASA Astrophysics Data System (ADS)
Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad
2012-03-01
Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.
How to calculate financial information for home energy raters, lenders and savvy home buyers
Vieira, R.K.; Cummings, J.E.; Fairey, P.W.; Hannani, K.
1998-07-01
Home ratings and energy-efficient mortgages are becoming the key vehicles in the process of moving more buyers and builders to energy efficiency that exceed minimum code limits. The energy-efficient mortgages industry requires both the projected savings of energy-conservation measures and other key financial information for builders, realtors, buyers and lenders. This paper presents the methodology used by the one state's home rating software for calculating and reporting key financial information and for selecting the most cost-effective upgrades automatically through an optimization process. Historically, many statistics have been calculated based on two pieces of information--the cost of the energy conservation measures and the projected savings from the measures. Unfortunately, when attempting to upgrade an existing or code-minimum new home up to more efficient level, such as EPA's Energy Star Home program level, a number of measures interact. The savings of a package of upgrades can be determined, but a methodology was required for attributing the savings due to each measure as required for certain national mortgage products. When examining the cash flow of measures there are a host of other factors - the amount of the upgrade that will be borrowed, the income tax rate used for deducting interest, any increase to the property that will result in higher property tax and insurance rates and the maintenance on the upgrade. The reporting of the financial analysis is of significant importance to the lending industry. This paper presents many report options contained in the Florida software, Energy Gauge, and its ability to meet the requirements of HUD, Fannie Mae, and the national HERS guidelines.
Calculation of Coster-Kronig energies and transition probabilities by linear interpolation method
NASA Astrophysics Data System (ADS)
Trivedi, R. K.; Shrivastava, Uma; Hinge, V. K.; Shrivastava, B. D.
2016-10-01
The X-ray emission spectrum consists of two types of spectral lines heaving different origins. The diagram lines originate because of transitions in singly ionized atom, while the nondiagram lines or satellites originate due to transitions in doubly or multiply ionized atom. The X- ray satellite energy is the difference between the energies of initial and final states which are both doubly or multiply ionized. Thus, the satellite has a different energy than the energy of the X-ray diagram line. Once the singly ionized state has been created, it is the probability of a particular subsequent process that will lead to the formation of two-hole state. The single hole may get converted through a Coster-Kronig transition to a double hole state. The probability of formation of double hole state via this process is written as σ.σ', where σ is the probability of creation of single hole state and σ' is the probability of the Coster-Kronig transition. The value of σ' can be taken from the tables of Chen et al. [1], who have presented the calculated values of σ' for almost all possible Coster-Kronig transitions in some elements. The energies of the satellites can be calculated by using the tables of Parente et al. [2]. Both of these tables do not give values for all the elements. The aim of the present work is to show that the values for other elements, for which values are not listed by Chen et al. and Parente et al., can be calculated by linear interpolation method.
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
Eggleston, J.E.; Abdou, M.A.; Tillack, M.S.
1994-12-31
One of the parameters affecting the feasibility of Inertial Fusion Energy (IFE) devices is the number of shots per unit time, i.e. the repetition rate. The repetition rate limits the achievable power that can be obtained from the reactor. To obtain an estimate of the allowable time between shots, a code named RECON was developed to model the response of the reaction chamber to the pellet explosion. This paper discusses how the code treats the thermodynamic response of the cavity gas and models the condensation/evaporation of this vapor to and from the first wall. A large amount of energy from the pellet microexplosion is carried by the pellet debris and the x-rays generated in the fusion reaction. Models of x-ray attenuation and ion slowing down are used to estimate the fraction of the pellet energy that is absorbed in the vapor. A large amount of energy is absorbed into the cavity gas, which causes it to become partially ionized. The ionization complicates the calculation of the temperature, pressure, and the radiative heat transfer from the gas to the first wall. To treat this problem, methods developed by Zel`dovich and Raizer are used in modeling the internal energy and the radiative heat flux. RECON was developed to run with a relatively short computational time, yet accurate enough for conceptual reactor design calculations.
NASA Astrophysics Data System (ADS)
Abdel Samad, B.; Ashrit, P. V.
2014-09-01
Vanadium pentoxide V2O5 thin films were grown on glass substrates by the LAMBD deposition system with different laser energies. The structure, composition and optical properties of the films have been investigated with atomic force microscopy, x-ray photoemission spectroscopy, ellipsometry and the transmittance analysis. Upon the increase of laser energy, the results showed that the changes in the optical constants are consistent with the thickness changes of the film. The refractive index increases and the absorption coefficient increases when the laser energy increases. The AFM analysis showed a change of the roughness and structure of the deposited films at different laser energies. The prepared films deposited by LAMBD showed interesting properties with correct V2O5 phase without need of annealing after deposition.
