Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS
2017-05-17
and generally requires more time to solve per particle . This means that roughly half of the MPI processes will have higher reaction run times, while...ARL-TR-8018 ● MAY 2017 US Army Research Laboratory Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS...Research Laboratory Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS by Christopher P Stone Computational
Nonadiabatic quantum dynamics calculations for the N + NH --> N(2) + H reaction.
Yang, Huan; Hankel, M; Varandas, Antonio; Han, Keli
2010-09-01
Nonadiabatic quantum dynamics calculations on the two coupled potential energy surfaces (PESs) (1(2)A' and 2(2)A') and also adiabatic quantum calculations on the lowest adiabatic PES are reported for the title reaction. Reaction probabilities for total angular momenta, J, varying from 0 to 160, are calculated to obtain the integral cross section (ICS) for collision energies ranging from 0.05 to 1.0 eV. Calculations using both the close coupling and the Centrifugal Sudden (CS) approximation are carried out to evaluate the role of Coriolis coupling effects for this reaction. The results of the nonadiabatic calculations show that the nonadiabatic effects in the title reaction for the initial state of NH (v = 0, j = 0) could be neglected, at least in the collision energy range considered in this study.
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
Xu, Zheng; Yasuda, Keiji; Liu, Xiao-Jun
2015-10-01
In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves. Project supported by the National Natural Science Foundation of China (Grant Nos. 11404245, 11204129, and 11211140039).
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
徐峥; 安田启司; 刘晓峻
2015-01-01
In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves.
Quantum dynamics calculation of reaction probability for H+Cl2→HCl+Cl
无
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + Cl2 based on the GHNS potential energy surface with total angular momentum J = 0. The effects of the translational, vibrational and rotational excitation of Cl2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Quantum dynamics calculation of reaction probability for H+Cl2→HC1+Cl
王胜龙; 赵新生
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + CI2 based on the GHNS potential energy surface with total angular momentum J= 0. The effects of the translational, vibrational and rotational excitation of CI2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Should Thermostatted Ring Polymer Molecular Dynamics be used to calculate reaction rates?
Hele, Timothy J H
2015-01-01
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to rigorous Quantum Transition-State Theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H+H$_2$, D+MuH and F+H$_2$, and the prototypical polyatomic reaction H+CH$_4$. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is less accurate than Ring Polymer Molecular Dynamics (RPMD) for symmetric reactions, and in certain asymmetric systems closer to the q...
Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?
Hele, Timothy J. H., E-mail: tjhh2@cam.ac.uk [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Suleimanov, Yury V. [Computation-based Science and Technology Research Center, Cyprus Institute, 20 Kavafi St., Nicosia 2121 (Cyprus); Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139 (United States)
2015-08-21
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H{sub 2}, D + MuH, and F + H{sub 2}, and the prototypical polyatomic reaction H + CH{sub 4}. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.
Monge-Palacios, M; Yang, M; Espinosa-García, J
2012-04-14
A detailed dynamics study, using both quasi-classical trajectory (QCT) and reduced-dimensional quantum mechanical (QM) calculations, was carried out to understand the reactivity and mechanism of the Cl((2)P) + NH(3)→ HCl + NH(2) gas-phase reaction, which evolves through deep wells in the entry and exit channels. The calculations were performed on an analytical potential energy surface recently developed by our group, PES-2010 [M. Monge-Palacios, C. Rangel, J. C. Corchado and J. Espinosa-Garcia, Int. J. Quantum. Chem., 2011], together with a simplified model surface, mod-PES, in which the reactant well is removed to analyze its influence. The main finding was that the QCT and QM methods show a change of the reaction probability with collision energy, suggesting a change of the atomic-level mechanism of reaction with energy. This change disappeared when the mod-PES was used, showing that the behaviour at low energies is a direct consequence of the existence of the reactant well. Analysis of the trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) > 5 kcal mol(-1)) practically all trajectories are direct, at low energies (E(coll) cross section results reinforce this change of mechanism, showing also the influence of the reactant well on this reaction. Thus, the PES-2010 surface yields a forward-backward symmetry in the scattering, while when the reactant well is removed with the mod-PES the shape is more isotropic.
Kinematically complete chemical reaction dynamics
Trippel, S.; Stei, M.; Otto, R.; Hlavenka, P.; Mikosch, J.; Eichhorn, C.; Lourderaj, U.; Zhang, J. X.; Hase, W. L.; Weidemüller, M.; Wester, R.
2009-11-01
Kinematically complete studies of molecular reactions offer an unprecedented level of insight into the dynamics and the different mechanisms by which chemical reactions occur. We have developed a scheme to study ion-molecule reactions by velocity map imaging at very low collision energies. Results for the elementary nucleophilic substitution (SN2) reaction Cl- + CH3I → ClCH3 + I- are presented and compared to high-level direct dynamics trajectory calculations. Furthermore, an improved design of the crossed-beam imaging spectrometer with full three-dimensional measurement capabilities is discussed and characterization measurements using photoionization of NH3 and photodissociation of CH3I are presented.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun
2011-05-14
We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.
Photochemical reaction dynamics
Moore, B.C. [Lawrence Berkeley Laboratory, Livermore, CA (United States)
1993-12-01
The purpose of the program is to develop a fundamental understanding of unimolecular and bimolecular reaction dynamics with application in combustion and energy systems. The energy dependence in ketene isomerization, ketene dissociation dynamics, and carbonyl substitution on organometallic rhodium complexes in liquid xenon have been studied. Future studies concerning unimolecular processes in ketene as well as energy transfer and kinetic studies of methylene radicals are discussed.
Cao, Jun
2015-06-01
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π* transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π* excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S1(1ππ*) and S2(1nNπ*) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.
Cao, Jun, E-mail: caojunbnu@mail.bnu.edu.cn [Guizhou Provincial Key Laboratory of Computational Nano-Material Sciences, Guizhou Normal College, Guiyang, Guizhou 550018, China and Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China)
2015-06-28
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.
LI; Jin-hai
2012-01-01
<正>The DTL is very important accelerator structure, and it is necessary for the proton linac accelerator. We did the dynamics simulation for the 20 MeV DTL, and obtained the physical and mechanical parameters. The input energy of the DTL is 3 MeV, and the pulsed beam current is 50 mA.
无
2011-01-01
Compared with ellipse cavity, the spoke cavity has many advantages, especially for the low and medium beam energy. It will be used in the superconductor accelerator popular in the future. Based on the spoke cavity, we design and calculate an accelerator
Kunxian Shu
2014-01-01
Full Text Available The response to ultrashort laser pulses of two stacked benzene molecules has been studied by semiclassical dynamics simulation; two typical pathways were found following excitation of one of the benzene molecules by a 25 fs (FWHM, 4.7 eV photon. With a fluence of 40.49 J/m2, the stacked molecules form a cyclobutane benzene dimer; the formation of the two covalent bonds linking two benzenes occurs asynchronously after the excimer decays to electronic ground state. With a fluence of 43.26 J/m2, only one bond is formed, which breaks about 50 fs after formation, followed by separation into the two molecules. The deformation of benzene ring is found to play an important role in the bond cleavage.
Density functional calculations on hydrocarbon isodesmic reactions
Fortunelli, Alessandro; Selmi, Massimo
1994-06-01
Hartree—Fock, Hartree—Fock-plus-correlation and self-consistent Kohn—Sham calculations are performed on a set of hydrocarbon isodesmic reactions, i.e. reactions among hydrocarbons in which the number and type of carbon—carbon and carbon—hydrogen bonds is conserved. It is found that neither Hartree—Fock nor Kohn—Sham methods correctly predict standard enthalpies, Δ Hr(298 K), of these reactions, even though — for reactions involving molecules containing strained double bonds — the agreement between the theoretical estimates and the experimental values of Δ Hr seems to be improved by the self-consistent solution of the Kohn—Sham equations. The remaining discrepancies are attributed to intramolecular dispersion effects, that are not described by ordinary exchange—correlation functionals, and are eliminated by introducing corrections based on a simple semi-empirical model.
Calculation of the energetics of chemical reactions
Dunning, T.H. Jr.; Harding, L.B.; Shepard, R.L.; Harrison, R.J.
1988-01-01
To calculate the energetics of chemical reactions we must solve the electronic Schroedinger equation for the molecular conformations of importance for the reactive encounter. Substantial changes occur in the electronic structure of a molecular system as the reaction progresses from reactants through the transition state to products. To describe these changes, our approach includes the following three elements: the use of multiconfiguration self-consistent field wave functions to provide a consistent zero-order description of the electronic structure of the reactants, transition state, and products; the use of configuration interaction techniques to describe electron correlation effects needed to provide quantitative predictions of the reaction energetics; and the use of large, optimized basis sets to provide the flexibility needed to describe the variations in the electronic distributions. With this approach we are able to study reactions involving as many as 5--6 atoms with errors of just a few kcal/mol in the predicted reaction energetics. Predictions to chemical accuracy, i.e., to 1 kcal/mol or less, are not yet feasible, although continuing improvements in both the theoretical methodology and computer technology suggest that this will soon be possible, at least for reactions involving small polyatomic species. 4 figs.
Meana-Pañeda, Rubén; Truhlar, Donald G; Fernández-Ramos, Antonio
2011-03-07
We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.
New methods for quantum mechanical reaction dynamics
Thompson, Ward Hugh [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
1996-12-01
Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L^{2}) representation of the outgoing wave scattering Green`s function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green`s function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC^{-} can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC^{-} geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H_{3}O^{-} system, providing information about the potential energy surface for the OH + H_{2} reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the
2017-01-01
A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of −0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than −0.6 V (RHE) ethylene, the major product, is produced via the Eley–Rideal (ER) mechanism using H2O + e–. The rate-determining step (RDS) is C–C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than −0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than −0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4. These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface. PMID:28167767
Dynamics Calculation of Travel Wave Tube
无
2011-01-01
During the dynamics calculating of the travel tube, we must obtain the field map in the tube. The field map can be affected by not only the beam loading, but also the attenuation coefficient. The calculation of the attenuation coefficient
Microscopic calculations for solar nuclear reactions
Csoto, A; Csoto, Attila; Langanke, Karlheinz
2001-01-01
We have studied the 4He(3He,gamma)7Be, 3He(3He,2p)4He, and 7Be(p,gamma)8B reactions of the solar p-p chain, using microscopic cluster models. Among other results, we showed that the 6Li+p channel has a nontrivial effect on the 7Be-producing reaction, that the existence of a resonance in 6Be close to the 3He+3He threshold is rather unlikely, and that the correlations between some properties of 7Be/8B and the low-energy cross section of 7Be(p,gamma)8B might help one to constrain the value of the S_17(0) astrophysical S-factor.
Lara, Manuel, E-mail: manuel.lara@uam.es [Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid (Spain); Jambrina, P. G.; Aoiz, F. J. [Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid (Spain); Launay, J.-M. [Institut de Physique de Rennes, UMR CNRS 6251, Université de Rennes I, F-35042 Rennes (France)
2015-11-28
Quantum reactive and elastic cross sections and rate coefficients have been calculated for D{sup +} + H{sub 2} (v = 0, j = 0) collisions in the energy range from 10{sup −8} K (deep ultracold regime), where only one partial wave is open, to 150 K (Langevin regime) where many of them contribute. In systems involving ions, the ∼R{sup −4} behavior extends the interaction up to extremely long distances, requiring a special treatment. To this purpose, we have used a modified version of the hyperspherical quantum reactive scattering method, which allows the propagations up to distances of 10{sup 5} a{sub 0} needed to converge the elastic cross sections. Interpolation procedures are also proposed which may reduce the cost of exact dynamical calculations at such low energies. Calculations have been carried out on the PES by Velilla et al. [J. Chem. Phys. 129, 084307 (2008)] which accurately reproduces the long range interactions. Results on its prequel, the PES by Aguado et al. [J. Chem. Phys. 112, 1240 (2000)], are also shown in order to emphasize the significance of the inclusion of the long range interactions. The calculated reaction rate coefficient changes less than one order of magnitude in a collision energy range of ten orders of magnitude, and it is found in very good agreement with the available experimental data in the region where they exist (10-100 K). State-to-state reaction probabilities are also provided which show that for each partial wave, the distribution of HD final states remains essentially constant below 1 K.
Ab Initio Calculations Of Nuclear Reactions And Exotic Nuclei
Quaglioni, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2014-05-05
Our ultimate goal is to develop a fundamental theory and efficient computational tools to describe dynamic processes between nuclei and to use such tools toward supporting several DOE milestones by: 1) performing predictive calculations of difficult-to-measure landmark reactions for nuclear astrophysics, such as those driving the neutrino signature of our sun; 2) improving our understanding of the structure of nuclei near the neutron drip line, which will be the focus of the DOE’s Facility for Rare Isotope Beams (FRIB) being constructed at Michigan State University; but also 3) helping to reveal the true nature of the nuclear force. Furthermore, these theoretical developments will support plasma diagnostic efforts at facilities dedicated to the development of terrestrial fusion energy.
Sequential Voronoi diagram calculations using simple chemical reactions
Costello, Ben de Lacy; Adamatzky, Andy
2012-01-01
In our recent paper [de Lacy Costello et al. 2010] we described the formation of complex tessellations of the plane arising from the various reactions of metal salts with potassium ferricyanide and ferrocyanide loaded gels. In addition to producing colourful tessellations these reactions are naturally computing generalised Voronoi diagrams of the plane. The reactions reported previously were capable of the calculation of three distinct Voronoi diagrams of the plane. As diffusion coupled with a chemical reaction is responsible for the calculation then this is achieved in parallel. Thus an increase in the complexity of the data input does not utilise additional computational resource. Additional benefits of these chemical reactions is that a permanent record of the Voronoi diagram calculation (in the form of precipitate free bisectors) is achieved, so there is no requirement for further processing to extract the calculation results. Previously it was assumed that the permanence of the results was also a potenti...
Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations
De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut
2011-01-01
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c
Theoretical Model Calculation for d + 8Li Reaction
HAN Yin-Lu; GUO Hai-Rui; ZHANG Yue; ZHANG Jing-Shang
2008-01-01
Based on the theoretical models for light nuclei, the calculations of reaction cross sections and the angular distributions for d+8Li reaction are performed. Since all of the particle emissions are from the compound nucleus to the discrete levels, the angular momentum coupling effect in pre-equilibrium mechanism is taken into account. The three-body break-up process and the recoil effect are involved. The theoretical calculated results are compared to existing experimental data.
Quantum dynamics of fast chemical reactions
Light, J.C. [Univ. of Chicago, IL (United States)
1993-12-01
The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.
Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions
Schultz, Emeric
2008-01-01
A highly flexible learning tool, referred to as a dynamic reaction figure, is described. Application of these figures can (i) yield the correct chemical equation by simply following a set of menu driven directions; (ii) present the underlying "mechanism" in chemical reactions; and (iii) help to solve quantitative problems in a number of different…
Gimondi, Ilaria; Cavallotti, Carlo; Vanuzzo, Gianmarco; Balucani, Nadia; Casavecchia, Piergiorgio
2016-07-14
The mechanism of the O((3)P) + CH3CCH reaction was investigated using a combined experimental/theoretical approach. Experimentally the reaction dynamics was studied using crossed molecular beams (CMB) with mass-spectrometric detection and time-of-flight analysis at 9.2 kcal/mol collision energy. Theoretically master equation (ME) simulations were performed on a potential energy surface (PES) determined using high-level ab initio electronic structure calculations. In this paper (II) the theoretical results are described and compared with experiments, while in paper (I) are reported and discussed the results of the experimental study. The PES was investigated by determining structures and vibrational frequencies of wells and transition states at the CASPT2/aug-cc-pVTZ level using a minimal active space. Energies were then determined at the CASPT2 level increasing systematically the active space and at the CCSD(T) level extrapolating to the complete basis set limit. Two separate portions of the triplet PES were investigated, as O((3)P) can add either on the terminal or the central carbon of the unsaturated propyne bond. Minimum energy crossing points (MECPs) between the triplet and singlet PESs were searched at the CASPT2 level. The calculated spin-orbit coupling constants between the T1 and S0 electronic surfaces were ∼25 cm(-1) for both PESs. The portions of the singlet PES that can be accessed from the MECPs were investigated at the same level of theory. The system reactivity was predicted integrating stochastically the one-dimensional ME using Rice-Ramsperger-Kassel-Marcus theory to determine rate constants on the full T1/S0 PESs, accounting explicitly for intersystem crossing (ISC) using the Landau-Zener model. The computational results are compared both with the branching ratios (BRs) determined experimentally in the companion paper (I) and with those estimated in a recent kinetic study at 298 K. The ME results allow to interpret the main system reactivity: CH
Calculation of individual isotope equilibrium constants for geochemical reactions
Thorstenson, D.C.; Parkhurst, D.L.
2004-01-01
Theory is derived from the work of Urey (Urey H. C. [1947] The thermodynamic properties of isotopic substances. J. Chem. Soc. 562-581) to calculate equilibrium constants commonly used in geochemical equilibrium and reaction-transport models for reactions of individual isotopic species. Urey showed that equilibrium constants of isotope exchange reactions for molecules that contain two or more atoms of the same element in equivalent positions are related to isotope fractionation factors by ?? = (Kex)1/n, where n is the number of atoms exchanged. This relation is extended to include species containing multiple isotopes, for example 13C16O18O and 1H2H18O. The equilibrium constants of the isotope exchange reactions can be expressed as ratios of individual isotope equilibrium constants for geochemical reactions. Knowledge of the equilibrium constant for the dominant isotopic species can then be used to calculate the individual isotope equilibrium constants. Individual isotope equilibrium constants are calculated for the reaction CO2g = CO2aq for all species that can be formed from 12C, 13C, 16O, and 18O; for the reaction between 12C18 O2aq and 1H218Ol; and among the various 1H, 2H, 16O, and 18O species of H2O. This is a subset of a larger number of equilibrium constants calculated elsewhere (Thorstenson D. C. and Parkhurst D. L. [2002] Calculation of individual isotope equilibrium constants for implementation in geochemical models. Water-Resources Investigation Report 02-4172. U.S. Geological Survey). Activity coefficients, activity-concentration conventions for the isotopic variants of H2O in the solvent 1H216Ol, and salt effects on isotope fractionation have been included in the derivations. The effects of nonideality are small because of the chemical similarity of different isotopic species of the same molecule or ion. The temperature dependence of the individual isotope equilibrium constants can be calculated from the temperature dependence of the fractionation
Bias in Dynamic Monte Carlo Alpha Calculations
Sweezy, Jeremy Ed [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nolen, Steven Douglas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Adams, Terry R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Trahan, Travis John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-02-06
A 1/N bias in the estimate of the neutron time-constant (commonly denoted as α) has been seen in dynamic neutronic calculations performed with MCATK. In this paper we show that the bias is most likely caused by taking the logarithm of a stochastic quantity. We also investigate the known bias due to the particle population control method used in MCATK. We conclude that this bias due to the particle population control method is negligible compared to other sources of bias.
Theoretical calculations and analysis for n + 6Li reaction
Tao, Xi; Wang, Jimin; Chen, Guochang; Shen, Qingbiao
2017-09-01
R-matrix theory is an important methodology for applications on light, medium and heavy mass nuclides nuclear reaction in the resonance energy range. Full R-matrix formalism contains the diagonal elements of the energy levels matrix and it is a rigorous theory. Because of different assumptions and approximations, many kinds of R-matrix derived methods are obtained. The new R-matrix code FDRR is presented and includes 4 kinds of R-matrix applications. It can be used for calculating integral cross sections and angular distributions of 2-bodies reactions. The cross sections and angular distributions of n+ 6Li reaction are calculated and analyzed by FDRR code. The results are in good agreement with experimental data below 20 MeV.
Reaction Dynamics and Spectroscopy of Hydrocarbons in Plasma
Braams, Bastiaan J.
2014-03-24
This grant supported research in theoretical and computational Chemical Physics that resulted in numerous publications on fitting ab initio potential energy surfaces and dipole moment surfaces of polyatomic molecules and cations. This work made use of novel fitting methods that ensures that these surfaces are invariant with respect to all permutations of like atoms. The surfaces were used in various dynamics calculations, ranging from quantum vibrational dynamics to(quasi)classical trajectory calculations of reaction dynamics. A number of these studies were done in collaboration with experimental groups where the theoretical analyses turned out to be essential to give a proper understanding of the experimental results.
Quantum dynamics of the abstraction reaction of H with cyclopropane.
Shan, Xiao; Clary, David C
2014-10-30
The dynamics of the abstraction reaction of H atoms with the cyclopropane molecule is studied using quantum mechanical scattering theory. The quantum scattering calculations are performed in hyperspherical coordinates with a two-dimensional (2D) potential energy surface. The ab initio energy calculations are carried out with CCSD(T)-F12a/cc-pVTZ-F12 level of theory with the geometry and frequency calculations at the MP2/cc-pVTZ level. The contribution to the potential energy surface from the spectator modes is included as the projected zero-point energy correction to the ab initio energy. The 2D surface is fitted with a 29-parameter double Morse potential. An R-matrix propagation scheme is carried out to solve the close-coupled equations. The adiabatic energy barrier and reaction enthalpy are compared with high level computational calculations as well as experimental data. The calculated reaction rate constants shows very good agreement when compared with the experimental data, especially at lower temperature highlighting the importance of quantum tunnelling. The reaction probabilities are also presented and discussed. The special features of performing quantum dynamics calculation on the chemical reaction of a cyclic molecule are discussed.
Excitation function calculations for α + 93Nb nuclear reactions
Yiğit, M.; Tel, E.; Sarpün, İ. H.
2016-10-01
In this study, the excitation functions of alpha-induced reactions on the 93Nb target nucleus were calculated by using ALICE-ASH code. The hybrid model, Weisskopf-Ewing model and geometry dependent hybrid model in this code were used to understand the alpha-niobium interaction. The contribution on the nuclear interaction of compound and pre-compound processes, with variation of the incident alpha particle energy, was presented. Furthermore, the reaction cross sections were calculated by using different level density models such as Superfluid nuclear model, Fermi gas model and Kataria-Ramamurthy Fermi gas model. Obtaining a good agreement between the calculated and the measured cross sections, the exciton numbers and the nuclear level density models were varied. Finally, the proper choice of the exciton numbers and the nuclear level density models was found to be quite important in order to obtain the more realistic cross section values.
Improved resonance reaction rate calculation for lattice physics subsystem
Finch, D.R.
1974-02-08
The resonance capture calculations of the HAMMER System and HAMBUR System are derived from a consistent statement of the integral slowing down equation and definitions of the resonance integral. The assumptions made in these treatments are explicitly stated, and and an attempt is made to estimate the possible error in the resonance integral arising from these assumptions. This analysis is made to pin-point those parts of the calculation that can be improved and updated. Based on the analysis of existing calculations a method of calculation is derived which avoids most of the problems encountered in HAMMER and HAMBUR. The chief improvements that result are as follows: Careful attention is paid to calculation of the resonance flux as most errors in existing calculations result from consistently overpredicting fluxes in all regions of a lattice cell. The calculation can be modified to produce as crude or detailed a resonance calculation, at the expense of computer time, as required by the user. Resonances that overlap group boundaries contribute the correct contribution to each group's reaction rates. Overlap between resonances of different isotopes is correctly accounted for. Up-to-date resonance formalisms are used including the Adler-Adler multi-level formulations. Provision is made to easily add new formalisms when required. Streaming effects from neutron leaking into a cell may optionally be included in the calculation of resonance reaction rates. A complete description of the physics contained in this new computational module is provided along with additional information on the numerical techniques employed in the module.
Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.
Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin
2014-06-25
Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.
Nuclear reaction rates and opacity in massive star evolution calculations
Bahena, D [Astronomical Institute of the Academy of Sciences, BocnI II 1401, 14131 Praha 4 (Czech Republic); Klapp, J [Instituto Nacional de Investigaciones Nucleares, Km. 36.5 Carr. Mexico-Toluca, 52750 Edo. de Mexico (Mexico); Dehnen, H, E-mail: jaime.klapp@inin.gob.m [Universitaet Konstanz, Fachbereich Physik, Fach M568, D-78457 Konstanz (Germany)
2010-07-01
Nuclear reaction rates and opacity are important parameters in stellar evolution. The input physics in a stellar evolution code determines the main theoretical characteristics of the stellar structure, evolution and nucleosynthesis of a star. For different input physics, in this work we calculate stellar evolution models of very massive first stars during the hydrogen and helium burning phases. We have considered 100 and 200M{sub s}un galactic and pregalactic stars with metallicity Z = 10{sup -6} and 10{sup 9}, respectively. The results show important differences from old to new formulations for the opacity and nuclear reaction rates, in particular the evolutionary tracks are significantly affected, that indicates the importance of using up to date and reliable input physics. The triple alpha reaction activates sooner for pregalactic than for galactic stars.
Potential energy surfaces and reaction dynamics of polyatomic molecules
Chang, Yan-Tyng.
1991-11-01
A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
2013-03-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
Reaction dynamics and photochemistry of divalent systems
Davis, H. Floyd [Univ. of California, Berkeley, CA (United States)
1992-05-01
Results are presented of molecular beam studies of bimolecular and unimolecular reactions of Ba. Chapter 1 discusses the reaction Ba + NO_{2}. Formation of the dominant BaO(^{1}Σ) + NO products resulted primarily from decay of long-lived Ba^{+}NO_{2}^{-} collision complexes. Secondary mechanisms led to formation of forward scattered, internally excited BaO, and BaNO + O. D_{o}(Ba-NO) = 65±20 kcal/mol. Reactions of ground state and electronically excited Ba with water and alcohols are examined in Chapter 2. Reaction of Ba(^{1}S) + H^{2}O led to BaO + H_{2}, whereas excited state Ba(^{1}D) + H_{2}O reacted to form BaOH + H. Collisions between Ba and CH_{3}OH led to BaOCH_{3} + H. Radical channels involve H-atom migration and are promoted by excitation of the incident Ba atom. In Chapter 3, reactions of Ba(^{1}S) with ClO_{2}2 and O_{3} are discussed. Again, direct and complex mechanisms were observed. Formation of BaCl + O_{2} from decomposition of Ba^{+}ClO_{2}^{-} accounted for 10% of total reaction crass section. Although Ba + O_{3} → BaO + 0_{2} occurs primarily by direct reaction mechanisms, the secondary channel Ba + 0_{3} → BaO_{2} + 0 involved decay of long lived Ba^{1+}O_{3}^{-} intermediates. D_{o}(Ba-O_{2}) = 120 ±20 kcal/mol. Photodissociation dynamics of NO_{3} is explored in chapter 4. Visible excitation leads to formation of NO + 0_{2} and NO_{2} + O. Wavelength dependence of branching ratios is investigated. D_{o}(O-NO_{2}) = 48.55 kcal/mole ;and calculate ΔH_{f}(NO_{3}) = 17.75 kcal/mole (298K). Chapter 5 discusses the photodissociation of OClO in a molecular beam. Although ClO(^{2}II) + O(^{3}P) is dominant, Cl(^{2}P) + O_{2 }
Improving the accuracy of dynamic mass calculation
Oleksandr F. Dashchenko
2015-06-01
Full Text Available With the acceleration of goods transporting, cargo accounting plays an important role in today's global and complex environment. Weight is the most reliable indicator of the materials control. Unlike many other variables that can be measured indirectly, the weight can be measured directly and accurately. Using strain-gauge transducers, weight value can be obtained within a few milliseconds; such values correspond to the momentary load, which acts on the sensor. Determination of the weight of moving transport is only possible by appropriate processing of the sensor signal. The aim of the research is to develop a methodology for weighing freight rolling stock, which increases the accuracy of the measurement of dynamic mass, in particular wagon that moves. Apart from time-series methods, preliminary filtration for improving the accuracy of calculation is used. The results of the simulation are presented.
Markovian Dynamics on Complex Reaction Networks
Goutsias, John
2012-01-01
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating...
Dynamical Model of Weak Pion Production Reactions
Sato, T; Lee, T S H
2003-01-01
The dynamical model of pion electroproduction has been extended to investigate the weak pion production reactions. The predicted cross sections of neutrino-induced pion production reactions are in good agreement with the existing data. We show that the renormalized(dressed) axial N-$\\Delta$ form factor contains large dynamical pion cloud effects and this renormalization effects are crucial in getting agreement with the data. We conclude that the N-$\\Delta$ transitions predicted by the constituent quark model are consistent with the existing neutrino induced pion production data in the $\\Delta$ region.
Chemical Reaction Dynamics in Nanoscle Environments
Evelyn M. Goldfield
2006-09-26
The major focus of the research in this program is the study of the behavior of molecular systems confined in nanoscale environments. The goal is to develop a theoretical framework for predicting how chemical reactions occur in nanoscale environments. To achieve this goal we have employed ab initio quantum chemistry, classical dynamics and quantum dynamics methods. Much of the research has focused on the behavior of molecules confined within single-walled carbon nanotubes (SWCNTs). We have also studied interactions of small molecules with the exterior surface of SWCNTs. Nonequilibrium molecular dynamics of interfaces of sliding surface interfaces have also been performed.
Reaction dynamics in polyatomic molecular systems
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Markovian dynamics on complex reaction networks
Goutsias, J., E-mail: goutsias@jhu.edu; Jenkinson, G., E-mail: jenkinson@jhu.edu
2013-08-10
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.
Mode-Specific SN2 Reaction Dynamics.
Wang, Yan; Song, Hongwei; Szabó, István; Czakó, Gábor; Guo, Hua; Yang, Minghui
2016-09-01
Despite its importance in chemistry, the microscopic dynamics of bimolecular nucleophilic substitution (SN2) reactions is still not completely elucidated. In this publication, the dynamics of a prototypical SN2 reaction (F(-) + CH3Cl → CH3F + Cl(-)) is investigated using a high-dimensional quantum mechanical model on an accurate potential energy surface (PES) and further analyzed by quasi-classical trajectories on the same PES. While the indirect mechanism dominates at low collision energies, the direct mechanism makes a significant contribution. The reactivity is found to depend on the specific reactant vibrational mode excitation. The mode specificity, which is more prevalent in the direct reaction, is rationalized by a transition-state-based model.
Effect of Coriolis coupling in chemical reaction dynamics.
Chu, Tian-Shu; Han, Ke-Li
2008-05-14
It is essential to evaluate the role of Coriolis coupling effect in molecular reaction dynamics. Here we consider Coriolis coupling effect in quantum reactive scattering calculations in the context of both adiabaticity and nonadiabaticity, with particular emphasis on examining the role of Coriolis coupling effect in reaction dynamics of triatomic molecular systems. We present the results of our own calculations by the time-dependent quantum wave packet approach for H + D2 and F(2P3/2,2P1/2) + H2 as well as for the ion-molecule collisions of He + H2 +, D(-) + H2, H(-) + D2, and D+ + H2, after reviewing in detail other related research efforts on this issue.
Theoretical studies of chemical reaction dynamics
Schatz, G.C. [Argonne National Laboratory, IL (United States)
1993-12-01
This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.
Electromagnetic Reactions and Few-Nucleon Dynamics
Bacca, Sonia
2013-01-01
We present an update on recent theoretical studies of electromagnetic reactions obtained by using the Lorentz integral transform method. The 4He nucleus will be the main focus of this report: results for the photo-disintegration and the electro-disintegration processes will be shown, as well as a recent calculation of polarizability effects in muonic atoms. We also discuss the exciting possibility to investigate inelastic reactions for medium-mass nuclei in coupled-cluster theory, highlighted by the recent application to the 16O photo-nuclear cross section.
Trinidad Pérez-Rivera, Danilo; Romani, Paul N.; Lopez-Encarnacion, Juan Manuel
2016-10-01
Titan's atmosphere is arguably the atmosphere of greatest interest that we have an abundance of data for from both ground based and spacecraft observations. As we have learned more about Titan's atmospheric composition, the presence of pre-biotic molecules in its atmosphere has generated more and more fascination about the photochemical process and pathways it its atmosphere. Our computational laboratory has been extensively working throughout the past year characterizing nitrile synthesis reactions, making significant progress on the energetics and dynamics of the reactions of .CN with the hydrocarbons acetylene (C2H2), propylene (CH3CCH), and benzene (C6H6), developing a clear picture of the mechanistic aspects through which these three reactions proceed. Specifically, first principles calculations of the reaction profiles and molecular dynamics studies for gas-phase reactions of .CN and C2H2, .CN and CH3CCH, and .CN and C6H6 have been carried out. A very accurate determination of potential energy surfaces of these reactions will allow us to compute the reaction rates which are indispensable for photochemical modeling of Titan's atmosphere.The work at University of Puerto Rico at Cayey was supported by Puerto Rico NASA EPSCoR IDEAS-ER program (2015-2016) and DTPR was sponsored by the Puerto Rico NASA Space Grant Consortium Fellowship. *E-mail: juan.lopez15@upr.edu
Ab initio calculations of reactions of light nuclei
Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr
2017-09-01
An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.
Neural Networks in Chemical Reaction Dynamics
Raff, Lionel; Hagan, Martin
2011-01-01
This monograph presents recent advances in neural network (NN) approaches and applications to chemical reaction dynamics. Topics covered include: (i) the development of ab initio potential-energy surfaces (PES) for complex multichannel systems using modified novelty sampling and feedforward NNs; (ii) methods for sampling the configuration space of critical importance, such as trajectory and novelty sampling methods and gradient fitting methods; (iii) parametrization of interatomic potential functions using a genetic algorithm accelerated with a NN; (iv) parametrization of analytic interatomic
Molecular beam studies of reaction dynamics
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Mielke, Steven L.; Truhlar, Donald G.; Schwenke, David W.
1991-01-01
Improved techniques and well-optimized basis sets are presented for application of the outgoing wave variational principle to calculate converged quantum mechanical reaction probabilities. They are illustrated with calculations for the reactions D + H2 yields HD + H with total angular momentum J = 3 and F + H2 yields HF + H with J = 0 and 3. The optimization involves the choice of distortion potential, the grid for calculating half-integrated Green's functions, the placement, width, and number of primitive distributed Gaussians, and the computationally most efficient partition between dynamically adapted and primitive basis functions. Benchmark calculations with 224-1064 channels are presented.
Coriolis-coupled wave packet dynamics of H + HLi reaction.
Padmanaban, R; Mahapatra, S
2006-05-11
We investigated the effect of Coriolis coupling (CC) on the initial state-selected dynamics of H+HLi reaction by a time-dependent wave packet (WP) approach. Exact quantum scattering calculations were obtained by a WP propagation method based on the Chebyshev polynomial scheme and ab initio potential energy surface of the reacting system. Partial wave contributions up to the total angular momentum J=30 were found to be necessary for the scattering of HLi in its vibrational and rotational ground state up to a collision energy approximately 0.75 eV. For each J value, the projection quantum number K was varied from 0 to min (J, K(max)), with K(max)=8 until J=20 and K(max)=4 for further higher J values. This is because further higher values of K do not have much effect on the dynamics and also because one wishes to maintain the large computational overhead for each calculation within the affordable limit. The initial state-selected integral reaction cross sections and thermal rate constants were calculated by summing up the contributions from all partial waves. These were compared with our previous results on the title system, obtained within the centrifugal sudden and J-shifting approximations, to demonstrate the impact of CC on the dynamics of this system.
Reaction dynamics studies for the system 7Be+58Ni
Torresi, D.; Mazzocco, M.; Acosta, L.; Boiano, A.; Boiano, C.; Diaz-Torres, A.; Fierro, N.; Glodariu, T.; Grilj, L.; Guglielmetti, A.; Keeley, N.; La Commara, M.; Martel, I.; Mazzocchi, C.; Molini, P.; Pakou, A.; Parascandolo, C.; Parkar, V. V.; Patronis, N.; Pierroutsakou, D.; Romoli, M.; Rusek, K.; Sanchez-Benitez, A. M.; Sandoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Stiliaris, E.; Strano, E.; Stroe, L.; Zerva, K.
2015-04-01
The study of reactions induced by exotic weakly bound nuclei at energies around the Coulomb barrier had attracted a large interest in the last decade, since the features of these nuclei can deeply affect the reaction dynamics. The discrimination between different reaction mechanisms is, in general, a rather difficult task. It can be achieved by using detector arrays covering high solid angle and with high granularity that allow to measure the reaction products and, possibly, coincidences between them, as, for example, recently done for stable weakly bound nuclei [1, 2]. We investigated the collision of the weakly bound nucleus 7Be on a 58Ni target at the beam energy of 1.1 times the Coulomb barrier, measuring the elastic scattering angular distribution and the energy and angular distributions of 3He and 4He. The 7Be radioactive ion beam was produced by the facility EXOTIC at INFN-LNL with an energy of 22 MeV and an intensity of ~3×105 pps. Results showed that the 4He yeld is about 4 times larger than 3He yield, suggesting that reaction mechanisms other than the break-up mostly produce the He isotopes. Theoretical calculations for transfer channels and compound nucleus reactions suggest that complete fusion accounts for (41±5%) of the total reaction cross section extracted from optical model analysis of the elastic scattering data, and that 3He and 4He stripping are the most populated reaction channels among direct processes. Eventually estimation of incomplete fusion contributions to the 3,4He production cross sections was performed through semi-classical calculations with the code PLATYPUS [3].
Dynamics Calculation of CH-DTL
无
2011-01-01
CH-DTL is a new development of accelerator structure, which has high shunt impedance and simple structure. The beam dynamics of CH-DTL is based on KONUS method, whose characteristic is that the longitudinal focus is small or none,
Unimolecular reaction dynamics of well characterized ionic reactions. Final report, 1993--1997
Baer, T.
1997-12-31
The dissociation dynamics of well characterized and energy selected ions have been investigated by photoelectron photoion coincidence (PEPICO) spectrometry. A number of ions have been found which dissociate in competition with isomerization and which thus lead to multi-component decay rates. The dissociation dynamics on such complex potential energy surfaces are common for many free radical reactions, including some of importance to combustion processes. Individual reaction rates for isomerization and dissociation have been extracted from the data. In addition, all rates have been successfully modeled with the RRKM theory in combination with ab initio molecular orbital calculations. The dissociation dynamics of a dimer ion system has been studied on the UNC PEPICO apparatus as well as at the Chemical Dynamics Beam line of the ALS. This proof of principle experiment shows that it is possible to investigate such systems and to determine the heats of formation of free radicals by this approach. Finally, a dissociation involving a loose transition state with no exit barrier has been successfully modeled with a simplified version of the variational transition state theory (VTST). The aim of all of these studies is to develop protocols for modeling moderately complex unimolecular reactions with simple models.
Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.
2013-11-01
The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.
Wang, Bi-Yao; Li, Ze-Rong; Tan, Ning-Xin; Yao, Qian; Li, Xiang-Yuan
2013-04-25
We present a further interpretation of reaction class transition state theory (RC-TST) proposed by Truong et al. for the accurate calculation of rate coefficients for reactions in a class. It is found that the RC-TST can be interpreted through the isodesmic reaction method, which is usually used to calculate reaction enthalpy or enthalpy of formation for a species, and the theory can also be used for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. A correction scheme based on this theory is proposed for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. To validate the scheme, 16 combinations of various ab initio levels with various basis sets are used as the approximate methods and CCSD(T)/CBS method is used as the benchmarking method in this study to calculate the reaction energies and energy barriers for a representative set of five reactions from the reaction class: R(c)CH(R(b))CR(a)CH2 + OH(•) → R(c)C(•)(R(b))CR(a)CH2 + H2O (R(a), R(b), and R(c) in the reaction formula represent the alkyl or hydrogen). Then the results of the approximate methods are corrected by the theory. The maximum values of the average deviations of the energy barrier and the reaction enthalpy are 99.97 kJ/mol and 70.35 kJ/mol, respectively, before correction and are reduced to 4.02 kJ/mol and 8.19 kJ/mol, respectively, after correction, indicating that after correction the results are not sensitive to the level of the ab initio method and the size of the basis set, as they are in the case before correction. Therefore, reaction energies and energy barriers for reactions in a class can be calculated accurately at a relatively low level of ab initio method using our scheme. It is also shown that the rate coefficients for the five representative reactions calculated at the BHandHLYP/6-31G(d,p) level of theory via our scheme are very close to the values calculated at CCSD(T)/CBS level. Finally, reaction
Semirigid vibrating rotor target calculation for reaction O(3p)+CH4 →CH3+OH
LIU; Xinguo; BAI; Lihua; ZHANG; Qinggang
2004-01-01
The time-dependent quantum dynamics calculation for reaction O(3p)+CH4→ CH3+OH is made, using of the semirigid vibrating rotor target (SVRT) model and the time-dependent wave packet (TDWP) method. The corresponding reaction probabilities of different initial states are provided. From the calculation of initial rovibrational state j= 0,v= 0, 1, we can see that the excitation of the H-CH3 stretching vibration gives significant enhancement of reaction probability and the reaction threshold decreases dramatically with the enhancement of the vibrating excitation, which indicates that the vibrating energy of reagent molecules contributes a lot to the molecular collision. As for the calculation of reaction probability of state v= 0, j= 0,1,2,3, the results show that the reaction probability rises significantly with the enhancement of rotational quantum number j while the reaction threshold has no changes. The spatial steric effect of the title reaction is studied and analyzed too after the calculation of reaction probability of states j= 5, k= 0-2, n= 0 and j=5, k=2, n=0-2 is made.
Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics.
Shemesh, Dorit; Nizkorodov, Sergey A; Gerber, R Benny
2016-09-15
Photochemistry of carbonyl compounds is of major importance in atmospheric and organic chemistry. The photochemistry of cyclohexanone is studied here using on-the-fly molecular dynamics simulations on a semiempirical multireference configuration interaction potential-energy surface to predict the distribution of photoproducts and time scales for their formation. Rich photochemistry is predicted to occur on a picosecond time scale following the photoexcitation of cyclohexanone to the first singlet excited state. The main findings include: (1) Reaction channels found experimentally are confirmed by the theoretical simulations, and a new reaction channel is predicted. (2) The majority (87%) of the reactive trajectories start with a ring opening via C-Cα bond cleavage, supporting observations of previous studies. (3) Mechanistic details, time scales, and yields are predicted for all reaction channels. These benchmark results shed light on the photochemistry of isolated carbonyl compounds in the atmosphere and can be extended in the future to photochemistry of more complex atmospherically relevant carbonyl compounds in both gaseous and condensed-phase environments.
Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Saria
2009-09-15
a SN2 -like transition geometry, Figure 3c, the axial O-C-H bond angle is slightly bent more for reaction 4, Figure 3d. The products of reaction 4 are...Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Sarin Patrick F. Conforti and Matthew Braunstein* Spectral...calculations were performed on the reaction systems O(3P) + sarin and O(3P) + dimethyl methylphosphonate (DMMP), a sarin simulant. Transition state
FROSSARD, Laurent; Cheze, Laurence; Dumas, Raphaël
2011-01-01
Background: Calculation of lower limb kinetics is limited by floor-mounted force-plates. Objectives: Comparison of hip joint moments, power and mechanical work on the prosthetic limb of a transfemoral amputee calculated by inverse dynamics using either the ground reactions (force-plates) or knee reactions (transducer). Study design: Comparative analysis. Methods: Kinematics, ground reaction and knee reaction data were collected using a motion analysis system, two forceplates, and a multi-axia...
Separable Potentials for (d,p) Reaction Calculations
Elster, Ch; Eremenko, V; Nunes, F M; Thompson, I J; Arbanas, G; Escher, J E
2015-01-01
An important ingredient for applications of nuclear physics to e.g. astrophysics or nuclear energy are the cross sections for reactions of neutrons with rare isotopes. Since direct measurements are often not possible, indirect methods like $(d,p)$ reactions must be used instead. Those $(d,p)$ reactions may be viewed as effective three-body reactions and described with Faddeev techniques. An additional challenge posed by $(d,p)$ reactions involving heavier nuclei is the treatment of the Coulomb force. To avoid numerical complications in dealing with the screening of the Coulomb force, recently a new approach using the Coulomb distorted basis in momentum space was suggested. In order to implement this suggestion, one needs to derive a separable representation of neutron- and proton-nucleus optical potentials and compute their matrix elements in this basis.
Numerical Calculation of Artillery-Fuze System Dynamic Characteristics
WANG Ya-bin; LIU Ming-jie; TAN Hui-min
2007-01-01
A numerical calculation method based on the finite element analysis of dynamic characteristics of artillery-fuze system is discussed in detail. Pretension element is used to mesh the couple structure between artillery and fuze to analyze the change of dynamic characteristics of artillery-fuze system when pre-tightening force varies between artillery and fuze. Numerical calculation of the finite element analysis and actual hammering test of a artillery-fuze system are carried out with the same input to verify the accuracy of numerical calculation. The results show that the finite element model of artillery-fuze system is credibl e and the calculation accuracy is perfect.
Reaction to Indispensable Manual Calculation Skills in a CAS Environment.
Monaghan, John
2001-01-01
Reacts to an article published in a previous issue of this journal on the effects of graphing calculators and computer algebra systems (CAS) on students' manual calculation and algebraic manipulation skills. Considers the contribution made by Jean-Baptiste Lagrange to thinking about the role of CAS in teaching algebra. (ASK)
Nagy, Tibor; Vikár, Anna; Lendvay, György, E-mail: lendvay.gyorgy@ttk.mta.hu [Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2., H-1117 Budapest (Hungary)
2016-01-07
The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH{sub 4} + H → CH{sub 3} + H{sub 2} and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C–H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C–H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling.
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.
De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut
2011-07-15
With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.
Rate Constant Calculation for Thermal Reactions Methods and Applications
DaCosta, Herbert
2011-01-01
Providing an overview of the latest computational approaches to estimate rate constants for thermal reactions, this book addresses the theories behind various first-principle and approximation methods that have emerged in the last twenty years with validation examples. It presents in-depth applications of those theories to a wide range of basic and applied research areas. When doing modeling and simulation of chemical reactions (as in many other cases), one often has to compromise between higher-accuracy/higher-precision approaches (which are usually time-consuming) and approximate/lower-preci
Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan
2014-10-01
The gas-phase reaction of an Np atom with H2O was investigated using density functional theory and ab initio molecular dynamics. The reaction mechanisms and the corresponding potential energy profiles for different possible spin states were analyzed. Three reaction channels were found in the mechanism study: the isomerization channel, the H2 elimination channel, and the H atom elimination channel. The latter two were observed in the dynamics simulation. It was found that the branching ratio of the title reaction depends on the initial kinetic energy along the transition vector. Product energy distributions for the reaction were evaluated by performing direct classical trajectory calculations on the lowest sextet potential energy surface. The results indicate that most of the available energy appears as the translational energy of the products. The overall results indicate that the H2 elimination channel with low kinetic energy is thermodynamically favored but competes with the H atom elimination channel with higher kinetic energy.