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.
Sanchez-Parcerisa, D; Cortés-Giraldo, M A; Dolney, D; Kondrla, M; Fager, M; Carabe, A
2016-02-21
In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm(-1)) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process.
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.
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.
Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.
Miao, Yinglong; McCammon, J Andrew
Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.
Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.
Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J Andrew
2011-06-02
The independent trajectory thermodynamic integration (IT-TI) approach (Lawrenz et. al J. Chem. Theory. Comput. 2009, 5:1106-1116(1)) for free energy calculations with distributed computing is employed to study two distinct cases of protein-ligand binding: first, the influenza surface protein N1 neuraminidase bound to the inhibitor oseltamivir, and second, the M. tuberculosis enzyme RmlC complexed with the molecule CID 77074. For both systems, finite molecular dynamics (MD) sampling and varied molecular flexibility give rise to IT-TI free energy distributions that are remarkably centered on the target experimental values, with a spread directly related to protein, ligand, and solvent dynamics. Using over 2 μs of total MD simulation, alternative protocols for the practical, general implementation of IT-TI are investigated, including the optimal use of distributed computing, the total number of alchemical intermediates, and the procedure to perturb electrostatics and van der Waals interactions. A protocol that maximizes predictive power and computational efficiency is proposed. IT-TI outperforms traditional TI predictions and allows a straightforward evaluation of the reliability of free energy estimates. Our study has broad implications for the use of distributed computing in free energy calculations of macromolecular systems.
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.
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
Energy gap of extended states in SiC-doped graphene nanoribbon: Ab initio calculations
NASA Astrophysics Data System (ADS)
Liu, Xiaoshi; Wu, Yong; Li, Zhongyao; Gao, Yong
2017-04-01
The energy gap of extended states in zigzag graphene nanoribbons (ZGNRs) was examined on the basis of density-functional theory. In isolated ZGNRs, the energy gap is inversely proportional to the width of ribbon. It agrees well with the results from the Dirac equation in spin-unpolarized ZGNRs, although the considered ZGNRs have spin-polarized edges. However, the energy gap in SiC-doped ZGNRs cannot be modeled by effective width approximation. The doping also lifts the spin-degenerate of edge states and results in a metallic-like band structure near the Fermi level in SiC-doped ZGNRs. Our calculations may be helpful for understanding the origin of the reported single-channel ballistic transport in epitaxial graphene nanoribbons.
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.
First-Principles Approach to Calculating Energy Level Alignment at Aqueous Semiconductor Interfaces
NASA Astrophysics Data System (ADS)
Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.
2014-10-01
A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b1 energy level in water. The application to the specific cases of nonpolar (101 ¯0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.
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.
Including the relativistic kinetic energy in a spline-augmented plane-wave band calculation
Fehrenbach, G.M.; Schmidt, G.
1997-03-01
The first-order relativistic correction to the kinetic energy of an electron, the mass-velocity term, is not bounded from below. It can, therefore, not be used within a variational framework. To overcome this deficiency we developed a method to include the entire relativistic kinetic energy {radical}(p{sup 2}c{sup 2}+m{sub 0}{sup 2}c{sup 4}){minus}m{sub 0}c{sup 2} in a spline-augmented plane-wave band calculation. The first results for silver are quite promising, especially for d and p states: The analysis of the energies of the core states as well as of the valence band structure suggests that the energies of d bands are reproduced within 1 mRy. However, the combination of the relativistic kinetic energy with the Darwin term leads to energies which are too low for s-like valence states by 10 mRy. Therefore, the s and d valence band complex is spread out and the Fermi level is lowered by the same amount as the s states. We expect to overcome these deficiencies in future investigations by using a alternative form of the relativistic potential correction along the lines proposed by Douglas and Kroll. {copyright} {ital 1997} {ital The American Physical Society}
NASA Astrophysics Data System (ADS)
Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.
2016-04-01
State-of-the-art directed self-assembly (DSA) of block copolymer (BCP) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication. The defect free energy of a dislocation pair or jog defect, one of the most common defects found in BCP-DSA, is calculated via thermodynamic integration using a coarse-grained molecular dynamics model as a function of χ and the degree of polymerization (N). It is found that χN is not the best predictor of defect free energy and that a single χN value can yield vastly different free energies when χ and N are different. Defect free energy was highly dependent on defect location relative to the underlayer, and free energy differences ˜100 kT were found among the three possible defect locations on a 1:3 guiding pattern. It was found that increasing molar mass dispersity (Ð) significantly reduced defect free energy. Extrapolating from Ð up to 1.5 suggests that the defect will occur in equal proportions to the defect free state at a Ð of around 1.6 for this system. It was found that long chains tended to concentrate near the defect and stabilize the defect.
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.
Chemical vapour deposition of thermochromic vanadium dioxide thin films for energy efficient glazing
NASA Astrophysics Data System (ADS)
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.
Mesoscale energy deposition footprint model for kiloelectronvolt cluster bombardment of solids.
Russo, Michael F; Garrison, Barbara J
2006-10-15
Molecular dynamics simulations have been performed to model 5-keV C60 and Au3 projectile bombardment of an amorphous water substrate. The goal is to obtain detailed insights into the dynamics of motion in order to develop a straightforward and less computationally demanding model of the process of ejection. The molecular dynamics results provide the basis for the mesoscale energy deposition footprint model. This model provides a method for predicting relative yields based on information from less than 1 ps of simulation time.
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.
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.
Betowski, Leon D; Enlow, Mark; Riddick, Lee; Aue, Donald H
2006-11-30
Electron affinities (EAs) and free energies for electron attachment (DeltaGo(a,298K)) have been directly calculated for 45 polynuclear aromatic hydrocarbons (PAHs) and related molecules by a variety of theoretical methods, with standard regression errors of about 0.07 eV (mean unsigned error = 0.05 eV) at the B3LYP/6-31 + G(d,p) level and larger errors with HF or MP2 methods or using Koopmans' Theorem. Comparison of gas-phase free energies with solution-phase reduction potentials provides a measure of solvation energy differences between the radical anion and neutral PAH. A simple Born-charging model approximates the solvation effects on the radical anions, leading to a good correlation with experimental solvation energy differences. This is used to estimate unknown or questionable EAs from reduction potentials. Two independent methods are used to predict DeltaGo(a,298K) values: (1) based upon DFT methods, or (2) based upon reduction potentials and the Born model. They suggest reassignments or a resolution of conflicting experimental EAs for nearly one-half (17 of 38) of the PAH molecules for which experimental EAs have been reported. For the antiaromatic molecules, 1,3,5-tri-tert-butylpentalene and the dithia-substituted cyclobutadiene 1, the reduction potentials lead to estimated EAs close to those expected from DFT calculations and provide a basis for the prediction of the EAs and reduction potentials of pentalene and cyclobutadiene. The Born model has been used to relate the electrostatic solvation energies of PAH and hydrocarbon radical anions, and spherical halide anions, alkali metal cations, and ammonium ions to effective ionic radii from DFT electron-density envelopes. The Born model used for PAHs has been successfully extended here to quantitatively explain the solvation energy of the C60 radical anion.
Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor.
Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad
2011-01-01
We report a Quantum mechanics/Molecular Mechanics-Poisson-Boltzmann/ Surface Area (QM/MM-PB/SA) method to calculate the binding free energy of c-Abl human tyrosine kinase by combining the QM and MM principles where the ligand is treated quantum mechanically and the rest of the receptor by classical molecular mechanics. To study the role of entropy and the flexibility of the protein ligand complex in a solvated environment, molecular dynamics calculations are performed using a hybrid QM/MM approach. This work shows that the results of the QM/MM approach are strongly correlated with the binding affinity. The QM/MM interaction energy in our reported study confirms the importance of electronic and polarization contributions, which are often neglected in classical MM-PB/SA calculations. Moreover, a comparison of semi-empirical methods like DFTB-SCC, PM3, MNDO, MNDO-PDDG, and PDDG-PM3 is also performed. The results of the study show that the implementation of a DFTB-SCC semi-empirical Hamiltonian that is derived from DFT gives better results than other methods. We have performed such studies using the AMBER molecular dynamic package for the first time. The calculated binding free energy is also in agreement with the experimentally determined binding affinity for c-Abl tyrosine kinase complex with Imatinib.Electronic supplementary material The online version of this article (doi:10.1007/s10867-010-9199-z) contains supplementary material, which is available to authorized users.
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.
An efficient method for the calculation of quantum mechanics/molecular mechanics free energies
NASA Astrophysics Data System (ADS)
Woods, Christopher J.; Manby, Frederick R.; Mulholland, Adrian J.