Systematic development of reduced reaction mechanisms for dynamic modeling
Frenklach, M.; Kailasanath, K.; Oran, E. S.
1986-01-01
A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.
Sekizawa, Kazuyuki
2016-01-01
Background: Multinucleon transfer (MNT) and quasifission (QF) processes are dominant processes in low-energy collisions of two heavy nuclei. They are expected to be useful to produce neutron-rich unstable nuclei. Nuclear dynamics leading to these processes depends sensitively on nuclear properties such as deformation and shell structure. Purpose: We elucidate reaction mechanisms of MNT and QF processes involving heavy deformed nuclei, making detailed comparisons between microscopic TDHF calculations and measurements for $^{64}$Ni+$^{238}$U reaction. Methods: Three-dimensional Skyrme-TDHF calculations are performed. Particle-number projection method is used to evaluate MNT cross sections from the TDHF wave function after collision. Results: Fragment masses, total kinetic energy (TKE), scattering angle, contact time, and MNT cross sections are investigated for $^{64}$Ni+$^{238}$U reaction. They show reasonable agreements with measurements. At small impact parameters, collision dynamics depends sensitively on th...
Statistical Model Calculations for (n,γ Reactions
Beard Mary
2015-01-01
Full Text Available Hauser-Feshbach (HF cross sections are of enormous importance for a wide range of applications, from waste transmutation and nuclear technologies, to medical applications, and nuclear astrophysics. It is a well-observed result that diﬀerent nuclear input models sensitively aﬀect HF cross section calculations. Less well known however are the eﬀects on calculations originating from model-specific implementation details (such as level density parameter, matching energy, back-shift and giant dipole parameters, as well as eﬀects from non-model aspects, such as experimental data truncation and transmission function energy binning. To investigate the eﬀects or these various aspects, Maxwellian-averaged neutron capture cross sections have been calculated for approximately 340 nuclei. The relative eﬀects of these model details will be discussed.
Imaging the dynamics of chlorine atom reactions with alkenes
Estillore, Armando D.; Visger, Laura M.; Suits, Arthur G.
2010-08-01
We report a study of chlorine atom reactions with a series of target monounsaturated alkene molecules: 1-pentene, 1-hexene, 2-hexene, and cyclohexene. These reactions were studied using crossed-beam dc slice ion imaging at collision energies of 4 and 7 kcal/mol. Images of the reactively scattered alkenyl radical products were obtained via single photon ionization at 157 nm. The angular distributions at low collision energy are largely isotropic, suggesting the formation of a complex that has a lifetime comparable to or longer than its rotational period, followed by HCl elimination. At high collision energy, the distributions show a sharp forward peak superimposed on the isotropic component accounting for ˜13% of the product flux. The translational energy distributions peak near zero for the backscattered product, in sharp contrast to the results for alkanes. In the forward direction, the translational energy distributions change dramatically with collision energy. At the high collision energy, a sharp forward peak at ˜80% of the collision energy appears, quite reminiscent of results of our recent study of Cl+pentane reactions. The scattering distributions for all target molecules are similar, suggesting similarity of the reaction dynamics among these molecules. Ab initio calculations of the energetics and ionization energies for the various product channels were performed at the CBS-QB3 level to aid in interpreting the results.
Calculation of the dynamic air flow resistivity of fibre materials
Tarnow, Viggo
1997-01-01
The acoustic attenuation of acoustic fiber materials is mainly determined by the dynamic resistivity to an oscillating air flow. The dynamic resistance is calculated for a model with geometry close to the geometry of real fibre material. The model constists of parallel cylinders placed randomly. ......-consistent procedure gives the same results as the more complicated procedure based on average over Voronoi cells. Graphs of the dynamic resistivity versus frequency are given for fiber densities and diameters typical for acoustic fiber materials.......The acoustic attenuation of acoustic fiber materials is mainly determined by the dynamic resistivity to an oscillating air flow. The dynamic resistance is calculated for a model with geometry close to the geometry of real fibre material. The model constists of parallel cylinders placed randomly...
王艳; 钱英; 冯文林; 刘若庄
2003-01-01
An implementation of the variational quantum RRKM program is presented to utilize the direct ab initio dynamics approach for calculating k(E, J), k(E) and k(T) within the framework of the microcanonical transition state (μTST) and microcanonical variational TST (μVT) theories. An algorithm including tunneling contributions in Beyer-Swinehart method for calculating microcanonical rate constants is also proposed. An efficient piece-wise interpolation method is developed to evaluate the Boltzmann integral in calculation of thermal rate constants. Calculations on several test reactions, namely the H(D)2CO→H(D)2 + CO, CH2CO→CH2 + CO and CH4 + H→CH3 + H2 reactions, show that the results are in good agreement with the previous rate constants calculations. This approach would require much less computational resource.
Implementing the Graphing Calculator in Cincinnati's Precalculus Classes: Teachers' Reactions.
Kaplan, Rose; Herrera, Terese
1995-01-01
Presents data from interviews of (n=15) precalculus teachers required to adopt the technology-intensive Demana/Waits Precalculus Mathematics textbook and to use graphing calculators in their precalculus classes. Results showed that teachers recognized the need for well-organized, extensive workshops. Teacher comments showed a disparity in their…
The molecular dynamics of atmospheric reaction
Polanyi, J. C.
1971-01-01
Detailed information about the chemistry of the upper atmosphere took the form of quantitative data concerning the rate of reaction into specified states of product vibration, rotation and translation for exothermic reaction, as well as concerning the rate of reaction from specified states of reagent vibration, rotation and translation for endothermic reaction. The techniques used were variants on the infrared chemiluminescence method. Emphasis was placed on reactions that formed, and that removed, vibrationally-excited hydroxyl radicals. Fundamental studies were also performed on exothermic reactions involving hydrogen halides.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
The quantum dynamics of electronically nonadiabatic chemical reactions
Truhlar, Donald G.
1993-01-01
Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally
Statistical theory for the kinetics and dynamics of roaming reactions.
Klippenstein, Stephen J; Georgievskii, Yuri; Harding, Lawrence B
2011-12-22
We present a statistical theory for the effect of roaming pathways on product branching fractions in both unimolecular and bimolecular reactions. The analysis employs a separation into three distinct steps: (i) the formation of weakly interacting fragments in the long-range/van der Waals region of the potential via either partial decomposition (for unimolecular reactants) or partial association (for bimolecular reactants), (ii) the roaming step, which involves the reorientation of the fragments from one region of the long-range potential to another, and (iii) the abstraction, addition, and/or decomposition from the long-range region to yield final products. The branching between the roaming induced channel(s) and other channels is obtained from a steady-state kinetic analysis for the two (or more) intermediates in the long-range region of the potential. This statistical theory for the roaming-induced product branching is illustrated through explicit comparisons with reduced dimension trajectory simulations for the decompositions of H(2)CO, CH(3)CHO, CH(3)OOH, and CH(3)CCH. These calculations employ high-accuracy analytic potentials obtained from fits to wide-ranging CASPT2 ab initio electronic structure calculations. The transition-state fluxes for the statistical theory calculations are obtained from generalizations of the variable reaction coordinate transition state theory approach. In each instance, at low energy the statistical analysis accurately reproduces the branching obtained from the trajectory simulations. At higher energies, e.g., above 1 kcal/mol, increasingly large discrepancies arise, apparently due to a dynamical biasing toward continued decomposition of the incipient molecular fragments (for unimolecular reactions). Overall, the statistical theory based kinetic analysis is found to provide a useful framework for interpreting the factors that determine the significance of roaming pathways in varying chemical environments.
Kılınç, F.; Karpuz, N.; ćetin, B.
2017-02-01
In medical physics, radionuclides are needed to diagnose functional disorders of organs and to diagnose and treat many diseases. Nuclear reactions are significant for the productions of radionuclides. It is important to analyze the cross sections for much different energy. In this study, reactional cross sections calculations on 13N, 18F radioisotopes are with TALYS 1.6 nuclear reaction simulation code. Cross sections calculated and experimental data taken from EXFOR library were compared
Effect of gamma-strength on nuclear reaction calculations
Kadenko, Igor; Bondar, Borys; Gorbachenko, Oleksandr; Leshchenko, Borys; Solodovnyk, Kateryna; Tkach, Oleksandr; Zheltonozhskyi, Viktor
2016-01-01
The results of the study of gamma-transition description in fast neutron capture and photofission are presented. Recent experimental data were used, namely, the spectrum of prompt gamma-rays in the energy range 2{\\div}18 MeV from 14-MeV neutron capture in natural Ni and isomeric ratios in primary fragments of photofission of the isotopes of U, Np and Pu by bremsstrahlung with end-point energies $E_e$= 10.5, 12 and 18 MeV. The data are compared with the theoretical calculations performed within EMPIRE 3.2 and TALYS 1.6 codes. The mean value of angular momenta and their distributions were determined in the primary fragments $^{84}$Br, $^{97}$Nb, $^{90}$Rb, $^{131,133}$Te, $^{132}$Sb, $^{132,134}$I, $^{135}$Xe of photofissions. An impact of the characteristics of nuclear excited states on the calculation results is studied using different models for photon strength function and nuclear level density.
CALCULATION AND IMPROVEMENT OF DYNAMIC CHARACTERISTICS OF CENTRIFUGE
无
2001-01-01
The modeling of the rotor-support system of a typical centrifuge is discussed. The impedance matching method, cooperating with Riccati transfer matrix method and modal analysis method are adopted to calculate its dynamic characteristics. The influences of the main parts to the critical speeds are analyzed. Based on the analysis, a critical speed in the operating speed range is tuned successfully, and thus the dynamic characteristics of the centrifuge are much improved.
Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing
Mähönen, Petri; Punkka, Veikko
A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
Gravitational field calculations on a dynamic lattice by distributed computing.
Mähönen, P.; Punkka, V.
A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
Bradforth, S.E.
1992-11-01
The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound {yields} bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN{sup {minus}}, NCO{sup {minus}} and NCS{sup {minus}}. Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH{sub 3}0H,F + C{sub 2}H{sub 5}OH,F + OH and F + H{sub 2}. A time dependent framework for the simulation and interpretation of the bound {yields} free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH {yields} O({sup 3}P, {sup 1}D) + HF and F + H{sub 2}. The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H{sub 2} system, comparisons with three-dimensional quantum calculations are made.
Quantum Dynamics Study on D+OD+ Reaction: Competition between Exchange and Abstraction Channels
Wen-wu Xu; Pei-yu Zhang; Guo-zhong He
2013-01-01
Quantum dynamics for the D+OD+ reaction at the collision energy range of 0.0-1.0 eV was studied on an accurate ab initio potential energy surface.Both of the endothermic abstraction (D+OD+-O++D2) and thermoneutral exchange (D+OD+-D+OD+) channels were investigated from the same set of time-dependent quantum wave packets method under centrifugal sudden approximation.The reaction probability dependence with collision energy,the integral cross sections,and the thermal rate constant of the both channels are calculated.It is found that there is a convex structure in the reaction path of the exchange reaction.The calculated time evolution of the wave packet distribution at J=0 clearly indicates that the convex structure significantly influences the dynamics of the exchange and abstraction channels of title reaction.
Forming the Calculated Dynamic Transmission Systems of Wheeled Vehicles
A. B. Fominykh
2017-01-01
Full Text Available To calculate dynamic loading of transmission parts of wheeled vehicles, it is necessary to build up the appropriate calculated dynamic systems and determine their inertial, elastic, and damping parameters.The initial point of this process is to form an initial dynamic system. Hereafter, to cut the time of computations there is a need to reduce the number of masses of this system, and sometimes simplify its structure. The main requirement to be fulfilled in this case is that the calculated dynamical system is to be equivalent to the initial one (in terms of similarity of the vibrational process characteristics in these systems, i.e., the frequencies and modes of oscillations of both systems, their amplitude-frequency characteristics. This is possible when the energy characteristics of the corresponding systems are equal, i.e. their kinetic and potential energies, dissipative functions, and external force energies.Usually, when forming the initial and calculated dynamic systems, all types of friction are reduced to a linearly viscous one. However, it disables us to investigate the motion of these systems if there is an arbitrary, in particular, poly-harmonic action (for example, on the side of the internal combustion engine, since in this case the linear friction coefficients given will depend on the frequency and amplitude of the oscillations.The paper is aimed at determining the equivalent parameters of calculated dynamic systems of wheeled vehicles, including the dissipative parameters for the general case of friction.On the basis of energy principles, the expressions are obtained to determine the equivalent inertial, elastic, and damping parameters of the calculated dynamical systems of wheeled vehicles when the structure is changed and the number of masses of the system is decreased. The presented technique enables us to investigate the motion of these systems under arbitrary, including poly-harmonic, action on the system, using the
The complex-forming dynamics of Ne + NeH(D)+ (v = 0, 1; j = 0) reactions
Li, Wenliang
2017-01-01
The quasi-classical trajectory method has been employed to investigate the dynamics of the title reactions based on an accurate potential energy surface. The agreement between the QCT and quantum wave packet results is good for the integral cross sections and the reaction probabilities. The influences of the collision energy on the average lifetime of the complex-forming are also predicted. The polarization dependent differential cross sections of the title reactions are also calculated to uncover the reaction mechanism. The calculated results indicated that the collision energies play an important role in the complex-forming dynamics of the title reactions.
A large scale molecular dynamics calculation of a lipid bilayer
Okazaki, Susumu [Tokyo Inst. of Tech. (Japan)
1998-03-01
Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such a atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2 chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (author)
Real-time electron dynamics simulation of two-electron transfer reactions induced by nuclear motion
Suzuki, Yasumitsu; Yamashita, Koichi
2012-04-01
Real-time electron dynamics of two-electron transfer reactions induced by nuclear motion is calculated by three methods: the numerically exact propagation method, the time-dependent Hartree (TDH) method and the Ehrenfest method. We find that, as long as the nuclei move as localized wave packets, the TDH and Ehrenfest methods can reproduce the exact electron dynamics of a simple charge transfer reaction model containing two electrons qualitatively well, even when nonadiabatic transitions between adiabatic states occur. In particular, both methods can reproduce the cases where a complete two-electron transfer reaction occurs and those where it does not occur.
Calculation of reaction energies and adiabatic temperatures for waste tank reactions
Burger, L.L.
1995-10-01
Continual concern has been expressed over potentially hazardous exothermic reactions that might occur in Hanford Site underground waste storage tanks. These tanks contain many different oxidizable compounds covering a wide range of concentrations. The chemical hazards are a function of several interrelated factors, including the amount of energy (heat) produced, how fast it is produced, and the thermal absorption and heat transfer properties of the system. The reaction path(s) will determine the amount of energy produced and kinetics will determine the rate that it is produced. The tanks also contain many inorganic compounds inert to oxidation. These compounds act as diluents and can inhibit exothermic reactions because of their heat capacity and thus, in contrast to the oxidizable compounds, provide mitigation of hazardous reactions. In this report the energy that may be released when various organic and inorganic compounds react is computed as a function of the reaction-mix composition and the temperature. The enthalpy, or integrated heat capacity, of these compounds and various reaction products is presented as a function of temperature; the enthalpy of a given mixture can then be equated to the energy release from various reactions to predict the maximum temperature which may be reached. This is estimated for several different compositions. Alternatively, the amounts of various diluents required to prevent the temperature from reaching a critical value can be estimated. Reactions taking different paths, forming different products such as N{sub 2}O in place of N{sub 2} are also considered, as are reactions where an excess of caustic is present. Oxidants other than nitrate and nitrite are considered briefly.
Ichikawa, Kazuhide; Fukushima, Akinori; Ishihara, Yoshio; Isaki, Ryuichiro; Takeguchi, Toshio; Tachibana, Akitomo; 10.1016/j.theochem.2009.08.026
2009-01-01
We investigate a reaction of boron trichloride (BCl3) with iron(III) hydroxide (Fe(OH)3) by ab initio quantum chemical calculation as a simple model for a reaction of iron impurities in BCl3 gas. We also examine a reaction with water. We find that compounds such as Fe(Cl)(OBCl2)2(OHBCl2) and Fe(Cl)2(OBCl2)(OHBCl2) are formed while producing HCl and reaction paths to them are revealed. We also analyze the stabilization mechanism of these paths using newly-developed interaction energy density derived from electronic stress tensor in the framework of the Regional DFT (Density Functional Theory) and Rigged QED (Quantum ElectroDynamics).
Alapati, Sudhakar V; Karl Johnson, J; Sholl, David S
2007-03-28
Hydrides of period 2 and 3 elements are promising candidates for hydrogen storage, but typically have heats of reaction that are too high to be of use for fuel cell vehicles. Recent experimental work has focused on destabilizing metal hydrides through mixing metal hydrides with other compounds. A very large number of possible destabilized metal hydride reaction schemes exist, but the thermodynamic data required to assess the enthalpies of these reactions are not available in many cases. We have used density functional theory calculations to predict the reaction enthalpies for more than 300 destabilization reactions that have not previously been reported. The large majority of these reactions are predicted not to be useful for reversible hydrogen storage, having calculated reaction enthalpies that are either too high or too low, and hence these reactions need not be investigated experimentally. Our calculations also identify multiple promising reactions that have large enough hydrogen storage capacities to be useful in practical applications and have reaction thermodynamics that appear to be suitable for use in fuel cell vehicles and are therefore promising candidates for experimental work.
S. Tolosa
2013-01-01
Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.
Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy
Piccini, GiovanniMaria; Alessio, Maristella
2016-01-01
Abstract The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude). PMID:27008460
Calculated disturbances for evaluation of dynamical properties of freight cars
I.A. Mashchenko
2013-08-01
Full Text Available Purpose. To form realizations of the calculated disturbances for studying the dynamic properties of railway vehicles. Methodology. Records of the track-test car for one of the typical track sections of the Pridneprovsk railroad are the basic data for building the disturbance components. To derive the true geometric parameters of the railway gauge the records of the track-test car using a double-point metering circuit are transformed considering the transfer function of the measuring system. A model of the calculated disturbances is presented as the four components: a symmetric vertical irregularity determined as a semi-sum of vertical irregularities of the right and left rails; an oblique-symmetric vertical irregularity of the track determined as a semi-difference of vertical irregularities of the right and left rails; horizontal irregularities of the right and left rails. Acceptability criterion of the constructed disturbances is a relationship between the values of the dynamical properties factors of cars and the corresponding experimental data. Findings. The three techniques for the calculated disturbances forming are proposed. The first technique uses records of the track-test car for the track with a sufficiently high amount for given track conditions as components of the calculated disturbances. In so doing symmetrical vertical components of disturbances resulting from records of settling are corrected with the mass and stiffness parameters of the car under consideration. The second technique uses building and applying the theoretical realizations of irregularities corresponding to a real track according to a spectral analysis. The third technique ensures a polyharmonic model of disturbances, the parameters of which are the values of the basic frequencies and amplitudes that are typical for irregularities of a railway track. A possibility of practical applying of the constructed models of disturbances are presented using an example for
VERIFICATION OF TORSIONAL OSCILLATING MECHANICAL SYSTEM DYNAMIC CALCULATION RESULTS
Peter KAŠŠAY
2014-09-01
Full Text Available On our department we deal with optimization and tuning of torsional oscillating mechanical systems. When solving these problems we often use results of dynamic calculation. The goal of this article is to compare values obtained by computation and experimentally. For this purpose, a mechanical system built in our laboratory was used. At first, classical HARDY type flexible coupling has been applied into the system, then we used a pneumatic flexible shaft coupling developed by us. The main difference of these couplings over conventional flexible couplings is that they can change their dynamic properties during operation, by changing the pressure of the gaseous medium in their flexible elements.
Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.
2017-01-01
Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations. PMID:28262694
Ulissi, Zachary W.; Medford, Andrew J.; Bligaard, Thomas; Nørskov, Jens K.
2017-03-01
Surface reaction networks involving hydrocarbons exhibit enormous complexity with thousands of species and reactions for all but the very simplest of chemistries. We present a framework for optimization under uncertainty for heterogeneous catalysis reaction networks using surrogate models that are trained on the fly. The surrogate model is constructed by teaching a Gaussian process adsorption energies based on group additivity fingerprints, combined with transition-state scaling relations and a simple classifier for determining the rate-limiting step. The surrogate model is iteratively used to predict the most important reaction step to be calculated explicitly with computationally demanding electronic structure theory. Applying these methods to the reaction of syngas on rhodium(111), we identify the most likely reaction mechanism. Propagating uncertainty throughout this process yields the likelihood that the final mechanism is complete given measurements on only a subset of the entire network and uncertainty in the underlying density functional theory calculations.
Dynamic CT of tuberculous meningeal reactions
Jinkins, J.R.
1987-07-01
The technique of intravenous dynamic cranial computed tomography has been applied to the patient population at this location in Saudi Arabia with meningeal tuberculosis. The various manifestations and sequelae including meningitis, arteritis, infarct, and true meningeal tuberculomata all have characteristic if not specific appearances. The dynamic study enhances an otherwise static examination and reveals a great deal about the pathophysiology of tuberculosis involving the cerebral meningeal surfaces.
VERIFICATION OF TORSIONAL OSCILLATING MECHANICAL SYSTEM DYNAMIC CALCULATION RESULTS
2014-01-01
On our department we deal with optimization and tuning of torsional oscillating mechanical systems. When solving these problems we often use results of dynamic calculation. The goal of this article is to compare values obtained by computation and experimentally. For this purpose, a mechanical system built in our laboratory was used. At first, classical HARDY type flexible coupling has been applied into the system, then we used a pneumatic flexible shaft coupling developed by us...
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Duality-based calculations for transition probabilities in stochastic chemical reactions
Ohkubo, Jun
2017-02-01
An idea for evaluating transition probabilities in chemical reaction systems is proposed, which is efficient for repeated calculations with various rate constants. The idea is based on duality relations; instead of direct time evolutions of the original reaction system, the dual process is dealt with. Usually, if one changes rate constants of the original reaction system, the direct time evolutions should be performed again, using the new rate constants. On the other hands, only one solution of an extended dual process can be reused to calculate the transition probabilities for various rate constant cases. The idea is demonstrated in a parameter estimation problem for the Lotka-Volterra system.
Programming the dynamics of biochemical reaction networks.
Simmel, Friedrich C
2013-01-22
The development of complex self-organizing molecular systems for future nanotechnology requires not only robust formation of molecular structures by self-assembly but also precise control over their temporal dynamics. As an exquisite example of such control, in this issue of ACS Nano, Fujii and Rondelez demonstrate a particularly compact realization of a molecular "predator-prey" ecosystem consisting of only three DNA species and three enzymes. The system displays pronounced oscillatory dynamics, in good agreement with the predictions of a simple theoretical model. Moreover, its considerable modularity also allows for ecological studies of competition and cooperation within molecular networks.
Bobbert, Maarten F; Gómez Alvarez, Constanza B; van Weeren, P René; Roepstorff, Lars; Weishaupt, Michael A
2007-06-01
The purpose of this study was to determine whether individual limb forces could be calculated accurately from kinematics of trotting and walking horses. We collected kinematic data and measured vertical ground reaction forces on the individual limbs of seven Warmblood dressage horses, trotting at 3.4 m s(-1) and walking at 1.6 m s(-1) on a treadmill. First, using a segmental model, we calculated from kinematics the total ground reaction force vector and its moment arm relative to each of the hoofs. Second, for phases in which the body was supported by only two limbs, we calculated the individual reaction forces on these limbs. Third, we assumed that the distal limbs operated as linear springs, and determined their force-length relationships using calculated individual limb forces at trot. Finally, we calculated individual limb force-time histories from distal limb lengths. A good correspondence was obtained between calculated and measured individual limb forces. At trot, the average peak vertical reaction force on the forelimb was calculated to be 11.5+/-0.9 N kg(-1) and measured to be 11.7+/-0.9 N kg(-1), and for the hindlimb these values were 9.8+/-0.7 N kg(-1) and 10.0+/-0.6 N kg(-1), respectively. At walk, the average peak vertical reaction force on the forelimb was calculated to be 6.9+/-0.5 N kg(-1) and measured to be 7.1+/-0.3 N kg(-1), and for the hindlimb these values were 4.8+/-0.5 N kg(-1) and 4.7+/-0.3 N kg(-1), respectively. It was concluded that the proposed method of calculating individual limb reaction forces is sufficiently accurate to detect changes in loading reported in the literature for mild to moderate lameness at trot.
Ring opening reaction dynamics in the reaction of hydrogen atoms with ethylene oxide
Shin, S. K.; Jarek, R. L.; Böhmer, E.; Wittig, C.
1994-10-01
Ethylene oxide, C2H4O, is a three-membered ring with a single oxygen atom bridging the two carbons. Reactions of H and D atoms with ethylene oxide have been studied in the gas phase to provide insight into the dynamics of three-membered ring opening. H atoms were produced by photolyzing HI in the wavelength range 240-266 nm. The channel leading to OH+C2H4 was monitored via laser-induced fluorescence (LIF) of the OH A 2Σ←X 2Π system. The D atom reaction yields OD with no hydrogen scrambling. With an available energy of 23 000 cm-1, the average OH D rotational energy is ˜350 cm-1 for OH(v=0) and OD(v=0) and ˜250 cm-1 for OD(v=1). OH(v=1) was not observed, while the OD(v=1) population was about one-tenth that of OD(v=0). There was no apparent bias in populations between Λ doublets in each of the spin-orbit states for both OH and OD. Doppler broadening of OH(v=0) rotational lines was measured to evaluate the average center-of-mass (c.m.) translational energy, which was found to be ˜2300 cm-1. On average, the ring opening process deposits ˜10% of the available energy into c.m. translation, ˜2% into OH rotation, and ˜88% into ethylene internal energy. Comparison with CH2CH2OH unimolecular dissociation dynamics and theoretical transition state calculations leads to a likely mechanism in which hydrogen abstracts oxygen via sequential C-O bond fission without involving a long-lived CH2CH2OH intermediate.
Dynamical theory of primary processes of charge separation in the photosynthetic reaction center.
Lakhno, Victor D
2005-05-01
A dynamical theory has been developed for primary separation of charges in the course of photosynthesis. The theory deals with both hopping and superexchange transfer mechanisms. Dynamics of electron transfer from dimeric bacteriochlorophyll to quinone has been calculated. The results obtained agree with experimental data and provide a unified explanation of both the hierarchy of the transfer time in the photosynthetic reaction center and the phenomenon of coherent oscillations accompanying the transfer process.
Kinetic calculations and mechanism definition for reactions in an ammonium perchlorate flame
Ermolin, N.E.; Fomin, V.M.; Korobeinichev, O.P.; Tereshchenko, A.G.
1982-09-01
This article reports on detailed calculations on the reaction kinetics in APC flames on the basis of a wide set of possible reactions and experimental data on the initial composition of the gas mixture (gasification products from APC). The purpose is to select the most important reactions in this system by comparing the calculations on the kinetics with experimental data on the concentration profiles in APC flames. Discusses kinetic equations; rate constants as the reaction mechanism; results from kinetic calculations; and identification of major stages. A laminar flame such as that provided by ammonium perchlorate is described in general form by a system of differential equations that incorporate the transport of heat and matter in the presence of chemical reactions. APC is a system consisting of 4 elements (N,H,Cl and O). Points out that the scheme enables one to determine which reactions are responsible for producing the final products. Suggests that in the future one will be able to analyze experimental data on the reaction-rate profiles for stable components in order to determine either the atom and radical concentrations or the rate constants of the reactions involving them.
Lísal, Martin; Brennan, John K.; Smith, William R.; Siperstein, Flor R.
2004-09-01
We present a simulation tool to study fluid mixtures that are simultaneously chemically reacting and adsorbing in a porous material. The method is a combination of the reaction ensemble Monte Carlo method and the dual control volume grand canonical molecular dynamics technique. The method, termed the dual control cell reaction ensemble molecular dynamics method, allows for the calculation of both equilibrium and nonequilibrium transport properties in porous materials such as diffusion coefficients, permeability, and mass flux. Control cells, which are in direct physical contact with the porous solid, are used to maintain the desired reaction and flow conditions for the system. The simulation setup closely mimics an actual experimental system in which the thermodynamic and flow parameters are precisely controlled. We present an application of the method to the dry reforming of methane reaction within a nanoscale reactor model in the presence of a semipermeable membrane that was modeled as a porous material similar to silicalite. We studied the effects of the membrane structure and porosity on the reaction species permeability by considering three different membrane models. We also studied the effects of an imposed pressure gradient across the membrane on the mass flux of the reaction species. Conversion of syngas (H2/CO) increased significantly in all the nanoscale membrane reactor models considered. A brief discussion of further potential applications is also presented.
Model Calculation of n + 6Li Reactions Below 20 MeV
ZHANG Jing-Shang; HAN Yin-Lu
2001-01-01
Based on the unified Hauser-Feshbach and exciton model for light nuclei, the calculations of reaction cross sections and the double-differential cross sections for n + 6Li are performed. Since all of the first-particle emissions are from the compound nucleus to the discrete levels, the angular momentum coupling effect in pre-equilibrium mechanism must be taken into account. The fitting of the measured data indicates that the three-body break-up process needs to be involved, and the pre-equilibrium reaction mechanism dominates the reaction processes. In light nucleus reactions the recoil effect must be taken into account.``
Skulason, Egill; Tripkovic, Vladimir; Björketun, Mårten
2010-01-01
Density functional theory calculations have been performed for the three elementary steps―Tafel, Heyrovsky, and Volmer―involved in the hydrogen oxidation reaction (HOR) and its reverse, the hydrogen evolution reaction (HER). For the Pt(111) surface a detailed model consisting of a negatively...... charged Pt(111) slab and solvated protons in up to three water bilayers is considered and reaction energies and activation barriers are determined by using a newly developed computational scheme where the potential can be kept constant during a charge transfer reaction. We determine the rate limiting...
Wilson, J. W.; Khandelwal, G. S.
1976-01-01
Calculational methods for estimation of dose from external proton exposure of arbitrary convex bodies are briefly reviewed. All the necessary information for the estimation of dose in soft tissue is presented. Special emphasis is placed on retaining the effects of nuclear reaction, especially in relation to the dose equivalent. Computer subroutines to evaluate all of the relevant functions are discussed. Nuclear reaction contributions for standard space radiations are in most cases found to be significant. Many of the existing computer programs for estimating dose in which nuclear reaction effects are neglected can be readily converted to include nuclear reaction effects by use of the subroutines described herein.
NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics
Capellos, Christos
1986-01-01
This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...
Transverse flow reactor studies of the dynamics of radical reactions
Macdonald, R.G. [Argonne National Laboratory, IL (United States)
1993-12-01
Radical reactions are in important in combustion chemistry; however, little state-specific information is available for these reactions. A new apparatus has been constructed to measure the dynamics of radical reactions. The unique feature of this apparatus is a transverse flow reactor in which an atom or radical of known concentration will be produced by pulsed laser photolysis of an appropriate precursor molecule. The time dependence of individual quantum states or products and/or reactants will be followed by rapid infrared laser absorption spectroscopy. The reaction H + O{sub 2} {yields} OH + O will be studied.
Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
Lipková, Jana
2011-01-01
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.
Diky, Vladimir; Chirico, Robert D; Kazakov, Andrei F; Muzny, Chris D; Frenkel, Michael
2009-12-01
ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. This paper describes the first application of this concept to the evaluation of thermodynamic properties for chemical reactions. Reaction properties evaluated are the enthalpies, entropies, Gibbs energies, and thermodynamic equilibrium constants. Details of key considerations in the critical evaluation of enthalpies of formation and of standard entropies for organic compounds are discussed in relation to their application in the calculation of reaction properties. Extensions to the class structure of the program are described that allow close linkage between the derived reaction properties and the underlying pure-component properties. Derivation of pure-component enthalpies of formation and of standard entropies through the use of directly measured reaction properties (enthalpies of reaction and equilibrium constants) is described. Directions for future enhancements are outlined.
Buss, R.J.
1979-04-01
The study of seven radical-molecule reactions using the crossed molecular beam technique with supersonic nozzle beams is reported. Product angular and velocity distributions were obtained and compared with statistical calculations in order to identify dynamical features of the reactions. In the reaction of chlorine and fluorine atoms with vinyl bromide, the product energy distributions are found to deviate from predictions of the statistical model. A similar effect is observed in the reaction of chlorine atoms with 1, 2 and 3-bromopropene. The reaction of oxygen atoms with ICl and CF/sub 3/I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol/sup -1/. In all reactions studied, the product energy and angular distributions are found to be coupled, and this is attributed to a kinematic effect of the conservation of angular momentum.
METHOD FOR CALCULATION OF STRESSED STATE SUBSTANTIATED BY DYNAMIC MICROTWIN
V. V. Vlashevich
2014-01-01
Full Text Available Method for calculation of the stressed state in a dynamic twin has been developed on the basis of a non-thin non-coherent micro-twin model with continuous distribution of twinning dislocations at twin boundaries. In this case there is no additional generation with the help of twinning dislocation source. The model takes into account that the twin has coherent and noncoherent boundary sections. The developed model has made it possible to take into consideration a form of non-coherent sections of twinning boundaries in calculations of stressed and deformed state at dynamic twins. It has been established that localized stresses are migrating together with non-coherent sections of the twin. Normal stresses σxx change their sign in relation to direction of the twin development. Shear stresses σxy are alternating in signs in relation to an axis which is perpendicular to the direction of the twin development and which is passing through a mid-point of non-coherent twin section. Distribution of stresses σyy и σyz has similar configuration. Stresses σzx in the second and fourth quarters of XOY plane are negative and the stresses in the first and third quarters are positive. Distribution of stresses σzz practically does not differ from distribution of stresses σyy according to configuration but numerical values of stress tensor component data are different.The results have been obtained without thin twin model that permits to consider only elastic stage of the twinning process. The executed stress calculations at dynamic twin are important for forecasting at the accumulation stage of damage origination which is caused by twinning destruction and permit to improve forecasting accuracy of technical system resources on the basis of twinning materials such as alloys based on iron, copper, zinc, aluminium, titanium.
Total Reaction Cross Section in an Isospin-Dependent Quantum Molecular Dynamics Model
魏义彬; 蔡翔舟; 沈文庆; 马余刚; 张虎勇; 钟晨; 郭威; 陈金根; 马国亮; 王鲲
2003-01-01
The isospin-dependent quantum molecular dynamics (IDQMD) model is used to study the total reaction cross section σR. The energy-dependent Pauli volumes of neutrons and protons have been discussed and introduced into the IDQMD calculation to replace the widely used energy-independent Pauli volumes. The modified IDQMD calculation can reproduce the experimental cr R well for both stable and exotic nuclei induced reactions. Comparisons of the calculated σn induced by 11Li with different initial density distributions have been performed. It is shown that the calculation by using the experimentally deduced density distribution with a long tail can fit the experimental excitation function better than that by using the Skyrme-Hartree-Fock calculated density without long tails. It is also found that σR at high energy is sensitive to the long tail of density distribution.
Advanced Dynamics Analytical and Numerical Calculations with MATLAB
Marghitu, Dan B
2012-01-01
Advanced Dynamics: Analytical and Numerical Calculations with MATLAB provides a thorough, rigorous presentation of kinematics and dynamics while using MATLAB as an integrated tool to solve problems. Topics presented are explained thoroughly and directly, allowing fundamental principles to emerge through applications from areas such as multibody systems, robotics, spacecraft and design of complex mechanical devices. This book differs from others in that it uses symbolic MATLAB for both theory and applications. Special attention is given to solutions that are solved analytically and numerically using MATLAB. The illustrations and figures generated with MATLAB reinforce visual learning while an abundance of examples offer additional support. This book also: Provides solutions analytically and numerically using MATLAB Illustrations and graphs generated with MATLAB reinforce visual learning for students as they study Covers modern technical advancements in areas like multibody systems, robotics, spacecraft and des...
Bayesian inversion analysis of nonlinear dynamics in surface heterogeneous reactions.
Omori, Toshiaki; Kuwatani, Tatsu; Okamoto, Atsushi; Hukushima, Koji
2016-09-01
It is essential to extract nonlinear dynamics from time-series data as an inverse problem in natural sciences. We propose a Bayesian statistical framework for extracting nonlinear dynamics of surface heterogeneous reactions from sparse and noisy observable data. Surface heterogeneous reactions are chemical reactions with conjugation of multiple phases, and they have the intrinsic nonlinearity of their dynamics caused by the effect of surface-area between different phases. We adapt a belief propagation method and an expectation-maximization (EM) algorithm to partial observation problem, in order to simultaneously estimate the time course of hidden variables and the kinetic parameters underlying dynamics. The proposed belief propagation method is performed by using sequential Monte Carlo algorithm in order to estimate nonlinear dynamical system. Using our proposed method, we show that the rate constants of dissolution and precipitation reactions, which are typical examples of surface heterogeneous reactions, as well as the temporal changes of solid reactants and products, were successfully estimated only from the observable temporal changes in the concentration of the dissolved intermediate product.
Three-body calculation of triple-alpha reaction at low energies
Ishikawa, Souichi
2011-09-01
The reaction rate of the triple-alpha (3α) process at low temperatures, where resonant reaction is not dominant, is calculated through the inverse process, the photodisintegration of a 12C nucleus. For this, Schrödinger equations in a three-alpha (3-α) model of 12C are directly solved by a Faddeev method, which has been successfully applied to three-nucleon problem so far. The nuclear Hamiltonian consists of an α-α potential, which reproduces the 8Be resonance state, together with three-body potentials to reproduce 12C properties. Our results of the 3α reaction rate are about 103 times larger at low temperature (T = 107 K) than a standard rate from the Nuclear Astrophysics Compilation of Reaction Rates (NACRE), which means our results are remarkably smaller than recent results of quantum-mechanical three-body calculations by Ogata et al.
Iftimie, R; Schofield, J P; Iftimie, Radu; Salahub, Dennis; Schofield, Jeremy
2003-01-01
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.
Modeling reaction pathways of low energy particle deposition on thiophene via ab initio calculations
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.
Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions
Gray, S.K. [Argonne National Laboratory, IL (United States)
1993-12-01
A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.
Nonlinear damping calculation in cylindrical gear dynamic modeling
Guilbault, Raynald; Lalonde, Sébastien; Thomas, Marc
2012-04-01
The nonlinear dynamic problem posed by cylindrical gear systems has been extensively covered in the literature. Nonetheless, a significant proportion of the mechanisms involved in damping generation remains to be investigated and described. The main objective of this study is to contribute to this task. Overall, damping is assumed to consist of three sources: surrounding element contribution, hysteresis of the teeth, and oil squeeze damping. The first two contributions are considered to be commensurate with the supported load; for its part however, squeeze damping is formulated using expressions developed from the Reynolds equation. A lubricated impact analysis between the teeth is introduced in this study for the minimum film thickness calculation during contact losses. The dynamic transmission error (DTE) obtained from the final model showed close agreement with experimental measurements available in the literature. The nonlinear damping ratio calculated at different mesh frequencies and torque amplitudes presented average values between 5.3 percent and 8 percent, which is comparable to the constant 8 percent ratio used in published numerical simulations of an equivalent gear pair. A close analysis of the oil squeeze damping evidenced the inverse relationship between this damping effect and the applied load.
A review of dynamical resonances in A + BC chemical reactions
Ren, Zefeng; Sun, Zhigang; Zhang, Donghui; Yang, Xueming
2017-02-01
The concept of the transition state has played an important role in the field of chemical kinetics and reaction dynamics. Reactive resonances in the transition-state region can dramatically enhance the reaction probability; thus investigation of the reactive resonances has attracted great attention from chemical physicists for many decades. In this review, we mainly focus on the recent progress made in probing the elusive resonance phenomenon in the simple A + BC reaction and understanding its nature, especially in the benchmark F/Cl + H2 and their isotopic variants. The signatures of reactive resonances in the integral cross section, differential cross section (DCS), forward- and backward-scattered DCS, and anion photodetachment spectroscopy are comprehensively presented in individual prototype reactions. The dynamical origins of reactive resonances are also discussed in this review, based on information on the wave function in the transition-state region obtained by time-dependent quantum wave-packet calculations.
Quantum Dynamics of Radical-Ion-Pair Reactions
Kominis, I. K.
2010-01-01
Radical-ion-pair reactions were recently shown to represent a rich biophysical laboratory for the application of quantum measurement theory methods and concepts, casting doubt on the validity of the theoretical treatment of these reactions and the results thereof that has been at the core of spin chemistry for several decades now. The ensued scientific debate, although exciting, is plagued with several misconceptions. We will here provide a comprehensive treatment of the quantum dynamics of r...
Dynamical dipole mode in heavy-ion fusion reactions
Parascandolo, C., E-mail: concetta.parascandolo@na.infn.i [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Pierroutsakou, D. [INFN - Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Martin, B. [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Agodi, C.; Alba, R. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); Boiano, A. [INFN - Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Coniglione, R. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); De Filippo, E. [INFN - Sezione di Catania, 95123, Catania (Italy); Del Zoppo, A. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); Emanuele, U. [INFN, Gruppo Collegato di Messina and Dip. di Fisica, Universita di Messina, Messina (Italy); Farinon, F. [GSI, Planckstrasse 1, D-64291, Darmstadt (Germany); Guglielmetti, A. [Universita degli Studi di Milano and INFN, Sezione di Milano, via Celoria 16, I-20133 Milano (Italy); Inglima, G.; La Commara, M. [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Maiolino, C. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); Mazzocchi, C. [Universita degli Studi di Milano and INFN, Sezione di Milano, via Celoria 16, I-20133 Milano (Italy); Mazzocco, M. [Dip. di Fisica and INFN, Universita di Padova, via F. Marzolo 8, I-35131 Padova (Italy); Romoli, M. [INFN - Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Sandoli, M. [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Santonocito, D. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy)
2010-03-01
The dynamical dipole mode, excited in charge asymmetric heavy-ion collisions, was investigated in the mass region of the {sup 192}Pb compound nucleus, formed by using the {sup 40,48}Ca + {sup 152,144}Sm reactions at approx11 MeV/nucleon. Preliminary results of this measurement, concerning both fusion-evaporation and fission events are presented. As a fast cooling mechanism on the fusion path, the dynamical dipole mode could be useful for the synthesis of super heavy elements through 'hot' fusion reactions.
Vagena, E.; Stoulos, S.
2017-01-01
Bremsstrahlung photon beam delivered by a linear electron accelerator has been used to experimentally determine the near threshold photonuclear cross section data of nuclides. For the first time, (γ, n) cross section data was obtained for the astrophysical important nucleus 162Er. Moreover, theoretical calculations have been applied using the TALYS 1.6 code. The effect of the gamma ray strength function on the cross section calculations has been studied. A satisfactorily reproduction of the available experimental data of photonuclear cross section at the energy region below 20 MeV could be achieved. The photon flux was monitored by measuring the photons yield from seven well known (γ, n) reactions from the threshold energy of each reaction up to the end-point energy of the photon beam used. An integrated cross-section 87 ± 14 mb is calculated for the photonuclear reaction 162Er (γ, n) at the energy 9.2-14 MeV. The effective cross section estimated using the TALYS code range between 89 and 96 mb depending on the γ-strength function used. To validate the method for the estimation of the average cross-section data of 162Er (γ, n) reaction, the same procedure has been performed to calculate the average cross-section data of 197Au (γ, n) and 55Mn (γ, n) reactions. In this case, the photons yield from the rest well known (γ, n) reactions was used in order to monitoring the photon flux. The results for 162Er (γ, n), 197Au (γ, n) and 55Mn (γ, n) are found to be in good agreement with the theoretical values obtained by TALYS 1.6. So, the present indirect process could be a valuable tool to estimate the effective cross section of (γ, n) reaction for various isotopes using bremsstrahlung beams.
Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.
Cross Sections Calculations of ( d, t) Nuclear Reactions up to 50 MeV
Tel, E.; Yiğit, M.; Tanır, G.
2013-04-01
In nuclear fusion reactions two light atomic nuclei fuse together to form a heavier nucleus. Fusion power is the power generated by nuclear fusion processes. In contrast with fission power, the fusion reaction processes does not produce radioactive nuclides. The fusion will not produce CO2 or SO2. So the fusion energy will not contribute to environmental problems such as particulate pollution and excessive CO2 in the atmosphere. Fusion powered electricity generation was initially believed to be readily achievable, as fission power had been. However, the extreme requirements for continuous reactions and plasma containment led to projections being extended by several decades. In 2010, more than 60 years after the first attempts, commercial power production is still believed to be unlikely before 2050. Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, there is still a long way to go to penetrate commercial fusion reactors to the energy market. In the fusion reactor, tritium self-sufficiency must be maintained for a commercial power plant. Therefore, for self-sustaining (D-T) fusion driver tritium breeding ratio should be greater than 1.05. Working out the systematics of ( d, t) nuclear reaction cross sections is of great importance for the definition of the excitation function character for the given reaction taking place on various nuclei at different energies. Since the experimental data of charged particle induced reactions are scarce, self-consistent calculation and analyses using nuclear theoretical models are very important. In this study, ( d, t) cross sections for target nuclei 19F, 50Cr, 54Fe, 58Ni, 75As, 89Y, 90Zr, 107Ag, 127I, 197Au and 238U have been investigated up to 50 MeV deuteron energy. The excitation functions for ( d, t) reactions have been calculated by pre-equilibrium reaction mechanism. Calculation results have been also compared with the available measurements in
Benjamin, Ilan; Pohorille, Andrew
1993-01-01
The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.
Benjamin, Ilan; Pohorille, Andrew
1993-01-01
The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.
Dynamic/Thermochemical Balance Drives Unusual Alkyl/F Exchange Reactions in Siloxides and Analogs.
Correra, Thiago C; Fernandes, André S; Riveros, José M
2016-03-17
A recent report has shown that siloxides can undergo an unusual Me/F exchange reaction promoted by NF3 in the gas phase ( Angew. Chem. Int. Ed. 2012, 51, 8632-8635). A more extensive study of this kind of exchange has been carried out using mass spectrometry techniques (FT-ICR), DFT calculations, natural bond orbital (NBO) analysis, and Born-Oppenheimer molecular dynamics simulations (BOMD), using NF3, SO2F2, and CF4 as fluorine donors and evaluating the effect of replacing the Si center by Ge and C. This comprehensive approach shows that NF3 is crucial for the exchange reaction, as SO2F2 forms SO3F(-) via a pentacoordinated channel whereas no reaction is observed for CF4. The uniqueness of NF3 is caused by favorable thermochemical consideration and by dynamic effects that preclude the formation of the ubiquitous Si-F pentacoordinated species. Me3GeO(-) was shown to be as reactive as siloxides toward NF3, whereas C analogs showed no reactions under our experimental conditions. The exchange reaction was also shown to take place for triethylsiloxides. These exchange reactions are examples of reaction systems that avoid the lower energy pathway and are driven by dynamic effects that cannot be explained by the potential energy surface.
Dynamics of synchrotron VUV-induced intracluster reactions
Grover, J.R. [Brookhaven National Laboratory, Upton, NY (United States)
1993-12-01
Photoionization mass spectrometry (PIMS) using the tunable vacuum ultraviolet radiation available at the National Synchrotron Light Source is being exploited to study photoionization-induced reactions in small van der Waals mixed complexes. The information gained includes the observation and classification of reaction paths, the measurement of onsets, and the determination of relative yields of competing reactions. Additional information is obtained by comparison of the properties of different reacting systems. Special attention is given to finding unexpected features, and most of the reactions investigated to date display such features. However, understanding these reactions demands dynamical information, in addition to what is provided by PIMS. Therefore the program has been expanded to include the measurement of kinetic energy release distributions.
Yu Angyang
2015-06-01
Full Text Available The theoretical background and basic definition of the resonances in chemical reaction dynamics have been introduced in this article. The historical breakthrough in the experimental search for the reaction resonances has been reviewed in this report, with an emphasis on the crossed molecular beam apparatus. The research of the chemical reaction resonances has attracted many scientists’ attention from 80s of last century. The chemical reaction resonances in the F+H2 reaction were firstly observed by the researchers of the Chinese Academy of Sciences in 2006. Besides, the partial wave resonances in the chemical reactions have been observed for the first time in 2010.
Dynamical resonances in the fluorine atom reaction with the hydrogen molecule.
Yang, Xueming; Zhang, Dong H
2008-08-01
[Reaction: see text]. The concept of transition state has played a crucial role in the field of chemical kinetics and reaction dynamics. Resonances in the transition state region are important in many chemical reactions at reaction energies near the thresholds. Detecting and characterizing isolated reaction resonances, however, have been a major challenge in both experiment and theory. In this Account, we review the most recent developments in the study of reaction resonances in the benchmark F + H 2 --> HF + H reaction. Crossed molecular beam scattering experiments on the F + H 2 reaction have been carried out recently using the high-resolution, highly sensitive H-atom Rydberg tagging technique with HF rovibrational states almost fully resolved. Pronounced forward scattering for the HF (nu' = 2) product has been observed at the collision energy of 0.52 kcal/mol in the F + H 2 (j = 0) reaction. Quantum dynamical calculations based on two new potential energy surfaces, the Xu-Xie-Zhang (XXZ) surface and the Fu-Xu-Zhang (FXZ) surface, show that the observed forward scattering of HF (nu' = 2) in the F + H 2 reaction is caused by two Feshbach resonances (the ground resonance and first excited resonance). More interestingly, the pronounced forward scattering of HF (nu' = 2) at 0.52 kcal/mol is enhanced considerably by the constructive interference between the two resonances. In order to probe the resonance potential more accurately, the isotope substituted F + HD --> HF + D reaction has been studied using the D-atom Rydberg tagging technique. A remarkable and fast changing dynamical picture has been mapped out in the collision energy range of 0.3-1.2 kcal/mol for this reaction. Quantum dynamical calculations based on the XXZ surface suggest that the ground resonance on this potential is too high in comparison with the experimental results of the F + HD reaction. However, quantum scattering calculations on the FXZ surface can reproduce nearly quantitatively the resonance
The oxygen reduction reaction mechanism on Pt(111) from density functional theory calculations
Tripkovic, Vladimir; Skulason, Egill; Siahrostami, Samira;
2010-01-01
We study the oxygen reduction reaction (ORR) mechanism on a Pt(1 1 1) surface using density functional theory calculations We find that at low overpotentials the surface is covered with a half dissociated water layer We estimate the barrier for proton transfer to this surface and the barrier for ...
Use of pressure insoles to calculate the complete ground reaction forces
Forner Cordero, A.; Koopman, H.F.J.M.; Helm, van der F.C.T.
2004-01-01
A method to calculate the complete ground reaction force (GRF) components from the vertical GRF measured with pressure insoles is presented and validated. With this approach it is possible to measure several consecutive steps without any constraint on foot placement and compute a standard inverse dy
Jensen, L; van Duijnen, PT; Snijders, JG
2003-01-01
A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discr
TIME SCALES OF FUSION-FISSION REACTIONS CALCULATED FROM PRESCISSION NEUTRON MULTIPLICITIES
SIWEKWILCZYNSKA, K; WILCZYNSKI, J; SIEMSSEN, RH; WILSCHUT, HW
1995-01-01
The time scale of fusion-fission reactions was found to be in the range from tau(f) = 5 . 10(-20) to 5 . 10(-19) s. This result was obtained from the analysis of the prescission neutron multiplicities with a new method combining the time-dependent statistical cascade calculations with the nuclear
An equation for calculating the volumetric ratios required in a ligation reaction.
Cranenburgh, R M
2004-08-01
The ligation of two DNA fragments to create a new plasmid DNA molecule is a key reaction in molecular biology. Where the fragment lengths and concentrations are known, existing equations allow the desired relative molar ratio to be calculated, but this must then be related to the required volumes. Further calculations are then necessary if the maximum available volume is to consist of DNA solutions. The equation presented here allows the simple calculation of volumes of DNA solutions required to obtain a desired molar insert-to-vector ratio, and these can comprise all of the available volume in a ligation if required, thus maximising the yield of the recombinant plasmid.
Doronin Fedor Leonidovich
2014-01-01
Full Text Available When designing residential buildings, additional measures for increasing the strength at dynamic effects indoors are not foreseen. The walls of the structure fixed in the framework are not designed for shock wave caused by explosion of utility gas. When designing a building, the task of the special dynamic load is often reduced to the calculation of the safe shock pressure, exceeding of which leads to the destruction of the structures. The wall with the window area under dynamic effects is a blast relief panel, which reduces the excess pressure inside the room. The proposed method of calculating a design with a window unit allows determining the dynamic reaction of the wall on explosive pulse. The proposed calculation technique of the constructions at shock loads allows tracing the changes of the inertial forces and displacements at any stage of dynamic response. The reaction to dynamic loads can be also set for non-monolithic structures, consisting of different materials with different conditions of fastening. Elastoplastic reaction of a brick wall with glass units was determined using step-by-step method of linear acceleration. The calculation of stress-strain state of brick walls with window panes determined the strength properties of the structures close to the monolithic version. The proposed technique of numerical solution of dynamic equations is applied only in the analysis of elastic systems, in which the dynamic characteristics remain unchanged throughout the reaction process.
DCHAIN: A user-friendly computer program for radioactive decay and reaction chain calculations
East, L.V.
1994-05-01
A computer program for calculating the time-dependent daughter populations in radioactive decay and nuclear reaction chains is described. Chain members can have non-zero initial populations and be produced from the preceding chain member as the result of radioactive decay, a nuclear reaction, or both. As presently implemented, chains can contain up to 15 members. Program input can be supplied interactively or read from ASCII data files. Time units for half-lives, etc. can be specified during data entry. Input values are verified and can be modified if necessary, before used in calculations. Output results can be saved in ASCII files in a format suitable for including in reports or other documents. The calculational method, described in some detail, utilizes a generalized form of the Bateman equations. The program is written in the C language in conformance with current ANSI standards and can be used on multiple hardware platforms.
Coriolis coupling and nonadiabaticity in chemical reaction dynamics.
Wu, Emilia L
2010-12-01
The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D(2), F+H(2)/D(2)/HD, D(+)+H(2), O+H(2), and He+H(2)(+), have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D(+)+H(2), Ne+H(2)(+), and He+H(2)(+) in both adiabatic and nonadiabatic context.
Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.
2013-11-01
Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.
Dynamics of anion-molecule reactions at low energy
Mikosch, J.
2007-11-15
Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S{sub N}2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S{sub N}2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S{sub N}2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S{sub N}2 mechanism involving CH{sub 3}-rotation. (orig.)
Welsch, Ralph, E-mail: rwelsch@uni-bielefeld.de; Manthe, Uwe, E-mail: uwe.manthe@uni-bielefeld.de [Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld (Germany)
2015-02-14
Initial state-selected reaction probabilities of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C{sub 3v} symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f{sub 2}-symmetric) stretching, or e-symmetric bending excited states of methane.
Welsch, Ralph; Manthe, Uwe
2015-02-14
Initial state-selected reaction probabilities of the H + CH4 → H2 + CH3 reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C3v symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f2-symmetric) stretching, or e-symmetric bending excited states of methane.
Welsch, Ralph; Manthe, Uwe
2015-02-01
Initial state-selected reaction probabilities of the H + CH4 → H2 + CH3 reaction are calculated in full and reduced dimensionality on a recent neural network potential [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. The quantum dynamics calculation employs the quantum transition state concept and the multi-layer multi-configurational time-dependent Hartree approach and rigorously studies the reaction for vanishing total angular momentum (J = 0). The calculations investigate the accuracy of the neutral network potential and study the effect resulting from a reduced-dimensional treatment. Very good agreement is found between the present results obtained on the neural network potential and previous results obtained on a Shepard interpolated potential energy surface. The reduced-dimensional calculations only consider motion in eight degrees of freedom and retain the C3v symmetry of the methyl fragment. Considering reaction starting from the vibrational ground state of methane, the reaction probabilities calculated in reduced dimensionality are moderately shifted in energy compared to the full-dimensional ones but otherwise agree rather well. Similar agreement is also found if reaction probabilities averaged over similar types of vibrational excitation of the methane reactant are considered. In contrast, significant differences between reduced and full-dimensional results are found for reaction probabilities starting specifically from symmetric stretching, asymmetric (f2-symmetric) stretching, or e-symmetric bending excited states of methane.
Krapf, Sebastian; Koslowski, Thorsten; Steinbrecher, Thomas
2010-08-28
DNA Photolyases are light sensitive oxidoreductases present in many organisms that participate in the repair of photodamaged DNA. They are capable of electron transfer between a bound cofactor and a chain of tryptophan amino acid residues. Due to their unique mechanism and important function, photolyases have been subject to intense study in recent times, with both experimental and computational efforts. In this work, we present a novel application of classical molecular dynamics based free energy calculations, combined with quantum mechanical computations, to biomolecular charge transfer. Our approach allows for the determination of all reaction parameters in Marcus' theory of charge transport. We were able to calculate the free energy profile for the movement of a positive charge along protein sidechains involved in the biomolecule's function as well as charge-transfer rates that are in good agreement with experimental results. Our approach to simulate charge-transfer reactions explicitly includes the influence of protein flexibility and solvent dynamics on charge-transfer energetics. As applied here to a biomolecular system of considerable scientific interest, we believe the method to be easily adaptable to the study of charge-transfer phenomena in biochemistry and other fields.
Quantum Dynamics of Radical-Ion-Pair Reactions
Kominis, I K
2010-01-01
Radical-ion-pair reactions were recently shown to represent a rich biophysical laboratory for the application of quantum measurement theory methods and concepts, casting doubt on the validity of the theoretical treatment of these reactions and the results thereof that has been at the core of spin chemistry for several decades now. The ensued scientific debate, although exciting, is plagued with several misconceptions. We will here provide a comprehensive treatment of the quantum dynamics of radical-ion-pair reactions, generalizing our recent work and elaborating on the analogy with the double-slit experiment having partial "which-path" information. This analogy directly leads to the general treatment of radical-ion pair reactions covering the whole range between the two extremes, that of perfect singlet-triplet coherence and that of complete incoherence.
Mauguière, F A L; Ezra, G S; Farantos, S C; Wiggins, S
2014-01-01
A model Hamiltonian for the reaction CH$_4^+ \\rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom NHIMS are unstable periodic orbits which, in conjunction with their stable and unstable manifolds, unambiguously define the (locally) non-recrossing dividing surfaces assumed in statistical theories of reaction rates. By constructing periodic orbit continuation/bifurcation diagrams for two values of the potential function parameter corresponding to late and early transition states, respectively, and using the total energy as another parameter, we dynamically assign different regions of phase space to reactants and product...
O Scholten; A Usov
2010-08-01
To describe photo- and meson-induced reactions on the nucleon, one is faced with a rather extensive coupled-channel problem. Ignoring the effects of channel coupling, as one would do in describing a certain reaction at the tree level, invariably creates a large inconsistency between the different reactions that are described. In addition, the imaginary parts of the amplitude, which are related through the optical theorem, to total cross-sections, are directly reflected in certain polarization observables. Performing a full coupled-channel calculation thus offers the possibility to implement the maximum number of constraints. The drawback one is faced with is to arrive at a simultaneous fit of a large number of reaction channels. While some of the parameters are common to many reactions, one is still faced with the challenge to optimize a large number of parameters in a highly non-linear calculation. Here we show that such an approach is possible and present some results for photoinduced strangeness production.
Nonadiabatic quantum wave packet dynamics of the H + H2 reaction including the coriolis coupling
B Jayachander Rao; S Mahapatra
2009-09-01
The effect of coriolis coupling on the dynamics of H + H2 reaction is examined by calculating the initial state-selected and energy resolved reaction probabilities on the coupled manifold of its degenerate 2 (') ground electronic state. H3 in this state is prone to the Jahn-Teller (JT) instability and consequently the degeneracy is split upon distortion from its 3ℎ equilibrium geometry. The orbital degeneracy is, however, restored along the 3ℎ symmetry configuration and it results into conical intersections of the two JT split component states. The energetically lower adiabatic component of latter is repulsive, and mainly (`rather solely’) drive the H + H2 reaction dynamics. On the otherhand, the upper adiabatic component is of bound type and can only impart non-adiabaticity on the dynamics of lower state. Comparison calculations are therefore also carried out on the uncoupled lower adiabatic sheet to assess the nonadiabatic effect. Exact quantum scattering calculations are performed by a chebyshev polynomial propagator and employing the double many body expansion potential energy surface of the electronic ground state of H3. Reaction probabilities are reported up to a total energy of ∼ 3.0 eV, slightly above the energetic minimum of the seam of conical intersections at ∼ 2.74 eV. Reaction probabilities are calculated up to the total angular momentum, = 20 and for each value of , the projection quantum number is varied from 0 to min (, max), with max = 4. Probability results are compared and discussed with those obtained without the coriolis coupling.
Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Theory and Practical Applications
Suleimanov, Yury V; Guo, Hua
2016-01-01
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze theory and its connection to quantum transition state theory. We then focus on its practical application to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rates in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rates. We also hope it will motivate further applications of RPMD to various chemical reactions.
Oxygenation mechanism of ions in dynamic reaction cell ICP-MS.
Narukawa, Tomohiro; Chiba, Koichi
2013-01-01
A dynamic reaction cell (DRC) is one of the most effective tools for eliminating spectral interferences caused by polyatomic molecules in inductively coupled plasma mass spectrometry (ICP-MS). Oxygen gas (O2), by producing oxygenated ions, is very effective in reducing some specific spectral interferences. In this study, the oxygenation of elemental ions (M(+)) in the DRC was investigated experimentally, and a new explanation for oxygenation based on the enthalpy changes in the oxygenating reactions is proposed. The enthalpy changes of each M(+) were calculated and the possibility of each reaction occurring was evaluated. The calculations were in good agreement with experimental observations. Theoretical and experimental results supported the hypothesis that the enthalpy changes (ΔH) of M(+)+ O2 → MO(+) + O and M(+) + O → MO(+) and the thermodynamic stability of M(+)-O are key factors controlling oxygenation of M(+) in the DRC.
Suleimanov, Yury V; Aoiz, F Javier; Guo, Hua
2016-11-03
This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.
Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.
Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R
2014-10-14
The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a
Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya
2015-01-14
Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.
Achakovskiy, Oleg; Tselyaev, Victor; Shitov, Mikhail
2015-01-01
The neutron capture cross sections and average radiative widths of neutron resonances for two double-magic nuclei 132Sn and 208Pb have been calculated using the microscopic photon strength functions, which were obtained within the microscopic self-consistent version of the extended theory of finite Fermi systems in the time blocking approximation. For the first time, the microscopic PSFs have been obtained within the fully self-consistent approach with exact accounting for the single particle continuum (for 208Pb). The approach includes phonon coupling effects in addition to the standard RPA approach. The known Skyrme force has been used. The calculations of nuclear reaction characteristics have been performed with the EMPIRE 3.1 nuclear reaction code. Here, three nuclear level density (NLD) models have been used: the so-called phenomenological GSM, the EMPIRE specific (or Enhanced GSM) and the microscopical combinatorial HFB NLD models. For both considered characteristics we found a significant disagreement ...
Gardner, D.G.; Gardner, M.A.
1990-12-05
p-Process modeling of some rare but stable proton-rich nuclei requires knowledge of a variety of neutron, charged particle, and photonuclear reaction rates at temperatures of 2 to 3 {times} 10{sup 9} {degrees}K. Detailed balance is usually invoked to obtain the stellar photonuclear rates, in spite of a number of well-known constraints. In this work we attempt to calculate directly the stellar rates for ({gamma},n) and ({gamma},{alpha}) reactions on {sup 151}Eu. These are compared with stellar rates obtained from detailed balance, using the same input parameters for the stellar (n,{gamma}) and ({alpha},{gamma}) reactions on {sup 150}Eu and {sup 147}Pm, respectively. The two methods yielded somewhat different results, which will be discussed along with some sensitivity studies. 16 refs., 7 figs.
The photodissociation and reaction dynamics of vibrationally excited molecules
Crim, F.F. [Univ. of Wisconsin, Madison (United States)
1993-12-01
This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.
Plummer, L.N.; Parkhurst, D.L.; Fleming, G.W.; Dunkle, S.A.
1988-01-01
The program named PHRQPITZ is a computer code capable of making geochemical calculations in brines and other electrolyte solutions to high concentrations using the Pitzer virial-coefficient approach for activity-coefficient corrections. Reaction-modeling capabilities include calculation of (1) aqueous speciation and mineral-saturation index, (2) mineral solubility, (3) mixing and titration of aqueous solutions, (4) irreversible reactions and mineral water mass transfer, and (5) reaction path. The computed results for each aqueous solution include the osmotic coefficient, water activity , mineral saturation indices, mean activity coefficients, total activity coefficients, and scale-dependent values of pH, individual-ion activities and individual-ion activity coeffients , and scale-dependent values of pH, individual-ion activities and individual-ion activity coefficients. A data base of Pitzer interaction parameters is provided at 25 C for the system: Na-K-Mg-Ca-H-Cl-SO4-OH-HCO3-CO3-CO2-H2O, and extended to include largely untested literature data for Fe(II), Mn(II), Sr, Ba, Li, and Br with provision for calculations at temperatures other than 25C. An extensive literature review of published Pitzer interaction parameters for many inorganic salts is given. Also described is an interactive input code for PHRQPITZ called PITZINPT. (USGS)
Chemical memory reactions induced bursting dynamics in gene expression.
Tian, Tianhai
2013-01-01
Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.
Untangling knots via reaction-diffusion dynamics of vortex strings
Maucher, Fabian
2016-01-01
We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings
Maucher, Fabian; Sutcliffe, Paul
2016-04-01
We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.
YANG,En-Cui(杨恩翠); ZHAO,Xiao-Jun(赵小军); TIAN,Peng(田鹏); HAO,Jin-Ku(郝金库)
2004-01-01
The two possible reaction paths of producing ethane on coupling reaction of methane through plasma were theoretically investigated by B3LYP and MP2 methods with 6-311G* respectively and further compared with the previous results calculated from B3LYP/6-31G*.The new investigated results consistently confirmed the previous conclusion.And the influences of the calculation methods and basis sets on the calculated results were also discussed.
A ring polymer molecular dynamics study of the Cl + O3 reaction.
de Tudela, R Pérez; Suleimanov, Y V; Menéndez, M; Castillo, J F; Aoiz, F J
2014-02-21
We have performed ring polymer molecular dynamics (RPMD) calculations on the Cl + O3 → ClO + O2 reaction at temperatures ranging from 200 K to 400 K, and compared the results with previous theoretical studies and also with the available experimental data. This reaction presents a couple of features which makes it a particularly interesting and challenging case to be studied using RPMD. First, classically, this is essentially a barrierless reaction, with a saddle point located below the reactants. However, the free energy profiles along the reaction coordinate display small barriers due to the fact that the decrease in enthalpy from reactants to the TS is somewhat compensated by a decrease in entropy. To our knowledge this is the first time such a process is studied using this technique. Second, the transition state is located early in the reactant valley, therefore the inclusion of the recrossing correction in the RPMD calculations is crucial to determine rate coefficients. Regarding quantum effects, our calculations show that RPMD results are within the error bars of the purely classical ones. This implies that tunnelling is negligible in this reaction at the temperatures studied, not surprisingly for a system including oxygen and chlorine atoms, and that the zero point energies of reactants, transition state and products are practically the same. Finally, the rate coefficients presented in this work are in a fairly good agreement with the recommended experimental values, somewhat better than those obtained using other approaches.
An efficient method for calculation of dynamic logarithmic gains in biochemical systems theory.
Shiraishi, Fumihide; Hatoh, Yuji; Irie, Toshinori
2005-05-07
Biochemical systems theory (BST) characterizes a given biochemical system based on the logarithmic gains, rate-constant sensitivities and kinetic-order sensitivities defined at a steady state. This paper describes an efficient method for calculation of the time courses of logarithmic gains, i.e. dynamic logarithmic gains L(Xi, Xj; t), which expresses the percentage change in the value of a dependent variable Xi at a time t in response to an infinitesimal percentage change in the value of an independent variable Xj at t=0. In this method, one first recasts the ordinary differential equations for the dependent variables into an exact canonical nonlinear representation (GMA system) through appropriate transformations of variables. Owing to the structured mathematical form of this representation, the recast system can be fully described by a set of numeric parameters, and the differential equations for the dynamic logarithmic gains can be set up automatically without resource to computer algebra. A simple general-purpose computer program can thus be written that requires only the relevant numeric parameters as input to calculate the time courses of the variables and of the dynamic logarithmic gains for both concentrations and fluxes. Unlike other methods, the proposed method does not require to derive any expression for the partial differentiation of flux expressions with respect to each independent variable. The proposed method has been applied to two kinds of reaction models to elucidate its usefulness.
Dynamic signaling cascades: reversible covalent reaction-coupled molecular switches.
Ren, Yulong; You, Lei
2015-11-11
The research of systems chemistry exploring complex mixtures of interacting synthetic molecules has been burgeoning recently. Herein we demonstrate for the first time the coupling of molecular switches with a dynamic covalent reaction (DCR) and the modulation of created chemical cascades with a variety of inputs, thus closely mimicking a biological signaling system. A novel Michael type DCR of 10-methylacridinium perchlorate and monothiols exhibiting excellent regioselectivity and tunable affinity was discovered. A delicate balance between the unique reactivity of the reactant and the stability of the adduct leads to the generation of a strong acid in a thermodynamically controlled system. The dynamic cascade was next created via coupling of the DCR and a protonation-induced configurational switch (E/Z isomerization) through a proton relay. Detailed examination of the interdependence of the equilibrium enabled us to rationally optimize the cascade and also shed light on the possible intermediate of the switching process. Furthermore, relative independence of the coupled reactions was verified by the identification of stimuli that are able to facilitate one reaction but suppress the other. To further enhance systematic complexity, a second DCR of electrophilic aldehydes and thiols was employed for the reversible inhibition of the binary system, thus achieving the interplay of multiple equilibria. Finally, a fluorescence switch was turned on through coupling with the DCR, showcasing the versatility of our strategy. The results described herein should pave the way for the exploitation of multifunctional dynamic covalent cascades.
Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.
Otto, R; Brox, J; Trippel, S; Stei, M; Best, T; Wester, R
2013-08-29
We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. We find a strong preference for the formation of unsolvated I(-) reaction products with respect to the energetically favored reaction toward solvated I(-)(H2O). Angle differential cross section measurements reveal similar velocity and angular distributions for all solvated and parts of the unsolvated reaction products. We furthermore find that the contribution of these two products to the total product flux can be described by the same collision energy dependence. We interpret our findings in terms of a joint reaction mechanism in which a CH3OH(H2O)···I(-) complex is formed that decays into either solvated or unsolvated products. Quantum chemical calculation are used to support this assumption.
Wefstaedt Patrick
2009-11-01
Full Text Available Abstract Background Among other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS- model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces. Methods The anatomical geometries of the MBS-model have been established using computer tomography- (CT- and magnetic resonance imaging- (MRI- data. The CT-data were collected from the pelvis, femora, tibiae and pads of a mixed-breed adult dog. Geometric information about 22 muscles of the pelvic extremity of 4 mixed-breed adult dogs was determined using MRI. Kinematic and kinetic data obtained by motion analysis of a clinically healthy dog during a gait cycle (1 m/s on an instrumented treadmill were used to drive the model in the multi-body simulation. Results and Discussion As a result the vertical ground reaction forces (z-direction calculated by the MBS-system show a maximum deviation of 1.75%BW for the left and 4.65%BW for the right hind limb from the treadmill measurements. The calculated peak ground reaction forces in z- and y-direction were found to be comparable to the treadmill measurements, whereas the curve characteristics of the forces in y-direction were not in complete alignment. Conclusion In conclusion, it could be demonstrated that the developed MBS-model is suitable for simulating ground reaction forces of dogs during walking. In forthcoming investigations the model will be developed further for the calculation of forces and moments acting on the hip joint during different movements, which can be of help in context with the in
Nitschke, Naomi; Atkovska, Kalina; Hub, Jochen S.
2016-09-01
Molecular dynamics simulations are capable of predicting the permeability of lipid membranes for drug-like solutes, but the calculations have remained prohibitively expensive for high-throughput studies. Here, we analyze simple measures for accelerating potential of mean force (PMF) calculations of membrane permeation, namely, (i) using smaller simulation systems, (ii) simulating multiple solutes per system, and (iii) using shorter cutoffs for the Lennard-Jones interactions. We find that PMFs for membrane permeation are remarkably robust against alterations of such parameters, suggesting that accurate PMF calculations are possible at strongly reduced computational cost. In addition, we evaluated the influence of the definition of the membrane center of mass (COM), used to define the transmembrane reaction coordinate. Membrane-COM definitions based on all lipid atoms lead to artifacts due to undulations and, consequently, to PMFs dependent on membrane size. In contrast, COM definitions based on a cylinder around the solute lead to size-independent PMFs, down to systems of only 16 lipids per monolayer. In summary, compared to popular setups that simulate a single solute in a membrane of 128 lipids with a Lennard-Jones cutoff of 1.2 nm, the measures applied here yield a speedup in sampling by factor of ˜40, without reducing the accuracy of the calculated PMF.
De Wispelaere, Kristof; Ensing, Bernd; Ghysels, An; Meijer, Evert Jan; Van Speybroeck, Veronique
2015-06-22
The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.
Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin
2015-11-12
High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.
Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan
2014-10-06
A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.
Geometrical Models of the Phase Space Structures Governing Reaction Dynamics
Waalkens, Holger
2009-01-01
Hamiltonian dynamical systems possessing equilibria of ${saddle} \\times {centre} \\times...\\times {centre}$ stability type display \\emph{reaction-type dynamics} for energies close to the energy of such equilibria; entrance and exit from certain regions of the phase space is only possible via narrow \\emph{bottlenecks} created by the influence of the equilibrium points. In this paper we provide a thorough pedagogical description of the phase space structures that are responsible for controlling transport in these problems. Of central importance is the existence of a \\emph{Normally Hyperbolic Invariant Manifold (NHIM)}, whose \\emph{stable and unstable manifolds} have sufficient dimensionality to act as separatrices, partitioning energy surfaces into regions of qualitatively distinct behavior. This NHIM forms the natural (dynamical) equator of a (spherical) \\emph{dividing surface} which locally divides an energy surface into two components (`reactants' and `products'), one on either side of the bottleneck. This di...
van Harrevelt, Rob; Honkala, Johanna Karoliina; Nørskov, Jens Kehlet
2005-01-01
Quantum-mechanical calculations of the reaction rate for dissociative adsorption of N-2 on stepped Ru(0001) are presented. Converged six-dimensional quantum calculations for this heavy-atom reaction have been performed using the multiconfiguration time-dependent Hartree method. A potential...
Resonances and reactions from mean-field dynamics
Stevenson P. D.
2016-01-01
Full Text Available The time-dependent version of nuclear density functional theory, using functionals derived from Skyrme interactions, is able to approximately describe nuclear dynamics. We present time-dependent results of calculations of dipole resonances, concentrating on excitations of valence neutrons against a proton plus neutron core in the neutron-rich doubly-magic 132Sn nucleus, and results of collision dynamics, highlighting potential routes to ternary fusion, with the example of a collision of 48Ca+48Ca+208Pb resulting in a compound nucleus of element 120 stable against immediate fission.
Modern Dynamical Coupled-Channels Calculations for Extracting and Understanding the Nucleon Spectrum
Kamano, Hiroyuki
2016-01-01
We give an overview of recent progress in the spectroscopic study of nucleon resonances within the dynamical coupled-channels analysis of meson-production reactions. The important role of multichannel reaction dynamics in understanding various properties of nucleon resonances is emphasized.
Nguyen, H.D.
1991-11-01
Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.
Nguyen, H.D.
1991-11-01
Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.
Li, Xifeng; Cai, Zhongli; Katsumura, Yosuke [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab
2000-03-01
The interaction of caffeic acid with e{sub aq}{sup -}, (CH{sub 3}){sub 2}(OH) CCH{sub 2}{sup {center_dot}}, CO{sub 2}{sup {center_dot}}{sup -}, H{sup {center_dot}}, {center_dot}OH and N{sub 3}{sup {center_dot}} radicals were studied by {gamma}-, pulse radiolysis and molecular orbital calculation. UV-visible spectra of electron/{center_dot}OH adducts, semi-quinone radicals of caffeic ions, and the stable products from the reactions were derived. The rate constants were determined. The attacked sites and the most favorable structures of the transient radicals were predicted. Reaction mechanisms were proposed. (author)
Dynamic biochemical reaction process analysis and pathway modification predictions.
Conejeros, R; Vassiliadis, V S
2000-05-05
Recently, the area of model predictive modification of biochemical pathways has received attention with the aim to increase the productivity of microbial systems. In this study, we present a generalization of previous work, where, using a sensitivity study over the fermentation as a dynamic system, the optimal selection of reaction steps for modification (amplification or attenuation) is determined. The influence of metabolites in the activity of enzymes has also been considered (through activation or inhibition). We further introduce a new concept in the dynamic modeling of biochemical reaction systems including a generalized continuous superstructure in which two artificial multiplicative terms are included to account for: (a) enzyme overexpression or underexpression (attenuation or amplification) for the whole enzyme pool; and (b) modification of the apparent order of a kinetic expression with respect to the concentration of a metabolite or any subset of metabolites participating in the pathway. This new formulation allows the prediction of the sensitivity of the pathway performance index (objective function) with respect to the concentration of the enzyme, as well as the interaction of the enzyme with other metabolites. Using this framework, a case study for the production of penicillin V is analyzed, obtaining the most sensitive reaction steps (or bottlenecks) and the most significant regulations of the system, due to the effect of concentration of intracellular metabolites on the activity of each enzyme.
Pérez de Tudela, Ricardo; Aoiz, F J; Suleimanov, Yury V; Manolopoulos, David E
2012-02-16
A fundamental issue in the field of reaction dynamics is the inclusion of the quantum mechanical (QM) effects such as zero point energy (ZPE) and tunneling in molecular dynamics simulations, and in particular in the calculation of chemical reaction rates. In this work we study the chemical reaction between a muonium atom and a hydrogen molecule. The recently developed ring polymer molecular dynamics (RPMD) technique is used, and the results are compared with those of other methods. For this reaction, the thermal rate coefficients calculated with RPMD are found to be in excellent agreement with the results of an accurate QM calculation. The very minor discrepancies are within the convergence error even at very low temperatures. This exceptionally good agreement can be attributed to the dominant role of ZPE in the reaction, which is accounted for extremely well by RPMD. Tunneling only plays a minor role in the reaction.
Reaction dynamics of molecular hydrogen on silicon surfaces
Bratu, P.; Brenig, W.; Gross, A.
1996-01-01
between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective...... of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...
Calculation for fission decay from heavy ion reactions at intermediate energies
Blaich, T.; Begemann-Blaich, M.; Fowler, M.M.; Wilhelmy, J.B. (Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)); Britt, H.C.; Fields, D.J.; Hansen, L.F.; Namboodiri, M.N.; Sangster, T.C. (Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)); Fraenkel, Z. (Weizmann Institute of Science, 76100 Rehovot (Israel))
1992-02-01
A detailed deexcitation calculation is presented for target residues resulting from intermediate-energy heavy ion reactions. The model involves an intranuclear cascade, subsequent fast nucleon emission, and final decay by statistical evaporation including fission. Results are compared to data from bombardments with Fe and Nb projectiles on targets of Ta, Au, and Th at 100 MeV/nucleon. The majority of observable features are reproduced with this simple approach, making obvious the need for involving new physical phenomena associated with multifragmentation or other collective dissipation mechanisms.
Hofmann, H.M.; Mertelmeier, T. (Erlangen-Nuernberg Univ., Erlangen (Germany, F.R.). Inst. fuer Theoretische Physik); Mello, P.A. (Instituto Nacional de Investigaciones Nucleares, Mexico City. Lab. del Acelerador); Seligman, T.H. (Universidad Nacional Autonoma de Mexico, Mexico City. Inst. de Fisica)
1981-12-14
A comparison is presented between predictions of the entropy approach to statistical nuclear reactions, and numerical calculations performed by generating an ensemble of S-matrices in terms of K-matrices with specified statistical distributions for their parameters. The comparison is done for: (a) the 2nd, 3rd and 4th moments of S in a 4-channel case and (b) the actual distribution of the S-matrix elements in a 2-channel case. In both cases the agreement is found to be very good in the domain of strong absorption.
Present status of coupled-channels calculations for heavy-ion subbarrier fusion reactions
Hagino, K
2015-01-01
The coupled-channels method has been a standard tool in analyzing heavy-ion fusion reactions at energies around the Coulomb barrier. We investigate three simplifications usually adopted in the coupled-channels calculations. These are i) the exclusion of non-collective excitations, ii) the assumption of coordinate independent coupling strengths, and iii) the harmonic oscillator approximation for multi-phonon excitations. In connection to the last point, we propose a novel microscopic method based on the beyond-mean-field approach in order to take into account the anharmonic effects of collective vibrations.
Body-Fitted Detonation Shock Dynamics and the Pseudo-Reaction-Zone Energy Release Model
Meyer, Chad; Quirk, James; Short, Mark; Chqiuete, Carlos
2016-11-01
Programmed-burn methods are a class of models used to propagate a detonation wave, without the high resolution cost associated with a direct numerical simulation. They separate the detonation evolution calculation into two components: timing and energy release. The timing component is usually calculated with a Detonation Shock Dynamics model, a surface evolution representation that relates the normal velocity of the surface (Dn) to its local curvature. The energy release component must appropriately capture the degree of energy change associated with chemical reaction while simultaneously remaining synchronized with the timing component. The Pseudo-Reaction-Zone (PRZ) model is a reactive burn like energy release model, converting reactants into products, but with a conversion rate that is a function of the DSD surface Dn field. As such, it requires the DSD calculation produce smooth Dn fields, a challenge in complex geometries. We describe a new body-fitted approach to the Detonation Shock Dynamics calculation which produces the required smooth Dn fields, and a method for calibrating the PRZ model such that the rate of energy release remains as synced as possible with the timing component. We show results for slab, rate-stick and arc geometries.
Molecular-dynamics study of detonation. II. The reaction mechanism
Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.
1996-01-01
In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.
Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea;
2014-01-01
We present a method to calculate 31P solid-state NMR spectra based on the dynamic input from extended molecular dynamics (MD) simulations. The dynamic information confered by MD simulations is much more comprehensive than the information provided by traditional NMR dynamics models based on......, for example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated 31P spectra obtained...
Analysis of Vibration Mode for H2+F→HF+H Reaction Mechanism: Density functional Theory Calculation
无
2001-01-01
Three density functional theory methods (DFT) have been used to investigate the H2+F?HF+H reaction comparing with the Hartree-Fock method and Moller-Plesset (MP2) perturbation theory method. Through the analysis of the vibrational mode and vibrational frequency in the reaction process, the reaction mechanism has been discussed. The activation energy, the reorganization energy and rate constant of the ET reaction are calculated at semi-quantitative level.
Quantum and quasiclassical dynamics of the multi-channel H + H2S reaction
Qi, Ji; Lu, Dandan; Song, Hongwei; Li, Jun; Yang, Minghui
2017-03-01
The prototypical multi-channel reaction H + H2S → H2 + SH/H + H2S has been investigated using the full-dimensional quantum scattering and quasi-classical trajectory methods to unveil the underlying competition mechanism between different product channels and the mode specificity. This reaction favors the abstraction channel over the exchange channel. For both channels, excitations in the two stretching modes promote the reaction with nearly equal efficiency and are more efficient than the bending mode excitation. However, they are all less efficient than the translational energy. In addition, the experimentally observed non-Arrhenius temperature dependence of the thermal rate constants is reasonably reproduced by the quantum dynamics calculations, confirming that the non-Arrhenius behavior is caused by the pronounced quantum tunneling.
Crossed-beam studies of the dynamics of radical reactions
Liu, K. [Argonne National Laboratory, IL (United States)
1993-12-01
The objective of this program is to characterize the detailed dynamics of elementary radical reactions and to provide a better understanding of radical reactivity in general. The radical beam is typically generated by a laser photolysis method. After colliding with the reacting molecule in a crossed-beam apparatus, the reaction product state distribution is interrogated by laser spectroscopic techniques. Several radicals of combustion significance, such as O, CH, OH, CN and NCO have been successfully generated and their collisional behavior at the state-to-state integral cross section level of detail has been studied in this manner. During the past year, the detection system has been converted from LIF to REMPI schemes, and the emphasis of this program shifted to investigate the product angular distributions. Both inelastic and reactive processes have been studied.
Recycling probability and dynamical properties of germinal center reactions
Meyer-Hermann, M; Or-Guil, M; Meyer-Hermann, Michael; Deutsch, Andreas; Or-Guil, Michal
2001-01-01
We introduce a new model for the dynamics of centroblasts and centrocytes in a germinal center. The model reduces the germinal center reaction to the elements considered as essential and embeds proliferation of centroblasts, point mutations of the corresponding antibody types represented in a shape space, differentiation to centrocytes, selection with respect to initial antigens, differentiation of positively selected centrocytes to plasma or memory cells and recycling of centrocytes to centroblasts. We use exclusively parameters with a direct biological interpretation such that, once determined by experimental data, the model gains predictive power. Based on the experiment of Han et al.(1995) we predict that a high rate of recycling of centrocytes to centroblasts is necessary for the germinal center reaction to work reliably. Furthermore, we find a delayed start of the production of plasma and memory cells with respect to the start of point mutations, which turns to be necessary for the optimization process ...
Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe
2014-09-28
We show how we can find the enthalpy of a chemical reaction under non-ideal conditions using the Small System Method to sample molecular dynamics simulation data for fluctuating variables. This method, created with Hill's thermodynamic analysis, is used to find properties in the thermodynamic limit, such as thermodynamic correction factors, partial enthalpies, volumes, heat capacities and compressibility. The values in the thermodynamic limit at (T,V, μj) are then easily transformed into other ensembles, (T,V,Nj) and (T,P,Nj), where the last ensemble gives the partial molar properties which are of interest to chemists. The dissociation of hydrogen from molecules to atoms was used as a convenient model system. Molecular dynamics simulations were performed with three densities; ρ = 0.0052 g cm(-3) (gas), ρ = 0.0191 g cm(-3) (compressed gas) and ρ = 0.0695 g cm(-3) (liquid), and temperatures in the range; T = 3640-20,800 K. The enthalpy of reaction was observed to follow a quadratic trend as a function of temperature for all densities. The enthalpy of reaction was observed to only have a small pressure dependence. With a reference point close to an ideal state (T = 3640 K and ρ = 0.0052 g cm(-3)), we were able to calculate the thermodynamic equilibrium constant, and thus the deviation from ideal conditions for the lowest density. We found the thermodynamic equilibrium constant to increase with increasing temperature, and to have a negligible pressure dependence. Taking the enthalpy variation into account in the calculation of the thermodynamic equilibrium constant, we found the ratio of activity coefficients to be in the order of 0.7-1.0 for the lowest density, indicating repulsive forces between H and H2. This study shows that the compressed gas- and liquid density values at higher temperatures are far from those calculated under ideal conditions. It is important to have a method that can give access to partial molar properties, independent of the ideality of
Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Sarin
Conforti, Patrick F.; Braunstein, Matthew; Dodd, James A.
2009-10-01
Electronic structure and molecular dynamics calculations were performed on the reaction systems O(3P) + sarin and O(3P) + dimethyl methylphosphonate (DMMP), a sarin simulant. Transition state geometries, energies, and heats of reaction for the major reaction pathways were determined at several levels of theory, including AM1, B3LYP/6-311+G(d,p), and CBS-QB3. The major reaction pathways for both systems are similar and include H-atom abstraction, H-atom elimination, and methyl elimination, in rough order from low to high energy. The H-atom abstraction channels have fairly low barriers (˜10 kcal mol-1) and are close to thermoneutral, while the other channels have relatively high energy barriers (>40 kcal mol-1) and a wide range of reaction enthalpies. We have also found a two-step pathway leading to methyl elimination through O-atom attack on the phosphorus atom for DMMP and sarin. For sarin, the two-step methyl elimination pathway is significantly lower in energy than the single-step pathway. We also present results of O(3P) + sarin and O(3P) + DMMP reaction cross sections over a broad range of collision energies (2-10 km s-1 collision velocities) obtained using the direct dynamics method with an AM1 semiempirical potential. These excitation functions are intended as an approximate guide to future hyperthermal measurements, which to our knowledge have not yet examined either of these systems. The reaction barriers, reaction enthalpies, transition state structures, and excitation functions are generally similar for DMMP and sarin, with some moderate differences for methyl elimination energetics, which indicates DMMP will likely be a good substitute for sarin in many O(3P) chemical investigations.
Angular momentum dependence of quasifission dynamics in the reaction 48Ca+244Pu
Yu, Chong; Guo, Lu
2017-09-01
The quasifission dynamics in the reaction 48Ca+244Pu is investigated in the framework of time-dependent Hartree-Fock (TDHF) theory. The calculations are performed in three-dimensional Cartesian coordinate without any symmetry restrictions. The full Skyrme energy functional is incorporated in our TDHF implementation. The quasifission dynamics is quite sensitive to the angular momentum of colliding system. The contact time of quasifission decreases as a function of angular momentum and then forms a plateau with small oscillations. The quasifission process is accompanied by an important multi-nucleon transfer. The quantum shell effect plays a crucial role in the mass and charge of quasifission fragments. The mass-angle distribution of the fragments is calculated, which can be compared directly with future experiments.
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
Bradforth, S.E.
1992-11-01
The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound [yields] bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN[sup [minus
Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics
Franz, Benjamin; Chapman, S Jonathan; Erban, Radek
2012-01-01
Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface which partitions the domain and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that to accurately compute variances using the PBD simulation requires the overlap region. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented.
New reaction rates for improved primordial D /H calculation and the cosmic evolution of deuterium
Coc, Alain; Petitjean, Patrick; Uzan, Jean-Philippe; Vangioni, Elisabeth; Descouvemont, Pierre; Iliadis, Christian; Longland, Richard
2015-12-01
Primordial or big bang nucleosynthesis (BBN) is one of the three historically strong evidences for the big bang model. Standard BBN is now a parameter-free theory, since the baryonic density of the Universe has been deduced with an unprecedented precision from observations of the anisotropies of the cosmic microwave background radiation. There is a good agreement between the primordial abundances of 4He, D, 3He, and 7Li deduced from observations and from primordial nucleosynthesis calculations. However, the 7Li calculated abundance is significantly higher than the one deduced from spectroscopic observations and remains an open problem. In addition, recent deuterium observations have drastically reduced the uncertainty on D /H , to reach a value of 1.6%. It needs to be matched by BBN predictions whose precision is now limited by thermonuclear reaction rate uncertainties. This is especially important as many attempts to reconcile Li observations with models lead to an increased D prediction. Here, we reevaluate the d (p ,γ )3He, d (d ,n ) 3H3, and d (d ,p ) 3H reaction rates that govern deuterium destruction, incorporating new experimental data and carefully accounting for systematic uncertainties. Contrary to previous evaluations, we use theoretical ab initio models for the energy dependence of the S factors. As a result, these rates increase at BBN temperatures, leading to a reduced value of D /H =(2.45 ±0.10 )×10-5 (2 σ ), in agreement with observations.