2008-01-01
The combination of quantum mechanics (QM) with molecular mechanics (MM) offers a route to improved accuracy in the study of biological systems, and there is now significant research effort being spent to develop QM/MM methods that can be applied to the calculation of relative free energies. Currently, the computational expense of the QM part of the calculation means that there is no single method that achieves both efficiency and rigor; either the QM/MM free energy method is rigorous and computationally expensive, or the method introduces efficiency-led assumptions that can lead to errors in the result, or a lack of generality of application. In this paper we demonstrate a combined approach to form a single, efficient, and, in principle, exact QM/MM free energy method. We demonstrate the application of this method by using it to explore the difference in hydration of water and methane. We demonstrate that it is possible to calculate highly converged QM/MM relative free energies at the MP2/aug-cc-pVDZ/OPLS level within just two days of computation, using commodity processors, and show how the method allows consistent, high-quality sampling of complex solvent configurational change, both when perturbing hydrophilic water into hydrophobic methane, and also when moving from a MM Hamiltonian to a QM/MM Hamiltonian. The results demonstrate the validity and power of this methodology, and raise important questions regarding the compatibility of MM and QM/MM forcefields, and offer a potential route to improved compatibility.
Vázquez, Juana; Harding, Michael E; Stanton, John F; Gauss, Jürgen
2011-05-10
A variational method for the calculation of low-lying vibrational energy levels of molecules with small amplitude vibrations is presented. The approach is based on the Watson Hamiltonian in rectilinear normal coordinates and characterized by a quasi-analytic integration over the kinetic energy operator (KEO). The KEO beyond the harmonic approximation is represented by a Taylor series in terms of the rectilinear normal coordinates around the equilibrium configuration. This formulation of the KEO enables its extension to arbitrary order until numerical convergence is reached for those states describing small amplitude motions and suitably represented with a rectilinear system of coordinates. A Gauss-Hermite quadrature grid representation of the anharmonic potential is used for all the benchmark examples presented. Results for a set of molecules with linear and nonlinear configurations, i.e., CO2, H2O, and formyl fluoride (HFCO), illustrate the performance of the method and the versatility of our implementation.
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.
TASK 2.5.4 DEVELOPMENT OF AN ENERGY SAVINGS CALCULATOR
Miller, William A; New, Joshua Ryan; Desjarlais, Andre Omer; Huang, Joe; Erdem, Ender; Ronnen, Levinson
2010-03-01
California s major energy utilities and the California Energy Commission (CEC) are seeking to allocate capital that yields the greatest return on investment for energy infrastructure that meets any part of the need for reliable supplies of energy. The utilities are keenly interested in knowing the amount of electrical energy savings that would occur if cool roof color materials are adopted in the building market. To meet this need the Oak Ridge National Laboratory and the Lawrence Berkeley National Laboratory (LBNL) have been collaborating on a Public Interest Energy Research (PIER) project to develop an industry-consensus energy-savings calculator. The task was coordinated with an ongoing effort supported by the DOE to develop one calculator to achieve both the DOE and the EPA objectives for deployment of cool roof products. Recent emphasis on domestic building energy use has made the work a top priority by the Department of Energy s (DOE) Building Technologies Program. The Roof Savings Calculator (RSC) tool is designed to help building owners, manufacturers, distributors, contractors and practitioners easily run complex simulations. The latest web technologies and usability design were employed to provide an easy input interface to an annual simulation of hour-by-hour, whole-building performance using the world-class simulation tools DOE-2.1E and AtticSim. Building defaults were assigned based on the best available statistical evidence and can provide energy and cost savings after the user selects nothing more than the building location. A key goal for the tool is to promote the energy benefits of cool color tile, metal and asphalt shingle roof products and other energy saving systems. The RSC tool focuses on applications for the roof and attic; however, the code conducts a whole building simulation that puts the energy and heat flows of the roof and attic into the perspective of the whole house. An annual simulation runs in about 30 sec. In addition to cool
Monte Carlo simulation of electrodeposition of copper: a multistep free energy calculation.
Harinipriya, S; Subramanian, Venkat R
2008-04-03
Electrodeposition of copper (Cu) involves length scales of a micrometer or even less. Several theoretical techniques such as continuum Monte Carlo, kinetic Monte Carlo (KMC), and molecular dynamics have been used for simulating this problem. However the multiphenomena characteristics of the problem pose a challenge for an efficient simulation algorithm. Traditional KMC methods are slow, especially when modeling surface diffusion with large number of particles and frequent particle jumps. Parameter estimation involving thousands of KMC runs is very time-consuming. Thus a less time-consuming and novel multistep continuum Monte Carlo simulation is carried out to evaluate the step wise free energy change in the process of electrochemical copper deposition. The procedure involves separate Monte Carlo codes employing different random number criterion (using hydrated radii, bare radii, hydration number of the species, redox potentials, etc.) to obtain the number of species (CuCl(2) or CuSO(4) or Cu as the case may be) and in turn the free energy. The effect of concentration of electrolyte, influence of electric field and presence of chloride ions on the free energy change for the processes is studied. The rate determining step for the process of electrodeposition of copper from CuCl(2) and CuSO(4) is also determined.