Fast LiH destruction in reaction with H: quantum calculations and astrophysical consequences
Bovino, S; Gianturco, F A; 10.1088/0004-637X/699/1/383
2009-01-01
We present a quantum-mechanical study of the exothermic 7LiH reaction with H. Accurate reactive probabilities and rate coefficients are obtained by solving the Schrodinger equation for the motion of the three nuclei on a single Born-Oppenheimer potential energy surface (PES) and using a coupled-channel hyperspherical coordinate method. Our new rates indeed confirm earlier, qualitative predictions and some previous theoretical calculations, as discussed in the main text. In the astrophysical domain we find that the depletion process largely dominates for redshift (z) between 400 and 100, a range significant for early Universe models. This new result from first-principle calculations leads us to definitively surmise that LiH should be already destroyed when the survival processes become important. Because of this very rapid depletion reaction, the fractional abundance of LiH is found to be drastically reduced, so that it should be very difficult to manage to observe it as an imprinted species in the cosmic back...
Refined Calculations of Secondary Nuclear Reactions in Magneto-Inertial Fusion Plasmas
Schmit, Paul; Knapp, Patrick; Hansen, Stephanie; Gomez, Matthew; Hahn, Kelly; Sinars, Daniel; Peterson, Kyle; Slutz, Stephen; Sefkow, Adam; Awe, Thomas; Harding, Eric; Jennings, Christopher
2014-10-01
Diagnosing the degree of magnetic flux compression at stagnation in magneto-inertial fusion (MIF) is critical for charting the performance of any MIF concept. In pure deuterium plasma, the transport of high-energy tritons produced by the aneutronic DD fusion reaction depends strongly on the magnetic field. The tritons probe and occasionally react with the fuel, emitting secondary DT neutrons. We show that the DT/DD neutron yield ratio and the secondary DT neutron spectra can be used to infer the magnetic field-radius product (BR), the critical confinement parameter for MIF. The amount of fuel-pusher mix also can be constrained by secondary reactions. We discuss the sensitivity to plasma inhomogeneities of the calculations and outline methods to relate secondary yields to alpha particle energy deposition in ignition-relevant experiments employing DT fuel. We compare our calculations to recent tests of the Magnetized Liner Inertial Fusion (MagLIF) concept on the Z Pulsed Power Facility. Supported in part by the SNL Truman Fellowship, which is part of the LDRD Program, and sponsored by Sandia Corporation (a wholly owned subsidiary of Lockheed Martin Corporation) as Operator of SNL under its U.S. DoE Contract No. DE-AC04-94AL85000.
Quasi-elastic reactions: an interplay of reaction dynamics and nuclear structure
Szilner, S; Jelavic-Malenica, D; Mijatovic, T; Soic, N [Ruder Botkovic Institute and University of Zagreb, Zagreb (Croatia); Corradi, L; Fioretto, E; Gadea, A; Mengoni, D; Stefanini, A M; Valiente-Dobon, J J [INFN - Laboratori Nazionali di Legnaro, Legnaro (Italy); Pollarolo, G [INFN and Universita di Torino (Italy); Beghini, S; Farnea, E; Lunardi, S; Montagnoli, G; Scarlassara, F; Ur, C A [INFN and Universita di Padova, Padova (Italy); Courtin, S; Haas, F; Lebhertz, D, E-mail: szilner@irb.hr [IPHC, CNRS/IN2P3 and Universite de Strasbourg, Strasbourg (France)
2011-02-01
The revival of transfer reaction studies benefited from the construction of the new generation large solid angle spectrometers based on trajectory reconstruction that reached an unprecedented efficiency and selectivity. The coupling of these spectrometers with large {gamma} arrays allowed the identification of individual excited states, their population pattern and decay modes via particle-{gamma} coincidences. In the present paper aspects of fragment-{gamma} coincidence studies measured with the Prisma-Clara set up in {sup 40}Ca+{sup 96}Zr and {sup 40}Ar+{sup 208}Pb are discussed. In particular, we report about states of particle-phonon character, supporting the idea that the relevant degrees of freedom acting in the reaction dynamics define the final yield distributions.
Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng
2006-12-28
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.
Four-body continuum-discretized coupled-channels calculations applied to {sup 6}He reactions
Rodriguez-Gallardo, M. [Consejo Superior de Investigaciones Cientificas (CSIC), Madrid (Spain). Inst. de Estructura de la Materia; Arias, J.M.; Gomez-Camacho, J.M.; Moro, A.M. [Universidad de Sevilla (Spain). Dept. de Fisica Atomica, Molecular y Nuclear; Thompson, I.J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical Science Directorate; Tostevin, J.A. [University of Surrey, Guildford (United Kingdom). Dept. of Physics
2010-07-01
Full text. The scattering of a weakly bound three-body system by a target is discussed. The continuum-discretized coupled-channels (CDCC) framework, recently extended to four-body reactions (three-body projectile plus target), is used for the scattering calculations. Two different methods are used to discretized the three-body continuum of the projectile. In the first case, we make use of a Pseudo-State (PS) method in which the states of the projectile are represented by the eigenstates of its internal Hamiltonian in a truncated basis of square-integrable functions. In particular, we use the transformed harmonic oscillator (THO) method, in which the PS basis is obtained by applying a local scale transformation to the Harmonic Oscillator basis. In the second case, we applied the binning procedure that has just been extended to three-body projectiles. This discretization method requires to calculate first the true continuum of the projectile and then this continuum is discretized making bins or packages of energy. This has been the method used for many years in standard three-body (two-body projectile plus target) CDCC calculations. Its extension to three-body projectiles uses the eigenchannel expansion of the three-body S-matrix. We applied this formalism to several reactions induced by the Borromean nucleus {sup 6}He at different energies, namely {sup 6}He+{sup 9}Be at 16.2 MeV, {sup 6}He+{sup 64}Zn at 13.6 MeV, {sup 6}He+{sup 120}Sn at 17.4 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV. Four-body CDCC calculations for elastic and breakup observables are presented for these reactions comparing both discretization methods, THO and binning. The effect of the mass of the target, which is clearly related to the influence of Coulomb couplings, is investigated. The elastic cross sections are also compared to existing experimental data. (author)
Calculation of Double-Differential Cross Sections of n+7Li Reactions Below 20 MeV
ZHANG Jing-Shang; HAN Ying-Lu
2002-01-01
A new reaction model for light nuclei is proposed to analyze the measured data,especially for analysis of the double-differential cross sections of the outgoing particles.Many channels arc opened in the n + 7Li reaction below En＜ 20 MeV.The reaction mechanism is very complex,beside the sequential emissions there are also three-body breakup processes.Because of a strong recoil effect of light nucleus reactions,the energy balance is strictly taken into account.The comparisons of the calculated results with the double-differential measurements indicate that the model calculations are successful for the total outgoing neutrons.
A series method applied to engineering calculations in structural dynamics
Reyes Márquez, Auxiliadora; Reyes Perales, José Antonio; Cortés Molina, Mónica; García Alonso, Fernando Luis
2014-01-01
This paper shows an application of the Φ-functions series method to calculate the response of structures in face of an earthquake, modelled by a 2DOF. The Φ-functions series method is an adaptation of the ideas of Scheifele to integrate forced and damped oscillators. This algorithm presents the advantage of integrating precisely the perturbed problem with only two Φ-functions. Method coefficients are calculated by simple algebraic recurrences in which the perturbation function is involved. Re...
Yang, Tiangang; Chen, Jun; Huang, Long; Wang, Tao; Xiao, Chunlei; Sun, Zhigang; Dai, Dongxu; Yang, Xueming; Zhang, Dong H
2015-01-02
The Cl + H2 reaction is an important benchmark system in the study of chemical reaction dynamics that has always appeared to proceed via a direct abstraction mechanism, with no clear signature of reaction resonances. Here we report a high-resolution crossed-molecular beam study on the Cl + HD (v = 1, j = 0) → DCl + H reaction (where v is the vibrational quantum number and j is the rotational quantum number). Very few forward scattered products were observed. However, two distinctive peaks at collision energies of 2.4 and 4.3 kilocalories per mole for the DCl (v' = 1) product were detected in the backward scattering direction. Detailed quantum dynamics calculations on a highly accurate potential energy surface suggested that these features originate from two very short-lived dynamical resonances trapped in the peculiar H-DCl (v' = 2) vibrational adiabatic potential wells that result from chemical bond softening. We anticipate that dynamical resonances trapped in such wells exist in many reactions involving vibrationally excited molecules.
Capote, R.; Herman, M.; Obložinský, P.; Young, P. G.; Goriely, S.; Belgya, T.; Ignatyuk, A. V.; Koning, A. J.; Hilaire, S.; Plujko, V. A.; Avrigeanu, M.; Bersillon, O.; Chadwick, M. B.; Fukahori, T.; Ge, Zhigang; Han, Yinlu; Kailas, S.; Kopecky, J.; Maslov, V. M.; Reffo, G.; Sin, M.; Soukhovitskii, E. Sh.; Talou, P.
2009-12-01
We describe the physics and data included in the Reference Input Parameter Library, which is devoted to input parameters needed in calculations of nuclear reactions and nuclear data evaluations. Advanced modelling codes require substantial numerical input, therefore the International Atomic Energy Agency (IAEA) has worked extensively since 1993 on a library of validated nuclear-model input parameters, referred to as the Reference Input Parameter Library (RIPL). A final RIPL coordinated research project (RIPL-3) was brought to a successful conclusion in December 2008, after 15 years of challenging work carried out through three consecutive IAEA projects. The RIPL-3 library was released in January 2009, and is available on the Web through http://www-nds.iaea.org/RIPL-3/. This work and the resulting database are extremely important to theoreticians involved in the development and use of nuclear reaction modelling (ALICE, EMPIRE, GNASH, UNF, TALYS) both for theoretical research and nuclear data evaluations. The numerical data and computer codes included in RIPL-3 are arranged in seven segments: MASSES contains ground-state properties of nuclei for about 9000 nuclei, including three theoretical predictions of masses and the evaluated experimental masses of Audi et al. (2003). DISCRETE LEVELS contains 117 datasets (one for each element) with all known level schemes, electromagnetic and γ-ray decay probabilities available from ENSDF in October 2007. NEUTRON RESONANCES contains average resonance parameters prepared on the basis of the evaluations performed by Ignatyuk and Mughabghab. OPTICAL MODEL contains 495 sets of phenomenological optical model parameters defined in a wide energy range. When there are insufficient experimental data, the evaluator has to resort to either global parameterizations or microscopic approaches. Radial density distributions to be used as input for microscopic calculations are stored in the MASSES segment. LEVEL DENSITIES contains
Measurements of Dynamical Dipole in isospin asymmetric fusion reactions
Giaz, A.; Corsi, A.; Camera, F.; Bracco, A.; Crespi, F. C. L.; Leoni, S.; Nicolini, R.; Vandone, V.; Benzoni, G.; Blasi, N.; Brambilla, S.; Million, B.; Wieland, O.; Cinausero, M.; Degelier, M.; Gramegna, F.; Kravchuk, V. L.; Marchi, T.; Rizzi, V.; Bardelli, L.; Barlini, S.; Bini, M.; Carboni, S.; Casini, G.; Chiari, M.; Nannini, A.; Pasquali, G.; Piantelli, S.; Poggi, G.; Baiocco, G.; Bruno, M.; D'agostino, M.; Morelli, L.; Vannini, V.; Colonna, M.; Di Toro, M.; Rizzo, C.; Bednarcyk, P.; Ciemala, M.; Kmiecik, M.; Maj, A.; Mazurek, K.; Menczynski, W.; Alba, R.; Maiolino, C.; Santonocito, D.; Montanari, D.; Ordine, A.
2012-05-01
In heavy ion nuclear reactions the process leading to complete fusion is expected to produce pre-equilibrium γ-ray emission, if particular conditions are met. Indeed, when there is an N/Z asymmetry between projectile and target, charge equilibration takes place with a collective dipole oscillation, called Dynamical Dipole (DD), associated to a γ-ray emission. The existing experimental data concerning this pre-equilibrium γ-ray emission are still rather scarce and manly concentrated in the A≊132 mass region. The very preliminary results concerning the measurement of the DD γ-ray emission in the fusion reaction 16O (Elab=192 MeV) + 116Sn at 12 MeV/u will be presented and compared with the γ yield measured for the same reaction at 8.1 and 15.6 MeV/u. The present experiment aims at the measurement of the total emission yield of the DD at 12 MeV/u where the predicted theoretical yield does not completely reproduce the experimental data. The experiment has been performed at the INFN Legnaro Laboratories using the GARFIELD-HECTOR array.
Vijaykumar, Adithya; Wolde, Pieter Rein ten; Bolhuis, Peter G
2016-01-01
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. {\\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.
Microscopic dynamics simulations of heavy-ion fusion reactions induced by neutron-rich nuclei
Wang, Ning; Zhang, Yingxun; Li, Zhuxia
2014-01-01
The heavy-ion fusion reactions induced by neutron-rich nuclei are investigated with the improved quantum molecular dynamics (ImQMD) model. With a subtle consideration of the neutron skin thickness of nuclei and the symmetry potential, the stability of nuclei and the fusion excitation functions of heavy-ion fusion reactions $^{16}$O+$^{76}$Ge, $^{16}$O+$^{154}$Sm, $^{40}$Ca+$^{96}$Zr and $^{132}$Sn+$^{40}$Ca are systematically studied. The fusion cross sections of these reactions at energies around the Coulomb barrier can be well reproduced by using the ImQMD model. The corresponding slope parameter of the symmetry energy adopted in the calculations is $L \\approx 78$ MeV and the surface energy coefficient is $g_{\\rm sur}=18\\pm 1.5$ MeVfm$^2$. In addition, it is found that the surface-symmetry term significantly influences the fusion cross sections of neutron-rich fusion systems. For sub-barrier fusion, the dynamical fluctuations in the densities of the reaction partners and the enhanced surface diffuseness at ...
Heavy ion collision dynamics of 10,11B+10,11B reactions
Singh BirBikram
2015-01-01
Full Text Available The dynamical cluster-decay model (DCM of Gupta and collaborators has been applied successfully to the decay of very-light (A ∼ 30, light (A ∼ 40−80, medium, heavy and super-heavy mass compound nuclei for their decay to light particles (evaporation residues, ER, fusion-fission (ff, and quasi-fission (qf depending on the reaction conditions. We intend to extend here the application of DCM to study the extreme case of decay of very-light nuclear systems 20,21,22Ne∗ formed in 10,11B+10,11B reactions, for which experimental data is available for their binary symmetric decay (BSD cross sections, i.e., σBSD. For the systems under study, the calculations are presented for the σBSD in terms of their preformation and barrier penetration probabilities P0 and P. Interesting results are that in the decay of such lighter systems there is a competing reaction mechanism (specifically, the deep inelastic orbiting of non-compound nucleus (nCN origin together with ff. We have emipirically estimated the contribution of σnCN. Moreover, the important role of nuclear structure characteristics via P0 as well as angular momentum ℓ in the reaction dynamics are explored in the study.
Kim, Ki Chul; Kulkarni, Anant D; Johnson, J Karl; Sholl, David S
2011-04-21
Systematic thermodynamics calculations based on density functional theory-calculated energies for crystalline solids have been a useful complement to experimental studies of hydrogen storage in metal hydrides. We report the most comprehensive set of thermodynamics calculations for mixtures of light metal hydrides to date by performing grand canonical linear programming screening on a database of 359 compounds, including 147 compounds not previously examined by us. This database is used to categorize the reaction thermodynamics of all mixtures containing any four non-H elements among Al, B, C, Ca, K, Li, Mg, N, Na, Sc, Si, Ti, and V. Reactions are categorized according to the amount of H(2) that is released and the reaction's enthalpy. This approach identifies 74 distinct single step reactions having that a storage capacity >6 wt.% and zero temperature heats of reaction 15 ≤ΔU(0)≤ 75 kJ mol(-1) H(2). Many of these reactions, however, are likely to be problematic experimentally because of the role of refractory compounds, B(12)H(12)-containing compounds, or carbon. The single most promising reaction identified in this way involves LiNH(2)/LiH/KBH(4), storing 7.48 wt.% H(2) and having ΔU(0) = 43.6 kJ mol(-1) H(2). We also examined the complete range of reaction mixtures to identify multi-step reactions with useful properties; this yielded 23 multi-step reactions of potential interest.
Ultrafast ring-closing reaction dynamics of a photochromic furan-based difurylethene
Khodko, A.; Khomenko, V.; Shynkarenko, Y.; Mamuta, O.; Kapitanchuk, O.; Sysoiev, D.; Kachalova, N.; Huhn, T.; Snegir, S.
2017-02-01
The ultrafast photoinduced ring-closing dynamics of a furan-based difurylethene (YnPhT) has been investigated by femtosecond transient absorption spectroscopy. We performed time-dependent density functional theory (TD-DFT) calculations to explain the experimental results in detail. The sub-picosecond time scale of the ring-closing reaction is comparable with thiophene-based analogues, but oxygen atoms at the photochromic core can avoid adverse interaction between switches and metal contacts in further applications. This observation proves that furan-based diarylethenes are potential optoelectronic elements with an ultrafast optical response.
Calculation of A x for the Proton-Deuteron Breakup Reaction at 135 MeV
Eslami-Kalantari, M.; Mehmandoost-Khajeh-Dad, A. A.; Shafaei, M. A.; Amir-Ahmadi, H. R.; Biegun, A.; Gašparic, I.; Joulaeizadeh, L.; Kalantar-Nayestanaki, N.; Kistryn, St.; Kozela, A.; Mardanpour, H.; Messchendorp, J. G.; Moeini, H.; Ramazani-Moghaddam-Arani, A.; Shende, S. V.; Stephan, E.; Sworst, R.
2013-08-01
Observables in proton-deuteron scattering are sensitive probes of the nucleon-nucleon interaction and three-nucleon force effects (3NF). Several facilities in the world, including Kernfysisch Versneller Instituut (KVI), allow a detailed study a few-nucleon interaction below the pion-production threshold exploiting polarized proton and deuteron beams. In this contribution we explored 3NF effects in the break-up scattering process by performing a measurement of differential cross section and the analyzing power, especially the x component of the analyzing power, using a 135 MeV polarized-proton beam impinging on a liquid-deuteron target. The proton-deuteron breakup reaction leads to a final state with three free particles and a rich phase space that allows us to study observables for continuous set of kinematical configurations of the outgoing nucleons. The results are interpreted with the help of state-of-the-art Faddeev calculations.
Fekete, Attila; Komáromi, István
2016-12-07
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to
Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
2015-05-07
The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum–classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute–solvent interactions.
Structural and dynamical control of the reaction rate in protein electron transfer
Balabin, Ilya A.
Electron transfer (ET) reactions in proteins are key steps in many vital bioenergetic processes, and the reaction rate is known to be highly sensitive to the protein structure in some cases. For most bioenergetic reactions, as described by the Fermi Golden rule, the rate is proportional to a product of the average square of the effective electronic donor to acceptor coupling and a Franck-Condon factor, which accounts for the nuclear control of the energy gap. The nuclear factor is reasonably well described in Marcus theory and its modifications, and this work is focused on the mechanisms that control the effective coupling. About ten years ago, the Pathways model described for the first time how protein environment may control the effective coupling. In this work, a novel theoretical approach is developed to explore the mechanisms of structural and dynamical control beyond the qualitative level of the Pathways model. In Chapter 1, the assumptions of the Pathways model, its limitations and effects of the structure and the electronic Hamiltonian are investigated for model chain-like bridges using the Dyson's equations. In Chapter II, the framework to explore the sensitivity of the effective coupling to quality of the electronic Hamiltonian, the interference among the dominant pathways and the bridge dynamics is presented. This analysis employs the Green's function technique and includes combined molecular dynamics and electronic structure calculations. Finally, in Chapter III, this framework is tested on the bacterial photosynthetic reaction center, and the mechanisms of the structural and dynamical control for different ET steps are discussed.
Calculations of three-nucleon reactions with N3LO chiral forces: achievements and challenges
Witala, Henryk; Skibinski, Roman; Topolnicki, Kacper
2013-01-01
We discuss the application of the chiral N3LO forces to three-nucleon reactions and point to the challenges which will have to be addressed. Present approaches to solve three-nucleon Faddeev equations are based on a partial-wave decomposition. A rapid increase of the number of terms contributing to the chiral three-nucleon force when increasing the order of the chiral expansion from N2LO to N3LO forced us to develop a fast and effective method of automatized partial wave decomposition. At low energies of the incoming nucleon below about 20MeV, where only a limited number of partial waves is required, this method allowed us to perform calculations of reactions in the three-nucleon continuum using N3LO two- and three-nucleon forces. It turns out that inclusion of consistent chiral interactions, with relativistic 1/m corrections and short-range 2pi-contact term omitted in the N3LO three-nucleon force, does not explain the long standing low energy Ay-puzzle. We discuss problems arising when chiral forces are appl...
Balasekaran, Samundeeswari Mariappan; Spandl, Johann; Hagenbach, Adelheid; Köhler, Klaus; Drees, Markus; Abram, Ulrich
2014-05-19
A mixture of [Tc(NO)F5](2-) and [Tc(NO)(NH3)4F](+) is formed during the reaction of pertechnetate with acetohydroxamic acid (Haha) in aqueous HF. The blue pentafluoridonitrosyltechnetate(II) has been isolated in crystalline form as potassium and rubidium salts, while the orange-red ammine complex crystallizes as bifluoride or PF6(-) salts. Reactions of [Tc(NO)F5](2-) salts with HCl give the corresponding [Tc(NO)Cl4/5](-/2-) complexes, while reflux in neat pyridine (py) results in the formation of the technetium(I) cation [Tc(NO)(py)4F](+), which can be crystallized as hexafluoridophosphate. The same compound can be synthesized directly from pertechnetate, Haha, HF, and py or by a ligand-exchange procedure starting from [Tc(NO)(NH3)4F](HF2). The technetium(I) cation [Tc(NO)(NH3)4F](+) can be oxidized electrochemically or by the reaction with Ce(SO4)2 to give the corresponding Tc(II) compound [Tc(NO)(NH3)4F](2+). The fluorido ligand in [Tc(NO)(NH3)4F](+) can be replaced by CF3COO(-), leaving the "[Tc(NO)(NH3)4](2+) core" untouched. The experimental results are confirmed by density functional theory calculations on [Tc(NO)F5](2-), [Tc(NO)(py)4F](+), [Tc(NO)(NH3)4F](+), and [Tc(NO)(NH3)4F](2+).
Dynamic simulation of flash drums using rigorous physical property calculations
F. M. Gonçalves
2007-06-01
Full Text Available The dynamics of flash drums is simulated using a formulation adequate for phase modeling with equations of state (EOS. The energy and mass balances are written as differential equations for the internal energy and the number of moles of each species. The algebraic equations of the model, solved at each time step, are those of a flash with specified internal energy, volume and mole numbers (UVN flash. A new aspect of our dynamic simulations is the use of direct iterations in phase volumes (instead of pressure for solving the algebraic equations. It was also found that an iterative procedure previously suggested in the literature for UVN flashes becomes unreliable close to phase boundaries and a new alternative is proposed. Another unusual aspect of this work is that the model expressions, including the physical properties and their analytical derivatives, were quickly implemented using computer algebra.
Calculated pKa Variations Expose Dynamic Allosteric Communication Networks.
Lang, Eric J M; Heyes, Logan C; Jameson, Geoffrey B; Parker, Emily J
2016-02-17
Allosteric regulation of protein function, the process by which binding of an effector molecule provokes a functional response from a distal site, is critical for metabolic pathways. Yet, the way the allosteric signal is communicated remains elusive, especially in dynamic, entropically driven regulation mechanisms for which no major conformational changes are observed. To identify these dynamic allosteric communication networks, we have developed an approach that monitors the pKa variations of ionizable residues over the course of molecular dynamics simulations performed in the presence and absence of an allosteric regulator. As the pKa of ionizable residues depends on their environment, it represents a simple metric to monitor changes in several complex factors induced by binding an allosteric effector. These factors include Coulombic interactions, hydrogen bonding, and solvation, as well as backbone motions and side chain fluctuations. The predictions that can be made with this method concerning the roles of ionizable residues for allosteric communication can then be easily tested experimentally by changing the working pH of the protein or performing single point mutations. To demonstrate the method's validity, we have applied this approach to the subtle dynamic regulation mechanism observed for Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, the first enzyme of aromatic biosynthesis. We were able to identify key communication pathways linking the allosteric binding site to the active site of the enzyme and to validate these findings experimentally by reestablishing the catalytic activity of allosterically inhibited enzyme via modulation of the working pH, without compromising the binding affinity of the allosteric regulator.
Development of a dynamic calculation tool forsimulation of ditching
Pilorget, Marc
2011-01-01
The present document is the final master thesis report written by Marc PILORGET,student at SUPAERO (home institution) and KTH (Royal Institute of Technology,Exchange University). This six months internship was done at DASSAULT AVIATION(Airframe engineering department) based in Saint-Cloud, France. It spanned from the 5thof July to the 23rd of December. The thesis work aims at developing an SPH (SmoothParticle Hydrodynamics) calculation method for ditching and implementing it in the finiteelem...
Trapp, O
2006-01-01
A unified equation to evaluate elution profiles of reversible as well as irreversible (pseudo-) first-order reactions in dynamic chromatography and on-column reaction chromatography has been derived. Rate constants k1 and k(-1) and Gibbs activation energies are directly obtained from the chromatographic parameters (retention times tR(A) and tR(B) of the interconverting or reacting species A and B, the peak widths at half-height wA and wB, and the relative plateau height h(p)), the initial amounts A0 and B0 of the reacting species, and the equilibrium constant K(A/B). The calculation of rate constants requires only a few iterative steps without the need of performing a computationally extensive simulation of elution profiles. The unified equation was validated by comparison with a data set of 125,000 simulated elution profiles to confirm the quality of this equation by statistical means and to predict the minimal experimental requirements. Surprisingly, the recovery rate from a defined data set is on average 35% higher using the unified equation compared to the evaluation by iterative computer simulation.
Mechanical reaction-diffusion model for bacterial population dynamics
Ngamsaad, Waipot
2015-01-01
The effect of mechanical interaction between cells on the spreading of bacterial population was investigated in one-dimensional space. A nonlinear reaction-diffusion equation has been formulated as a model for this dynamics. In this model, the bacterial cells are treated as the rod-like particles that interact, when contacting each other, through the hard-core repulsion. The repulsion introduces the exclusion process that causes the fast diffusion in bacterial population at high density. The propagation of the bacterial density as the traveling wave front in long time behavior has been analyzed. The analytical result reveals that the front speed is enhanced by the exclusion process---and its value depends on the packing fraction of cell. The numerical solutions of the model have been solved to confirm this prediction.
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
Franz, Benjamin
2013-06-19
Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.
New reaction rates for improved primordial D/H calculation and the cosmic evolution of deuterium
Coc, Alain; Uzan, Jean-Philippe; Vangioni, Elisabeth; Descouvemont, Pierre; Illiadis, Christian; Longland, Richard
2015-01-01
Primordial or big bang nucleosynthesis (BBN) is one of the three historical strong evidences for the big bang model. Standard BBN is now a parameter free theory, since the baryonic density of the Universe has been deduced with an unprecedented precision from observations of the anisotropies of the cosmic microwave background (CMB) radiation. There is a good agreement between the primordial abundances of 4He, D, 3He and 7Li deduced from observations and from primordial nucleosynthesis calculations. However, the 7Li calculated abundance is significantly higher than the one deduced from spectroscopic observations and remains an open problem. In addition, recent deuterium observations have drastically reduced the uncertainty on D/H, to reach a value of 1.6%. It needs to be matched by BBN predictions whose precision is now limited by thermonuclear reaction rate uncertainties. This is especially important as many attempts to reconcile Li observations with models lead to an increased D prediction. Here, we re-evalua...
Jensen, Lasse; van Duijnen, Piet Th.; Snijders, Jaap G.
2003-12-01
We present a discrete solvent reaction field (DRF) model for the calculation of frequency-dependent hyperpolarizabilities of molecules in solution. In this model the solute is described using density functional theory (DFT) and the discrete solvent molecules are described with a classical polarizable model. The first hyperpolarizability is obtained in an efficient way using time-dependent DFT and the (2n+1) rule. The method was tested for liquid water using a model in which a water molecule is embedded in a cluster of 127 classical water molecules. The frequency-dependent first and second hyperpolarizabilities related to the electric field induced second harmonic generation (EFISH) experiment, were calculated both in the gas phase and in the liquid phase. For water in the gas phase, results are obtained in good agreement with correlated wave function methods and experiments by using the so-called shape-corrected exchange correlation (xc)-potentials. In the liquid phase the effect of using asymptotically correct functionals is discussed. The model reproduced the experimentally observed sign change in the first hyperpolarizaibility when going from the gas phase to the liquid phase. Furthermore, it is shown that the first hyperpolarizability is more sensitive to damping of the solvent-solute interactions at short range than the second hyperpolarizability.
Calculation of radiation reaction effect on orbital parameters in Kerr spacetime
Sago, Norichika
2015-01-01
We calculate the secular changes of the orbital parameters of a point particle orbiting a Kerr black hole, due to the gravitational radiation reaction. For this purpose, we use the post-Newtonian (PN) approximation in the first order black hole perturbation theory, with the expansion with respect to the orbital eccentricity. In this work, the calculation is done up to the fourth post-Newtonian (4PN) order and to the sixth order of the eccentricity, including the effect of the absorption of gravitational waves by the black hole. We confirm that, in the Kerr case, the effect of the absorption appears at the 2.5PN order beyond the leading order in the secular change of the particle's energy and may induce a superradiance, as known previously for circular orbits. In addition, we find that the superradiance may be suppressed when the orbital plane inclines with respect to the equatorial plane of the central black hole. We also investigate the accuracy of the 4PN formulae by comparing to numerical results. If we re...
Calculations of the dynamic dipole polarizabilities for the Li+ ion
Zhang, Yong-Hui; Tang, Li-Yan; Zhang, Xian-Zhou; Shi, Ting-Yun
2016-10-01
The B-spline configuration-interaction method is applied to the investigations of dynamic dipole polarizabilities for the four lowest triplet states (2 3S, 33S, 23P, and 33P) of the Li+ ion. The accurate energies for the triplet states of n 3S, n 3P, and n 3D, the dipole oscillator strengths for 23S(33S) → n 3P, 23P(33P) → n 3S, and 23P(33P) → n 3D transitions, with the main quantum number n up to 10 are tabulated for references. The dynamic dipole polarizabilities for the four triplet states under a wide range of photon energy are also listed, which provide input data for analyzing the Stark shift of the Li+ ion. Furthermore, the tune-out wavelengths in the range from 100 nm to 1.2 μm for the four triplet states, and the magic wavelengths in the range from 100 nm to 600 nm for the 23S → 33S, 23S → 23P, and 23S → 33P transitions are determined accurately for the experimental design of the Li+ ion. Project supported by the National Basic Research Program of China (Grant No. 2012CB821305) and the National Natural Science Foundation of China (Grant Nos. 11474319, 11274348, and 91536102).
Molecular-dynamics calculation of the vacancy heat of transport
Schelling, Patrick K.; Ernotte, Jacques; Shokeen, Lalit; Tucker, William C. [Advanced Material Processing and Analysis Center and Department of Physics, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816 (United States); Woods Halley, J. [Department of Physics, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota 555455 (United States)
2014-07-14
We apply the recently developed constrained-dynamics method to elucidate the thermodiffusion of vacancies in a single-component material. The derivation and assumptions used in the method are clearly explained. Next, the method is applied to compute the reduced heat of transport Q{sub v}{sup *}−h{sub fv} for vacancies in a single-component material. Results from simulations using three different Morse potentials, with one providing an approximate description of Au, and an embedded-atom model potential for Ni are presented. It is found that the reduced heat of transport Q{sub v}{sup *}−h{sub fv} may take either positive or negative values depending on the potential parameters and exhibits some dependence on temperature. It is also found that Q{sub v}{sup *}−h{sub fv} may be correlated with the activation entropy. The results are discussed in comparison with experimental and previous simulation results.
The calculation of robot dynamics using articulated-body inertias
Featherstone, R.
1983-05-01
This paper describes a new method for calculating the acceleration of a robot in response to given actuator forces. The method is applicable to open-loop kinematic chains containing revolute and prismatic joints. The algorithm is based on recursive formulas involving quantities called articulated-body inertias, which represent the inertia properties of collections of rigid bodies connected together by joints allowing constrained relative motion between the bodies. A new, matrix-based notation is introduced to represent articulated-body inertias and other spatial quantities. This notation is used to develop the algorithm, and results in a compact representation of the equations. The new algorithm has a computational requirement that varies linearly with the number of joints, and its efficiency is compared with other published algorithms.
Body drop into a fluid tank and dynamic loads calculation
Komarov Aleksandr Andreevich
2014-05-01
Full Text Available The theory of a body striking a fluid began intensively developing due to the tasks of hydroplanes landing. For the recent years the study of a stroke and submersion of bodies into fluid became even more current. We face them in the process of strength calculation of ship hulls and other structures in modern technology. These tasks solution represents great mathematical difficulty even in case of the mentioned simplifications. These difficulties emerge due to the unsteady character of fluid motion in case of body submersion, and also jet and spray phenomena, which lead to discontinuous motions. On the basis of G.V. Logvinovich’s concept the problem of loads determination with consideration for air gap is solved for both a body and reservoir enclosing structures when a body falls into a fluid. Numerical method is based on the decay of an arbitrary discontinuity.
A Brownian Dynamics Approach to ESR Line Shape Calculations
Wright, Matthew P.
The work presented in this thesis uses a Monte Carlo technique to simulate spectra for 14N spin-labels and 15N spin labels. The algorithm presented here also has the capability to produce simulated spectra for any admixture of 14N and 15N. The algorithm makes use of `iterative loops' to model Brownian rotational diffusion and for the repeated evaluation of the spectral correlation function (relaxation function). The method described in this work starts with a derivation of an angular dependent "Spin Hamiltonian" that when diagonalized yields orientation dependent eigenvalues. The resulting eigenvalue equations are later used to calculate the energy trajectories of a nitroxide spin-label undergoing rotational diffusion. The energy trajectories are then used to evaluate the relaxation function. The absorption spectrum is obtained by applying a Fourier transform to the relaxation function. However, the application of the Fourier transform to the relaxation function produces "leakage" effects that manifest as spurious peaks in the first derivative spectrum. To counter "leakage" effects a data windowing function was applied to the relaxation function prior to the Fourier transform. In order to test the accuracy of this algorithm, simulated spectra for 14N, and 15N spin labels diffusing in a glycerol-water mixture as well as a 14N-15N admixture diffusing in the same solvent were produced and compared to experimental spectra. An attempt to quantify the level of agreement was made by calculating the mean square residual of the simulated and experimental spectra. The main spectral features were reproduced with reasonable fidelity by the simulated spectra.
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
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
LI Jian-jie; LAN Ming-jian; LI Fang-yu
2008-01-01
To describe properties of the high frequency gravitational wave (HFGW) propagating through the vacuum gravitational field in Robertson-Walker background space-time, we calculated its energy momentum pseudo-tensor (EMPT) in the limit of short wavelengths by taking the Brill-Hartle average on the second order perturbation of the Einstein tensor over several wavelengths. By rewriting the EMPT as a form of perfect fluid, the dynamical back-reaction of HFGW on the background space-time was discussed. The result shows that the energy density of HFGW, which is in the gauge we chose, is positive definite. The HFGW serves as a source for curving the background space-time and affects the dynamical evolution and time evolution of the scale factor of the Robertson-Walker metric.
Spectra for the A = 6 reactions calculated from a three-body resonance model
Paris Mark W.
2016-01-01
Full Text Available We develop a resonance model of the transition matrix for three-body breakup reactions of the A = 6 system and present calculations for the nucleon observed spectra, which are important for inertial confinement fusion and Big Bang nucleosynthesis (BBN. The model is motivated by the Faddeev approach where the form of the T matrix is written as a sum of the distinct Jacobi coordinate systems corresponding to particle configurations (α, n-n and (n; n-α to describe the final state. The structure in the spectra comes from the resonances of the two-body subsystems of the three-body final state, namely the singlet (T = 1 nucleon-nucleon (NN anti-bound resonance, and the Nα resonances designated the ground state (Jπ = 3−2${{{3^ - }} \\over 2}$ and first excited state (Jπ = 1−2${{{1^ - }} \\over 2}$ of the A = 5 systems 5He and 5Li. These resonances are described in terms of single-level, single-channel R-matrix parameters that are taken from analyses of NN and Nα scattering data. While the resonance parameters are approximately charge symmetric, external charge-dependent effects are included in the penetrabilities, shifts, and hard-sphere phases, and in the level energies to account for internal Coulomb differences. The shapes of the resonance contributions to the spectrum are fixed by other, two-body data and the only adjustable parameters in the model are the combinatorial amplitudes for the compound system. These are adjusted to reproduce the observed nucleon spectra from measurements at the Omega and NIF facilities. We perform a simultaneous, least-squares fit of the tt neutron spectra and the 3He3He proton spectra. Using these amplitudes we make a prediction of the α spectra for both reactions at low energies. Significant differences in the tt and 3He3He spectra are due to Coulomb effects.
Spectra for the A = 6 reactions calculated from a three-body resonance model
Paris, Mark W.; Hale, Gerald M.
2016-06-01
We develop a resonance model of the transition matrix for three-body breakup reactions of the A = 6 system and present calculations for the nucleon observed spectra, which are important for inertial confinement fusion and Big Bang nucleosynthesis (BBN). The model is motivated by the Faddeev approach where the form of the T matrix is written as a sum of the distinct Jacobi coordinate systems corresponding to particle configurations (α, n-n) and (n; n-α) to describe the final state. The structure in the spectra comes from the resonances of the two-body subsystems of the three-body final state, namely the singlet (T = 1) nucleon-nucleon (NN) anti-bound resonance, and the Nα resonances designated the ground state (Jπ = {{{3^ - }} over 2}) and first excited state (Jπ = {{{1^ - }} over 2}) of the A = 5 systems 5He and 5Li. These resonances are described in terms of single-level, single-channel R-matrix parameters that are taken from analyses of NN and Nα scattering data. While the resonance parameters are approximately charge symmetric, external charge-dependent effects are included in the penetrabilities, shifts, and hard-sphere phases, and in the level energies to account for internal Coulomb differences. The shapes of the resonance contributions to the spectrum are fixed by other, two-body data and the only adjustable parameters in the model are the combinatorial amplitudes for the compound system. These are adjusted to reproduce the observed nucleon spectra from measurements at the Omega and NIF facilities. We perform a simultaneous, least-squares fit of the tt neutron spectra and the 3He3He proton spectra. Using these amplitudes we make a prediction of the α spectra for both reactions at low energies. Significant differences in the tt and 3He3He spectra are due to Coulomb effects.
Excitation of the dynamical dipole in the charge asymmetric reaction 16O + 116Sn
Corsi, A.; Wieland, O.; Kravchuk, V. L.; Bracco, A.; Camera, F.; Benzoni, G.; Blasi, N.; Brambilla, S.; Crespi, F. C. L.; Giussani, A.; Leoni, S.; Million, B.; Montanari, D.; Moroni, A.; Gramegna, F.; Lanchais, A.; Mastinu, P.; Brekiesz, M.; Kmiecik, M.; Maj, A.; Bruno, M.; D'Agostino, M.; Geraci, E.; Vannini, G.; Barlini, S.; Casini, G.; Chiari, M.; Nannini, A.; Ordine, A.; Di Toro, M.; Rizzo, C.; Colonna, M.; Baran, V.
2009-08-01
The γ-ray emission from the dynamical dipole formed in heavy-ion collisions during the process leading to fusion was measured for the N/Z asymmetric reaction 16O + 116Sn at beam energies of 8.1 and 15.6 MeV/nucleon. High-energy γ-rays and charged particles were measured in coincidence with the heavy recoiling residual nuclei. The data are compared with those from the N/Z symmetric reaction 64Ni + 68Zn at bombarding energies of 4.7 and 7.8 MeV/nucleon, leading to the same CN with the same excitation energies as calculated from kinematics. The measured yield of the high-energy γ-rays from the 16O-induced reaction is found to exceed that of the thermalized CN and the excess yield increases with bombarding energy. The data are in rather good agreement with the predictions for the dynamical dipole emission based on the Boltzmann-Nordheim-Vlasov model. In addition, a comparison with existing data in the same mass region is performed to extract information on the dipole moment dependence.
Excitation of the dynamical dipole in the charge asymmetric reaction {sup 16}O + {sup 116}Sn
Corsi, A. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Wieland, O. [INFN Sezione di Milano, Milano (Italy); Kravchuk, V.L. [Laboratori Nazionali INFN di Legnaro, Legnaro (Italy); Bracco, A. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Camera, F. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy)], E-mail: franco.camera@mi.infn.it; Benzoni, G.; Blasi, N.; Brambilla, S. [INFN Sezione di Milano, Milano (Italy); Crespi, F.C.L.; Giussani, A.; Leoni, S. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Million, B. [INFN Sezione di Milano, Milano (Italy); Montanari, D.; Moroni, A. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Gramegna, F.; Lanchais, A.; Mastinu, P. [Laboratori Nazionali INFN di Legnaro, Legnaro (Italy); Brekiesz, M.; Kmiecik, M.; Maj, A. [Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, Krakow (Poland)] (and others)
2009-08-24
The {gamma}-ray emission from the dynamical dipole formed in heavy-ion collisions during the process leading to fusion was measured for the N/Z asymmetric reaction {sup 16}O + {sup 116}Sn at beam energies of 8.1 and 15.6 MeV/nucleon. High-energy {gamma}-rays and charged particles were measured in coincidence with the heavy recoiling residual nuclei. The data are compared with those from the N/Z symmetric reaction {sup 64}Ni + {sup 68}Zn at bombarding energies of 4.7 and 7.8 MeV/nucleon, leading to the same CN with the same excitation energies as calculated from kinematics. The measured yield of the high-energy {gamma}-rays from the {sup 16}O-induced reaction is found to exceed that of the thermalized CN and the excess yield increases with bombarding energy. The data are in rather good agreement with the predictions for the dynamical dipole emission based on the Boltzmann-Nordheim-Vlasov model. In addition, a comparison with existing data in the same mass region is performed to extract information on the dipole moment dependence.
Comparative dynamics of the two channels of the reaction of D + MuH.
Aoiz, F J; Aldegunde, J; Herrero, V J; Sáez-Rábanos, V
2014-06-07
The dynamics of the asymmetric D + MuH (Mu = Muonium) reaction leading to Mu exchange, DMu + H, and H abstraction, DH + Mu, channels has been investigated using time-independent quantum mechanical (QM) calculations. Reaction probabilities, cross sections, cumulative reaction probabilities, and rate coefficients were determined for the two exit channels of the reaction. Quasiclassical trajectory (QCT) calculations were also performed in order to check the reliability of the method for this reaction and to discern the genuine quantum effects. Overall, the Mu exchange channel exhibits more structured reaction probabilities and cross sections with much larger rate coefficients than the H abstraction counterpart. Over the 100-1000 K temperature interval considered in this study, the QM rate coefficients for the Mu exchange vary between ≈5 × 10(-15) and 2 × 10(-11) cm(3) s(-1) and those for the generation of DH + Mu between 2 × 10(-18) and 3.5 × 10(-12) cm(3) s(-1). In common with the rest of the isotopologues of the H + H2 system, the height of the respective barriers in the collinear (symmetric stretch) vibrationally adiabatic potential energy curves matches the classical total energy threshold very accurately. Indeed, the lower and narrower vibrationally adiabatic collinear barrier as compared with that for the DH + Mu formation determines the preponderance of the DMu + H channel. Comparison of QM and QCT results and their analysis show that tunneling accounts for the reactivity at energies below the height of these barriers and that its effect on the rate coefficients becomes appreciable below 300 K. As expected, with growing temperature the contribution of tunneling to the global reactivity decreases markedly, but the rate coefficients are still much higher for the Mu exchange channel due to the effect of MuH rotational excitation that boosts the formation of DMu while diminishing the H abstraction channel that leads to DH formation. The analysis of the
N-dimensional switch function for energy conservation in multiprocess reaction dynamics.
Mogo, César; Brandão, João
2016-06-15
The MReaDy program was designed for studying Multiprocess Reactive Dynamic systems, that is, complex chemical systems involving different and concurrent reactions. It builds a global potential energy surface integrating a variety of potential energy surfaces, each one of them representing an elementary reaction expected to play a role in the chemical process. For each elementary reaction, energy continuity problems may happen in the transition between potential energy surfaces due to differences in the functional form for each of the fragments, especially if built by different authors. A N-dimensional switch function is introduced in MReaDy in order to overcome such a problem. As an example, results of a collision trajectory calculation for H2 + OH → H3 O are presented, showing smooth transition in the potential energy, leading to conservation in the total energy. Calculations for a hydrogen combustion system from 1000 K up to 4000 K shows a variation of 0.012% when compared to the total energy of the system. © 2016 Wiley Periodicals, Inc.
Calculation of the local rupture speed of dynamically propagating earthquakes
Andrea Bizzarri
2014-01-01
Full Text Available The velocity at which a propagating earthquake advances on the fault surface is of pivotal importance in the contest of the source dynamics and in the modeling of the ground motions generation. In this paper the problem of the determination of the rupture speed (v_r is considered. The comparison of different numerical schemes to compute vr from the rupture time (t_r shows that, in general, central finite differences schemes are more accurate than forward or backward schemes, regardless the order of accuracy. Overall, the most efficient and accurate algorithm is the five–points stencil method at the second–order of accuracy. It is also shown how the determination of t_r can affect v_r ; numerical results indicate that if the fault slip velocity threshold (v_l used to define t_r is too high (v_l ≥ 0.1 m/s the details of the rupture are missed, for instance the rupture tip bifurcation occurring for 2–D supershear rupture. On the other hand, for v_l ≤ 0.01 m/s the results appear to be stable and independent on the choice of v_l . Finally, it is demonstrated that in the special case of the linear slip–weakening friction law the definitions of t_r from the threshold criterion on the fault slip velocity and from the achievement of the maximum yield stress are practically equivalent.
Jensen, Lasse; van Duijnen, Piet Th.; Snijders, Jaap G.
2003-08-01
A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discrete solvent molecules. The classical solvent molecules are represented using distributed atomic charges and polarizabilities. All the atomic parameters have been chosen so as to describe molecular gas phase properties of the solvent molecule, i.e., the atomic charges reproduce the molecular dipole moment and the atomic polarizabilities reproduce the molecular polarizability tensor using a modified dipole interaction model. The QM/MM interactions are introduced into the Kohn-Sham equations and all interactions are solved self-consistently, thereby allowing for the solute to be polarized by the solvent. Furthermore, the inclusion of polarizabilities in the MM part allows for the solvent molecules to be polarized by the solute and by interactions with other solvent molecules. Initial applications of the model to calculate the vertical electronic excitation energies and frequency-dependent molecular polarizability of a water molecule in a cluster of 127 classical water molecules are presented. The effect of using different exchange correlation (xc)-potentials is investigated and the results are compared with results from wave function methods combined with a similar solvent model both at the correlated and uncorrelated level of theory. It is shown that accurate results in agreement with correlated wave function results can be obtained using xc-potentials with the correct asymptotic behavior.
Esposito, Fabrizio; Coppola, Carla Maria; De Fazio, Dario
2015-12-24
In this work we present a dynamical study of the H + HeH+ → H2+ + He reaction in a collision energy range from 0.1 meV to 10 eV, suitable to be used in applicative models. The paper extends and complements a recent work [ Phys. Chem. Chem. Phys. 2014, 16, 11662] devoted to the characterization of the reactivity from the ultracold regime up to the three-body dissociation breakup. In particular, the accuracy of the quasi-classical trajectory method below the three-body dissociation threshold has been assessed by a detailed comparison with previous calculations performed with different reaction dynamics methods, whereas the reliability of the results in the high energy range has been checked by a direct comparison with the available experimental data. Integral cross sections for several HeH+ roto-vibrational states have been analyzed and used to understand the extent of quantum effects in the reaction dynamics. By using the quasi-classical trajectory method and quantum mechanical close coupling data, respectively, in the high and low collision energy ranges, we obtain highly accurate thermal rate costants until 15 000 K including all (178) the roto-vibrational bound and quasi-bound states of HeH+. The role of the collision-induced dissociation is also discussed and explicitly calculated for the ground roto-vibrational state of HeH+.
Dreij, Kristian; Chaudhry, Qasim Ali; Jernström, Bengt; Morgenstern, Ralf; Hanke, Michael
2011-01-01
A general description of effects of toxic compounds in mammalian cells is facing several problems. Firstly, most toxic compounds are hydrophobic and partition phenomena strongly influence their behaviour. Secondly, cells display considerable heterogeneity regarding the presence, activity and distribution of enzymes participating in the metabolism of foreign compounds i.e. bioactivation/biotransformation. Thirdly, cellular architecture varies greatly. Taken together, complexity at several levels has to be addressed to arrive at efficient in silico modelling based on physicochemical properties, metabolic preferences and cell characteristics. In order to understand the cellular behaviour of toxic foreign compounds we have developed a mathematical model that addresses these issues. In order to make the system numerically treatable, methods motivated by homogenization techniques have been applied. These tools reduce the complexity of mathematical models of cell dynamics considerably thus allowing to solve efficiently the partial differential equations in the model numerically on a personal computer. Compared to a compartment model with well-stirred compartments, our model affords a more realistic representation. Numerical results concerning metabolism and chemical solvolysis of a polycyclic aromatic hydrocarbon carcinogen show good agreement with results from measurements in V79 cell culture. The model can easily be extended and refined to include more reactants, and/or more complex reaction chains, enzyme distribution etc, and is therefore suitable for modelling cellular metabolism involving membrane partitioning also at higher levels of complexity.
Kristian Dreij
Full Text Available A general description of effects of toxic compounds in mammalian cells is facing several problems. Firstly, most toxic compounds are hydrophobic and partition phenomena strongly influence their behaviour. Secondly, cells display considerable heterogeneity regarding the presence, activity and distribution of enzymes participating in the metabolism of foreign compounds i.e. bioactivation/biotransformation. Thirdly, cellular architecture varies greatly. Taken together, complexity at several levels has to be addressed to arrive at efficient in silico modelling based on physicochemical properties, metabolic preferences and cell characteristics. In order to understand the cellular behaviour of toxic foreign compounds we have developed a mathematical model that addresses these issues. In order to make the system numerically treatable, methods motivated by homogenization techniques have been applied. These tools reduce the complexity of mathematical models of cell dynamics considerably thus allowing to solve efficiently the partial differential equations in the model numerically on a personal computer. Compared to a compartment model with well-stirred compartments, our model affords a more realistic representation. Numerical results concerning metabolism and chemical solvolysis of a polycyclic aromatic hydrocarbon carcinogen show good agreement with results from measurements in V79 cell culture. The model can easily be extended and refined to include more reactants, and/or more complex reaction chains, enzyme distribution etc, and is therefore suitable for modelling cellular metabolism involving membrane partitioning also at higher levels of complexity.
Yalcin, C; Rauscher, T; Kiss, G G; Özkan, N; Güray, R T; Halász, Z; Szücs, T; Fülöp, Zs; Korkulu, Z; Somorjai, E
2015-01-01
Astrophysical reaction rates, which are mostly derived from theoretical cross sections, are necessary input to nuclear reaction network simulations for studying the origin of $p$ nuclei. Past experiments have found a considerable difference between theoretical and experimental cross sections in some cases, especially for ($\\alpha$,$\\gamma$) reactions at low energy. Therefore, it is important to experimentally test theoretical cross section predictions at low, astrophysically relevant energies. The aim is to measure reaction cross sections of $^{107}$Ag($\\alpha$,$\\gamma$)$^{111}$In and $^{107}$Ag($\\alpha$,n)$^{110}$In at low energies in order to extend the experimental database for astrophysical reactions involving $\\alpha$ particles towards lower mass numbers. Reaction rate predictions are very sensitive to the optical model parameters and this introduces a large uncertainty into theoretical rates involving $\\alpha$ particles at low energy. We have also used Hauser-Feshbach statistical model calculations to s...
Three-Body Model Calculation of Spin Distribution in Two-Nucleon Transfer Reaction
Ogata, Kazuyuki; Chiba, Satoshi
2011-01-01
The differential cross sections of two-nucleon transfer reactions 238U(18O,16O)240U around 10 MeV per nucleon are calculated by one-step Born-approximation with a 16O+2n+238U three-body model. The three-body wave function in the initial channel is obtained with the continuum-discretized coupled-channels method, and that in the final channel is evaluated with adiabatic approximation. The resulting cross sections have a peak around the grazing angle, and the spin distribution, i.e., the cross section at the peak as a function of the transferred spin, is investigated. The shape of the spin distribution is found not sensitive to the incident energies, optical potentials, and treatment of the breakup channels both in the initial and final states, while it depends on the excitation energy of the residual nucleus 240U. The peak of the spin distribution moves to the large-spin direction as the excitation energy increases. To fulfill the condition that the peak position should not exceeds 10 hbar, which is necessary f...
Battaglia, Francine [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Agblevor, Foster [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Klein, Michael [Univ. of Delaware, Newark, DE (United States); Sheikhi, Reza [Northeastern Univ., Boston, MA (United States)
2015-12-31
A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important results was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.
Battaglia, Francine [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Agblevor, Foster [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Klein, Michael [Univ. of Delaware, Newark, DE (United States); Sheikhi, Reza [Northeastern Univ., Boston, MA (United States)
2015-09-30
A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important results was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.
Vasil'ev, Sergej; Bruce, Doug
2006-05-01
Molecular dynamics simulations have been performed to study photosystem II structure and function. Structural information obtained from simulations was combined with ab initio computations of chromophore excited states. In contrast to calculations based on the x-ray structure, the molecular-dynamics-based calculations accurately predicted the experimental absorbance spectrum. In addition, our calculations correctly assigned the energy levels of reaction-center (RC) chromophores, as well as the lowest-energy antenna chlorophyll. The primary and secondary quinone electron acceptors, Q(A) and Q(B), exhibited independent changes in position over the duration of the simulation. Q(B) fluctuated between two binding sites similar to the proximal and distal sites previously observed in light- and dark-adapted RC from purple bacteria. Kinetic models were used to characterize the relative influence of chromophore geometry, site energies, and electron transport rates on RC efficiency. The fluctuating energy levels of antenna chromophores had a larger impact on quantum yield than did their relative positions. Variations in electron transport rates had the most significant effect and were sufficient to explain the experimentally observed multi-component decay of excitation in photosystem II. The implications of our results are discussed in the context of competing evolutionary selection pressures for RC structure and function.
Farberow, Carrie A.; Dumesic, James A.; Mavrikakis, Manos
2014-10-03
Reaction pathways are explored for low temperature (e.g., 400 K) reduction of nitric oxide by hydrogen on Pt(111). First-principles electronic structure calculations based on periodic, self-consistent density functional theory(DFT-GGA, PW91) are employed to obtain thermodynamic and kinetic parameters for proposed reaction schemes on Pt(111). The surface of Pt(111) during NO reduction by H₂ at low temperatures is predicted to operate at a high NO coverage, and this environment is explicitly taken into account in the DFT calculations. Maximum rate analyses are performed to assess the most likely reaction mechanisms leading to formation of N₂O, the major product observed experimentally at low temperatures. The results of these analyses suggest that the reaction most likely proceeds via the addition of at least two H atoms to adsorbed NO, followed by cleavage of the N-O bond.
Yalçin, C.
2017-02-01
The theoretical cross section calculations for the astrophysical p process are very crucial due to the most of the related reactions are technically very difficult to measure at the laboratory. On the other hand, the theoretical cross sections are not in agreement with the experimental results, especially for the (α,γ) reactions. One of the main reason of the difference between theoretical and experimental cross section is description of the α+nucleus optical model potential. In order to understand current situation and improvement of the theoretical calculations, the 112Sn(α,γ)116Te reaction were investigated for different global optical model potentials at the astrophysically interested energies. Astrophysical S factors were also calculated and compared with experimental data available at EXFOR database.
Can post-error dynamics explain sequential reaction time patterns?
Stephanie eGoldfarb
2012-07-01
Full Text Available We investigate human error dynamics in sequential two-alternative choice tasks. When subjects repeatedly discriminate between two stimuli, their error rates and mean reaction times (RTs systematically depend on prior sequences of stimuli. We analyze these sequential effects on RTs, separating error and correct responses, and identify a sequential RT tradeoff: a sequence of stimuli which yields a relatively fast RT on error trials will produce a relatively slow RT on correct trials and vice versa. We reanalyze previous data and acquire and analyze new data in a choice task with stimulus sequences generated by a first-order Markov process having unequal probabilities of repetitions and alternations. We then show that relationships among these stimulus sequences and the corresponding RTs for correct trials, error trials, and averaged over all trials are significantly influenced by the probability of alternations; these relationships have not been captured by previous models. Finally, we show that simple, sequential updates to the initial condition and thresholds of a pure drift diffusion model can account for the trends in RT for correct and error trials. Our results suggest that error-based parameter adjustments are critical to modeling sequential effects.
Isospin dynamics on neck fragmentation in isotopic nuclear reactions
Feng, Zhao-Qing
2016-01-01
The neck dynamics in Fermi-energy heavy-ion collisions, to probe the nuclear symmetry energy in the domain of sub-saturation densities, is investigated within an isospin dependent transport model. The single and double ratios of neutron/proton from free nucleons and light clusters (complex particles) in the isotopic reactions are analyzed systematically. Isospin effects of particles produced from the neck fragmentations are explored, which are constrained within the midrapidities ($|y/y_{proj}|<$0.3) and azimuthal angles (70$^{o}\\sim$110$^{o}$, 250$^{o}\\sim$290$^{o}$) in semiperipheral nuclear collisions. It is found that the ratios of the energetic isospin particles strongly depend on the stiffness of nuclear symmetry energy and the effects increase with softening the symmetry energy, which would be a nice probe for extracting the symmetry energy below the normal density in experimentally. A flat structure appears at the tail spectra from the double ratio distributions. The neutron to proton ratio of ligh...
Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew
experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....
Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew
experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....
Minomo, Kosho
2016-01-01
We analyze the $\\alpha$-$^{12}$C inelastic scattering to the $0^+_2$ state of $^{12}$C, the Hoyle state, in a fully microscopic framework. With no free adjustable parameter, the inelastic cross sections at forward angles are well reproduced by the microscopic reaction calculation using the transition density of $^{12}$C obtained by the resonating group method and the nucleon-nucleon $g$ matrix interaction developed by the Melbourne group. It is thus shown that the monopole transition strength obtained by the structural calculation is consistent with that extracted from the reaction observable, suggesting no missing monopole strength of the Hoyle state.
Gaohong Zhai
2014-01-01
Full Text Available A realistic semiclassical dynamics simulation study is reported for the photoinduced ring-opening reaction of spiropyran. The main simulation results show that one pathway involves hydrogen out-of-plane (HOOP torsion of phenyl ring nearby N atom in 254 fs on the excited state and the isomerization from cis- to trans-SP that is complete in about 10 ps on the ground state after the electron transition πσ*; the other dominate pathway corresponds to the ring-opening reaction of trans-SP to form the most stable merocyanine (MC product. Unlike the previous theoretical finding, one C−C bond cleavage on the real molecule rather than the C−N dissociation of the model one is more probable than the ring-opening reaction after the photoexcitation of SP. The simulation findings provide more important complementarity for interpreting experimental observations, confirming the previously theoretical studies of photochromic ring-opening process and even supplying other possible reaction mechanisms.
Jonathan S. Merritt
2008-01-01
Full Text Available The equine distal forelimb is a common location of injuries related to mechanical overload. In this study, a two-dimensional model of the musculoskeletal system of the region was developed and applied to kinematic and kinetic data from walking and trotting horses. The forces in major tendons and joint reaction forces were calculated. The components of the joint reaction forces caused by wrapping of tendons around sesamoid bones were found to be of similar magnitude to the reaction forces between the long bones at each joint. This finding highlighted the importance of taking into account muscle-tendon wrapping when evaluating joint loading in the equine distal forelimb.
Molecular Dynamics Simulations of Chemical Reactions for Use in Education
Qian Xie; Tinker, Robert
2006-01-01
One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…
Molecular Dynamics Simulations of Chemical Reactions for Use in Education
Qian Xie; Tinker, Robert
2006-01-01
One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…
Naumov, Sergej; von Sonntag, Clemens
2011-11-01
Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.
Multi-Loop Calculations of Anomalous Exponents in the Models of Critical Dynamics
Adzhemyan L. Ts.
2016-01-01
Full Text Available The Renormalization group method (RG is applied to the investigation of the E model of critical dynamics, which describes the transition from the normal to the superfluid phase in He4. The technique “Sector decomposition” with R’ operation is used for the calculation of the Feynman diagrams. The RG functions, critical exponents and critical dynamical exponent z, which determines the growth of the relaxation time near the critical point, have been calculated in the two-loop approximation in the framework of ε-expansion. The relevance of a fixed point for helium, where the dynamic scaling is weakly violated, is briefly discussed.
Dynamical mean field theory-based electronic structure calculations for correlated materials.
Biermann, Silke
2014-01-01
We give an introduction to dynamical mean field approaches to correlated materials. Starting from the concept of electronic correlation, we explain why a theoretical description of correlations in spectroscopic properties needs to go beyond the single-particle picture of band theory.We discuss the main ideas of dynamical mean field theory and its use within realistic electronic structure calculations, illustrated by examples of transition metals, transition metal oxides, and rare-earth compounds. Finally, we summarise recent progress on the calculation of effective Hubbard interactions and the description of dynamical screening effects in solids.
Maiti, Buddhadev; Sadeghi, Raymond; Austin, Anthony; Morales, Jorge A.
2007-11-01
Results of a complete investigation of the H + + HF reaction at ELab = 30 eV with the electron nuclear dynamics (END) and the coherent-states dynamics (CSD) theories are herein presented. Current END-CSD methodology employs frozen Gaussian wave packet in the semiclassical limit of ℏ → 0 for the nuclei, and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 400 CS trajectories from five independent HF target orientations provide a complete description of the reactive processes in this system, including: non-charge-transfer scattering (NCTS), charge-transfer scattering (CTS), hydrogen fluoride dissociation (H-F D), and hydrogen rearrangement (HR). Several aspects of the reactions dynamics, such as mechanistic details and rainbow angles effects, are discussed. Differential and integral cross sections are evaluated via a novel CS formulation of those properties in conjunction with semiclassical techniques. The calculated total differential cross section shows an excellent agreement with available experimental results.
Choi, Sungjun; Sang, Byoung-In; Hong, Jongsup; Yoon, Kyung Joong; Son, Ji-Won; Lee, Jong-Ho; Kim, Byung-Kook; Kim, Hyoungchul
2017-01-01
High-temperature chemical reactions are ubiquitous in (electro) chemical applications designed to meet the growing demands of environmental and energy protection. However, the fundamental understanding and optimization of such reactions are great challenges because they are hampered by the spontaneous, dynamic, and high-temperature conditions. Here, we investigated the roles of metal catalysts (Pd, Ni, Cu, and Ag) in the high-temperature reverse water-gas shift (RWGS) reaction using in-situ surface analyses and density functional theory (DFT) calculations. Catalysts were prepared by the deposition-precipitation method with urea hydrolysis and freeze-drying. Most metals show a maximum catalytic activity during the RWGS reaction (reaching the thermodynamic conversion limit) with formate groups as an intermediate adsorbed species, while Ag metal has limited activity with the carbonate species on its surface. According to DFT calculations, such carbonate groups result from the suppressed dissociation and adsorption of hydrogen on the Ag surface, which is in good agreement with the experimental RWGS results.
Tachikawa, Hiroto
2005-01-01
Direct ab initio molecular dynamics (MD) calculations have been carried out for the reaction of cyclopropenyl chloride with halide ion (F–) (F– + (CH)3Cl → F(CH)3 + Cl–) in gas phase. Both SN2 and SN2′ channels were found as product channels. These channels are strongly dependent on the collision angle of F– to the target (CH)3Cl molecule. The collision at one of the carbon atoms of the C=C double bond leads to the SN2′ reaction channel; whereas the collision at the methylene carbon atom lead...
Precise integration method without inverse matrix calculation for structural dynamic equations
Wang Mengfu; F. T. K. Au
2007-01-01
The precise integration method proposed for linear time-invariant homogeneous dynamic systems can provide accurate numerical results that approach an exact solution at integration points. However, difficulties arise when the algorithm is used for non-homogeneous dynamic systems due to the inverse matrix calculation required. In this paper, the structural dynamic equalibrium equations are converted into a special form, the inverse matrix calculation is replaced by the Crout decomposition method to solve the dynamic equilibrium equations, and the precise integration method without the inverse matrix calculation is obtained. The new algorithm enhances the present precise integration method by improving both the computational accuracy and efficiency. Two numerical examples are given to demonstrate the validity and efficiency of the proposed algorithm.
Manson, G; Worden, K, E-mail: graeme.manson@sheffield.ac.u, E-mail: k.worden@sheffield.ac.u [Dynamics Research Group, Department of Mechanical Engineering, University of Sheffield, Mappin St, Sheffield S1 3JD (United Kingdom)
2009-08-01
Although a great deal of work has been carried out on structural dynamic systems under random excitation, there has been a comparatively small amount of this work concentrating on the calculation of the quantities commonly measured in structural dynamic tests. Among the existing work, the Volterra series, a means of predicting nonlinear system response for weakly nonlinear systems, has allowed the computation of various measurable quantities of interest for structural dynamics, including: auto- and cross-spectra, FRFs, coherences and higher-order spectra. These calculations are quite intensive and are typically only possible using computer algebra. A previous calculation by the authors for the coherence for a Duffing oscillator yielded results which showed some qualitatitive disagreement with numerical simulation; the object of the current paper is simply to extend the calculation in order to see if better agreement can be achieved.
Mixed quantum-classical reaction path dynamics of C2H5F --> C2H4 + HF.
Stopera, Christopher J; Bladow, Landon L; Thweatt, W David; Page, Michael
2008-11-20
A mixed quantum-classical method for calculating product energy partitioning based on a reaction path Hamiltonian is presented and applied to HF elimination from fluoroethane. The goal is to describe the effect of the potential energy release on the product energies using a simple model of quantized transverse vibrational modes coupled to a classical reaction path via the path curvature. Calculations of the minimum energy path were done at the B3LYP/6-311++G(2d,2p) and MP2/6-311++G** levels of theory, followed by energy-partitioning dynamics calculations. The results for the final HF vibrational state distribution were found to be in good qualitative agreement with both experimental studies and quasiclassical trajectory simulations.
Dynamical resonance in F+H2 chemical reaction and rotational excitation effect
YANG XueMing; XIE DaiQian; ZHANG DongHui
2007-01-01
Reaction resonance is a frontier topic in chemical dynamics research, and it is also essential to the understanding of mechanisms of elementary chemical reactions. This short article describes an important development in the frontier of research. Experimental evidence of reaction resonance has been detected in a full quantum state resolved reactive scattering study of the F+H2 reaction. Highly accurate full quantum scattering theoretical modeling shows that the reaction resonance is caused by two Feshbach resonance states. Further studies show that quantum interference is present between the two resonance states for the forward scattering product. This study is a significant step forward in our understanding of chemical reaction resonance in the benchmark F+H2 system. Further experimental studies on the effect of H2 rotational excitation on dynamical resonance have been carried out. Dynamical resonance in the F+H2 (j = 1) reaction has also been observed.
DEVELOPMENT OF CALCULATING MODEL APPLICABLE FOR CYLINDER WALL DYNAMIC HEAT TRANSFER
ZHONG Minjun; SHI Tielin
2007-01-01
In the calculation of submarine air conditioning load of the early stage, the obtained heat is regarded as cooling load. The confusion of the two words causing the cooling load figured out is abnormally high, and the change of air conditioning cooling load can not be indicated. In accordance with submarine structure and heat transfer characteristics of its inner components, Laplace transformation to heat conduction differential equation of cylinder wall is carried out. The dynamic calculation of submarine conditioning load based on this model is also conducted, and the results of calculation are compared with those of static cooling load calculation. It is concluded that the dynamic cooling load calculation methods can illustrate the change of submarine air conditioning cooling load more accurate than the static one.
Equation of State of Al Based on Quantum Molecular Dynamics Calculations
Minakov, Dmitry V.; Levashov, Pavel R.; Khishchenko, Konstantin V.
2011-06-01
In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and values of isentropic sound velocity behind the shock front for aluminum. We use the VASP code with an ultrasoft pseudopotential and GGA exchange-correlation functional. Up to 108 particles have been used in calculations. For the Hugoniots of Al we solve the Hugoniot equation numerically. To calculate 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 along isentropes. The results of our calculations are in good agreement with experimental data. 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. This work is supported by RFBR, grants 09-08-01129 and 11-08-01225.
Naumov, Vladimir S; Ignatov, Stanislav K
2017-08-01
The GROMOS 56ACARBO force field for the description of carbohydrates was modified for calculations of chitosan (poly-1,4-(N-acetyl)-β-D-glucopyranosamine-2) with protonated and non-protonated amino groups and its derivatives. Additional parameterization was developed on the basis of quantum chemical calculations. The modified force field (56ACARBO_CHT) allows performing the molecular dynamic calculations of chitosans with different degrees of protonation corresponding to various acidity of medium. Test calculations of the conformational transitions in the chitosan rings and polymeric chains as well as the chitosan nanocrystal dissolution demonstrate good agreement with experimental data. Graphical abstract The GROMOS 56ACARBO_CHT force field allows performing the molecular dynamic calculations of chitosans with different types of amio-group: free, protonated, substituted.
Umar, A S; Simenel, C
2016-01-01
Background: Synthesis of superheavy elements (SHE) with fusion-evaporation reactions is strongly hindered by the quasifission (QF) mechanism which prevents the formation of an equilibrated compound nucleus and which depends on the structure of the reactants. New SHE have been recently produced with doubly-magic $^{48}$Ca beams. However, SHE synthesis experiments with single-magic $^{50}$Ti beams have so far been unsuccessful. Purpose: In connection with experimental searches for $Z=117,119$ superheavy elements, we perform a theoretical study of fusion and quasifission mechanisms in $^{48}$Ca,$^{50}$Ti+$^{249}$Bk reactions in order to investigate possible differences in reaction mechanisms induced by these two projectiles. Methods: The collision dynamics and the outcome of the reactions are studied using unrestricted time-dependent Hartree-Fock (TDHF) calculations as well as the density-constrained TDHF method to extract the nucleus-nucleus potentials and the excitation energy in each fragment. Results: Nucleu...
Tachikawa, Hiroto
2006-01-12
Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.
Josip Sertić
2014-01-01
Full Text Available The values of reaction forces in the boiler supports are the basis for the dimensioning of bearing steel structure of steam boiler. In this paper, the application of the method of equivalent stiffness of membrane wall is proposed for the calculation of reaction forces. The method of equalizing displacement, as the method of homogenization of membrane wall stiffness, was applied. On the example of “Milano” boiler, using the finite element method, the calculation of reactions in the supports for the real geometry discretized by the shell finite element was made. The second calculation was performed with the assumption of ideal stiffness of membrane walls and the third using the method of equivalent stiffness of membrane wall. In the third case, the membrane walls are approximated by the equivalent orthotropic plate. The approximation of membrane wall stiffness is achieved using the elasticity matrix of equivalent orthotropic plate at the level of finite element. The obtained results were compared, and the advantages of using the method of equivalent stiffness of membrane wall for the calculation of reactions in the boiler supports were emphasized.
Sertić, Josip; Kozak, Dražan; Samardžić, Ivan
2014-01-01
The values of reaction forces in the boiler supports are the basis for the dimensioning of bearing steel structure of steam boiler. In this paper, the application of the method of equivalent stiffness of membrane wall is proposed for the calculation of reaction forces. The method of equalizing displacement, as the method of homogenization of membrane wall stiffness, was applied. On the example of "Milano" boiler, using the finite element method, the calculation of reactions in the supports for the real geometry discretized by the shell finite element was made. The second calculation was performed with the assumption of ideal stiffness of membrane walls and the third using the method of equivalent stiffness of membrane wall. In the third case, the membrane walls are approximated by the equivalent orthotropic plate. The approximation of membrane wall stiffness is achieved using the elasticity matrix of equivalent orthotropic plate at the level of finite element. The obtained results were compared, and the advantages of using the method of equivalent stiffness of membrane wall for the calculation of reactions in the boiler supports were emphasized.
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Yajiang Hao
2015-07-01
Full Text Available We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin
2015-01-01
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
Variational RRKM calculation of thermal rate constant for C–H bond fission reaction of nitro methane
Afshin Taghva Manesh
2017-02-01
Full Text Available The present work provides quantitative results for the rate constants of unimolecular C–H bond fission reactions in the nitro methane at elevated temperatures up to 2000 K. In fact, there are three different hydrogen atoms in the nitro methane. The potential energy surface for each C–H bond fission reaction of nitro methane was investigated by ab initio calculations. The geometry and vibrational frequencies of the species involved in this process were optimized at the MP2 level of theory, using the cc-pvdz basis set. Since C–H bond fission channel is a barrierless reaction, we have used variational RRKM theory to predict rate coefficients. By means of calculated rate coefficients at different temperatures, the Arrhenius expression of the channel over the temperature range of 100–2000 K is k(T = 5.9E19∗exp(−56274.6/T.
Calculation and analysis of cross-sections for p+184W reactions up to 200 MeV
Sun, Jian-Ping; Zhang, Zheng-Jun; Han, Yin-Lu
2015-08-01
A set of optimal proton optical potential parameters for p+ 184W reactions are obtained at incident proton energy up to 250 MeV. Based on these parameters, the reaction cross-sections, elastic scattering angular distributions, energy spectra and double differential cross sections of proton-induced reactions on 184W are calculated and analyzed by using theoretical models which integrate the optical model, distorted Born wave approximation theory, intra-nuclear cascade model, exciton model, Hauser-Feshbach theory and evaporation model. The calculated results are compared with existing experimental data and good agreement is achieved. Supported by National Basic Research Program of China, Technology Research of Accelerator Driven Sub-critical System for Nuclear Waste Transmutation (2007CB209903) and Strategic Priority Research Program of Chinese Academy of Sciences, Thorium Molten Salt Reactor Nuclear Energy System (XDA02010100)
Welsch, Ralph; Manthe, Uwe
2014-08-07
The mode-selective chemistry of the title reaction is studied by full-dimensional quantum dynamics simulation on an accurate ab initio potential energy surface for vanishing total angular momentum. Using a rigorous transition state based approach and multi-configurational time-dependent Hartree wave packet propagation, initial state-selected reaction probabilities for many ro-vibrational states of methane are calculated. The theoretical results are compared with experimental trends seen in reactions of methane. An intuitive interpretation of the ro-vibrational control of the chemical reactivity provided by a sudden model based on the quantum transition state concept is discussed.
Physical chemistry of reaction dynamics in ionic liquid
Maroncelli, Mark [Pennsylvania State Univ., University Park, PA (United States)
2016-10-02
Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.
Physical Chemistry of Reaction Dynamics in Ionic Liquid
Maroncelli, Mark [Pennsylvania State Univ., University Park, PA (United States)
2016-10-02
Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.
The Reaction Dynamics of the Reactions Ba+CmH2m+1Br（m=1,2,3,4,5）
韩克利; 郑锡光; 张瑞勤; 孙本繁; 何国钟; 楼南泉
1994-01-01
The internal energy distributions of the nascent BaBr products formed in the reactions ofBa+BrR(R=CH3,C2H5,C3H7,C4H9,C5H11) under the single collision condition have been first studied bylaser-induced fluorescence method.With computer simulations of the experimental spectra,we obtained thevibrational distributions of the BaBr products,and found that the vibrational excitation and reaction cross-section increase with the number of the carbon atoms in the alkyl radical R.The quasitriatomic LEPS poten-tial of the Ba+CH3 reaction has been deduced reversely from the experimental results.The dynamics of thereactions Ba+BrR have been studied by the classical trajectory calculations based on the model LEPS poten-tials.It is concluded that the mass factor and the C-Br bond strength are the major factors affecting the rela-tionship between vibrational excitation and reaction cross-section with the number of the carbon atoms in thealkyl radical R.Furthermore,we obtained all the LEPS potentials of the reactive systems Ba+CmH2m+1 andconfirmed its reliability with ab initio calculations.
Ultrafast infrared studies of chemical reaction dynamics in room-temperature liquids
Yang, Haw [Univ. of California, Berkeley, CA (United States)
1999-11-01
Femtosecond infrared spectroscopy provides sufficient spectral and temporal resolution to support a detailed investigation of the early events of a photochemical reaction. Previously unreported transient species that arise as intermediates during the course of a reaction may have lifetimes that are too short for conventional characterization. For these species, quantum-mechanical (density functional theoretical and ab initio) electronic structure calculations provide invaluable insight into chemical properties including molecular structure and energetic. With the combination of experimental and theoretical results, it is possible to assemble a comprehensive picture of the reaction dynamics of a system that is intricately influenced by the surrounding solvent molecules. The mechanisms of several important organometallic reactions, such as alkane C– H bond activation by η^{3}-Tp*Rh(CO), silane Si–H bond activation by η^{5}-CpMn(CO)_{2} and η^{5}-CpRe(CO)_{2}, as well as chlorinated methane C–Cl bond cleavage by the Re(CO)_{5} radical are elucidated. The results demonstrate the importance of molecular morphology change (C–H and Si–H act ivat ion), solvent rearrangement (Si–H activation), intersystem crossing (Si–H activation), and solvent caging (C–Cl cleavage) in understanding the reactivity of the organometallic species, The nature of the apparent free-energy barrier for C–H, Si–H, and C–Cl bond activation reaction is found to be- cleavage of an alkane C–H bond, rearrangement of a silane molecule HSiR_{3} (R = alkyl group) from a nonreactive alkyl site to the reactive Si–H bond, and Cl atom transfer from a chlorinated methane molecule to Re(CO)_{5}, respectively. These results support previous d initio calculations for C–H and Si–H bond activation reaction profiles which suggest that cleavage of an alkane C–H bond by a transition metal center, unlike that of a silane
Quantum molecular dynamics approach to estimate spallation yield from + 208Pb reaction at 800 MeV
P K Sarkar; Maitreyee Nandy
2003-10-01
The spallation yield of neutrons and other mass fragments produced in 800 MeV proton induced reaction on 208Pb have been calculated in the framework of quantum molecular dynamics (QMD) model. The energy spectra and angular distribution have been calculated. Also, multiplicity distributions of the emitted neutrons and kinetic energy carried away by them have been estimated and compared with the available experimental data. The agreement is satisfactory. A major contribution to the neutron emission comes from statistical decay of the fragments. For mass and charge distributions of spallation productsthe QMD process gives rise to target-like and projectile-like fragments only.
Calculation of excitation functions of the 54,56,57,58Fe(, ) reaction from threshold to 30 MeV
Damewan Suchiang; J Joseph Jeremiah; B M Jyrwa
2014-10-01
The cross-sections for the formation of 54,56,57,58Co in the 54,56,57,58Fe(, ) reaction from threshold to 30 MeV protons have been theoretically calculated using the TALYS-1.4 nuclear model code, whereby we have studied major nuclear reaction mechanisms, including direct, preequilibrium and compound nuclear reaction. Subsequently, the level density and shell damping parameters have been adjusted and at the same time, the odd–even effects are well comprehended. The excitation functions have been compared with experimental nuclear data. It is observed that the theoretical cross-sections match fairly well. Proton-induced reaction cross-sections provide clues to understand the nuclear structure and offers a good testing ground for ideas about nuclear forces. In addition, complete information in this field is very much required for application in accelerator-driven subcritical system.
Reaction dynamics: The view from a transition state
Continetti, Robert E.
2017-10-01
Ejecting electrons from negative ions using light can create structures that very closely resemble the transition states of bimolecular reactions. Now, using this technique, trapped quantum states, or 'resonances', have been observed in a seven-atom reaction, and theory has been shown to be up to the task of capturing such complex phenomena.
The effect of dynamical quark mass on the calculation of a strange quark star's structure
Gholam Hossein Bordbar; Babak Ziaei
2012-01-01
We discuss the dynamical behavior of strange quark matter components,in particular the effects of density dependent quark mass on the equation of state of strange quark matter.The dynamical masses of quarks are computed within the Nambu-Jona-Lasinio model,then we perform strange quark matter calculations employing the MIT bag model with these dynamical masses.For the sake of comparing dynamical mass interaction with QCD quark-quark interaction,we consider the one-gluon-exchange term as the effective interaction between quarks for the MIT bag model.Our dynamical approach illustrates an improvement in the obtained equation of state values.We also investigate the structure of the strange quark star using TolmanOppenheimer-Volkoff equations for all applied models.Our results show that dynamical mass interaction leads to lower values for gravitational mass.
Theoretical Calculations and Analysis for n+59Co Reaction up to 20 MeV
2008-01-01
<正>All cross-sections of neutron-induced reactions, angular distributions, double differential cross sections, and energy spectra for neutron, proton, deuteron, triton, helium and alpha-particle emissions are
New Systematic CFD Methods to Calculate Static and Single Dynamic Stability Derivatives of Aircraft
Bai-gang Mi
2017-01-01
Full Text Available Several new systematic methods for high fidelity and reliability calculation of static and single dynamic derivatives are proposed in this paper. Angle of attack step response is used to obtain static derivative directly; then translation acceleration dynamic derivative and rotary dynamic derivative can be calculated by employing the step response motion of rate of the angle of attack and unsteady motion of pitching angular velocity step response, respectively. Longitudinal stability derivative calculations of SACCON UCAV are taken as test cases for validation. Numerical results of all cases achieve good agreement with reference values or experiments data from wind tunnel, which indicate that the proposed methods can be considered as new tools in the process of design and production of advanced aircrafts for their high efficiency and precision.
Yang, Xueming
In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The studies of the O(1D) + H2 → OH + H reaction has also been reviewed here. A prototype example of state-to-state dynamics of pure insertion chemical reaction is provided. Effect of the reagent rotational excitation and the isotope effect on the dynamics of this reaction have also been investigated. The detailed mechanism for abstraction channel in this reaction has also been closely studied. The experimental investigations of the simplest chemical reaction, the H3 system, have also been described here. Through extensive collaborations between theory and experiment, the mechanism for forward scattering product at high collision energies for the H + HD reaction was clarified, which is attributed to a slow down mechanism on the top of a quantized barrier transition state. Oscillations in the product quantum state resolved different cross sections have also been observed in the H + D2 reaction, and were attributed to the interference of adiabatic transition state pathways from detailed theoretical analysis. The results reviewed here clearly show the significant advances we have made in the studies of the state-to-state molecular reaction dynamics.
Yu, Feng
2016-03-24
We have investigated the dynamic reaction mechanisms of *ClO¯ with CH3Cl (the asterisk is utilized to label a different Cl atom). Ab initio molecular dynamics simulations at the MP2/6-31+G(d,p) level of theory have been employed to compute the dynamic trajectories. On the basis of our simulations, the dynamic reaction pathways for the bimolecular nucleophilic substitution (SN2) reaction channel and SN2-induced elimination reaction channel are clearly illustrated. For the SN2 reaction channel, some trajectories directly dissociate to the final products of CH3O*Cl and Cl¯, whereas the others involve the dynamic Cl¯···CH3O*Cl intermediate complex. As to the SN2-induced elimination reaction channel, the trajectories lead to the final products of CH2O, HCl, and *Cl¯ through the dynamic Cl¯···CH3O*Cl intermediate complex. More significantly, the product branching ratios of Cl¯ and *Cl¯ predicted by our simulations are basically consistent with previous experimental results (Villano et al. J. Am. Chem. Soc. 2009, 131, 8227-8233).
Calculations of Bose-Einstein correlations from Relativistic Quantum Molecular Dynamics
Sullivan, J.P.; Berenguer, M.; Fields, D.E.; Jacak, B.V.; Sarabura, M.; Simon-Gillo, J.; Sorge, H.; van Hecke, H. [Los Alamos National Lab., NM (United States); Pratt, S. [Michigan State Univ., East Lansing, MI (United States)
1993-10-01
Bose-Einstein correlation functions which are in good agreement with pion data can be calculated from an event generator. Here pion and (preliminary) kaon data from CERN experiment NA44 are compared to the calculations. The dynamics of 200 GeV/nucleon {sup 32}S + Pb collisions are calculated, without correlations due to interference patterns of a many-body wavefunction for identical particles, using the Relativistic Quantum Molecular Dynamics model (RQMD). The model is used to generate the phase-space coordinates of the emitted hadrons at the time they suffer their last strong interaction (freeze-out). Using the freeze-out position and momentum of pairs of randomly selected identical particles, a two-particle symmetrized wave-function is calculated and used to add two-body correlations. Details of the technique have been described previously. The method is similar to that used in the Spacer program.
Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach
Adomaitis, Raymond A., E-mail: adomaiti@umd.edu [Department of Chemical and Biomolecular Engineering, Institute for Systems Research, University of Maryland, College Park, Maryland 20742 (United States)
2016-01-15
A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies.
Calculation of the coefficient and dynamics of water diffusion in graphite joints
WANG Jun; LIU Wen-bin
2006-01-01
The coefficient and dynamics of water diffusion in adhesive-graphite joints were calculated insitu with energy dispersive X-ray (EDX) analysis, a method that is significantly simpler than elemental analysis. Water diffusion coefficient and dynamics of adhesive-graphite joints treated by different surface treatment methods were also investigated. Calculation results indicated that the water diffusion rate in adhesive-graphite joints treated by sandpaper was higher than that treated by chemical oxidation or by silane couple agent. Also the durability of graphite joints treated by coupling agent is superior to that treated by chemical oxidation or sandpaper burnishing.
Mathematical Models For Calculating The Value Of Dynamic Viscosity Of A Liquid
Ślęzak M.
2015-06-01
Full Text Available The objective of this article is to review models for calculating the value of liquid dynamic viscosity. Issues of viscosity and rheological properties of liquid ferrous solutions are important from the perspective of modelling, along with the control of actual production processes related to the manufacturing of metals, including iron and steel. Conducted analysis within literature indicates that there are many theoretical considerations concerning the effect of viscosity of liquid metals solutions. The vast majority of models constitute a group of theoretical or semi-empirical equations, where thermodynamic parameters of solutions, or some parameters determined by experimental methods, are used for calculations of the dynamic viscosity coefficient.
A New Parallel Algorithm in Power Flow Calculation: Dynamic Asynchronous Parallel Algorithm
无
2000-01-01
Based on the general methods in power flow calculation of power system and onconceptions and classifications of parallel algorithm, a new approach named DynamicAsynchronous Parallel Algorithm that applies to the online analysis and real-time dispatching and controlling of large-scale power network was put forward in this paper. Its performances of high speed and dynamic following have been verified on IEEE-14 bus system.
Structural parameter identifiability analysis for dynamic reaction networks
Davidescu, Florin Paul; Jørgensen, Sten Bay
2008-01-01
. The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...... method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...
Quantum dynamics of the Walden inversion reaction Cl - +CH3Cl --> ClCH3+Cl -
Clary, David C.; Palma, Juliana
1997-01-01
Quantum scattering calculations on the SN2 reaction Cl-+CH3Cl→ClCH3+Cl- are reported. The rotating bond approximation (RBA) has been adapted so that three degrees of freedom including the C-Cl stretching vibration and the CH3 umbrella mode are treated explicitly. The calculations have been done with minor modifications of a potential due to Vande Linde and Hase. It is found that initial excitation of the C-Cl vibration has a large effect on the reaction probabilities, while excitation of the CH3 umbrella vibration is less significant. The reaction is dominated by scattering resonances with lifetimes ranging from 0.1 to 10 ps. It is found that the length of the C-Cl bond at the transition state of the reaction has a particularly pronounced effect on the reaction probabilities. The magnitude of the quantum reaction probabilities compares quite well with those calculated using the quasiclassical trajectory method.
Fan, Zheyong; Siro, Topi; Harju, Ari
2012-01-01
In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme where a whole block is used for one particle and each thread in the block calcula...
Kaplan Abdullah
2015-01-01
Full Text Available Implementation of projects of new generation nuclear power plants requires the solving of material science and technological issues in developing of reactor materials. Melts of heavy metals (Pb, Bi and Pb-Bi due to their nuclear and thermophysical properties, are the candidate coolants for fast reactors and accelerator-driven systems (ADS. In this study, α, γ, p, n and 3He induced fission cross section calculations for 209Bi target nucleus at high-energy regions for (α,f, (γ,f, (p,f, (n,f and (3He,f reactions have been investigated using different fission reaction models. Mamdouh Table, Sierk, Rotating Liquid Drop and Fission Path models of theoretical fission barriers of TALYS 1.6 code have been used for the fission cross section calculations. The calculated results have been compared with the experimental data taken from the EXFOR database. TALYS 1.6 Sierk model calculations exhibit generally good agreement with the experimental measurements for all reactions used in this study.
Nuclear model calculations of (n,p) and (n,n'p) reactions on molybdenum isotopes
Ivascu, M.; Avrigeanu, M.; Avrigeanu, V.
1983-06-01
Cross sections for the (n,p) and (n,n'p) reactions on stable molybdenum isotopes have been calculated in the energy range from threshold up to 20 MeV. The calculations have involved the optical model (SCAT2 code), the statistical model (Kauser-Feshbach STAPRE code) and the preequilibrium decay exciton and hybrid models (incorporated in STAPRE). The input model parameters have been determined or checked analyzing against the available experimental data the calculated neutron strength functions, potential scattering radius, total, differential shape elastic and inelastic scattering cross sections (SPRT method), the excitation function of the reaction /sup 93/Nb(p,n)/sup 93/Mo, neutron resonance data and discrete levels at low excitation energies, neutron radiative capture cross sections on /sup 93/Nb and /sup 98,100/Mo target nuclei, the excitation function of the reaction /sup 92/Mo(n,2n)/sup 91/Mo cross section and isomer ratio, and the proton - emission spectrum for 15 MeV neutron incident energy on /sup 92/Mo target. The calculation of nuclear level density for excitation energies higher than approx.23 MeV are more reliable done by means of the liquid drop model predictions for the back - shifted Fermi gas model parameters. That enables also to use in a unified way the average level density parameter anti a = A/8 MeV/sup -1/ in both statistical and exciton models. The calculated (n,p) and (n,n'p) reaction cross sections are compared with the available experimental data and their sensitivity to the input parameter variations are discussed. 132 refs., 25 figs., 11 tabs.
Dorofeeva, Olga V; Ryzhova, Oxana N
2014-05-15
Accurate gas-phase enthalpies of formation (ΔfH298°) of 20 common α-amino acids, seven uncommon amino acids, and three small peptides were calculated by combining G4 theory calculations with an isodesmic reaction approach. The internal consistency over a set of ΔfH298°(g) values was achieved by sequential adjustment of their values through the isodesmic reactions. Four amino acids, alanine, β-alanine, sarcosine, and glycine, with reliable internally self-consistent experimental data, were chosen as the key reference compounds. These amino acids together with about 100 compounds with reliable experimental data (their accuracy was supported by G4 calculations) were used to estimate the enthalpies of formation of remaining amino acids. All of the amino acids with the previously established enthalpies of formation were later used as the reference species in the isodesmic reactions for the other amino acids. A systematic comparison was made of 14 experimentally determined enthalpies of formation with the results of calculations. The experimental enthalpies of formation for 10 amino acids were reproduced with good accuracy, but the experimental and calculated values for 4 compounds differed by 11–21 kJ/mol. For these species, the theoretical ΔfH298°(g) values were suggested as more reliable than the experimental values. On the basis of theoretical results, the recommended values for the gas-phase enthalpies of formation were also provided for amino acids for which the experimental ΔfH298°(g) were not available. The enthalpies of sublimation were evaluated for all compounds by taking into account the literature data on the solid-phase enthalpies of formation and the ΔfH298°(g) values recommended in our work. A special attention was paid to the accurate prediction of enthalpies of formation of amino acids from the atomization reactions. The problems associated with conformational flexibility of these compounds and harmonic treatment of low frequency torsional
Direct Dynamics Study on CH2O + CH·3 → CHO + CH4 Reaction
无
2006-01-01
It is still a formidable challenge to study CH2O + CH·3 → CHO + CH4 reaction in the gas phase by traditional dynamics, because of the large number of freedom degrees for the system.In this paper, direct dynamics, in which trajectories were run directly on the DFT potential energy surface, have been applied to the reaction, which gave a direct look in the reaction processes.Two sets of trajectories at different initial orientations of reactants and temperature have been simulated. And the detailed reaction mechanisms have been described.