Singh, Nidhi; Warshel, Arieh
2010-01-01
Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic Linear Response Approximation (LRA/β version) and its variants including the Linear Interaction Energy (LIE) to the more approximated and considerably faster scaled Protein Dipoles Langevin Dipoles (PDLD/S-LRA version), as well as the less rigorous Molecular Mechanics Poisson–Boltzmann/Surface Area (MM/PBSA) and Generalized Born/Surface Area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/β, the LIE, the PDLD/S-LRA/β and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the non-electrostatic term. On the average, the PDLD/S-LRA/β performs effectively. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies due to its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/β appears to offer an appealing option for the final stages of massive screening approaches. PMID:20186976
Pham, Tri T; Shirts, Michael R
2011-07-21
Improving the efficiency of free energy calculations is important for many biological and materials design applications, such as protein-ligand binding affinities in drug design, partitioning between immiscible liquids, and determining molecular association in soft materials. We show that for any pair potential, moderately accurate estimation of the radial distribution function for a solute molecule is sufficient to accurately estimate the statistical variance of a sampling along a free energy pathway. This allows inexpensive analytical identification of low statistical error free energy pathways. We employ a variety of methods to estimate the radial distribution function (RDF) and find that the computationally cheap two-body "dilute gas" limit performs as well or better than 3D-RISM theory and other approximations for identifying low variance free energy pathways. With a RDF estimate in hand, we can search for pairwise interaction potentials that produce low variance. We give an example of a search minimizing statistical variance of solvation free energy over the entire parameter space of a generalized "soft core" potential. The free energy pathway arising from this optimization procedure has lower curvature in the variance and reduces the total variance by at least 50% compared to the traditional soft core solvation pathway. We also demonstrate that this optimized pathway allows free energies to be estimated with fewer intermediate states due to its low curvature. This free energy variance optimization technique is generalizable to solvation in any homogeneous fluid and for any type of pairwise potential and can be performed in minutes to hours, depending on the method used to estimate g(r).
Calculation of excitation energies from the CC2 linear response theory using Cholesky decomposition
Baudin, Pablo; Marín, José Sánchez; Cuesta, Inmaculada García; Sánchez de Merás, Alfredo M. J.
2014-03-14
A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitioning form of the CC2 equations which reduces the dimension of the problem and avoids the storage of doubles amplitudes. We present calculation of excitation energies of benzene using a hierarchy of basis sets and compare the results with conventional CC2 calculations. The reduction of the scaling is evaluated as well as the effect of the Cholesky decomposition parameter on the quality of the results. The new algorithm is used to perform an extrapolation to complete basis set investigation on the spectroscopically interesting benzylallene conformers. A set of calculations on medium-sized molecules is carried out to check the dependence of the accuracy of the results on the decomposition thresholds. Moreover, CC2 singlet excitation energies of the free base porphin are also presented.
On the importance of full-dimensionality in low-energy molecular scattering calculations
Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof
2016-01-01
Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm−1 in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870
NASA Technical Reports Server (NTRS)
Baily, N. A.; Steigerwalt, J. E.; Hilbert, J. W.
1972-01-01
The frequency distributions of event size in the deposition of energy over small pathlengths have been measured after penetration of 44.3 MeV protons through various thicknesses of tissue-equivalent material. Results show that particle energy straggling of an initially monoenergetic proton beam after passage through an absorber causes the frequency distributions of energy deposited in short pathlengths of low atomic number materials to remain broad. In all cases investigated, the ratio of the most probable to the average energy losses has been significantly less than unity.
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.
NASA Astrophysics Data System (ADS)
Youroukov, S.; Kitova, S.; Danev, G.
2008-05-01
The possibility is studied of growing thin silicon oxynitride films by e-gun evaporation of SiO and SiO2 together with concurrent bombardment with low energy N2+ ions from a cyclotron resonance (ECR) source at room temperature of substrates. The degree of nitridation and oxidation of the films is investigated by means of X-ray spectroscopy. The optical characteristics of the films, their environmental stability and adhesion to different substrates are examined. The results obtained show than the films deposited are transparent. It is found that in the case of SiO evaporation with concurrent N2+ ion bombardment, reactive implantation of nitrogen within the films takes place at room temperature of the substrate with the formation of a new silicon oxynitride compound even at low ion energy (150-200 eV).