Thakur Meenu
2015-01-01
Full Text Available The reaction mechanism of 19F + 232Th and 28Si + 232Th systems populating the near-super-heavy compound nuclei 251Es and 260Rf respectively are investigated using neutron multiplicity as a probe. The prescission neutron multiplicities of these compound nuclei are calculated at different excitation energies using a statistical model code. These calculations are performed using the Bohr-Wheeler transition state fission width as well as the dissipative dynamical fission width based on the Kramers’ prescription. For 19F + 232Th system, the measured yield of pre-scission is compared with the statistical model calculations for the decay of a compound nucleus in the excitation energy range of 54-90 MeV. The comparison between the measured and the calculated values indicates that the Bohr-Wheeler fission width underestimates the pre-scission neutron yield and a large amount of dissipation strength is required to reproduce the experimental pre-scission neutron multiplicities. The excitation energy dependence of the fitted values of the dissipation coefficient is also discussed. In addition, exploratory statistical model calculations of pre-scission neutron multiplicity for the 28Si + 232Th system are presented in the above range of excitation energy.
Calculation method of quantum efficiency to TiO2 nanocrystal photocatalysis reaction
无
2002-01-01
The quantum yield is an important factor to evaluate the efficiency of photoreactor. This article gives an overall calculation method of the quantum efficiency(ф) and the apparent quantum efficiency(ф2) to the TiO2/UV photocatalysis system. Furthermore, for the immobility system (IS), the formulation of the faction of light absorbed by the TiO2 thin film is proposed so as to calculate the quantum efficiency by using the measured value and theoretic calculated value of transmissivity (T). For the suspension system(SS), due to the difficulty to obtain the absorption coefficient (α) of TiO2 particulates, the quantum efficiency is calculated by means of the relative photonic efficiency (ξr) and the standard quantum yield (фstandard).
Imaoka, Haruna; Kinugawa, Kenichi
2017-03-01
Thermal conductivity, shear viscosity, and bulk viscosity of normal liquid 4He at 1.7-4.0 K are calculated using path integral centroid molecular dynamics (CMD) simulations. The calculated thermal conductivity and shear viscosity above lambda transition temperature are on the same order of magnitude as experimental values, while the agreement of shear viscosity is better. Above 2.3 K the CMD well reproduces the temperature dependences of isochoric shear viscosity and of the time integral of the energy current and off-diagonal stress tensor correlation functions. The calculated bulk viscosity, not known in experiments, is several times larger than shear viscosity.
钟晨; 蔡翔舟; 沈文庆; 张虎勇; 魏义彬; 陈金根; 马余刚; 郭威; 方德清
2003-01-01
The Boltzmann-Uehling-Uhlenbeck (BUU) model, which includes the Fermi motion, the mean field, individual nucleon-nucleon (N-N) interactions and the Pauli blocking effect, etc., is used to calculate the total reaction cross section σR induced by α-particles on different targets in the incident energy range from 17.4 to 48.1 MeV/u. The calculation result can well reproduce the experimental data. The nucleus-nucleus interaction radius parameterγ0 was extracted from experimental σR. It is found that γ0 becomes constant with the increasing mass number of target.
Calculation of dynamic load impact on reinforced concrete arches in the ground
Barbashev Nikita Petrovich
2016-01-01
Full Text Available Concrete arches are widely used in the construction of underground facilities. The analysis of their work under dynamic loads (blasting, shock, seismic will improve the efficiency of design and application. The article addresses the problems of calculation of reinforced concrete arches in the ground in terms of the action of dynamic load - compression wave. The calculation is made basing on the decision of a closed system of equations that allows performing the calculation of elastic-plastic curved concrete structures under dynamic loads. Keeping in mind the properties of elastic-plastic reinforcement and concrete in the process of design variations, σ-ε diagrams are variable. The calculation is performed by the direct solution of differential equations in partial derivatives. The result is based on a system of ordinary differential equations of the second order (expressing the transverse and longitudinal oscillations of the structure and the system of algebraic equations (continuity condition of deformation. The computer program calculated three-hinged reinforced concrete arches. The structural calculations were produced by selection of the load based on the criteria of reaching the first limit state: ultimate strain of compressed concrete; ultimate strain tensile reinforcement; the ultimate deformation of the structure. The authors defined all the characteristics of the stress-strain state of the structure. The presented graphs show the change of bending moment and shear force in time for the most loaded section of the arch, the dependence of stresses and strains in concrete and reinforcement, stress changes in time for the cross-sectional height. The peculiarity of the problem is that the action of the load provokes the related dynamic forces - bending moment and longitudinal force. The calculations allowed estimating the carrying capacity of the structure using the criteria of settlement limit states. The decisive criterion was the
Veli ÇAPALI
2016-05-01
Full Text Available BeO is one of the most common moderator material for neutron moderation; due to its high density, neutron capture cross section and physical-chemical properties that provides usage at elevated temperatures. As it’s known, for various applications in the field of reactor design and neutron capture, reaction cross–section data are required. The cross–sections of (n,α, (n,2n, (n,t, (n,EL and (n,TOT reactions for 9Be and 16O nuclei have been calculated by using TALYS 1.6 Two Component Exciton model and EMPIRE 3.2 Exciton model in this study. Hadronic interactions of low energetic neutrons and generated isotopes–particles have been investigated for a situation in which BeO was used as a neutron moderator by using GEANT4, which is a powerful simulation software. In addition, energy deposition along BeO material has been obtained. Results from performed calculations were compared with the experimental nuclear reaction data exist in EXFOR.
Chen, Liuyang; Shao, Kejie; Chen, Jun; Yang, Minghui; Zhang, Dong H.
2016-05-01
This work performs a time-dependent wavepacket study of the H2 + C2H → H + C2H2 reaction on a new ab initio potential energy surface (PES). The PES is constructed using neural network method based on 68 478 geometries with energies calculated at UCCSD(T)-F12a/aug-cc-pVTZ level and covers H2 + C2H↔H + C2H2, H + C2H2 → HCCH2, and HCCH2 radial isomerization reaction regions. The reaction dynamics of H2 + C2H → H + C2H2 are investigated using full-dimensional quantum dynamics method. The initial-state selected reaction probabilities are calculated for reactants in eight vibrational states. The calculated results showed that the H2 vibrational excitation predominantly enhances the reactivity while the excitation of bending mode of C2H slightly inhibits the reaction. The excitations of two stretching modes of C2H molecule have negligible effect on the reactivity. The integral cross section is calculated with J-shift approximation and the mode selectivity in this reaction is discussed. The rate constants over 200-2000 K are calculated and agree well with the experimental measured values.
Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino
2016-06-27
This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies.
Theoretical Study on the Dynamics of the Reaction of HNO((1)A') with HO2((2)A″).
Mousavipour, S Hosein; Asemani, S Somayeh
2015-06-04
We used stochastic one-dimensional chemical master equation (CME) simulation to gain insight into the dynamics of the reaction of HNO((1)A') with HO2((2)A″). The reaction takes place over a multiwell, multichannel potential energy surface that is based on the computations at the CBS-QB3 level of theory. The calculated multipath potential energy surface consists of three potential wells and three van der Waals complexes. In solving the master equation, the Lennard-Jones potential is used to model the collision between the collider gases. The fractional population of different intermediates and products in the early stages of the reaction is examined to determine the role of the energized intermediates and van der Waals complexes on the kinetics of the title reaction. The major products of the title reaction at lower temperatures are OH, HNO2, HNOH, and O2(X(3)Σg(-)). The temperature- and pressure-dependence of the reaction over a wide range of temperature (300-3000 K) and pressure (0.1-2000 Torr) are studied. No sign of pressure dependence was being observed for the title reaction over the stated range of pressure. The calculated rate constants from the CME simulation are compared with those obtained from the RRKM-SSA method that is based on strong collision assumption. Our results indicate that the strong collision assumption increases the calculated rate constant for the formation of the main products (HNO2 + OH) by a factor of 2 at 300 K and 1 atm pressure, compared to the results of CME simulation, although the results are in good agreement at higher temperatures.
vanVlimmeren, BAC; Fraaije, JGEM
1996-01-01
We present a simple method for the numerical calculation of the noise distribution in multicomponent functional Langevin models. The topic is of considerable importance, in view of the increased interest in the application of mesoscopic dynamics simulation models to phase separation of complex
A very simple dynamic soil acidification model for scenario analyses and target load calculations
Posch, M.; Reinds, G.J.
2009-01-01
A very simple dynamic soil acidification model, VSD, is described, which has been developed as the simplest extension of steady-state models for critical load calculations and with an eye on regional applications. The model requires only a minimum set of inputs (compared to more detailed models) and
Seethaler, Pamela M.; Fuchs, Lynn S.; Fuchs, Douglas; Compton, Donald L.
2012-01-01
The purpose of this study was to assess the value of dynamic assessment (DA; degree of scaffolding required to learn unfamiliar mathematics content) for predicting 1st-grade calculations (CAs) and word problems (WPs) development, while controlling for the role of traditional assessments. Among 184 1st graders, predictors (DA, Quantity…
Svizhenko, Alexel; Anantram, M. P.; Maiti, Amitesh
2003-01-01
This paper presents viewgraphs on the modeling of the electromechanical response of carbon nanotubes, utilizing molecular dynamics and transport calculations. The topics include: 1) Simulations of the experiment; 2) Effect of diameter, length and temperature; and 3) Study of sp3 coordination-"The Table experiment".
Comparison of inverse dynamics calculated by two- and three-dimensional models during walking
Alkjaer, T; Simonsen, E B; Dyhre-Poulsen, P
2001-01-01
The purpose of the study was to compare joint moments calculated by a two- (2D) and a three-dimensional (3D) inverse dynamics model to examine how the different approaches influenced the joint moment profiles. Fifteen healthy male subjects participated in the study. A five-camera video system rec...
BUU calculations for {sup 12}C+{sup 26}Mg reaction at 6-11 MeV/u
Kicinska-Habior, M. [Warsaw Univ., Inst. of Experimental Physics, Nuclear Physics Div., Warsaw (Poland)]|[Washington Univ., Nuclear Physics Lab., Seattle, WA (United States); Trznadel, Z. [Warsaw Univ., Inst. of Experimental Physics, Nuclear Physics Div., Warsaw (Poland); Snover, K.A.; Kelly, M.P. [Washington Univ., Nuclear Physics Lab., Seattle, WA (United States); Maj, A. [Washington Univ., Nuclear Physics Lab., Seattle, WA (United States)]|[Inst. of Nuclear Physics, Cracow (Poland)
1997-12-31
High energy gamma spectra measured in the {sup 12}C +{sup 26}Mg reaction at energies of 5, 8.5 and 11 MeV/u have been analysed using the BUU computer code (cascade model). In the calculation the statistical and nonstatistical gamma-ray emission as well as the Bremsstrahlung have been taken into account. The parameters of the Giant Dipole Resonance have been extracted. 4 refs, 1 fig., 2 tabs.
Bassem Elshahat; Akhtar Naqvi; Nabil Maalej
2015-01-01
Purpose: Boron neutron capture therapy (BNCT) is a promising technique for the treatment of malignant disease targeting organs of the human body. Monte Carlo simulations were carried out to calculate optimum design parameters of an accelerator based beam shaping assembly (BSA) for BNCT of brain cancer setup.Methods: Epithermal beam of neutrons were obtained through moderation of fast neutrons from 3H(p,n) reaction in a high density polyethylene moderator and a graphite reflector. The dimensio...
Deltuva, A
2016-01-01
Angular-momentum or parity-dependent nonlocal optical potentials for nucleon-${}^{16}\\mathrm{O}$ scattering able to fit differential cross section data over the whole angular regime are developed and applied to the description of deuteron-${}^{16}\\mathrm{O}$ scattering in the framework of three-body Faddeev-type equations for transition operators. Differential cross sections and deuteron analyzing powers for elastic scattering and ${}^{16}\\mathrm{O}(d,p){}^{17}\\mathrm{O}$ transfer reactions are calculated using a number of local and nonlocal optical potentials and compared with experimental data. Angular-momentum or parity-dependence of the optical potential turns out to be quite irrelevant in the considered three-body reactions while nonlocality is essential for a successful description of the differential cross section data, especially in transfer reactions.
An eight-dimensional quantum dynamics study of the Cl + CH4→ HCl + CH3 reaction
Liu, Na; Yang, Minghui
2015-10-01
In this work, the later-barrier reaction Cl + CH4 → HCl + CH3 is investigated with an eight-dimensional quantum dynamics method [R. Liu et al., J. Chem. Phys. 137, 174113 (2012)] on the ab initio potential energy surface of Czakó and Bowman [J. Chem. Phys. 136, 044307 (2012)]. The reaction probabilities with CH4 initially in its ground and vibrationally excited states are calculated with a time-dependent wavepacket method. The theoretical integral cross sections (ICSs) are extensively compared with the available experimental measurements. For the ground state reaction, the theoretical ICSs excellently agree with the experimental ones. The good agreements are also achieved for ratios between ICSs of excited reactions. For ICS ratios between various states, the theoretical values are also consistent with the experimental observations. The rate constants over 200-2000 K are calculated and the non-Arrhenius effect has been observed which is coincident with the previous experimental observations and theoretical calculations.
A New Calculation Method of Dynamic Kill Fluid Density Variation during Deep Water Drilling
Honghai Fan
2017-01-01
Full Text Available There are plenty of uncertainties and enormous challenges in deep water drilling due to complicated shallow flow and deep strata of high temperature and pressure. This paper investigates density of dynamic kill fluid and optimum density during the kill operation process in which dynamic kill process can be divided into two stages, that is, dynamic stable stage and static stable stage. The dynamic kill fluid consists of a single liquid phase and different solid phases. In addition, liquid phase is a mixture of water and oil. Therefore, a new method in calculating the temperature and pressure field of deep water wellbore is proposed. The paper calculates the changing trend of kill fluid density under different temperature and pressure by means of superposition method, nonlinear regression, and segment processing technique. By employing the improved model of kill fluid density, deep water kill operation in a well is investigated. By comparison, the calculated density results are in line with the field data. The model proposed in this paper proves to be satisfactory in optimizing dynamic kill operations to ensure the safety in deep water.
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
Lespade, Laure
2016-08-01
Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.
The Lower Extremities Exoskeleton Actuator Dynamics Research Taking into Account Support Reaction
A. A. Vereikin
2014-01-01
Full Text Available The article shows high relevance of research, aimed at the robotic exoskeleton creation. It defines some problems related to the process of their designing; including a lack of power supply to provide enough autonomy, and difficulties of man-machine complex control. There is a review of literature on the walking robots with tree-like kinematic structure development. This work reflects the continuing investigations, currently conducted by the authors, and relies heavily on the results of previous works, devoted to this subject.The article presents the exoskeleton dynamics equation, taking into account the impact of external forces and torques, as well as external relations imposed. Using a model of lower extremities exoskeleton developed in SolidWorks software complex, baricentric parameters of the actuator links were found. The different types of movements, committed due to harmonic changes of generalized coordinates in exoskeleton degrees of mobility, equipped with electrohydraulic actuators, were analyzed. The laws of generalized coordinate changes in time, corresponding to the worst case loading, were found. All the necessary input data for the exoskeleton dynamics equation solution were determined.The numerical values of all components of the dynamics equation were obtained as result of the dynamics equation simulation. In this case, the exoskeleton actuator load capacity was assumed to be 50 kg. The article shows dependences of torque and power in the actuator degrees of mobility on the time, as well as a curve of total capacity of all drives both, ignoring and taking into consideration the support surface reactions. Obtained dependences are the initial data for the calculation of the drive system.The proposed method for determination of exoskeleton energy parameters allows developer to perform a prompt evaluation of various options for the actuator design in accordance with the selected criteria. As a main evaluation criterion, a minimum
Singh, Jagdev; Rashidi, M. M.; Kumar, Devendra; Swroop, Ram
2016-12-01
In this paper, we study a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions with time fractional Caputo derivative. The present article involves a more generalized effective approach, proposed for the Brusselator system say q-homotopy analysis transform method (q-HATM), providing the family of series solutions with nonlocal generalized effects. The convergence of the q-HATM series solution is adjusted and controlled by auxiliary parameter ℏ and asymptotic parameter n. The numerical results are demonstrated graphically. The outcomes of the study show that the q-HATM is computationally very effective and accurate to analyze nonlinear fractional differential equations.
Dynamical coupled-channels study of meson production reactions from EBAC@Jlab
Hiroyuki Kamano
2011-10-01
We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.
Stereo-dynamics of the exchange reaction Ha+LiHb→LiHa+Hb and its isotopic variants
Zhai Hong-Sheng; Yin Shu-Hui
2012-01-01
The quasi-classical trajectory (QCT) method is used to calculate the stereo-dynamics of the exchange reaction Ha+LiHb→LiHa+Hb and its isotopic variants based on an accurate potential energy surface reported by Prudente et al.[Prudente F V,Marques J M C and Maniero A M 2009 Chem.Phys.Lett.474 18].The reactive probability of the title reaction is computed.The vector correlations and four polarization-dependent generalized differential cross sections (PDDCSs) at different collision energies are presented.The influences of the collision energy and the reagent rotation on the product polarization are studied in the present work.The results indicate that the product rotational angular momentum j' is not only aligned,but also oriented along the direction perpendicular to the scattering plane.The product polarization distributions of the title reaction and its isotopic variants exhibit distinct differences which may arise from different mass combinations.
Xie, Jing; Sun, Rui; Siebert, Matthew R; Otto, Rico; Wester, Roland; Hase, William L
2013-08-15
Electronic structure and direct dynamics calculations were used to study the potential energy surface and atomic-level dynamics for the OH(-) + CH3I reactions. The results are compared with crossed molecular beam, ion imaging experiments. The DFT/B97-1/ECP/d level of theory gives reaction energetics in good agreement with experiment and higher level calculations, and it was used for the direct dynamics simulations that were performed for reactant collision energies of 2.0, 1.0, 0.5, and 0.05 eV. Five different pathways are observed in the simulations, forming CH3OH + I(-), CH2I(-) + H2O, CH2 + I(-) + H2O, IOH(-) + CH3, and [CH3--I--OH](-). The SN2 first pathway and the proton-transfer second pathway dominate the reaction dynamics. Though the reaction energetics favor the SN2 pathway, the proton-transfer pathway is more important except for the lowest collision energy. The relative ion yield determined from the simulations is in overall good agreement with experiment. Both the SN2 and proton-transfer pathways occur via direct rebound, direct stripping, and indirect mechanisms. Except for the highest collision energy, 70-90% of the indirect reaction for the SN2 pathway occurs via formation of the hydrogen-bonded OH(-)---HCH2I prereaction complex. For the proton-transfer pathway the indirect reaction is more complex with the roundabout mechanism and formation of the OH(-)---HCH2I and CH2I(-)---HOH complexes contributing to the reaction. The majority of the SN2 reaction is direct at 2.0, 1.0, and 0.5 eV, dominated by stripping. At 0.05 eV the two direct mechanisms and the indirect mechanisms have nearly equal contributions. The majority of the proton-transfer pathway is direct stripping at 2.0, 1.0, and 0.5 eV, but the majority of the reaction is indirect at 0.05 eV. The product relative translational energy distributions are in good agreement with experiment for both the SN2 and proton-transfer pathways. For both, direct reaction preferentially transfers the product
Fu, Bina; Zhang, Dong H.
2015-02-01
We employ the initial state-selected time-dependent wave packet approach to an atom-triatom reaction to study the H + HOD → OH + HD/OD + H2 reaction without the centrifugal sudden approximation, based on an accurate potential energy surface which was recently developed by neural network fitting to high level ab initio energy points. The total reaction probabilities and integral cross sections, which are the exact coupled-channel results, are calculated for the HOD reactant initially in the ground and several vibrationally excited states, including the bending excited state, OD stretching excited states, OH stretching excited states, and combined excitations of them. The reactivity enhancements from different initial states of HOD are presented, which feature strong bond-selective effects of the reaction dynamics. The current results for the product branching ratios, reactivity enhancements, and relative cross sections are largely improved over the previous calculations, in quantitatively good agreement with experiment. The thermal rate constant for the title reaction and the contributions from individual vibrational states of HOD are also obtained.
Sornek Krzysztof
2016-01-01
Full Text Available The proper design of renewable energy based systems is really important to provide their efficient and safe operation. The aim of this paper is to compare the results obtained during traditional static calculations, with the results of dynamic simulations. For this reason, simulations of solar water heating (SWH system, designed for a typical residential building, were conducted in the TRNSYS (Transient System Simulation Tool. Carried out calculations allowed to determine the heat generation in the discussed system as well as to estimate the efficiency of considered installation. Obtained results were compared with the results from other available tool based on the static calculations. It may be concluded, that using dynamic simulations at the designing stage of renewable energy based systems may help to avoid many exploitation problems (including low efficiency, overheating etc. and allows to provide safe exploitation of such installations.
Quantum three-body calculation of the nonresonant triple-\\alpha reaction rate at low temperatures
Ogata, Kazuyuki; Kamimura, Masayasu
2009-01-01
The triple-\\alpha reaction rate is re-evaluated by directly solving the three-body Schroedinger equation. The resonant and nonresonant processes are treated on the same footing using the continuum-discretized coupled-channels method for three-body scattering. Accurate description of the \\alpha-\\alpha nonresonant states significantly quenches the Coulomb barrier between the two-\\alpha's and the third \\alpha particle. Consequently, the \\alpha-\\alpha nonresonant continuum states below the resonance at 92.04 keV, i.e., the ground state of 8Be, give markedly larger contribution at low temperatures than in foregoing studies. We find about 20 orders-of-magnitude enhancement of the triple-\\alpha reaction rate around 10^7 K compared to the rate of the NACRE compilation.
Dynamical Dipole mode in heavy-ion fusion reactions in the 192Pb mass region
Parascandolo, C.; Pierroutsakou, D.; Alba, R.; Del Zoppo, A.; Maiolino, C.; Santonocito, D.; Agodi, C.; Baran, V.; Boiano, A.; Colonna, M.; Coniglione, R.; De Filippo, E.; Di Toro, M.; Emanuele, U.; Farinon, F.; Guglielmetti, A.; La Commara, M.; Martin, B.; Mazzocchi, C.; Mazzocco, M.; Rizzo, C.; Romoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Strano, E.; Torresi, D.; Trifiró, A.; Trimarchi, M.
2015-04-01
The dynamical dipole mode was investigated in the mass region of the 192Pb compound nucleus, by using the 40Ca + 152Sm and 48Ca + 144Sm reactions at Elab=11 and 10.1 MeV/nucleon, respectively. Both fusion-evaporation and fission events were studied simultaneously for the first time. Our results for evaporation and fission events (preliminary) show that the dynamical dipole mode survives in reactions involving heavier nuclei than those studied previously.
Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina
2009-10-01
The reactions of 1-naphthyl radicals with acetylene were studied behind reflected shock waves in a single-pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals. The [acetylene]/[1-iodonaphthalene] ratio in all of the experiments was approximately 100 to channel the free radicals into reactions with acetylene rather than iodonaphthalene. Only two major products resulting from the reactions of 1-naphthyl radicals with acetylene and with hydrogen atoms were found in the post shock samples. They were acenaphthylene and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from an attack of various free radicals on acetylene, were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of acetylene is negligible. One potential energy surface describes the production of acenaphthylene and 1-naphthyl acetylene, although the latter was not found experimentally due to the high barrier (calculated) required for its production. Using quantum chemical methods, the rate constants for three unimolecular elementary steps on the surface were calculated using transition state theory. A kinetics scheme containing 16 elementary steps was constructed, and computer modeling was performed. An excellent agreement between the experimental yields of the two major products and the calculated yields was obtained. Differences and similarities in the potential energy surfaces of 1-naphthyl radical + acetylene and those of ethylene are presented, and the kinetics mechanisms are discussed.
Hankel, M
2011-05-01
We present exact and estimated quantum differential and integral cross sections as well as product state distributions for the title reaction. We employ a time-dependent wavepacket method including all Coriolis couplings and also an adapted code where the helicity quantum number and with this the Coriolis couplings have been truncated. Results from helicity truncated as well as helicity conserving (HC) calculation are presented. The HC calculations fail to reproduce the exact results due to the influence of the centrifugal barrier. While the truncated calculation overestimate the exact integral cross sections they reproduce the features of the integral cross section very well. We also find that the product rotational state distributions are well reproduced if the maximum helicity state is chosen carefully. The helicity truncated calculations fail to give a good approximation of differential cross sections.
Saritas, Kayahan; Grossman, Jeffrey C.
2015-03-01
Molecules that undergo pericyclic isomerization reactions find interesting optical and energy storage applications, because of their usually high quantum yields, large spectral shifts and small structural changes upon light absorption. These reactions induce a drastic change in the conjugated structure such that substituents that become a part of the conjugated system upon isomerization can play an important role in determining properties such as enthalpy of isomerization and HOMO-LUMO gap. Therefore, theoretical investigations dealing with such systems should be capable of accurately capturing the interplay between electron correlation and exchange effects. In this work, we examine the dihydroazulene isomerization as an example conjugated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict thermochemical properties and to benchmark results from density functional theory (DFT) methods. Although DFT provides sufficient accuracy for similar systems, in this particular system, DFT predictions of ground state and reaction paths are inconsistent and non-systematic errors arise. We present a comparison between QMC and DFT results for enthalpy of isomerization, HOMO-LUMO gap and charge densities with a range of DFT functionals.
Theoretical studies of the dynamics of chemical reactions
Wagner, A.F. [Argonne National Laboratory, IL (United States)
1993-12-01
Recent research effort has focussed on several reactions pertinent to combustion. The formation of the formyl radical from atomic hydrogen and carbon monoxide, recombination of alkyl radicals and halo-alkyl radicals with halogen atoms, and the thermal dissociation of hydrogen cyanide and acetylene have been studied by modeling. In addition, the inelastic collisions of NCO with helium have been investigated.
Trapp, Oliver
2006-08-01
An analytical solution for the unified equation for degenerated (pseudo-) first-order reactions, e.g., enantiomerization processes, in dynamic CE is presented, and validated with a dataset of 31 250 elution profiles covering typical experimental parameters. The unified equation was applied to determine the enantiomerization barrier of the hypnotic glutarimide derivative thalidomide (Contergan(R)) by dynamic capillary electrokinetic chromatography (DEKC). The enantiomer separation of thalidomide was performed in an aqueous 50 mM sodium borate buffer at pH 9.3 in the presence of the chiral mobile phase additive carboxymethyl-beta-CD. Interconversion profiles featuring pronounced plateau formation were observed. Activation parameters DeltaH( not equal) and DeltaS( not equal) were obtained from temperature-dependent measurements between 20.0 and 37.5 degrees C in 2.5K steps. From the activation parameters the enantiomerization barrier of thalidomide at 37 degrees C under basic conditions were calculated to be DeltaG( not equal) = 93.2 kJ/mol. Comparison of the kinetic data with results obtained at pH 8.0 reveals the catalytic influence of the base on the enantiomerization barrier.
Bifurcations of Normally Hyperbolic Invariant Manifolds and Consequences for Reaction Dynamics
Mauguiere, F A L; Ezra, G S; Wiggins, S
2013-01-01
In this paper we study the breakdown of normal hyperbolicity and its consequences for reaction dynamics; in particular, the dividing surface, the flux through the dividing surface (DS), and the gap time distribution. Our approach is to study these questions using simple, two degree-of-freedom Hamiltonian models where calculations for the different geometrical and dynamical quantities can be carried out exactly. For our examples, we show that resonances within the normally hyperbolic invariant manifold may, or may not, lead to a `loss of normal hyperbolicity'. Moreover, we show that the onset of such resonances results in a change in topology of the dividing surface, but does not affect our ability to define a DS. The flux through the DS varies continuously with energy, even as the energy is varied in such a way that normal hyperbolicity is lost. For our examples the gap time distributions exhibit singularities at energies corresponding to the existence of homoclinic orbits in the DS, but these singularities a...
Dynamics of Surface Exchange Reactions Between Au and Pt for HER and HOR
Abrams, Billie; Vesborg, Peter Christian Kjærgaard; Bonde, Jacob Lindner;
2009-01-01
Cyclic voltammetric analysis of the Pt-on-Au system for hydrogen evolution and oxidation reactions (HER/HOR) indicates that dynamic surface exchange reactions occur between Pt and Au. HER/HOR activities depend on the dominant surface species present, which is controllable by the potential applied...
Reif, Maria M; Oostenbrink, Chris
2014-01-30
The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.
Analysis of dynamical behavior of reactions associated with 118,120,122Xe* isotopes
Grover, Neha; Sharma, Ishita; Kaur, Gurvinder; Sharma, Manoj K.
2017-03-01
In reference to recent experiment, the dynamical aspects of reactions forming even mass isotopes of 118,120,122Xe* nuclei are examined using the collective clusterization approach and the ℓ-summed Wong model. The role of excitation energy (or temperature), deformations, orientations and angular momentum etc. has been investigated for the 28Si + 90,92,94Zr reactions. In order to account for the role of deformations, the evaporation residue (ER) cross sections of 122Xe* nucleus have been studied in reference to the available experimental data by using spherical as well as deformed fragmentation approach. We have used optimum and compact orientations respectively for β2 alone and for β4 included, which inturn provide nice agreement with the available experimental cross-sections. Also, the effect of isospin (N/Z ratio) of decay fragments has been explored in view of the fragmentation analysis and preformation probability of 118,120,122Xe* nuclei. Additionally, the role of projectile nucleus is also explored by studying the fragmentation path of 118Xe* nucleus in comparison to 123Ba* system. Further, the ER cross-sections have been predicted for various even mass isotopes of 116,118,120,124Xe. In addition to this, to explore the fusion characteristics of 28Si + 90,92,94Zr reactions, the Wong model as well as the ℓ-summed Wong model has also been employed. Here also, the role of deformation in formation of 122Xe* nucleus has been examined and the calculated cross-sections find decent agreement with the experimental data.
Reaction dynamics of initial O2 sticking on Pd(100).
den Dunnen, Angela; Wiegman, Sandra; Jacobse, Leon; Juurlink, Ludo B F
2015-06-07
We have determined the initial sticking probability of O2 on Pd(100) using the King and Wells method for various kinetic energies, surface temperatures, and incident angles. The data suggest two different mechanisms to sticking and dissociation. Dissociation proceeds mostly through a direct process with indirect dissociation contributing only at low kinetic energies. We suggest a dynamical precursor state to account for the indirect dissociation channel, while steering causes the high absolute reactivity. A comparison of our results to those previously obtained for Pd(111) and Pd(110) highlights how similar results for different surfaces are interpreted to suggest widely varying dynamics.
Reaction dynamics of initial O2 sticking on Pd(100)
den Dunnen, Angela; Wiegman, Sandra; Jacobse, Leon; Juurlink, Ludo B. F.
2015-06-01
We have determined the initial sticking probability of O2 on Pd(100) using the King and Wells method for various kinetic energies, surface temperatures, and incident angles. The data suggest two different mechanisms to sticking and dissociation. Dissociation proceeds mostly through a direct process with indirect dissociation contributing only at low kinetic energies. We suggest a dynamical precursor state to account for the indirect dissociation channel, while steering causes the high absolute reactivity. A comparison of our results to those previously obtained for Pd(111) and Pd(110) highlights how similar results for different surfaces are interpreted to suggest widely varying dynamics.
Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina
2008-02-07
The reactions of 1-naphthyl radicals with ethylene were studied behind reflected shock waves in a single pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals as its C-I bond dissociation energy is relatively small. It is only approximately 65 kcal/mol as compared to the C-H bond strength in naphthalene which is approximately 112 kcal/mol and can thus produce naphthyl radicals at rather low reflected shock temperatures. The [ethylene]/[1-iodo-naphthalene] ratio in all of the experiments was approximately 100 in order to channel the free radicals into reactions with ethylene rather than iodonaphthalene. Four products resulting from the reactions of 1-naphthyl radicals with ethylene were found in the post shock samples. They were vinyl naphthalene, acenaphthene, acenaphthylene, and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from the attack of various free radicals on ethylene were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of ethylene is negligible. Three potential energy surfaces describing the production of vinyl naphthalene, acenaphthene, and acenaphthylene were calculated using quantum chemical methods and rate constants for the elementary steps on the surfaces were calculated using transition state theory. Naphthalene is not part of the reactions on the surfaces. Acenaphthylene is obtained only from acenaphthene. A kinetics scheme containing 27 elementary steps most of which were obtained from the potential energy surfaces was constructed and computer modeling was performed. An excellent agreement between the experimental yields of the four major products and the calculated yields was obtained.
De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.
2015-01-01
The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first
Yuan Xiaoming; Sun Jing; Sun Rui
2006-01-01
An error analysis of the dynamic shear modulus of stiff specimens from tests performed by a new resonant column device developed by the Institute of Engineering Mechanics, China was conducted. A modified approach for calculating the dynamic shear modulus of the stiff specimens is presented. The error formula of the tests was deduced and parameters that impact the accuracy of the test were identified. Using six steel specimens with known standard stiffness as a base, a revised dynamic shear modulus calculation for stiff specimens was formulated by comparing three of the models.The maximum error between the test results and the calculated results shown by curves from both the free-vibration and the resonant-vibration tests is less than 6%. The free-vibration and resonant-vibration tests for three types of stiff samples with a known modulus indicate that the maximum deviation between the actual and the tested value using the modified approach were less than 10%. As a result, the modified approach presented here is shown to be reliable and the new device can be used for testing dynamic shear modulus of any stiff materials at low shear strain levels
Isaacson, A.D.
1978-08-01
Using an approximate evaluation of Miller's golden rule formula to calculate autoionization widths which allows for the consideration only of L/sup 2/ functions, the positions and lifetimes of the lowest /sup 1/,/sup 3/P autoionizing states of He have been obtained to reasonable accuracy. This method has been extended to molecular problems, and the ab initio configuration interaction potential energy and width surfaces for the He(2/sup 3/S) + H/sub 2/ system have been obtained. Quantum mechanical close-coupling calculations of ionization cross sections using the complex V* - (i/2) GAMMA-potential have yielded rate constants in good agreement with the experimental results of Lindinger, et al. The potential energy surface of the He(2/sup 1/S) + H/sub 2/ system has also been obtained and exhibits not only a high degree of anisotropy, but also contains a relative maximum for a perpendicular (C/sub 2//sub v/) approach which appears to arise from s-p hybridization of the outer He orbital. However, similar ab initio calculations on the He(2/sup 1/S) + Ar system do not show such anomalous structure. In addition, the complex poles of the S-matrix (Siegert eigenvalues) were calculated for several autoionizing states of He and H/sup -/, with encouraging results even for quite modest basis sets. This method was extended to molecular problems, and results obtained for the He(2/sup 3/S) + H and He(2/sup 1/S) + H systems. 75 references.
The dynamics of reaction of Cl atoms with tetramethylsilane.
Retail, Bertrand; Rose, Rebecca A; Pearce, Julie K; Greaves, Stuart J; Orr-Ewing, Andrew J
2008-03-28
Rotational state distributions and state-selected CM-frame angular distributions were measured for HCl (v' = 0, j') products from the reaction of Cl-atoms with tetramethylsilane (TMS) under single collision conditions at a collision energy, E(coll), of 8.2 +/- 2.0 kcal mol(-1). The internal excitation of these products was very low with only 2% of the total energy available partitioned into HCl rotation. A transition state with a quasi-linear C-H-Cl moiety structure was computed and used to explain this finding. A backward peaking differential cross section was also reported together with a product translational energy (T') distribution with a maximum at T' approximately E(coll). This scattering behaviour is accounted for by reactions proceeding through a tight transition state on a highly skewed potential energy surface, which favours collisions at low impact parameters with a strong kinematic constraint on the internal excitation of the products. The large Arrhenius pre-exponential factor previously reported for this reaction is reconciled with the tight differential scattering observed in our study by considering the large size of the TMS molecule.
Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.
Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E
2016-05-10
Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.
Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.
2017-03-01
The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.
Shizgal, Bernie D.
2016-08-01
Nonclassical quadratures based on a new set of half-range polynomials, Tn(x) , orthogonal with respect to w(x) =e - x - b /√{ x } for x ∈ [ 0 , ∞) are employed in the efficient calculation of the nuclear fusion reaction rate coefficients from cross section data. The parameter b = B /√{kB T } in the weight function is temperature dependent and B is the Gamow factor. The polynomials Tn(x) satisfy a three term recurrence relation defined by two sets of recurrence coefficients, αn and βn. These recurrence coefficients define in turn the tridiagonal Jacobi matrix whose eigenvalues are the quadrature points and the weights are calculated from the first components of the eigenfunctions. For nonresonant nuclear reactions for which the astrophysical function can be expressed as a lower order polynomial in the relative energy, the convergence of the thermal average of the reactive cross section with this nonclassical quadrature is extremely rapid requiring in many cases 2-4 quadrature points. The results are compared with other libraries of nuclear reaction rate coefficient data reported in the literature.
Knowles, R.
1982-07-01
A general theory of moments for electrodynamic magnetic levitation systems has been developed using double Fourier series and dynamic circuit principles. Both employ Parseval's theorem using either wave constant derivatives or the polar waveconstant principle of the Fourier-Bessel/double Fourier series equivalence. A method for calculating angular derivatives of moments and forces is explained, and for all of these methods comparisons are made with experimental results obtained for single and split rail configurations. Extensions of dynamic circuit theory for tilted nonflat and circular magnets are also explained.
A 3-dimensional finite-difference method for calculating the dynamic coefficients of seals
Dietzen, F. J.; Nordmann, R.
1989-01-01
A method to calculate the dynamic coefficients of seals with arbitrary geometry is presented. The Navier-Stokes equations are used in conjunction with the k-e turbulence model to describe the turbulent flow. These equations are solved by a full 3-dimensional finite-difference procedure instead of the normally used perturbation analysis. The time dependence of the equations is introduced by working with a coordinate system rotating with the precession frequency of the shaft. The results of this theory are compared with coefficients calculated by a perturbation analysis and with experimental results.
Dynamical Calculations of bar K and MULTI-bar K Nuclei
Gazda, D.; Mareš, J.; Friedman, E.; Gal, A.
We report on our recent calculations of bar K and multi-bar K nuclei. Calculations were performed fully self-consistently across the periodic table using the relativistic mean-field approach. We aimed at detailed analysis of dynamical processes and various thresholds that determine the K- absorption width. Further, we studied the behavior of the nuclear medium under the influence of increasing strangeness in order to search for bar K condensation precursor phenomena. Last, we explored possibly self-bound strange hadronic configurations consisting of neutrons and bar K0 mesons and studied their properties.
Chao, S.; Jiao, C. W.; Liu, S.
2016-08-01
At this stage of the development of China's highway, the quantity and size of traffic signs are growing with the guiding information increasing. In this paper, a calculation method is provided for special sign board with reducing wind load measures to save construction materials and cost. The empirical model widely used in China is introduced for normal sign structure design. After that, this paper shows a computational fluid dynamics method, which can calculate both normal and special sign structures. These two methods are compared and analyzed with examples to ensure the applicability and feasibility of CFD method.
Collins, Peter; Ezra, Gregory S; Wiggins, Stephen
2013-01-01
We study reaction dynamics on a model potential energy surface exhibiting post-transition state bifurcation in the vicinity of a valley ridge inflection point. We compute fractional yields of products reached after the VRI region is traversed, both with and without dissipation. It is found that apparently minor variations in the potential lead to significant changes in the reaction dynamics. Moreover, when dissipative effects are incorporated, the product ratio depends in a complicated and highly non-monotonic fashion on the dissipation parameter. Dynamics in the vicinity of the VRI point itself play essentially no role in determining the product ratio, except in the highly dissipative regime.
郑娜; 钟春来; 樊铁栓
2012-01-01
An attempt is made to improve the evaluation of the prompt fission neutron emis- sion from 233U(n, f) reaction for incident neutron energies below 6 MeV. The multi-modal fission approach is applied to the improved version of Los Alamos model and the point by point model. The prompt fission neutron spectra and the prompt fission neutron as a function of fragment mass (usually named "sawtooth" data) v(A) are calculated independently for the three most dominant fission modes (standard I, standard II and superlong), and the total spectra and v(A) are syn- thesized. The multi-modal parameters are determined on the basis of experimental data of fission fragment mass distributions. The present calculation results can describe the experimental data very well, and the proposed treatment is thus a useful tool for prompt fission neutron emission prediction.
Low-energy heavy-ion reactions: a link between nuclear structure and reaction dynamics
Corradi, L; Beghini, S; Lin, C J; Montagnoli, G; Pollarolo, G; Scarlassara, F; Segato, G F; Stefanini, A M; Zheng, L F
1999-01-01
High precision data recently obtained in the study of multinucleon transfer and sub-barrier fusion reactions at LNL are presented. The studies of transfer channels in the systems sup 4 sup 0 sup , sup 4 sup 8 Ca+ sup 1 sup 2 sup 4 Sn and sup 6 sup 4 Ni+ sup 2 sup 3 sup 8 U revealed important effects not identified in the past, and demonstrated the possibility of a quantitative understanding of the role played by the various degrees of freedom in the reaction mechanism. Evidence of their influence on the fusion enhancements seem to show-up in the systems sup 4 sup 0 Ca+ sup 1 sup 2 sup 4 sup , sup 1 sup 1 sup 6 Sn and sup 4 sup 0 Ca+ sup 9 sup 0 sup , sup 9 sup 6 Zr, but, in general, the data still escape a consistent treatment.
Bottoni S.
2014-03-01
Full Text Available The heavy ion reaction 22Ne+208Pb at 128 MeV of bombarding energy has been studied using the PRISMA-CLARA experimental setup at Legnaro National Laboratories. Elastic, inelastic and one nucleon transfer cross sections have been measured. The experimental results are presented in parallel with the analysis on existing data for the unstable 24Ne nucleus, from the reaction 24Ne+208Pb at 182 MeV (measured at SPIRAL with the VAMOS-EXOGAM setup. The β2C charge deformation parameter for both 22Ne and 24Ne has been determined by a DWBA analysis of the experimental angular dis- tributions, showing a strong reduction for 24Ne.
Fasano, C.G.; Locher, M.P. (Paul Scherrer Inst., Villigen (Switzerland). Theory Group)
1991-02-01
We present a fully relativistic calculation for anti pd {yields} 5 {pi}p and anti pd {yields} 3 {pi}p that includes angular momentum and spin dynamics. We calculate the inclusive proton distributions from two diagrams: the leading 'tree' diagram, and the diagram for pion rescattering. Pion-nucleon rescattering proceeds through the {Delta} , in the Rarita-Swinger formalism, thus preserving the correct angular dependence. We use realistic parameterizations of the deuteron, keeping both the S and D states. The loop integrations for the rescattering amplitude and the phase space integrations have been done numerically. We find that the combined effects of a correct treatment of the rescattered pion and relativity are small in comparison with a simple non-relativistic calculation. (orig.).
Quantum Tunneling Rates of Gas-Phase Reactions from On-the-Fly Instanton Calculations.
Beyer, Adrian N; Richardson, Jeremy O; Knowles, Peter J; Rommel, Judith; Althorpe, Stuart C
2016-11-03
The instanton method obtains approximate tunneling rates from the minimum-action path (known as the instanton) linking reactants to the products at a given temperature. An efficient way to find the instanton is to search for saddle-points on the ring-polymer potential surface, which is obtained by expressing the quantum Boltzmann operator as a discrete path-integral. Here we report a practical implementation of this ring-polymer form of instanton theory into the Molpro electronic-structure package, which allows the rates to be computed on-the-fly, without the need for a fitted analytic potential-energy surface. As a test case, we compute tunneling rates for the benchmark H + CH4 reaction, showing how the efficiency of the instanton method allows the user systematically to converge the tunneling rate with respect to the level of electronic-structure theory.
Global dynamics of a reaction-diffusion system
Yuncheng You
2011-02-01
Full Text Available In this work the existence of a global attractor for the semiflow of weak solutions of a two-cell Brusselator system is proved. The method of grouping estimation is exploited to deal with the challenge in proving the absorbing property and the asymptotic compactness of this type of coupled reaction-diffusion systems with cubic autocatalytic nonlinearity and linear coupling. It is proved that the Hausdorff dimension and the fractal dimension of the global attractor are finite. Moreover, the existence of an exponential attractor for this solution semiflow is shown.
Zhang, Chao-Zhi; Li, Shi-Juan; Cao, Hui; Song, Ming-Xia; Kong, Qing-Gang
2015-05-01
A convenient method was reported to synthesize 3-(4‧-nitrophenyl)iminocoumarin by a cyclization reaction following a Knoevenagel reaction of 2-hydroxybenzaldehyde with 4-nitrophenylacenitrile in an ethanol solution. Piperidine or piperazine was employed respectively as catalyst. Crystal structure of 3-(4‧-nitrophenyl)iminocoumarin shows that the molecules are H-aggregation due to π-π stacking and hydrogen bonds between adjacent molecules, as a result, electrons would transfer easily from a molecule to an adjacent molecule. Based on theoretical calculations of the electronic structures and thermodynamic parameters of the reactive intermediates in these cyclization reactions, the reaction mechanisms were postulated. Data of single crystal and spectrum of UV-vis absorption show that 3-(4‧-nitrophenyl)iminocoumarin is good π-conjugated compound and would be potentially employed as donor-acceptor polymer units for developing bulk heterojunction solar cell. This paper suggests a convenient and effective method for synthesizing ring-locked D-A copolymer units for developing solar cell materials.
Liu, Peng; Li, Chen; Wang, Dunyou
2017-09-25
The Cl(-) + CH3I → CH3Cl + I(-) reaction in water was studied using combined multi-level quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculations with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 kcal/mol and 19.0 kcal/mol respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.
Michel, K. H.; ćakır, D.; Sevik, C.; Peeters, F. M.
2017-03-01
The elastic constant C11 and piezoelectric stress constant e1 ,11 of two-dimensional (2D) dielectric materials comprising h-BN, 2 H -MoS2 , and other transition-metal dichalcogenides and dioxides are calculated using lattice dynamical theory. The results are compared with corresponding quantities obtained with ab initio calculations. We identify the difference between clamped-ion and relaxed-ion contributions with the dependence on inner strains which are due to the relative displacements of the ions in the unit cell. Lattice dynamics allows us to express the inner-strain contributions in terms of microscopic quantities such as effective ionic charges and optoacoustical couplings, which allows us to clarify differences in the piezoelectric behavior between h-BN and MoS2. Trends in the different microscopic quantities as functions of atomic composition are discussed.
王岩国; 刘红荣; 杨奇斌; 张泽
2003-01-01
Off-axis electron holography in a field emission gun transmission-electron microscope and electron dynamic calculation are used to determine the absorption coefficient and inelastic mean free path (IMFP) of copper.Dependence of the phase shift of the exit electron wave on the specimen thickness is established by electron dynamic simulation. The established relationship makes it possible to determine the specimen thickness with the calculated phase shift by match of the phase shift measured in the reconstructed phase image. Based on the measured amplitudes in reconstructed exit electron wave and reference wave in the vacuum, the examined IMFP of electron with energy of 200kV in Cu is obtained to be 96nm.
Probing the role of Skyrme interactions on the fission dynamics of the 6Li + 238U reaction
Sharma, Ishita; Kumar, Raj; Sharma, Manoj K.
2017-06-01
The performance of selected five Skyrme forces (out of a set of 240), tested by Dutra et al., is analyzed in view of fusion-fission dynamics. These forces are assumed to perform better for neutron-rich systems, so the choice of the reaction is accordingly made by opting for a neutron-rich target in 6Li + 238U reaction. This reaction is diagnosed further in reference to fusion hindrance within the dynamical approach of the cluster-decay model (DCM). In order to reduce the computational time, three Skyrme forces are figured out with the criteria that these forces cover the barrier characteristics of the remaining two forces as well. The fission cross-sections are successfully addressed at low energies for the 6Li + 238U reaction. However, at relatively higher energies, the excitation functions show theoretical suppression with respect to experimental data, which may be associated with the possible existence of incomplete fusion (ICF). For ICF, we have considered that the 6Li broke into 4He + 2H, as mentioned in the experimental work. The calculations of ICF are carried out for the 4He + 238U reaction with the selected Skyrme forces at E_{c.m.} = 26.20 and 27.51 MeV. These forces address the data nicely for the compound nucleus (CN) as well as ICF processes. Here, the NRAPR force seems to require lesser barrier modification as compared to the other forces, therefore it can be used as an alternate choice for calculating the interaction potential. Additionally, the prediction of cross-sections at lower energies has been done with DCM using the NRAPR force. The ℓ-dependent % barrier modification of the Skyrme forces undertaken is also worked out in reference to fusion hindrance at below barrier energies.
Closed Loop Adaptive Refinement of Dynamical Models for Complex Chemical Reactions
2008-06-26
CH3Br, Ar + H2O are given below. 3.1 Cl− + CH3Br Reaction A global RS-HDMR input/output map for the SN2 reaction Cl− +CH3Br→ ClCH3 +Br − (9) 3 was...2257-2266. [16] Wang H. B., Hase W. L. (1996). Reaction path Hamiltonian analysis of the dynamics for Cl− + CH3Br→ ClCH3 + Br − SN2 nucleophilic... reaction Cl − + CH3Br → ClCH3 + Br −, J. Chem. Phys., 111(24), 10887- 10894. [18] Sun, L., Hase, W. L., Song, K. (2001). Trajectory studies of SN2
Kanai, Y; Takeuchi, N
2009-10-14
We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.
Lattice dynamics and spin-phonon interactions in multiferroic RMn2O5: Shell model calculations
Litvinchuk, A. P.
2009-08-01
The results of the shell model lattice dynamics calculations of multiferroic RMn2O5 materials (space group Pbam) are reported. Theoretical even-parity eigenmode frequencies are compared with those obtained experimentally in polarized Raman scattering experiments for R=Ho,Dy. Analysis of displacement patterns allows to identify vibrational modes which facilitate spin-phonon coupling by modulating the Mn-Mn exchange interaction and provides explanation of the observed anomalous temperature behavior of phonons.
Lattice dynamics of wurtzite CdS: Neutron scattering and ab-initio calculations
Debernardi, A.; Pyka, N. M.; Göbel, A.; Ruf, T.; Lauck, R.; Kramp, S.; Cardona, M.
1997-08-01
We have measured the phonon dispersion of wurtzite CdS by inelastic neutron scattering in a single crystal made from the nonabsorbing isotope 114Cd. One of the two silent B 1-modes occurs at 3.96 THz ( k = 0 ). It is significantly lower and less dispersive than so far assumed. Previous semiempirical lattice dynamical models need to be reanalyzed. However, the observed dispersion branches compare favorably with an ab-initio calculation.
Krykunov, Mykhaylo; Autschbach, Jochen
2007-01-14
We report implementations and results of time-dependent density functional calculations (i) of the frequency-dependent magnetic dipole-magnetic dipole polarizability, (ii) of the (observable) translationally invariant linear magnetic response, and (iii) of a linear intensity differential (LID) which includes the dynamic dipole magnetizability. The density functional calculations utilized density fitting. For achieving gauge-origin independence we have employed time-periodic magnetic-field-dependent basis functions as well as the dipole velocity gauge, and have included explicit density-fit related derivatives of the Coulomb potential. We present the results of calculations of static and dynamic magnetic dipole-magnetic dipole polarizabilities for a set of small molecules, the LID for the SF6 molecule, and dispersion curves for M-hexahelicene of the origin invariant linear magnetic response as well as of three dynamic polarizabilities: magnetic dipole-magnetic dipole, electric dipole-electric dipole, and electric dipole-magnetic dipole. We have also performed comparison of the linear magnetic response and magnetic dipole-magnetic dipole polarizability over a wide range of frequencies for H2O and SF6.
Calculation of heat capacities of light and heavy water by path-integral molecular dynamics
Shiga, Motoyuki; Shinoda, Wataru
2005-10-01
As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2O at 300 K, 6.9 in the liquid H2O at 300 K, and 4.1 in the ice IhH2O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10% higher than that of H2O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions.
Chiral dynamics in the gamma p --> p pi0 reaction
Blin, A N Hiller; Vacas, M J Vicente
2014-01-01
We investigate the neutral pion photoproduction on the proton near threshold in covariant chiral perturbation theory with the explicit inclusion of Delta degrees of freedom. This channel is specially sensitive to chiral dynamics and the advent of very precise data from the Mainz microtron has shown the limits of the convergence of the chiral series for both the heavy baryon and the covariant approaches. We show that the inclusion of the Delta resonance substantially improves the convergence leading to a good agreement with data for a wider range of energies.
Yang, Huan; Han, Keli; Schatz, George C; Smith, Sean C; Hankel, Marlies
2010-10-21
We present exact quantum differential cross sections and exact and estimated integral cross sections and branching ratios for the title reaction. We employ a time-dependent wavepacket method as implemented in the DIFFREALWAVE code including all Coriolis couplings and also an adapted DIFFREALWAVE code where the helicity quantum number and with this the Coriolis couplings have been truncated. Our exact differential cross sections at 0.453 eV total energy, one of the experimental energies, show good agreement with the experimental results for one of the product channels. While the truncated calculation present a significant reduction in the computational effort needed they overestimate the exact integral cross sections.
Brons, S; Elsässer, T; Ferrari, A; Gadioli, E; Mairani, A; Parodi, K; Sala, P; Scholz, M; Sommerer, F
2010-01-01
Monte Carlo codes are rapidly spreading among hadron therapy community due to their sophisticated nuclear/electromagnetic models which allow an improved description of the complex mixed radiation field produced by nuclear reactions in therapeutic irradiation. In this contribution results obtained with the Monte Carlo code FLUKA are presented focusing on the production of secondary fragments in carbon ion interaction with water and on CT-based calculations of absorbed and biological effective dose for typical clinical situations. The results of the simulations are compared with the available experimental data and with the predictions of the GSI analytical treatment planning code TRiP.
Quasi-elastic reactions: an interplay of reaction dynamics and nuclear structure
Recchia F.
2011-10-01
Full Text Available Multinucleon transfer reactions have been investigated in 40Ar+208Pb with the Prisma+Clara set-up. The experimental differential cross sections of different neutron transfer channels have been obtained at three different angular settings taking into account the transmission through the spectrometer. The experimental yields of the excited states have been determined via particle-γ coincidences. In odd Ar isotopes, we reported a signif cant population of 11/2− states, reached via neutron transfer. Their structure matches a stretched conf guration of the valence neutron coupled to vibration quanta.
The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak
Jing Li
2014-01-01
Full Text Available The stability and bifurcations of multiple limit cycles for the physical model of thermonuclear reaction in Tokamak are investigated in this paper. The one-dimensional Ginzburg-Landau type perturbed diffusion equations for the density of the plasma and the radial electric field near the plasma edge in Tokamak are established. First, the equations are transformed to the average equations with the method of multiple scales and the average equations turn to be a Z2-symmetric perturbed polynomial Hamiltonian system of degree 5. Then, with the bifurcations theory and method of detection function, the qualitative behavior of the unperturbed system and the number of the limit cycles of the perturbed system for certain groups of parameter are analyzed. At last, the stability of the limit cycles is studied and the physical meaning of Tokamak equations under these parameter groups is given.
Spur Gears Static and Dynamic Meshing Simulation and Tooth Stress Calculation
Jammal Ali
2015-01-01
Full Text Available Gear meshing is a complicated process, and is subjected to the simulation process in the following paper. A flexible quasi-static and dynamic finite element analysis (FEA models were built, to calculate contact principal and shear stresses. Full sized 3D spur gears are simulated under different boundary conditions. The first model, was a quasi-static analysis, where torque was used as input; and the second model, which was transient dynamic analysis, where rotational speed was used as input. The static analysis showed high stress concentration at the tooth contact point and under the contacting surface. The dynamic analysis provided the highest stress value at the different stages of gear engagement points along the line of action. Analytical and simulation result were in agreement in general, and the use of the new simulation model was discussed.
Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida
2009-06-01
A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.
Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida
2009-06-01
A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.
Platelet reactions to modified surfaces under dynamic conditions.
Rhodes, N P; Shortland, A P; Rattray, A; Williams, D F
1998-12-01
The influence of surfaces on the reactions of platelets in whole blood under laminar flow was investigated in a cone and plate viscometer. Citrated whole blood was exposed to steel, PMMA and PMMA modified with PEO at low (500 s(-1)) and high (4000 s(-1)) wall shear rates at room temperature for a period of 100 s. Treated blood samples were fixed with paraformaldehyde, stained with a monoclonal antibody for CD41 (platelet GPIIb/IIIa) conjugated with phycoerythrin and analyzed by flow cytometry. The reactions of platelets (microparticle generation and formation of platelet-platelet, platelet-red blood cell and red blood cell-microparticle aggregates) to these environments were quantified. Additionally, the size of platelet-platelet aggregates was assessed. The percentage platelet aggregation and numbers of microparticles generated were independent of surface type at any shear rate. The composition of the aggregates formed was influenced by the surface: at low and high shear rates PMMA caused the generation of platelet-platelet aggregates of the greatest size. The numbers of red blood cell-platelet and red blood cell-microparticle aggregates also varied depending on the surface. Fewer red blood cell-platelet aggregates were formed at higher shear rates, whereas the reverse was true for red blood cell-microparticle aggregates. It is concluded that these variations may help to explain the differential effects of surfaces to the induction of distant thrombotic events: microparticles may be protected from loss from the blood stream by their association with red blood cells at high shear rates.
V. A. Gribkov
2015-01-01
Full Text Available We consider the multilink pendulum system consisting of six physical pendulums. A pendulum (carrier has inertia parameters, which significantly exceed the remaining (carried ones placed on the carrier. In addition to the system under analysis, in particular, the paper presents a design scheme for a two-stage liquid fuel rocket using pendulums as the analogues of fluctuating fuel. Pendulum models also find application to solve problems of stabilization of space tether systems. The objective of the study is to determine dynamic characteristics of the said sixmembered pendulum system, as well as to identify specific dynamic properties inherent in objects of this kind. Dynamic characteristics of the system are determined by calculations. A physical model of the pendulum allowed us to compare the calculated and experimental results. To conduct the frequency tests of the pendulum model three pilot units have been created. The first two units turned out to be inappropriate for fulfilling the experimental tasks for various reasons. The third unit enabled us to obtain desirable experimental results. The "calculation–experiment” discrepancy on the natural frequencies of the pendulum model for the majority of frequencies was less than 5%. We analyzed the dynamic features of multilink pendulum systems "carried by the carrier unit links". The analysis results are applicable to the above-noted object classes of rocket and space technology.
Adsorption and Reaction of CO on (100) Surface of SrTiO3 by Density Function Theory Calculation
YUN Jiang-Ni; ZHANG Zhi-Yong; ZHANG Fu-Chun
2008-01-01
Adsorption and reaction of CO on two possible terminations of SrTi03 (100) surface are investigated by the first-principles calculation of plane wave ultrasoft pseudopotential based on the density function theory. The adsorption energy, Mulliken population analysis, density of states (DOS) and electronic density difference of CO on SrTi03 (100) surface, which have never been investigated before as far as we know are performed. The calculated results reveal that the Ti-CO orientation is the most stable configuration and the adsorption energy (0.449eV) is quite small. CO molecules adsorb weakly on the SrTiO3 (100) surface, there is predominantly electrostatic attraction between CO and the surface rather than a chemical bonding mechanism.
Al-abyad, Mogahed; Mohamed, Gehan Y. [Atomic Energy Authority, Cairo (Egypt). Experimental Nuclear Physics Dept.
2017-08-01
Neutron capture cross section (σ{sub 0}) and resonance integral (I{sub 0}) of the reaction {sup 186}W(n,γ){sup 187}W were measured experimentally using the research reactor (ETRR-2) and an Am-Be neutron source, also calculated using TALYS-1.6 code. The present results of σ{sub 0} are (39.08±2.6, 38.75±0.98 and 38.33 barn) and I{sub 0} are (418.5±74, 439.3±36 and 445.5 barn) by using the reactor, neutron source and TALYS-1.6, respectively. The present results are in acceptable agreement with most of the previous experimental and evaluated data as well as the theoretical calculations.
A method of moments for calculating dynamic responses beyond linear response theory
Kang Yan-Mei; Xu Jian-Xue; Xie Yong
2005-01-01
A method of moments for calculating the dynamic response of periodically driven overdamped nonlinear stochastic systems in the general response sense is proposed, which is a modification of the method of moments confined within linear response theory. The calculating experience suggests that the proposed technique is simple and efficient in implementation, and the comparison with stochastic simulation shows that the first three orders of susceptibilities calculated by the proposed technique have high accuracy. The dependence of the spectral amplification parameters at the first three harmonics on the noise intensity is also investigated, and another observed phenomenon of stochastic resonance in the systems induced by the location of a single periodic orbit is disclosed and explained.
Leaf trajectory calculation for dynamic multileaf collimation to realize optimized fluence profiles
Dirkx, M.L.P.; Heijmen, B.J.M.; Santvoort, J.P.C. van [University Hospital Rotterdam/Daniel den Hoed Cancer Center, Groene Hilledijk 301, 3075 EA Rotterdam (Netherlands)
1998-05-01
An algorithm for the calculation of the required leaf trajectories to generate optimized intensity modulated beam profiles by means of dynamic multileaf collimation is presented. This algorithm iteratively accounts for leaf transmission and collimator scatter and fully avoids tongue-and-groove underdosage effects. Tests on a large number of intensity modulated fields show that only a limited number of iterations, generally less than 10, are necessary to minimize the differences between optimized and realized fluence profiles. To assess the accuracy of the algorithm in combination with the dose calculation algorithm of the Cadplan 3D treatment planning system, predicted absolute dose distributions for optimized fluence profiles were compared with dose distributions measured on the MM50 Racetrack Microtron and resulting from the calculated leaf trajectories. Both theoretical and clinical cases yield an agreement within 2%, or within 2 mm in regions with a high dose gradient, showing that the accuracy is adequate for clinical application. (author)
Leaf trajectory calculation for dynamic multileaf collimation to realize optimized fluence profiles
Dirkx, M. L. P.; Heijmen, B. J. M.; van Santvoort, J. P. C.
1998-05-01
An algorithm for the calculation of the required leaf trajectories to generate optimized intensity modulated beam profiles by means of dynamic multileaf collimation is presented. This algorithm iteratively accounts for leaf transmission and collimator scatter and fully avoids tongue-and-groove underdosage effects. Tests on a large number of intensity modulated fields show that only a limited number of iterations, generally less than 10, are necessary to minimize the differences between optimized and realized fluence profiles. To assess the accuracy of the algorithm in combination with the dose calculation algorithm of the Cadplan 3D treatment planning system, predicted absolute dose distributions for optimized fluence profiles were compared with dose distributions measured on the MM50 Racetrack Microtron and resulting from the calculated leaf trajectories. Both theoretical and clinical cases yield an agreement within 2%, or within 2 mm in regions with a high dose gradient, showing that the accuracy is adequate for clinical application.
STUDY OF THE REACTION DYNAMICS OF Li + HF, HCl BY THE CROSSED MOLECULAR BEAMS METHOD
Becker, Christopher H.; Casavecchia, Piergiorgio; Tiedemann, Peter W.; Valentini, James J.; Lee, Yuan T.
1980-05-01
The reactions of (I) Li + HF {yields} LiF + H and (II) Li + HCl {yields} LiCl + H have been studied by the crossed molecular beams method. Angular distributions [N({theta})] of product molecules have been measured at 4 collision energies (E{sub c}) ranging from about 2 to 9 kcal/mole and time-of-flight (TOF) measurements of product velocity distribution were made at approximately E{sub c} = 3 and 9 kcal/mole for both reactions (I) and (II). The combined N({theta}) and TOF results were used to generate contour maps of lithium-halide product flux in angle and recoil velocity in the center-of-mass (c.m.) frame. For reaction (I) at E{sub c} = 3 kcal/mole the c.m. angular distribution [T({theta})] shows evidence of complex formation with near forward-backward symmetry; slightly favored backward peaking is observed. The shape of this T({theta}) indicates there is significant parallel or antiparallel spatial orientation of initial and final orbital angular momentum {rvec L} and {rvec L}', even though with H departing L' must be rather small and {rvec L} = {rvec J}', where {rvec J}' is the final rotational angular momentum vector. It is deduced that coplanar reaction geometries are strongly favored. At E{sub c} = 8.7 kcal/mole the T({theta}) of reaction (I) becomes strongly forward peaked. The product translational energy distributions P(E{sub T}') at both these collision energies give an average E{sub T}' of ~55% of the total available energy; this appears consistent with a theoretically calculated late exit barrier to reaction. The T({theta}) at E{sub c} = 2.9 and 9.2 kcal/mole for reaction (II) are forward-sideways peaked. Most of the available energy (~70%) goes into recoil velocity at both E{sub c} for LiCl formation. This suggests a late energy release for this 11 kcal/mole exoergic reaction. Both reactions (I) and (II) show evidence of no more than a minor partitioning of energy into product vibrational excitation. Integral reactive cross sections ({sigma}{sub R
Tan, Rui Shan; Yan, Wei; Lin, Shi Ying
2017-01-01
A computational study for the title reaction is carried out employing recent ab initio potential energy surface. J = 0 reaction probability is obtained using both quasiclassical trajectory (QCT) and wave packet methods. The total and state resolved integral as well as differential cross sections are also obtained by means of QCT method. Dynamics of the title reaction shows qualitative similarity with its isotopic counterpart, the H + CaCl reaction, but quantitatively, reactivity is significantly enhanced in the title reaction. In addition, the effect of initial rotational state excitation on H + CaCl reaction is investigated.
Time-resolved imaging of purely valence-electron dynamics during a chemical reaction
Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.
2011-01-01
Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...... the non-adiabatic photodissociation of carbon disulphide demonstrate how the purely electronic rearrangements of the valence electrons can be projected from inherently coupled electronic-vibrational dynamics. Combined with ongoing efforts in molecular frame alignment(20) and orientation(21,22), TRMFPADs...
Shi, Qicun; Meroueh, Samy O; Fisher, Jed F; Mobashery, Shahriar
2008-07-23
Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2
Valero, Rosendo; Truhlar, Donald G
2007-09-06
A diabatic representation is convenient in the study of electronically nonadiabatic chemical reactions because the diabatic energies and couplings are smooth functions of the nuclear coordinates and the couplings are scalar quantities. A method called the fourfold way was devised in our group to generate diabatic representations for spin-free electronic states. One drawback of diabatic states computed from the spin-free Hamiltonian, called a valence diabatic representation, for systems in which spin-orbit coupling cannot be ignored is that the couplings between the states are not zero in asymptotic regions, leading to difficulties in the calculation of reaction probabilities and other properties by semiclassical dynamics methods. Here we report an extension of the fourfold way to construct diabatic representations suitable for spin-coupled systems. In this article we formulate the method for the case of even-electron systems that yield pairs of fragments with doublet spin multiplicity. For this type of system, we introduce the further simplification of calculating the triplet diabatic energies in terms of the singlet diabatic energies via Slater's rules and assuming constant ratios of Coulomb to exchange integrals. Furthermore, the valence diabatic couplings in the triplet manifold are taken equal to the singlet ones. An important feature of the method is the introduction of scaling functions, as they allow one to deal with multibond reactions without having to include high-energy diabatic states. The global transformation matrix to the new diabatic representation, called the spin-valence diabatic representation, is constructed as the product of channel-specific transformation matrices, each one taken as the product of an asymptotic transformation matrix and a scaling function that depends on ratios of the spin-orbit splitting and the valence splittings. Thus the underlying basis functions are recoupled into suitable diabatic basis functions in a manner that
Spectroscopy and reaction dynamics of collision complexes containing hydroxyl radicals
Lester, M.I. [Univ. of Pennsylvania, Philadelphia (United States)
1993-12-01
The DOE supported work in this laboratory has focused on the spectroscopic characterization of the interaction potential between an argon atom and a hydroxyl radical in the ground X{sup 2}II and excited A {sup 2}{summation}{sup +} electronic states. The OH-Ar system has proven to be a test case for examining the interaction potential in an open-shell system since it is amenable to experimental investigation and theoretically tractable from first principles. Experimental identification of the bound states supported by the Ar + OH (X {sup 2}II) and Ar + OH(A {sup 2}{summation}{sup +}) potentials makes it feasible to derive realistic potential energy surfaces for these systems. The experimentally derived intermolecular potentials provide a rigorous test of ab initio theory and a basis for understanding the dramatically different collision dynamics taking place on the ground and excited electronic state surfaces.
Effect of the geometric phase on the dynamics of the hydrogen-exchange reaction.
Juanes-Marcos, Juan Carlos; Althorpe, Stuart C; Wrede, Eckart
2007-01-28
A recent puzzle in nonadiabatic quantum dynamics is that geometric phase (GP) effects are present in the state-to-state opacity functions of the hydrogen-exchange reaction, but cancel out in the state-to-state integral cross sections (ICSs). Here the authors explain this result by using topology to separate the scattering amplitudes into contributions from Feynman paths that loop in opposite senses around the conical intersection. The clockwise-looping paths pass over one transition state (1-TS) and scatter into positive deflection angles; the counterclockwise-looping paths pass over two transition states (2-TS) and scatter into negative deflection angles. The interference between the 1-TS and 2-TS paths thus integrates to a very small value, which cancels the GP effects in the ICS. Quasiclassical trajectory (QCT) calculations reproduce the scattering of the 1-TS and 2-TS paths into positive and negative deflection angles and show that the 2-TS paths describe a direct insertion mechanism. The inserting atom follows a highly constrained "S-bend" path, which allows it to avoid both the other atoms and the conical intersection and forces the product diatom to scatter into high rotational states. By contrast, the quantum 2-TS paths scatter into a mainly statistical distribution of rotational states, so that the quantum 2-TS total ICS is roughly twice the QCT ICS at 2.3 eV total energy. This suggests that the S-bend constraint is relaxed by tunneling in the quantum system. These findings on H+H(2) suggest that similar cancellations or reductions in GP effects are likely in many other reactions.
Analysis of dynamic foot pressure distribution and ground reaction forces
Ong, F. R.; Wong, T. S.
2005-04-01
The purpose of this study was to assess the relationship between forces derived from in-shoe pressure distribution and GRFs during normal gait. The relationship served to demonstrate the accuracy and reliability of the in-shoe pressure sensor. The in-shoe pressure distribution from Tekscan F-Scan system outputs vertical forces and Centre of Force (COF), while the Kistler force plate gives ground reaction forces (GRFs) in terms of Fz, Fx and Fy, as well as vertical torque, Tz. The two systems were synchronized for pressure and GRFs measurements. Data was collected from four volunteers through three trials for both left and right foot under barefoot condition with the in-shoe sensor. The forces derived from pressure distribution correlated well with the vertical GRFs, and the correlation coefficient (r2) was in the range of 0.93 to 0.99. This is a result of extended calibration, which improves pressure measurement to give better accuracy and reliability. The COF from in-shoe sensor generally matched well with the force plate COP. As for the maximum vertical torque at the forefoot during toe-off, there was no relationship with the pressure distribution. However, the maximum torque was shown to give an indication of the rotational angle of the foot.
Yu, Feng
2012-02-05
The bimolecular nucleophilic substitution (S(N)2) reaction of F(a)(-) with NH(2)F(b) has been investigated with the ab initio direct classical trajectory method. According to our trajectory calculations, a dynamic behavior of nonstatistical central barrier recrossing is revealed. Among the 64 trajectories calculated in this work, 45 trajectories follow the dynamic reaction pathways as assumed by statistical theory and other 19 trajectories with central barrier recrossings are nonstatistical. For the nonstatistical trajectories, the central barrier recrossings may originate from the inefficient kinetic energy transfer from the intramolecular modes of the NH(2)F(a) moiety in the dynamic F(b)(-)…H-NH-F(a) complex to the intermolecular modes of the dynamic F(b)(-)…H-NH-F(a) complex on the exit-channel potential energy surface. With respect to the dynamic behavior of the nonstatistical central barrier recrossing, the statistical theories such as the Rice-Ramsperger-Kassel-Marcus and transition state theories without further corrections cannot be used to model the reaction kinetics for this S(N)2 reaction.
V.O. Kharchenko
2015-06-01
Full Text Available Within this paper we have the studied structural and electronic properties of zirconium crystal with vacancies from the first principles. We have defined the optimal values for the lattice constants. The corresponding densities of states and energetic spectrum were calculated. These results gave a possibility to define the Fermi structure of the zirconium crystal with vacancies. In the framework of the molecular dynamics simulations we have studied the dynamics of the ensemble of periodically located vacancies in the zirconium crystal with an increase in temperature. We have analyzed the reconstruction of atomic structure and change in the total volume of the crystal with the temperature growth. The dependencies of the volume expansion coefficient for the pure zirconium without vacancies end zirconium crystal with different vacancies concentration on the temperature were studied.
Kuo, Nathanael, E-mail: nkuo8@jhmi.edu; Prince, Jerry L. [Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Dehghan, Ehsan [Philips Research North America, Briarcliff Manor, New York 10510 (United States); Deguet, Anton [Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Mian, Omar Y.; Le, Yi; Song, Danny Y. [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland 21231 (United States); Burdette, E. Clif [Acoustic MedSystems Inc., Savoy, Illinois 61974 (United States); Fichtinger, Gabor [School of Computing, Queen' s University, Kingston, Ontario K7L3N6 (Canada); Lee, Junghoon [Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, Maryland 21218 and Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland 21231 (United States)
2014-09-15
Purpose: Brachytherapy is a standard option of care for prostate cancer patients but may be improved by dynamic dose calculation based on localized seed positions. The American Brachytherapy Society states that the major current limitation of intraoperative treatment planning is the inability to localize the seeds in relation to the prostate. An image-guidance system was therefore developed to localize seeds for dynamic dose calculation. Methods: The proposed system is based on transrectal ultrasound (TRUS) and mobile C-arm fluoroscopy, while using a simple fiducial with seed-like markers to compute pose from the nonencoded C-arm. Three or more fluoroscopic images and an ultrasound volume are acquired and processed by a pipeline of algorithms: (1) seed segmentation, (2) fiducial detection with pose estimation, (3) seed matching with reconstruction, and (4) fluoroscopy-to-TRUS registration. Results: The system was evaluated on ten phantom cases, resulting in an overall mean error of 1.3 mm. The system was also tested on 37 patients and each algorithm was evaluated. Seed segmentation resulted in a 1% false negative rate and 2% false positive rate. Fiducial detection with pose estimation resulted in a 98% detection rate. Seed matching with reconstruction had a mean error of 0.4 mm. Fluoroscopy-to-TRUS registration had a mean error of 1.3 mm. Moreover, a comparison of dose calculations between the authors’ intraoperative method and an independent postoperative method shows a small difference of 7% and 2% forD{sub 90} and V{sub 100}, respectively. Finally, the system demonstrated the ability to detect cold spots and required a total processing time of approximately 1 min. Conclusions: The proposed image-guidance system is the first practical approach to dynamic dose calculation, outperforming earlier solutions in terms of robustness, ease of use, and functional completeness.
Siddik, Tarik
2013-01-01
Fusion serves an inexhaustible energy for humankind. Although there have been significant research and development studies on the inertial and magnetic fusion reactor technology, Furthermore, there are not radioactive nuclear waste problems in the fusion reactors. In this study, (n, p) reactions for some structural fusion materials such as 27Al, 51V, 52Cr, 55Mn and 56Fe have been investigated. The new calculations on the excitation functions of 27 Al(n,p) 27 Mg, 51 V(n,p) 51 Ti, 52 Cr(n,p) 52 V, 55 Mn(n,p) 55 Cr and 56 Fe(n,p) 56 Mn reactions have been carried out up to 30 MeV incident neutron energy. Statistical model calculations, based on the Hauser-Feshbach formalism, have been carried out using the TALYS-1.0 and were compared with available experimental data in the literature and with ENDF/B-VII, T=300k; JENDL-3.3, T=300k and JEFF3.1, T=300k evaluated libraries .
Calculating gravitationally self-consistent sea level changes driven by dynamic topography
Austermann, J.; Mitrovica, J. X.
2015-12-01
We present a generalized formalism for computing gravitationally self-consistent sea level changes driven by the combined effects of dynamic topography, geoid perturbations due to mantle convection, ice mass fluctuations and sediment redistribution on a deforming Earth. Our mathematical treatment conserves mass of the surface (ice plus ocean) load and the solid Earth. Moreover, it takes precise account of shoreline migration and the associated ocean loading. The new formalism avoids a variety of approximations adopted in previous models of sea level change driven by dynamic topography, including the assumption that a spatially fixed isostatic amplification of `air-loaded' dynamic topography accurately accounts for ocean loading effects. While our approach is valid for Earth models of arbitrary complexity, we present numerical results for a set of simple cases in which a pattern of dynamic topography is imposed, the response to surface mass loading assumes that Earth structure varies only with depth and that isostatic equilibrium is maintained at all times. These calculations, involving fluid Love number theory, indicate that the largest errors in previous predictions of sea level change driven by dynamic topography occur in regions of shoreline migration, and thus in the vicinity of most geological markers of ancient sea level. We conclude that a gravitationally self-consistent treatment of long-term sea level change is necessary in any effort to use such geological markers to estimate ancient ice volumes.
The unified equation for the evaluation of first order reactions in dynamic electrophoresis.
Trapp, Oliver
2006-02-01
The unified equation was validated for first order reactions in dynamic CE with a data set of 31 250 elution profiles. Comparison with the results from conventional iterative computer simulation revealed that the unified equation is superior in terms of success rate and precision. The unified equation was applied to determine the cis-trans isomerization rate constants of the angiotensin converting enzyme inhibitor captopril. The separation of the rotational cis-trans isomeric drug has been performed in an aqueous 66 mM citric acid/Tris buffer at pH 3.0 in a 50 cm polyacrylamide-coated fused-silica capillary. Interconversion profiles featuring pronounced plateau formation and peak broadening were observed. Activation parameters DeltaH not equal and DeltaS not equal were obtained from temperature-dependent measurements between 10 and 25 degrees C in 2.5 K steps. From the activation parameters the isomerization barriers of captopril at 37 degrees C under acidic conditions were calculated to be DeltaG not equal trans-->cis=90.6 kJ/mol and DeltaG not equal cis-->trans=84.6 kJ/mol. By comparison of the kinetic data with the results obtained under basic conditions (pH 9.3) a mechanism of isomerization could be proposed.
Fission dynamics of 240Cf* formed in 34,36S induced reactions
Jain Deepika
2015-01-01
Full Text Available We have studied the entrance channel effects in the decay of Compound nucleus 240Cf* formed in 34S+206Pb and 36S+204Pb reactions by using energy density dependent nuclear proximity potential in the framework of dynamical cluster-decay model (DCM. At different excitation energies, the fragmentation potential and preformation probability of decaying fragments are almost identical for both the entrance channels, which seem to suggest that decay is independent of its formation and entrance channel excitation energy. It is also observed that, with inclusion of deformation effects upto quadrupole within the optimum orientation approach, the fragmentation path governing potential energy surfaces gets modified significantly. Beside this, the fission mass distribution of Cf* isotopes is also investigated. The calculated fission cross-sections using SIII force for both the channels find nice agreement with the available experimental data for deformed choice of fragments, except at higher energies. In addition to this, the comparative analysis with Blocki based nuclear attraction is also worked out. It is observed that Blocki proximity potential accounts well for the CN decay at all energies whereas the use of EDF based nuclear potential suggests the presence of some non-compound nucleus process (such as quasi-fission (qf at higher energies.
Plyasunov, S
2005-01-01
This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and elimination of degrees of freedom via the renormalization of transition rates of slow reactions. The method suggested in this work is more general than other approaches presented previously: it is not limited to a particular type of stochastic processes and can be applied to different types of processes describing fast dynamics, and also provides crossover to the case when separation of time scales is not well pronounced. We derive a family of exact fluctuation-dissipation relations which establish the connection between effective rates and the statistics of the reaction events in fast reaction channels. An illustration of the technique is provided. Examples show that renormalized transition rates exhibit in general non-exponential relaxation behavior with a broad range of pos...
Reaction dynamics of small molecules at metal surfaces
Samson, P A
1999-01-01
directed angular distributions suggest the influence of a trapping mechanism, recombining molecules scattering through a molecularly adsorbed state, with a transition state of large d sub N sub N responsible for the product vibrational excitation. Although N sub 2 dissociation on Fe(100) forms a simple overlayer structure, on Fe(110), molecular chemisorption does not occur at or above room temperature and the sticking is extremely small (approx 10 sup - sup 6 to 10 sup - sup 7). Activated nitrogen bombardment can be used to prepare a 'surface nitride' with a structure related to the geometry of bulk Fe sub 4 N. Scanning tunnelling microscopy yields atomic scale features that cannot be explained by simple overlayers. It is proposed that the uppermost iron layer reconstructs to generate quasi-octahedral sites between the top two layers, with sub-surface nitrogen in these sites forming a model for the 'surface nitride' structure. The dissociation-desorption dynamics of D sub 2 upon the Sn/Pt(111) surface alloy a...
Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro
2016-02-01
Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
MODEL STUDIES OF MODE-SPECIFICITY IN UNIMOLECULAR REACTION DYNAMICS
Waite, Boyd A.; Miller, William H.
1980-06-01
Essentially exact quantum mechanical calculations are carried out to determine the energies and lifetimes of the quasi-bound states for a system of two (non~linearly) coupled oscillators (one of which is harmonic, the other being able to dissociate). For weak coupling the system displays mode-specificity, i.e., the unimolecular rate constants are not a monotonic function of the total energy, but increased coupling and frequency degeneracy tends to destroy mode-specificity. A somewhat surprising result is that for a given coupling the degree of modespecificity is roughly independent of the energy, in marked contrast to the fact that there is an energetic threshold for the onset of "stochastic trajectories" of the corresponding classical system; i.e., there seems to be no relation between statistical/mode-specific behavior of the unimolecular rate constants and stochastic/regular classical trajectories. In order to be able to treat more physically relevant models--i.e., those with more than two degrees of freedom--a semiclassical model is constructed and seen to be able to reproduce the accurate quantum mechanical rates reasonably well.
Wang, Yuping; Li, Yida; Wang, Dunyou
2017-01-01
A time-dependent, quantum reaction dynamics approach in full dimensional, six degrees of freedom was carried out to study the energy requirement on reactivity for the HBr + OH reaction with an early, negative energy barrier. The calculation shows both the HBr and OH vibrational excitations enhance the reactivity. However, even this reaction has a negative energy barrier, the calculation shows not all forms of energy are equally effective in promoting the reactivity. On the basis of equal amount of total energy, the vibrational energies of both the HBr and OH are more effective in enhancing the reactivity than the translational energy, whereas the rotational excitations of both the HBr and OH hinder the reactivity. The rate constants were also calculated for the temperature range between 5 to 500 K. The quantal rate constants have a better slope agreement with the experimental data than quasi-classical trajectory results.
Zhang, Y. C.; Zhang, J. Z. H.; Kouri, D. J.; Haug, K.; Schwenke, D. W.
1988-01-01
Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.
Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region
T.-S. H. Lee; A. Matsuyama; T. Sato
2006-11-15
A dynamical coupled-channel model is presented for investigating the nucleon resonances (N*) in the meson production reactions induced by pions and photons. Our objective is to extract the N* parameters and to investigate the meson production reaction mechanisms for mapping out the quark-gluon substructure of N* from the data. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method.
[Age-related dynamics of the motion reaction in school children].
Makarenko, M V; Petrenko, Iu O; Baĭda, O H; Men'shykh, O E
2009-01-01
We studied functional state of the central nervous system of boys and girls aged from 7 to 17 years old. Peculiarities of age-dependent dynamics of functional level of the central nervous system, stability of the reactions, levels of functional possibilities were described. The age-dependent periods of strengthening and weakening of correlation between the indexes of motive reaction and the criteria of the functional state of central nervous system were determined.
Calculation of the neutron electric dipole moment with two dynamical flavors of domain wall fermions
Berruto, F; Orginos, K; Soni, A
2005-01-01
We present a study of the neutron electric dipole moment ($\\vec d_N$) within the framework of lattice QCD with two flavors of dynamical lig ht quarks. The dipole moment is sensitive to the topological structure of the gaug e fields, and accuracy can only be achieved by using dynamical, or sea quark, calc ulations. However, the topological charge evolves slowly in these calculations, le ading to a relatively large uncertainty in $\\vec d_N$. It is shown, using quenched configurations, that a better sampling of the charge d istribution reduces this problem, but because the CP even part of the fermion determinant is absent, both the topological charge dis tribution and $\\vec d_N$ are pathological in the chiral limit. We discuss the statistical and systematic uncertainties arising from the topological charge distr ibution and unphysical size of the quark mass in our calculations and prospects fo r eliminating them. Our calculations employ the RBC collaboration two flavor domain wall fermion and DBW2 gauge action l...
Peters, Baron; Bolhuis, Peter G; Mullen, Ryan G; Shea, Joan-Emma
2013-02-01
We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths.
Influence of the leaving group on the dynamics of a gas-phase SN2 reaction
Stei, Martin; Carrascosa, Eduardo; Kainz, Martin A.; Kelkar, Aditya H.; Meyer, Jennifer; Szabó, István; Czakó, Gábor; Wester, Roland
2016-02-01
In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F- + CH3Cl and compared it to F- + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.
Matsuura, Tomoaki; Tanimura, Naoki; Hosoda, Kazufumi; Yomo, Tetsuya; Shimizu, Yoshihiro
2017-02-21
To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions.
Bassem Elshahat
2015-09-01
Full Text Available Purpose: Boron neutron capture therapy (BNCT is a promising technique for the treatment of malignant disease targeting organs of the human body. Monte Carlo simulations were carried out to calculate optimum design parameters of an accelerator based beam shaping assembly (BSA for BNCT of brain cancer setup.Methods: Epithermal beam of neutrons were obtained through moderation of fast neutrons from 3H(p,n reaction in a high density polyethylene moderator and a graphite reflector. The dimensions of the moderator and the reflector were optimized through optimization of epithermal / fast neutron intensity ratio as a function of geometric parameters of the setup. Results: The results of our calculation showed the capability of our setup to treat the tumor within 4 cm of the head surface. The calculated peak therapeutic ratio for the setup was found to be 2.15. Conclusion: With further improvement in the polyethylene moderator design and brain phantom irradiation arrangement, the setup capabilities can be improved to reach further deep-seated tumor.
Dynamics of surface-migration: Electron-induced reaction of 1,2-dihaloethanes on Si(100)
Huang, Kai; MacLean, Oliver; Guo, Si Yue; McNab, Iain R.; Ning, Zhanyu; Wang, Chen-Guang; Ji, Wei; Polanyi, John C.
2016-10-01
Scanning Tunneling Microscopy was used to investigate the electron-induced reaction of 1,2-dibromoethane (DBE) and 1,2-dichloroethane (DCE) on Si(100).We observed a long-lived physisorbed molecular state of DBE at 75 K and of DCE at 110 K. As a result we were able to characterize by experiment and also by ab initio theory the dynamics of ethylene production in the electron-induced surface-reaction of these physisorbed species. For both DBE and DCE the ethylene product was observed to migrate across the surface. In the case of DBE the recoil of the ethylene favored the silicon rows, migrating by an average distance of 22 Å, and up to 100 Å. Trajectory calculations were performed for this electron-induced reaction, using an 'Impulsive Two-State' model involving an anionic excited state and a neutral ground-potential. The model agreed with experiment in reproducing both migration and desorption of the ethylene product. The computed migration exhibited a 'ballistic' launch and subsequent 'bounces', thereby accounting for the observed long-range migratory dynamics.
Maiti, Buddhadev [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, TX 79409-1061 (United States); Sadeghi, Raymond [Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249-0698 (United States); Austin, Anthony [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, TX 79409-1061 (United States); Morales, Jorge A. [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, TX 79409-1061 (United States)], E-mail: jorge.morales@ttu.edu
2007-11-09
Results of a complete investigation of the H{sup +} + HF reaction at E{sub Lab} = 30 eV with the electron nuclear dynamics (END) and the coherent-states dynamics (CSD) theories are herein presented. Current END-CSD methodology employs frozen Gaussian wave packet in the semiclassical limit of h {yields} 0 for the nuclei, and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 400 CS trajectories from five independent HF target orientations provide a complete description of the reactive processes in this system, including: non-charge-transfer scattering (NCTS), charge-transfer scattering (CTS), hydrogen fluoride dissociation (H-F D), and hydrogen rearrangement (HR). Several aspects of the reactions dynamics, such as mechanistic details and rainbow angles effects, are discussed. Differential and integral cross sections are evaluated via a novel CS formulation of those properties in conjunction with semiclassical techniques. The calculated total differential cross section shows an excellent agreement with available experimental results.
Proceedings of the Workshop on open problems in heavy ion reaction dynamics at VIVITRON energies
Beck, F.A.
1993-07-01
Some problems of heavy ion reaction dynamics at the VIVITRON tandem accelerator and the experimental facilities are discussed at the meeting. Topics include light dinuclear systems, collision dynamics at low energies, fission evaporation and fusion of heavy nuclei and others. Most documents consist of transparencies presented at the workshop, texts of papers are missing. All items are indexed and abstracted for the INIS database. (K.A.).
Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems
Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em
2015-01-01
We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux a...
Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús
2015-01-01
Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2.
Calculation technique for simulation of wave and fracture dynamics in a reinforced sheet
Ayzenberg-Stepanenko, M; Osharovich, G
2011-01-01
Mathematical models and computer algorithms are developed to calculate dynamic stress concentration and fracture wave propagation in a reinforced composite sheet. The composite consists of a regular system alternating extensible fibers and pliable adhesive layers. In computer simulations, we derive difference algorithms preventing or minimizing the parasite distortions caused by the mesh dispersion and obtain precise numerical solutions in the plane fracture problem of a pre-stretched sheet along the fibers. Interactive effects of microscale dynamic deformation and multiple damage in fibers and adhesive are studied. Two engineering models of the composite are considered: the first assumes that adhesive can be represented by inertionless bonds of constant stiffness, while in the second one an adhesive is described by inertial medium perceived shear stresses. Comparison of results allows the evaluation of facilities of models in wave and fracture patterns analysis.
Wei, Xing
2016-01-01
For understanding magnetic effects on dynamical tides, we study the rotating magneto-hydrodynamic (MHD) flow driven by harmonic forcing. The linear responses are analytically derived in a periodic box under the local WKB approximation. Both the kinetic and Ohmic dissipations at the resonant frequencies are calculated and the various parameters are investigated. Although magnetic pressure may be negligible compared to thermal pressure, magnetic field can be important for the first-order perturbation, e.g. dynamical tides. It is found that magnetic field splits the resonant frequency, namely the rotating hydrodynamic flow has only one resonant frequency but the rotating MHD flow has two, one positive and the other negative. In the weak field regime the dissipations are asymmetric around the two resonant frequencies and this asymmetry is more striking with a weaker magnetic field. It is also found that both the kinetic and Ohmic dissipations at the resonant frequencies are inversely proportional to the Ekman num...
Belyaev, Andrey K.; Domcke, Wolfgang; Lasser, Caroline; Trigila, Giulio
2015-03-01
The Landau-Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn-Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.
Takaba, Hiromitsu; Kimura, Shou; Alam, Md. Khorshed
2017-03-01
Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MA0.5X0.5PbI3 (MA = CH3NH3+, X = NH4+ or (NH2)2CH+ or Cs+). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. DFT calculations show that electronic structures of the investigated partially substituted perovskites were similar with that of MAPbI3, while their bandgaps slightly decrease compared to that of MAPbI3. Our results mean that partial substitution in halide perovskite is effective technique to suppress diffusion of intrinsic ions and tune the band gap.