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.
Configurational space discretization and free energy calculation in complex molecular systems
Wang, Kai; Long, Shiyang; Tian, Pu
2016-01-01
We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy. PMID:26974524
Variational Monte Carlo calculations for the binding energy of sub. Lambda. Lambda. sup 31 Si
Ahsan, M.H. ); Kaykobad, M. ); Ali, S. )
1991-01-01
The binding energy of the {Lambda}{Lambda} hypernucleus {sub {Lambda}{Lambda}}{sup 31}Si has been calculated variationally with a {sup 28}Si+{ital n}+{Lambda}+{Lambda} four-body model. The integrations have been carried out with the help of a Monte Carlo technique. Three different types of {Lambda}-{Lambda} and {Lambda}-{ital N} potentials have been used. {ital n}-{sup 28}Si and {Lambda}-{sup 28}Si potentials have been generated by folding the {ital N}-{ital N} and {Lambda}-{ital N} potentials into the harmonic-oscillator shell-model density distribution of {sup 28}Si. The calculated values of the binding energy for the three different potentials are 40.19, 46.30, and 39.90 MeV. These values are compared with the reported experimental value of 38.2{plus minus}6.3 MeV. The dependence of the binding energy on the depth of the {Lambda}-{Lambda} interaction has also been investigated.
Slavícek, Petr; Winter, Bernd; Faubel, Manfred; Bradforth, Stephen E; Jungwirth, Pavel
2009-05-13
Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.
Configurational space discretization and free energy calculation in complex molecular systems.
Wang, Kai; Long, Shiyang; Tian, Pu
2016-03-14
We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy.
Path integral calculation of free energies: quantum effects on the melting temperature of neon.
Ramírez, R; Herrero, C P; Antonelli, A; Hernández, E R
2008-08-14
The path integral formulation has been combined with several methods to determine free energies of quantum many-body systems, such as adiabatic switching and reversible scaling. These techniques are alternatives to the standard thermodynamic integration method. A quantum Einstein crystal is used as a model to demonstrate the accuracy and reliability of these free energy methods in quantum simulations. Our main interest focuses on the calculation of the melting temperature of Ne at ambient pressure, taking into account quantum effects in the atomic dynamics. The free energy of the solid was calculated by considering a quantum Einstein crystal as reference state, while for the liquid, the reference state was defined by the classical limit of the fluid. Our findings indicate that, while quantum effects in the melting temperature of this system are small, they still amount to about 6% of the melting temperature, and are therefore not negligible. The particle density as well as the melting enthalpy and entropy of the solid and liquid phases at coexistence is compared to results obtained in the classical limit and also to available experimental data.
CALCULATING ENERGY STORAGE DUE TO TOPOLOGICAL CHANGES IN EMERGING ACTIVE REGION NOAA AR 11112
Tarr, Lucas; Longcope, Dana
2012-04-10
The minimum current corona model provides a way to estimate stored coronal energy using the number of field lines connecting regions of positive and negative photospheric flux. This information is quantified by the net flux connecting pairs of opposing regions in a connectivity matrix. Changes in the coronal magnetic field, due to processes such as magnetic reconnection, manifest themselves as changes in the connectivity matrix. However, the connectivity matrix will also change when flux sources emerge or submerge through the photosphere, as often happens in active regions. We have developed an algorithm to estimate the changes in flux due to emergence and submergence of magnetic flux sources. These estimated changes must be accounted for in order to quantify storage and release of magnetic energy in the corona. To perform this calculation over extended periods of time, we must additionally have a consistently labeled connectivity matrix over the entire observational time span. We have therefore developed an automated tracking algorithm to generate a consistent connectivity matrix as the photospheric source regions evolve over time. We have applied this method to NOAA Active Region 11112, which underwent a GOES M2.9 class flare around 19:00 on 2010 October 16th, and calculated a lower bound on the free magnetic energy buildup of {approx}8.25 Multiplication-Sign 10{sup 30} erg over 3 days.
Higher energy states in the CO dimer: millimeter-wave spectra and rovibrational calculations.
Surin, Leonid A; Fourzikov, Dmitri N; Giesen, Thomas F; Schlemmer, Stephan; Winnewisser, Gisbert; Panfilov, Victor A; Dumesh, Boris S; Vissers, Gé W M; van der Avoird, Ad
2007-12-13
New extensive millimeter-wave measurements of the 12C16O dimer have been made, and more than 300 new spectral transitions have been observed in the frequency range 81-135 GHz. A joint analysis of these and previous millimeter-wave data yielded the precise location of 33 new energy levels of A+ symmetry and 20 levels of A- symmetry. These energy levels are located at 8-18 cm(-1) above the zero-point level. Some of them belong to already known stacks, and others make up 9 new stacks of the dimer. Newly determined stacks have K=0, 1, and, for the first time, 2, where K is the projection of the total angular momentum on the intermolecular axis. The energy levels from accompanying rovibrational calculations with the use of a recently developed hybrid CCSD(T)/DFT-SAPT potential are in very good agreement with experiment. Analysis of the calculated wave functions revealed that two new stacks of A+ symmetry with K=2 correspond to overall rotation of the dimer while the other newly observed stacks belong to the geared bend overtone modes. The ground vibrational states of the two "isomers" found are more or less localized at the two minima in the potential surface, whereas all the geared bend excited states show a considerable amount of delocalization.
NASA Astrophysics Data System (ADS)
Mashouf, Shahram; Lechtman, Eli; Beaulieu, Luc; Verhaegen, Frank; Keller, Brian M.; Ravi, Ananth; Pignol, Jean-Philippe
2013-09-01
The American Association of Physicists in Medicine Task Group No. 43 (AAPM TG-43) formalism is the standard for seeds brachytherapy dose calculation. But for breast seed implants, Monte Carlo simulations reveal large errors due to tissue heterogeneity. Since TG-43 includes several factors to account for source geometry, anisotropy and strength, we propose an additional correction factor, called the inhomogeneity correction factor (ICF), accounting for tissue heterogeneity for Pd-103 brachytherapy. This correction factor is calculated as a function of the media linear attenuation coefficient and mass energy absorption coefficient, and it is independent of the source internal structure. Ultimately the dose in heterogeneous media can be calculated as a product of dose in water as calculated by TG-43 protocol times the ICF. To validate the ICF methodology, dose absorbed in spherical phantoms with large tissue heterogeneities was compared using the TG-43 formalism corrected for heterogeneity versus Monte Carlo simulations. The agreement between Monte Carlo simulations and the ICF method remained within 5% in soft tissues up to several centimeters from a Pd-103 source. Compared to Monte Carlo, the ICF methods can easily be integrated into a clinical treatment planning system and it does not require the detailed internal structure of the source or the photon phase-space.
Nagel, J A; Beck, C; Harms, H; Stiller, P; Guth, H; Stachs, O; Bretthauer, G
2010-12-01
Presbyopia and cataract are gaining more and more importance in the ageing society. Both age-related complaints are accompanied with a loss of the eye's ability to accommodate. A new approach to restore accommodation is the Artificial Accommodation System, an autonomous micro system, which will be implanted into the capsular bag instead of a rigid intraocular lens. The Artificial Accommodation System will, depending on the actual demand for accommodation, autonomously adapt the refractive power of its integrated optical element. One possibility to measure the demand for accommodation non-intrusively is to analyse eye movements. We present an efficient algorithm, based on the CORDIC technique, to calculate the demand for accommodation from magnetic field sensor data. It can be shown that specialised algorithms significantly shorten calculation time without violating precision requirements. Additionally, a communication strategy for the wireless exchange of sensor data between the implants of the left and right eye is introduced. The strategy allows for a one-sided calculation of the demand for accommodation, resulting in an overall reduction of calculation time by 50 %. The presented methods enable autonomous microsystems, such as the Artificial Accommodation System, to save significant amounts of energy, leading to extended autonomous run-times.
Mashouf, Shahram; Lechtman, Eli; Beaulieu, Luc; Verhaegen, Frank; Keller, Brian M; Ravi, Ananth; Pignol, Jean-Philippe
2013-09-21
The American Association of Physicists in Medicine Task Group No. 43 (AAPM TG-43) formalism is the standard for seeds brachytherapy dose calculation. But for breast seed implants, Monte Carlo simulations reveal large errors due to tissue heterogeneity. Since TG-43 includes several factors to account for source geometry, anisotropy and strength, we propose an additional correction factor, called the inhomogeneity correction factor (ICF), accounting for tissue heterogeneity for Pd-103 brachytherapy. This correction factor is calculated as a function of the media linear attenuation coefficient and mass energy absorption coefficient, and it is independent of the source internal structure. Ultimately the dose in heterogeneous media can be calculated as a product of dose in water as calculated by TG-43 protocol times the ICF. To validate the ICF methodology, dose absorbed in spherical phantoms with large tissue heterogeneities was compared using the TG-43 formalism corrected for heterogeneity versus Monte Carlo simulations. The agreement between Monte Carlo simulations and the ICF method remained within 5% in soft tissues up to several centimeters from a Pd-103 source. Compared to Monte Carlo, the ICF methods can easily be integrated into a clinical treatment planning system and it does not require the detailed internal structure of the source or the photon phase-space.