Dynamical analysis of tRNA Gln-GlnRS complex using normal mode calculation
Nakamura, Shugo; Ikeguchi, Mitsunori; Shimizu, Kentaro
2003-04-01
We applied normal mode calculation in internal coordinates to a complex of glutamine transfer RNA (tRNA Gln) and glutaminyl-tRNA synthetase (GlnRS). Calculated deviations of atoms agreed well with those obtained from X-ray data. The differences of motions corresponding to low mode frequencies between the free state and the complex state were analyzed. For GlnRS, many motions in the free state were conserved in the complex state, while the dynamics of tRNA Gln was largely affected by the complex formation. Superimposed images of the conserved and non-conserved motions of tRNA Gln clearly indicated the restricted direction of motions in the complex.
Time-reversed particle dynamics calculation with field line tracing at Titan - an update
Bebesi, Zsofia; Erdos, Geza; Szego, Karoly; Juhasz, Antal; Lukacs, Katalin
2014-05-01
We use CAPS-IMS Singles data of Cassini measured between 2004 and 2010 to investigate the pickup process and dynamics of ions originating from Titan's atmosphere. A 4th order Runge-Kutta method was applied to calculate the test particle trajectories in a time reversed scenario, in the curved magnetic environment. We evaluated the minimum variance directions along the S/C trajectory for all Cassini flybys during which the CAPS instrument was in operation, and assumed that the field was homogeneous perpendicular to the minimum variance direction. We calculated the magnetic field lines with this method along the flyby orbits and we could determine those observational intervals when Cassini and the upper atmosphere of Titan could be magnetically connected. We used three ion species (1, 2 and 16 amu ions) for time reversed tracking, and also considered the categorization of Rymer et al. (2009) and Nemeth et al. (2011) for further features studies.
NATO Advanced Research Workshop on The Theory of Chemical Reaction Dynamics
1986-01-01
The calculation of cross sections and rate constants for chemical reactions in the gas phase has long been a major problem in theoretical chemistry. The need for reliable and applicable theories in this field is evident when one considers the significant recent advances that have been made in developing experimental techniques, such as lasers and molecular beams, to probe the microscopic details of chemical reactions. For example, it is now becoming possible to measure cross sections for chemical reactions state selected in the vibrational rotational states of both reactants and products. Furthermore, in areas such as atmospheric, combustion and interstellar chemistry, there is an urgent need for reliable reaction rate constant data over a range of temperatures, and this information is often difficult to obtain in experiments. The classical trajectory method can be applied routinely to simple reactions, but this approach neglects important quantum mechanical effects such as tunnelling and resonances. For al...
Cis/trans Coordination in olefin metathesis by static and molecular dynamic DFT calculations
Poater, Albert
2014-05-25
In regard to [(N-heterocyclic carbene)Ru]-based catalysts, it is still a matter of debate if the substrate binding is preferentially cis or trans to the N-heterocyclic carbene ligand. By means of static and molecular dynamic DFT calculations, a simple olefin, like ethylene, is shown to be prone to the trans binding. Bearing in mind the higher reactivity of trans isomers in olefin metathesis, this insight helps to construct small alkene substrates with increased reactivity. © 2014 Springer Science+Business Media New York.
Dynamic mathematical model and numerical calculation method on spontaneous combustion of loose coal
WEN Hu(文虎)
2003-01-01
Through the experiment of coal spontaneous combustion and relationship particle size with oxidation character of loose coal, some calculation formula of characteristic parameters is got in the process of coal spontaneous combustion. According to these theories of porous medium hydrodynamics, mass transfer and heat transfer, mathematical models of air leak field, oxygen concentration field and temperature field are set up. Through experimental and theoretical analysis, 3-D dynamic mathematical model of coal spontaneous combustion is set up. The method of ascertaining boundary condition of model is analyzed, and finite difference method is adopted to solve 2-D mathematical model.
Influence of Marangoni flows on the dynamics of isothermal A + B → C reaction fronts
Tiani, R.; Rongy, L.
2016-09-01
The nonlinear dynamics of A + B → C fronts is analyzed both numerically and theoretically in the presence of Marangoni flows, i.e., convective motions driven by surface tension gradients. We consider horizontal aqueous solutions where the three species A, B, and C can affect the surface tension of the solution, thereby driving Marangoni flows. The resulting dynamics is studied by numerically integrating the incompressible Navier-Stokes equations coupled to reaction-diffusion-convection (RDC) equations for the three chemical species. We show that the dynamics of the front cannot be predicted solely on the basis of the one-dimensional reaction-diffusion profiles as is the case for buoyancy-driven convection around such fronts. We relate this observation to the structure of Marangoni flows which lead to more complex and exotic dynamics. We find in particular the surprising possibility of a reversal of the front propagation direction in time for some sets of Marangoni numbers, quantifying the influence of each chemical species concentration on the solution surface tension. We explain this reversal analytically and propose a new classification of the convective effects on A + B → C reaction fronts as a function of the Marangoni numbers. The influence of the layer thickness on the RDC dynamics is also presented. Those results emphasize the importance of flow symmetry properties when studying convective front dynamics in a given geometry.
Structure of thallium and lead calculated from Shaw local pseudopotential and molecular dynamics
Gasser J. G.
2011-05-01
Full Text Available Recently, we (Es Sbihi Phil. Mag 2010 have successfully calculated, by molecular dynamics, the static structure factor of liquid bismuth at different temperatures. Our results were in very good agreement with the Waseda experimental data. Our assumption was to consider the true density of states which presents a gap as measured by Indlekofer (J. Non-Cryst. Solids 1989 and calculated by Hafner-Jank (Phys. Rev. B 1990 for liquid bismuth. The number of electrons at the Fermi energy has been calculated with three conduction electrons for bismuth (number of p electrons. With this assumption, the structures were determined with an effective ion-ion potential constructed from the Shaw local Optimised Model Potential (OMP and the Ichimaru-Utsumi dielectric function. In the present paper, we generalize our assumptions to liquid thallium and lead which also present such a gap. Their calculated structures are also very close to the experimental ones. This confirms that the number of conduction electrons on the Fermi sphere is consistent with the number of p electrons as has been even shown for our electronic transport properties of liquid lead (A. Ben Abdellah, Phys. Rev. B 2003.
Compressive Loads on the Lumbar Spine During Lifting: 4D WATBAK versus Inverse Dynamics Calculations
M. H. Cole
2005-01-01
Full Text Available Numerous two- and three-dimensional biomechanical models exist for the purpose of assessing the stresses placed on the lumbar spine during the performance of a manual material handling task. More recently, researchers have utilised their knowledge to develop specific computer-based models that can be applied in an occupational setting; an example of which is 4D WATBAK. The model used by 4D WATBAK bases its predications on static calculations and it is assumed that these static loads reasonably depict the actual dynamic loads acting on the lumbar spine. Consequently, it was the purpose of this research to assess the agreement between the static predictions made by 4D WATBAK and those from a comparable dynamic model. Six individuals were asked to perform a series of five lifting tasks, which ranged from lifting 2.5 kg to 22.5 kg and were designed to replicate the lifting component of the Work Capacity Assessment Test used within Australia. A single perpendicularly placed video camera was used to film each performance in the sagittal plane. The resultant two-dimensional kinematic data were input into the 4D WATBAK software and a dynamic biomechanical model to quantify the compression forces acting at the L4/L5 intervertebral joint. Results of this study indicated that as the mass of the load increased from 2.5 kg to 22.5 kg, the static compression forces calculated by 4D WATBAK became increasingly less than those calculated using the dynamic model (mean difference ranged from 22.0% for 2.5 kg to 42.9% for 22.5 kg. This study suggested that, for research purposes, a validated three-dimensional dynamic model should be employed when a task becomes complex and when a more accurate indication of spinal compression or shear force is required. Additionally, although it is clear that 4D WATBAK is particularly suited to industrial applications, it is suggested that the limitations of such modelling tools be carefully considered when task-risk and employee
Calculation of the neutron electric dipole moment with two dynamical flavors of domain wall fermions
F. Berruto; T. Blum; K. Orginos; A. Soni
2005-12-08
We present a study of the neutron electric dipole moment ({rvec d}{sub N}) within the framework of lattice QCD with two flavors of dynamical light quarks. The dipole moment is sensitive to the topological structure of the gauge fields, and accuracy can only be achieved by using dynamical, or sea quark, calculations. However, the topological charge evolves slowly in these calculations, leading to a relatively large uncertainty in {rvec d}{sub N}. It is shown, using quenched configurations, that a better sampling of the charge distribution reduces this problem, but because the CP even part of the fermion determinant is absent, both the topological charge distribution and {rvec d}{sub N} are pathological in the chiral limit. We discuss the statistical and systematic uncertainties arising from the topological charge distribution and unphysical size of the quark mass in our calculations and prospects for eliminating them. Our calculations employ the RBC collaboration two flavor domain wall fermion and DBW2 gauge action lattices with inverse lattice spacing a{sup -1} {approx} 1.7 GeV, physical volume V {approx} (2 fm){sup 3}, and light quark mass roughly equal to the strange quark mass (m{sub sea} = 0.03 and 0.04). We determine a value of the electric dipole moment that is zero within (statistical) errors, |{rvec d}{sub N}| = -0.04(20) e-{theta}-fm at the smaller sea quark mass. Satisfactory results for the magnetic and electric form factors of the proton and neutron are also obtained and presented.
Liu, Jianbo; Song, Kihyung; Hase, William L; Anderson, Scott L
2005-12-22
Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state. The reaction is sharply orientation-dependent, even at high collision energies, and both trajectories and experiment find that H2CO+ vibration inhibits reaction. On the other hand, the trajectories do not reproduce the anomalously strong effect of nu2(+) (the CO stretch). The origin of the discrepancy and approaches for minimizing such problems in quasiclassical trajectories are discussed.
Ray, Sara E.; Vissers, Gé W. M.; McCoy, Anne B.
2009-06-01
Hydrogen-transfer reactions are probed through vibrational excitation of the HCl bond in the pre-reactive F\\cdotsHCl complex. Such open-shell species provide a challenge for quantum dynamical calculations due to the need to take into account multiple potential energy surfaces to accurately describe the system.A three-dimensional, fully-coupled potential energy surface has been constructed based on electronic energies calculated at the multireference configuration interaction+Davidson correction (MRCI+Q) level of theory with an aug-cc-pVnZ (n=2,3,4) basis. Spin orbit calculations have also been included. Here we present the results of time-dependent quantum wave packet calculations on the asymmetric hydrogen-transfer reaction of F(^2P) + HCl. In these calculations, the reaction is initiated by vibrationally exciting the HCl stretching motion in the pre-reactive F\\cdotsHCl complex. The wave packet is propagated on the coupled potential energy surfaces. Product state distributions were calculated for reactions initiated in the first three vibrationally excited states of HCl, v=1-3. M. P. Deskevich, M. Y. Hayes, K. Takahashi, R. T. Skodje, and D. J. Nesbitt J. Chem. Phys. 124 (22) 224303 (2006) M. P. Deskevich and D. J. Nesbitt private communication(2007)
Tamiya, K.; Tamagaki, R.
1981-10-01
Results obtained by applying a formulation based on the reaction matrix theory developed in I are given. Calculations by making use of a modified realistic potential, the Reid soft-core potential with the OPEP-part enhanced due to the isobar (Δ)-mixing, show that the transition to the [ALS] phase of quasi-neutrons corresponding to a typical π0 condensation occurs in the region of (2 ˜ 3) times the nuclear density. The most important ingredients responsible for this transition are the growth of the attractive 3P2 + 3F2 contribution mainly from the spin-parallel pairs in the same leyers and the reduction of the repulsive 3P1 contribution mainly from the spin-antiparallel pairs in the nearest layers; these mainfest themselves as the [ALS]-type localization develops. Properties of the matter under the new phase thus obtained such as the shape of the Fermi surface and the effective mass are discussed.
Bellesia, Giovanni
2015-01-01
We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.
Addari, D.; Aglietti, G. S.; Remedia, M.
2017-01-01
Microvibrations of a satellite reaction wheel assembly are commonly analysed in either hard-mounted or coupled boundary conditions, though coupled wheel-to-structure disturbance models are more representative of the real environment in which the wheel operates. This article investigates the coupled microvibration dynamics of a cantilever configured reaction wheel assembly mounted on either a stiff or flexible platform. Here a method is presented to cope with modern project necessities: (i) need of a model which gives accurate estimates covering a wide frequency range; (ii) reduce the personnel and time costs derived from the test campaign, (iii) reduce the computational effort without affecting the quality of the results. The method involves measurements of the disturbances induced by the reaction wheel assembly in a hard-mounted configuration and of the frequency and speed dependent dynamic mass of the reaction wheel. In addition, it corrects the approximation due to missing speed dependent dynamic mass in conventional reaction wheel assembly microvibration analysis. The former was evaluated experimentally using a previously designed and validated platform. The latter, on the other hand, was estimated analytically using a finite element model of the wheel assembly. Finally, the validation of the coupled wheel-structure disturbance model is presented, giving indication of the level of accuracy that can be achieved with this type of analyses.
Dynamics of Pickering Emulsions in the Presence of an Interfacial Reaction: A Simulation Study.
Zhao, Shuangliang; Zhan, Bicai; Hu, Yaofeng; Fan, Zhaoyu; Pera-Titus, Marc; Liu, Honglai
2016-12-13
Pickering emulsions combining surface-active and catalytic properties offer a promising platform for conducting interfacial reactions between immiscible reagents. Despite the significant progress in the design of Pickering interfacial catalysts for a broad panel of reactions, the dynamics of Pickering emulsions under reaction conditions is still poorly understood. Herein, using benzene hydroxylation with aqueous H2O2 as a model system, we explored the dynamics of benzene/water Pickering emulsions during reaction by dissipative particle dynamics. Our study points out that the surface wettability of the silica nanoparticles is affected to a higher extent by the degree of polymer grafting rather than an increase of the chain length of hydrophobic polymer moieties. A remarkable decline of the oil-in-water (O/W) interfacial tension was observed when increasing the yield of the reaction product (phenol), affecting the emulsion stability. However, phenol did not alter to an important extent the distribution of immiscible reagents around the nanoparticles sitting at the benzene/water interface. A synergistic effect between phenol and silica nanoparticles on the O/W interfacial tension of the biphasic system could be ascertained.
Dynamics of the Spiral Tip in a Closed Belousov-Zhabotinsky Reaction
ZHANG Hui-Jie; WANG Peng-Ye; ZHAO Ying-Ying
2005-01-01
@@ Dynamics of spiral tip rotating in a closed system of the light sensitive Belousov-Zhabotinsky reaction is studied under a homogeneous and steady illumination. The time dependence of the kinematical parameters of meandering spiral is presented and the experimental evidence is obtained for self-synchronization of the spiral tip in a closed B-Z system without external feedback.
MATLAB在反应工程计算中的应用%Application of MATLAB in Reaction Engineering Calculation
宋颖韬; 党明岩
2012-01-01
反应工程计算复杂,常需采用数值方法求解。文中以MATLAB为编程语言,将计算机辅助计算应用于反应工程问题求解,并列举典型实例。实践表明,基于MATLAB的计算机辅助计算引入课程的教学中可为学生理解课程内容和解答习题提供方便,并有助于调动学生的学习兴趣,提高其计算机应用能力。%Numerical method was often used to deal with the complex problems in reaction engineering.Several application examples in actual reaction engineering were presented and solved with the compute program complier by MATLAB.The practice showed that the introduction of computer-aided calculating based on MATLAB could facilitate effectively the understanding and answering to exercises for students.The learning interest and computer application capability were also improved dramatically.
无
2010-01-01
A dynamic calculation model of frame supporting structures with prestressed anchors for the slope stability is proposed. The frame and soil are closely contacted in the role of prestressed anchors and they cannot be separated along the whole slope. The lateral displacement of frame and soil is nearly in phase. The movement characteristic satisfies the theory of elastic foundation beam. The frame is treated with elastic foundation beam in this model. The influence of prestressed anchors is simplified as linear spring and damped system related with velocity. Under the condition of horizontal earthquake excitation, the equation of vibration response is established by using the model of dynamic Winkler beam and the analytical solutions are obtained for simple harmonic vibration. This method is applied to a case record for illustration of its capability, in order to verify the method, 3D nonlinear FEM (ADINA) is used to analyze the seismic performance of this case, the comparative results show that the design and the analysis are safe and credible by using the proposed method. The calculation model provides a new way for earthquake analysis and seismic design of slope stability supported by frame structure with prestressed anchors.
Chen, Li; Ueta, Hirokazu; Bisson, Régis; Beck, Rainer D
2013-05-01
We report the design and characterization of a new molecular-beam/surface-science apparatus for quantum state-resolved studies of gas/surface reaction dynamics combining optical state-specific reactant preparation in a molecular beam by rapid adiabatic passage with detection of surface-bound reaction products by reflection absorption infrared spectroscopy (RAIRS). RAIRS is a non-invasive infrared spectroscopic detection technique that enables online monitoring of the buildup of reaction products on the target surface during reactant deposition by a molecular beam. The product uptake rate obtained by calibrated RAIRS detection yields the coverage dependent state-resolved reaction probability S(θ). Furthermore, the infrared absorption spectra of the adsorbed products obtained by the RAIRS technique provide structural information, which help to identify nascent reaction products, investigate reaction pathways, and determine branching ratios for different pathways of a chemisorption reaction. Measurements of the dissociative chemisorption of methane on Pt(111) with this new apparatus are presented to illustrate the utility of RAIRS detection for highly detailed studies of chemical reactions at the gas/surface interface.
Dynamical Modes and Mechanisms in Ternary Reaction of 197Au+197Au
Tian, Jun-Long; Hao, Hong-Jun; Yuan, Su-Zhen; Li, Xue-Qin
2011-08-01
The modes of ternary reaction of 197Au+197Au at an energy of 15A MeV are dynamically studied by the improved quantum molecular dynamics model. Three kinds of modes are found by the time evolution of the configurations of the composite reaction systems: One is the direct mode for which the two time separations of the system happen almost simultaneously. Another is the cascade mode for which a two-step process is clearly shown. The third is oblate mode, a kind of very rare fission event. In this case the composite system deforms to a triangle-like configuration with three necks, and then it forms three equally sized fragments along space-symmetric directions in the reaction plane.
Dynamical Dipole mode in heavy-ion fusion reactions by using stable and radioactive beams
Molini P.
2011-10-01
Full Text Available The existence of the dynamical dipole mode in the 192Pb composite system was investigated through the study of its prompt γ decay employing the 40Ca + 152Sm and 48Ca + 144Sm reactions at Elab =11 and 10.1 MeV/u, respectively. The γ-rays and light charged particles were detected in coincidence with evaporation residues and ﬁssion fragments. First results of this experiment show that the dynamical dipole mode survives in collisions involving heavier mass reaction partners than those studied previously. As a fast cooling mechanism on the fusion path, the prompt dipole γ radiation could be of interest for the synthesis of super-heavy elements through ”hot” fusion reactions. Furthermore, by using radioactive beams and the prompt γ radiation as a probe we could get information on the symmetry energy at sub-saturation densities.
Dynamical Behavior of Core 3 He Nuclear Reaction-Diffusion Systems and Sun's Gravitational Field
DU Jiulin; SHEN Hong
2005-01-01
The coupling of the sun's gravitational field with processes of diffusion and convection exerts a significant influence on the dynamical behavior of the core 3He nuclear reaction-diffusion system. Stability analyses of the system are made in this paper by using the theory of nonequilibrium dynamics. It is showed that, in the nuclear reaction regions extending from the center to about 0.38 times of the radius of the sun, the gravitational field enables the core 3He nuclear reaction-diffusion system to become unstable and, after the instability, new states to appear in the system have characteristic of time oscillation. This may change the production rates of both 7Be and 8B neutrinos.
Chiral Dynamics and Dubna-Mainz-Taipei Dynamical Model for Pion-Photoproduction Reaction
Yang, Shin Nan
2010-01-01
We demonstrate that the Dubna-Mainz-Taipei (DMT) meson-exchange dynamical model, which starts from an effective chiral Lagrangian, for pion photoproduction provides an excellent and economic framework to describe both the pi^0 threshold production and the Delta deformation, two features dictated by chiral dynamics.
On the study of nonlinear dynamics of complex chemical reaction systems
无
2006-01-01
With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.
Kinetic calculation for the reaction of H with Si2H6 using the variational transition state theory
ZHANG; Qingzhu
2001-01-01
［1］Gates, S. M., Kuna, R. R., Greenlief, C. M., Silicon hydride etch products from the reaction of atomic hydrogen with Si(100), Surf. Sci., 1989, 207: 364.［2］Abrefah, J., Olander, D. R., Reaction of atomic hydrogen with crystalline silicon, Surf. Sci., 1989, 209: 291.［3］Kerwin, D. D., Douglas, J. D., Mechanistic insight into gas-phase of H+Si2H6 and hydrogen atom etching of silicon surface, J. Am. Chem. Soc., 1993, 115: 3731.［4］Pollock, T. L., Sandhu, H. S., Jodhan, A. et al., Photochemistry of silicon compounds, IV. Mercury photosensitization of disilane, J. Am. Chem. Soc., 1973, 95: 1017.［5］Austin, E. R., Lampe, F W., Rate constants for the reactions of hydrogen atoms with some silicanes and germanes, J. Phys. Chem., 1977, 81(12): 1134.［6］Fabry, L., Potzinger, P, Reimann, B. et al., Gas-phase homolytic substitution reactions of hydrogen atoms at silicon centers. Organometallics. 1986, 5: 1231.［7］Oberhammer, H., Lobreyer, T., Sundermeyer, W., The Ge-Si bond in silylgermane discrepancy between experiment and theory, J. Mol. Struct., 1994, 323: 125.［8］Durig. J. R., Church, J. S., Vibrational spectra of crystalline disilane and disilane, barrier to internal rotation and some normal coordinate calculations on H3SiSiH3, H3SiNCO, H3SiNCS, J. Chem. Phys., 1980, 73: 4784.［9］Espinosa-Garcia, J., Sanson, J., Corchado, J. C., The SiH4+H→SiH3+H2 reaction: potential energy surface, rate constants, and kinetic isotope effects, J. Chem. Phys., 1998, 109(2): 466.［10］Charles, B. M., Siddharth, D., William, A. G., Hessian biased force field for polysilane polymers, J. Phys. Chem,, 1995, 99:13321.［11］Wu, Y. D., Wong, C. L., Substituion effect on the dissociation energy of the Si-H bond: a density functional study, J. Org. Chem., 1995, 60: 821.［12］Taylor. C. A.. Marshall, P., A discharge-fluoro/chemiluminescence study of the reaction O+SiH at room temperature, Chem. Phys. Lett., 1993, 205(6): 493.［13］Doncaster, A. M., Walsh, R
Belyaev, Andrey K; Lasser, Caroline; Trigila, Giulio
2014-01-01
The Landau--Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs the recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Four different time scales are detected for the nuclear dynamics: Ultrafast Jahn--Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs; and nearly constant ...
Molecular dynamics calculation of thermophysical properties for a highly reactive liquid.
Wang, H P; Luo, B C; Wei, B
2008-10-01
In order to further understand the physical characteristics of liquid silicon, the thermophysical properties are required over a broad temperature range. However, its high reactivity brings about great difficulties in the experimental measurement. Here we report the thermophysical properties by molecular dynamics calculation, including density, specific heat, diffusion coefficient, and surface tension. The calculation is performed with a system consisting of 64,000 atoms, and employing the Stillinger-Weber (SW) potential model and the modified embedded atom method (MEAM) potential model. The results show that the density increases as a quadratic function of undercooling, and the value calculated by SW potential model is only 2-4 % smaller than the reported experimental data. The specific heat is obtained to be 30.95 J mol;{-1}K;{-1} by SW potential model and 32.50 J mol;{-1}K;{-1} by MEAM potential model, both of which are constants in the corresponding ranges of temperature. The self-diffusion coefficient is exponentially dependent on the temperature and consistent with the Arrhenius equation. The surface tension increases linearly with the rise of undercooling and agrees well with the reported experimental results. This work provides reasonable data in much wider temperature range, especially for the undercooled metastable state.
V.I. Milykh
2015-12-01
Full Text Available Attention is paid to the popular FEMM (Finite Element Method Magnetics program which is effective in the numerical calculations of the magnetic fields of electrical machines. The principles of the automated calculations providing the analysis of the dynamics of electromagnetic processes in turbo-generators are presented. This is realized in the form of a script on the algorithmic language Lua integrated with FEMM. The temporal functions of electromagnetic quantities are obtained by multi-position calculations of the magnetic field with ensuring its rotation together with the turbo-generator rotor. The developed program is universal in terms of the geometry and dimensions of turbo-generators, as well as the modes of their work with a minimum of input data in numerical form. This paper shows "extraction" of discrete temporal functions: the magnetic flux linkage of the phase stator winding; forces acting on the current-carrying and ferromagnetic elements of the structure; the magnetic induction at the fixed points; electromagnetic moment. This list can be expanded as part of the created program, as well as the use of the program can be extended to other types of electrical machines. The obtaining of a change period of any functions is provided by rotating the rotor to 60°.
Poirier, Bill; Salam, A
2004-07-22
In a previous paper [J. Theo. Comput. Chem. 2, 65 (2003)], one of the authors (B.P.) presented a method for solving the multidimensional Schrodinger equation, using modified Wilson-Daubechies wavelets, and a simple phase space truncation scheme. Unprecedented numerical efficiency was achieved, enabling a ten-dimensional calculation of nearly 600 eigenvalues to be performed using direct matrix diagonalization techniques. In a second paper [J. Chem. Phys. 121, 1690 (2004)], and in this paper, we extend and elaborate upon the previous work in several important ways. The second paper focuses on construction and optimization of the wavelength functions, from theoretical and numerical viewpoints, and also examines their localization. This paper deals with their use in representations and eigenproblem calculations, which are extended to 15-dimensional systems. Even higher dimensionalities are possible using more sophisticated linear algebra techniques. This approach is ideally suited to rovibrational spectroscopy applications, but can be used in any context where differential equations are involved.
Neutrino-nucleus reactions and their role for supernova dynamics and nucleosynthesis
Balasi, K G; Martínez-Pinedo, G
2015-01-01
The description of nuclear reactions induced by supernova neutrinos has witnessed significant progress during the recent years. At the energies and momentum transfers relevant for supernova neutrinos neutrino-nucleus cross sections are dominated by allowed transitions, however, often with non-negligible contributions from (first) forbidden transitions. For several nuclei allowed Gamow-Teller strength distributions could be derived from charge-exchange reactions and from inelastic electron scattering data. Importantly the diagonalization shell model has been proven to accurately describe these data and hence became the appropriate tool to calculate the allowed contributions to neutrino-nucleus cross sections for supernova neutrinos. Higher multipole contributions are usually calculated within the framework of the Quasiparticle Random Phase Approximation, which describes the total strength and the position of the giant resonances quite well. This manuscript reviews the recent progress achieved in calculating su...
Moore-Russo, Deborah A.; Cortes-Figueroa, Jose E.; Schuman, Michael J.
2006-01-01
The use of Calculator-Based Laboratory (CBL) technology, the graphing calculator, and the cooling and heating of water to model the behavior of consecutive first-order reactions is presented, where B is the reactant, I is the intermediate, and P is the product for an in-class demonstration. The activity demonstrates the spontaneous and consecutive…
Molecular dynamics study of phase separation in fluids with chemical reactions.
Krishnan, Raishma; Puri, Sanjay
2015-11-01
We present results from the first d=3 molecular dynamics (MD) study of phase-separating fluid mixtures (AB) with simple chemical reactions (A⇌B). We focus on the case where the rates of forward and backward reactions are equal. The chemical reactions compete with segregation, and the coarsening system settles into a steady-state mesoscale morphology. However, hydrodynamic effects destroy the lamellar morphology which characterizes the diffusive case. This has important consequences for the phase-separating structure, which we study in detail. In particular, the equilibrium length scale (ℓ(eq)) in the steady state suggests a power-law dependence on the reaction rate ε:ℓ(eq)∼ε(-θ) with θ≃1.0.
Xie, Jing; Kohale, Swapnil C; Hase, William L; Ard, Shaun G; Melko, Joshua J; Shuman, Nicholas S; Viggiano, Albert A
2013-12-27
Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of
Li, Yongle; Suleimanov, Yury V; Green, William H; Guo, Hua
2014-03-20
Thermal rate coefficients and kinetic isotope effect have been calculated for prototypical heavy-light-heavy polyatomic bimolecular reactions Cl + CH4/CD4 → HCl/DCl + CH3/CD3, using a recently proposed quantum dynamics approach: ring polymer molecular dynamics (RPMD). Agreement with experimental rate coefficients, which are quite scattered, is satisfactory. However, differences up to 50% have been found between the RPMD results and those obtained from the harmonic variational transition-state theory on one of the two full-dimensional potential energy surfaces used in the calculations. Possible reasons for such discrepancy are discussed. The present work is an important step in a series of benchmark studies aimed at assessing accuracy for RPMD for chemical reaction rates, which demonstrates that this novel method is a quite reliable alternative to previously developed techniques based on transition-state theory.
Kaur, Arshdeep; Chopra, Sahila; Gupta, Raj K.
2014-08-01
The compound nucleus (CN) fusion/formation probability PCN is defined and its detailed variations with the CN excitation energy E*, center-of-mass energy Ec .m., fissility parameter χ, CN mass number ACN, and Coulomb interaction parameter Z1Z2 are studied for the first time within the dynamical cluster-decay model (DCM). The model is a nonstatistical description of the decay of a CN to all possible processes. The (total) fusion cross section σfusion is the sum of the CN and noncompound nucleus (nCN) decay cross sections, each calculated as the dynamical fragmentation process. The CN cross section σCN is constituted of evaporation residues and fusion-fission, including intermediate-mass fragments, each calculated for all contributing decay fragments (A1, A2) in terms of their formation and barrier penetration probabilities P0 and P. The nCN cross section σnCN is determined as the quasi-fission (qf) process, where P0=1 and P is calculated for the entrance-channel nuclei. The DCM, with effects of deformations and orientations of nuclei included in it, is used to study the PCN for about a dozen "hot" fusion reactions forming a CN of mass number A ˜100 to superheavy nuclei and for various different nuclear interaction potentials. Interesting results are that PCN=1 for complete fusion, but PCNPCN≪1 due to the nCN contribution, depending strongly on different parameters of the entrance-channel reaction but found to be independent of the nuclear interaction potentials used.
Eisenbach, Markus [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Perera, Meewanage Dilina N. [Univ. of Georgia, Athens, GA (United States). Center for Simulational Physics; Landau, David P [Univ. of Georgia, Athens, GA (United States). Center for Simulational Physics; Nicholson, Don M. [Univ. of North Carolina, Asheville, NC (United States). Dept. of Physics; Yin, Junqi [Univ. of Tennessee, Knoxville, TN (United States). National Inst. for Computational Sciences; Brown, Greg [Florida State Univ., Tallahassee, FL (United States). Dept. of Physics
2015-01-01
We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.
Gabbasov Radek Fatykhovich
Full Text Available Bending plate is widely used in the construction of large-span structures. Its advantage is light weight, industrial production, low cost and easy installation. Implementing the algorithm for calculating bending plates in engineering practice is an important issue of the construction science. The generalized equations of finite difference method is a new trend in the calculation of building construction. FDM with generalized equation provides additional options for an engineer along with other methods (FEM. In the article the algorithm for dynamic calculation of thin bending plates basing on FDM was developed. The computer programs for dynamic calculation were created on the basis of the algorithm. The authors come to the conclusion that the more simple equations of FDM can be used in case of solving the impulse load problems in dynamic load calculation of thin bending plate.
Ab initio many-body calculations of the (3)H(d,n)(4)He and (3)He(d,p)(4)He fusion reactions.
Navrátil, Petr; Quaglioni, Sofia
2012-01-27
We apply the ab initio no-core shell model combined with the resonating-group method approach to calculate the cross sections of the (3)H(d,n)(4)He and (3)He(d,p)(4)He fusion reactions. These are important reactions for the big bang nucleosynthesis and the future of energy generation on Earth. Starting from a selected similarity-transformed chiral nucleon-nucleon interaction that accurately describes two-nucleon data, we performed many-body calculations that predict the S factor of both reactions. Virtual three-body breakup effects are obtained by including excited pseudostates of the deuteron in the calculation. Our results are in satisfactory agreement with experimental data and pave the way for microscopic investigations of polarization and electron-screening effects, of the (3)H(d,γn)(4)He bremsstrahlung and other reactions relevant to fusion research.
CALCULATION OF THE UNIQUE HIGH-RISE BUILDING FOR EARTHQUAKES IN NONLINEAR DYNAMIC FORMULATION
Mkrtychev Oleg Vartanovich
2016-06-01
Full Text Available The article contains the calculation of a 80-storey high-rise building on 3-component accelerograms with different dominant frequencies. The “Akhmat Tower” belongs to the complex “Grozny-city 2” and is classified as a unique construction, its height is 400 m. During the construction unique high-rise buildings and high-rise buildings in seismic areas an additional computational studies are required, which should take into account the nonlinear nature of the design. For the case of linear instrumental-synthesized accelerograms, it is necessary to apply nonlinear dynamic methods. The studies were conducted using the software LS-DYNA, implementing the methods of direct integration of the equations of motion by the explicit scheme. The constructive scheme of the building frame is braced, the spatial stability is ensured by load-bearing interior walls, columns and hard disks, and frame metal coatings. The choice of the type and dimensions of the finite element and the step of integration is due to the ability to perform calculations in reasonable time, and to the required accuracy of calculation. For this aim the issues of convergence of the solutions on a number of settlement schemes were investigated with the terms of thickened mesh of finite elements: 0.5 m; 1 m; 2 m; 3 m. As a result of the research it was obtained that the best is to split into finite elements with a characteristic size of 2 m. The calculation of the building is made on rigid foundation. The authors used accelerograms normalized for earthquakes of 8 and 9 points on the MSK-64 scale. The destruction of the elements in the process of loading, and the interaction of the elements during their contact was taken into account, i.e. the calculation was made taking into account physical, geometrical and structural nonlinearities. The article analyzes the results of the calculation. The authors evaluated the seismic stability of the building. Possible ways to improve the seismic
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
Gurtovenko, Andrey A; Vattulainen, Ilpo
2009-01-01
that it is employed in conjunction with tin-foil boundary conditions, which exactly balance a nonzero surface charge of a periodically replicated multibilayer system. Furthermore, we show that vacuum boundary conditions give qualitatively similar potential profiles for asymmetric lipid bilayers as compared......The electrostatic properties of lipid membranes are of profound importance as they are directly associated with membrane potential and, consequently, with numerous membrane-mediated biological phenomena. Here we address a number of methodological issues related to the computation...... of the electrostatic potential from atomic-scale molecular dynamics simulations of lipid bilayers. We discuss two slightly different forms of Poisson equation that are normally used to calculate the membrane potential: (i) a classical form when the potential and the electric field are chosen to be zero on one...
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.
Molecular dynamics simulation method for calculating fluence-dependent range profiles
Peltola, J; Keinonen, J
2003-01-01
Molecular dynamics has proven to be successful in calculating range profiles for low energy (keV) ions implanted into crystalline materials. However, for high fluences the structure of the material changes during the implantation process. The crystalline material becomes amorphized, which changes the range profiles. This damage build-up process has usually been taken into account with probabilities for changing the crystal structure during the simulation, and typically only BCA methods have been used. We present a fast MD method that simulates the damage build-up process in silicon, without bringing any free parameters to the simulation. Damage accumulation during the implantation is simulated by changing the material structure in front of path of the incoming ion. The amorphization level at each depth is proportional to the nuclear deposited energy in that depth region. The amorphization states are obtained from MD simulations of cascade damage. Silicon was used as a target material because of the large amou...
Lattice dynamics calculations for ferropericlase with internally consistent LDA+U method
Fukui, Hiroshi; Tsuchiya, Taku; Baron, Alfred Q. R.
2012-12-01
Vibrational densities of states and phonon dispersion relations for Mg0.875Fe0.125O ferropericlase in the high- and low-spin (HS and LS) states were calculated from first principles lattice dynamics using the internally consistent LDA+Utechnique. Finite-temperature thermodynamic properties were determined based on the quasi-harmonic approximation including the HS and LS mixing entropy and the magnetic entropy effects, which gave pressure and temperature variations of the low-spin fraction. Our results suggest that for thermodynamic modeling of the earth's interior, the effect of the mixed spin state cannot be ignored in the lower mantle, especially the lowermost part. The anomaly in the seismic wave velocity due to the spin crossover transition of ferropericlase, if it exists, is difficult to detect because of the wide pressure range of the transition, which is broadened by the temperature effect and the damping of the amplitude of the slow seismic wave.
Andrade, Xavier; Botti, Silvana; Marques, Miguel A. L.; Rubio, Angel
2007-05-01
The authors present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a frequency-dependent Sternheimer equation, within the formalism of time-dependent density functional theory, and allows the calculation of the response both in resonance and out of resonance. Furthermore, the excellent scaling with the number of atoms opens the way to the investigation of response properties of very large molecular systems. To demonstrate the capabilities of this method, they implemented it in a real-space (basis-set-free) code and applied it to benchmark molecules, namely, CO, H2O, and para-nitroaniline. Their results are in agreement with experimental and previous theoretical studies and fully validate their approach.
Calculation of two-particle quantities in the typical medium dynamical cluster approximation
Zhang, Y.; Zhang, Y. F.; Yang, S. X.; Tam, K.-M.; Vidhyadhiraja, N. S.; Jarrell, M.
2017-04-01
The mean-field theory for disordered electron systems without interaction is widely and successfully used to describe equilibrium properties of materials over the whole range of disorder strengths. However, it fails to take into account the effects of quantum coherence and information of localization. Vertex corrections due to multiple backscatterings may drive the electrical conductivity to zero and make expansions around the mean field in strong disorder problematic. Here, we present a method for the calculation of two-particle quantities which enables us to characterize the metal-insulator transitions in disordered electron systems by using the typical medium dynamical cluster approximation. We show how to include vertex corrections and information about the mobility edge in the typical mean-field theory. We successfully demonstrate the application of the developed method by showing that the conductivity formulated in this way properly characterizes the metal-insulator transition in disordered systems.
Dimitriou Konstantinos
2015-01-01
Full Text Available A simple yet accurate model is developed for the dynamical simulation of profile-modified gears, considering the effects of progressive tooth engagement, stiffness, elastohydrodynamic lubricant film formation and hysteresis. The real path of contact, stiffness and elastohydrodynamic lubricant film thickness are calculated for various operating conditions and the results are input to the dynamical simulation, resulting in a prediction of the dynamic transmission error.
Analysis of dynamical process with mass distribution of fission fragmentin heavy ion reactions
Aritomo Y.
2010-03-01
Full Text Available We analyzed experimental data obtained for the mass distribution of fission fragments in the reactions 36S+238U and 30Si+238U at several incident energies, which were performed by the JAEA group. Using the dynamical model with the Langevin equation, we precisely investigate the incident energy dependence of the mass distribution of fission fragments. We also consider the fine structures in the mass distribution of fission fragments caused by the nuclear structure at a low incident energy. It is explained why the mass distribution of fission fragments has different features in the two reactions. The fusion cross sections are also estimated.
7Be- and 8B-reaction dynamics at Coulomb barrier energies
Mazzocco M.
2016-01-01
Full Text Available We investigated the reaction dynamics induced by the Radioactive Ion Beams 7Be and 8B on a 208Pb target at energies around the Coulomb barrier. The two measurements are strongly interconnected, being 7Be (Sα = 1.586 MeV the loosely bound core of the even more exotic 8B (Sp = 0.1375 MeV nucleus. Here we summarize the present status of the data analysis for the measurement of the elastic scattering process for both reactions and the preliminary results for the optical model analysis of the collected data.
7Be- and 8B-reaction dynamics at Coulomb barrier energies
Mazzocco, M.; Boiano, A.; Boiano, C.; La Commara, M.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Signorini, C.; Strano, E.; Torresi, D.; Yamaguchi, H.; Kahl, D.; Acosta, L.; Di Meo, P.; Fernandez-Garcia, J. P.; Glodariu, T.; Grebosz, J.; Guglielmetti, A.; Imai, N.; Hirayama, Y.; Ishiyama, H.; Iwasa, N.; Jeong, S. C.; Jia, H. M.; Keeley, N.; Kim, Y. H.; Kimura, S.; Kubono, S.; Lay, J. A.; Lin, C. J.; Marquinez-Duran, G.; Martel, I.; Miyatake, H.; Mukai, M.; Nakao, T.; Nicoletto, M.; Pakou, A.; Rusek, K.; Sakaguchi, Y.; Sánchez-Benítez, A. M.; Sava, T.; Sgouros, O.; Stefanini, C.; Soramel, F.; Soukeras, V.; Stiliaris, E.; Stroe, L.; Teranishi, T.; Toniolo, N.; Wakabayashi, Y.; Watanabe, Y. X.; Yang, L.; Yang, Y. Y.
2016-05-01
We investigated the reaction dynamics induced by the Radioactive Ion Beams 7Be and 8B on a 208Pb target at energies around the Coulomb barrier. The two measurements are strongly interconnected, being 7Be (Sα = 1.586 MeV) the loosely bound core of the even more exotic 8B (Sp = 0.1375 MeV) nucleus. Here we summarize the present status of the data analysis for the measurement of the elastic scattering process for both reactions and the preliminary results for the optical model analysis of the collected data.
Untangling the Energetics and Dynamics of Boron Monoxide Radical Reactions (11BO; X2Sigma+)
2015-04-15
energy-density molecules and builds up on our previously successful synthesis of higher carbon oxides COx (x=3-6). Higher-order carbon sulfides - carbon...3.1. Crossed Beam Reactions of Boron Monoxide with Acetylene anmd Ethylene (P1, P8) The reaction dynamics of boron monoxide (BO; X2Σ...with acetylene (C2H2; X1Σg+) and with ethylene (C2H4; X1Ag) were investigated under single collision conditions at collision energy of 12 to 13 kJ mol
On the role of dynamical barriers in barrierless-reactions at low energies: S($^1$D) + H$_2$
Lara, Manuel; Varandas, A J C; Launay, J -M; Aoiz, F J
2011-01-01
Reaction probabilities as a function of total angular momentum and the resulting reaction cross-sections for the collision of open shell S($^1$D) atoms with para-hydrogen have been calculated in the kinetic energy range 0.09--10 meV (1--120 K). The quantum mechanical (QM) hyperspherical reactive scattering method and quasi--classical trajectory (QCT) and statistical quasiclassical trajectory (SQCT) approaches were used. Two different ab initio potential energy surfaces (PESs) have been considered. The widely used RKHS PES by Ho et al. (J. Chem. Phys. 116, 4124, 2002) and the recently published DMBE/CBS PES by Song and Varandas (J. Chem. Phys. 130, 134317, 2009). The calculations at low collision energies reveal very different dynamical behaviors on the two PESs. The reactivity on the RKHS PES is found to be considerably larger than that on the DMBE/CBS PES. The observed differences have their origin in two major distinct topography features. Although both PESs are essentially barrierless for equilibrium H--H ...
The effect of walking speed on local dynamic stability is sensitive to calculation methods
Stenum, Jan; Bruijn, Sjoerd M; Jensen, Bente Rona
2014-01-01
Local dynamic stability has been assessed by the short-term local divergence exponent (λS), which quantifies the average rate of logarithmic divergence of infinitesimally close trajectories in state space. Both increased and decreased local dynamic stability at faster walking speeds have been......% and 140% of preferred walking speed) for 3min each, while upper body accelerations in three directions were sampled. From these time-series, λS was calculated by three different methods using: (a) a fixed time interval and expressed as logarithmic divergence per stride-time (λS-a), (b) a fixed number...... of strides and expressed as logarithmic divergence per time (λS-b) and (c) a fixed number of strides and expressed as logarithmic divergence per stride-time (λS-c). Mean preferred walking speed was 1.16±0.09m/s. There was only a minor effect of walking speed on λS-a. λS-b increased with increasing walking...
Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers.
Strümpfer, Johan; Schulten, Klaus
2012-08-14
Calculating the evolution of an open quantum system, i.e., a system in contact with a thermal environment, has presented a theoretical and computational challenge for many years. With the advent of supercomputers containing large amounts of memory and many processors, the computational challenge posed by the previously intractable theoretical models can now be addressed. The hierarchy equations of motion present one such model and offer a powerful method that remained under-utilized so far due to its considerable computational expense. By exploiting concurrent processing on parallel computers the hierarchy equations of motion can be applied to biological-scale systems. Herein we introduce the quantum dynamics software PHI, that solves the hierarchical equations of motion. We describe the integrator employed by PHI and demonstrate PHI's scaling and efficiency running on large parallel computers by applying the software to the calculation of inter-complex excitation transfer between the light harvesting complexes 1 and 2 of purple photosynthetic bacteria, a 50 pigment system.
Mathematical simulation and calculation of the soil compaction under dynamic loads
Zolotarevskaya, D. I.
2011-04-01
The deformation and compaction of loamy sandy soddy-podzolic soils under linear dynamic changes in the compressive stresses and in the course of the soil creeping were studied in field experiments. The rheological properties of these soils occurring in the viscoelastic state were described by a first-order differential equation relating the compressive stresses, the rates of their changes, and the velocities of the relative vertical compressive deformation. Regression equations were derived for the viscoelastic properties of the studied soil as functions of its density, moisture, and linear compaction velocity. Methods were proposed for the calculation of indices of the stress-strain state and the compaction of soils under specified conditions of changes in their compressive stresses with time and in the course of the soil creeping after the initial linear increase in load. Corresponding computer programs were developed. The effect of the main factors due to the linear increase in the compressive loads and in the course of the soil creeping on the rheological properties, the stress-strain state, and the density of soils was quantitatively estimated. The calculation showed that the values of the soil deformation and the density under compressive stresses lower than the ultimate strength were stabilized with time, and the properties of the viscoelastic soil approached elastic ones.