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.
Study of hot electron spatial energy deposition in spherical targets relevant to shock ignition
NASA Astrophysics Data System (ADS)
Zhang, Shu; Wei, M. S.; Krauland, C.; Reynolds, H.; Hoppe, M.; Peebles, J.; Beg, F. N.; Theobald, W.; Borwick, E.; Li, J.; Ren, C.; Stoeckl, C.; Seka, W.; Betti, R.; Campbell, M.
2016-10-01
Understanding hot electron generation and coupling is important for the high-intensity shock ignition (SI) inertial confinement fusion concept. Recent hard x-ray experimental data from a SI-relevant platform on OMEGA-60 suggest that <100 keV hot electrons may augment shock pressure by depositing their energy in the solid density region behind the ablation front. These results deduced from simulation are convincing support for electron assisted SI. To further investigate beneficial hot electron characteristics from both high intensity UV and IR lasers in this relevant regime, we performed a joint OMEGA-60/OMEGA EP experiment in the spherical geometry. 60 UV laser beams (18 kJ, 1.8 ns, up to 1015 W/cm2) irradiated a low-density Cu foam ball target with a CH ablator followed by a single IR short pulse laser (2.6 kJ, 100 ps, 1017 W/cm2) at various delays. The electron spatial energy deposition was diagnosed via imaging Cu K α emission with a spherical crystal imager; total K α photon yield and bremsstrahlung radiation were also measured to infer electron spectra. Experimental results are compared with radiation hydrodynamic modeling and will be presented at the meeting. Work supported by the U.S. DOE under contracts DE-NA0002730 (NLUF) and DE-SC0014666.
Production of High Energy Particles Using the Pd/D Co-Deposition Process
NASA Astrophysics Data System (ADS)
Mosier-Boss, Pamela A.; Szpak, Stanislaw; Gordon, Frank E.
2007-03-01
Using the Pd/D co-deposition technique, we have obtained evidence (i.e., heat generation, hot spots, mini-explosions, radiation, and tritium production) suggestive that nuclear reactions can and do occur within the Pd lattice. It was found that these reactions are enhanced in the presence of either an external electric or magnetic field. SEM analysis of the cathodes shows morphological features suggestive of localized melting of the palladium. EDX analysis of these features show the presence of new elements which result form transmutation. To verify that these new elements are indeed nuclear in origin, experiments have been conducted using CR-39 detectors, a commonly used etch-track detector for recording the emission of high energy particles such as alphas and protons. When the co-deposition reaction was conducted in either an external electric or magnetic field, numerous tracks due to high energy particles were clearly observed on the CR-39 detector in those areas where the cathode is in direct contact with the detector. S. Szpak et al, J. Electroanal. Chem., v 580, 284(2005). S. Szpak et al, Naturwissenschaften, v 92, 394-397(2005).
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.
Guan, Cao; Zeng, Zhiyuan; Li, Xianglin; Cao, Xiehong; Fan, Yu; Xia, Xinhui; Pan, Guoxiang; Zhang, Hua; Fan, Hong Jin
2014-01-29
Nanostructured carbon is widely used in energy storage devices (e.g., Li-ion and Li-air batteries and supercapacitors). A new method is developed for the generation of carbon nanoflakes on various metal oxide nanostructures by combining atomic layer deposition (ALD) and glucose carbonization. Various metal oxide@nanoflake carbon (MO@f-C) core-branch nanostructures are obtained. For the mechanism, it is proposed that the ALD Al2 O3 and glucose form a composite layer. Upon thermal annealing, the composite layer becomes fragmented and moves outward, accompanied by carbon deposition on the alumina skeleton. When tested as electrochemical supercapacitor electrode, the hierarchical MO@f-C nanostructures exhibit better properties compared with the pristine metal oxides or the carbon coating without ALD. The enhancement can be ascribed to increased specific surface areas and electric conductivity due to the carbon flake coating. This peculiar carbon coating method with the unique hierarchical nanostructure may provide a new insight into the preparation of 'oxides + carbon' hybrid electrode materials for energy storage applications.
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.