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Sample records for dynamic reaction cell

  1. Dual control cell reaction ensemble molecular dynamics: A method for simulations of reactions and adsorption in porous materials

    Science.gov (United States)

    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.

  2. Oxygenation mechanism of ions in dynamic reaction cell ICP-MS.

    Science.gov (United States)

    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.

  3. Photochemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters

    Science.gov (United States)

    Li, Fangting

    2017-01-01

    The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical compositions x = (x1,x2, … ,xN) in a cell, where xℓ is the concentration of the ℓth biochemical species. Equivalently, for heterogeneous cell population dynamics xℓ is the number density of cells of the ℓth cell type. One of the insights derived from the landscape perspective is that the life history of an individual organism, which occurs on the hillsides of a landscape, is nearly deterministic and ‘programmed’, while population-wise an asynchronous non-equilibrium steady state resides mostly in the lowlands of the landscape. We argue that a dynamic ‘blue-sky’ bifurcation, as a representation of Waddington's landscape, is a more robust mechanism for a cell fate decision and subsequent differentiation than the widely pictured pitch-fork bifurcation. We revisit, in terms of the chemostatic driving forces upon active, living matter, the notions of near-equilibrium thermodynamic branches versus far-from-equilibrium states. The emergent

  5. Element fingerprinting of marine organisms by dynamic reaction cell inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Cubadda, Francesco; Raggi, Andrea; Coni, Ettore

    2006-02-01

    A method for the determination of sixteen elements (Al, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Se, Sn, V, Zn) in seafood by dynamic reaction cell inductively coupled plasma mass spectrometry (ICP-DRC-MS) is presented. A preliminary study of polyatomic interferences was carried out in relation to the chemical composition of marine organisms belonging to different taxa. Acid effects and other matrix effects in marine organisms submitted to closed-vessel microwave digestion were investigated as well. Ammonia was the reactive gas used in the DRC to remove polyatomic ions interfering with 27Al, 52Cr, 56Fe and 51V. Optimal conditions for the simultaneous determination of analytes were identified in order to develop a fast multielement method. A suite of real samples (mussels and various fish species) were used during method development along with three certified reference materials: BCR CRM 278R (mussel tissue), BCR CRM 422 (cod muscle) and DORM-2 (dogfish muscle). The proposed analytical approach can be used in conjunction with suitable chemometric procedures to address quality and safety issues in aquaculture and fisheries. As an example, a case study is described in which mussels from three farming sites in the Venice Lagoon were distinguished by multivariate analysis of element fingerprints.

  6. Kinematically complete chemical reaction dynamics

    Science.gov (United States)

    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.

  7. Determination of total selenium and Se-77 in isotopically enriched human samples by ICP-dynamic reaction cell-MS

    DEFF Research Database (Denmark)

    Sloth, Jens Jørgen; Larsen, Erik Huusfeldt; Bügel, Susanne H.;

    2003-01-01

    This paper describes an analytical method for the simultaneous quantitative determination of total selenium (Se) and Se-77 in isotopically enriched human plasma, urine and faeces by inductively coupled plasma- dynamic reaction cell- mass spectrometry ( ICP- DRC- MS). The samples originated from...... and the digested faecal samples were diluted using an aqueous diluent containing 0.5% Triton X-100, 2% nitric acid and 3% methanol. Selenium was detected as Se-76, Se-77 and Se-80 by ICP- DRC- MS. Selenium originating from the natural isotope abundance yeast and other selenium sources from the diet was determined...

  8. Monitoring dynamic reactions of red blood cells to UHF electromagnetic waves radiation using a novel micro-imaging technology.

    Science.gov (United States)

    Ruan, Ping; Yong, Junguang; Shen, Hongtao; Zheng, Xianrong

    2012-12-01

    Multiple state-of-the-art techniques, such as multi-dimensional micro-imaging, fast multi-channel micro-spetrophotometry, and dynamic micro-imaging analysis, were used to dynamically investigate various effects of cell under the 900 MHz electromagnetic radiation. Cell changes in shape, size, and parameters of Hb absorption spectrum under different power density electromagnetic waves radiation were presented in this article. Experimental results indicated that the isolated human red blood cells (RBCs) do not have obviously real-time responses to the ultra-low density (15 μW/cm(2), 31 μW/cm(2)) electromagnetic wave radiation when the radiation time is not more than 30 min; however, the cells do have significant reactions in shape, size, and the like, to the electromagnetic waves radiation with power densities of 1 mW/cm(2) and 5 mW/cm(2). The data also reveal the possible influences and statistical relationships among living human cell functions, radiation amount, and exposure time with high-frequency electromagnetic waves. The results of this study may be significant on protection of human being and other living organisms against possible radiation affections of the high-frequency electromagnetic waves.

  9. Laser ablation inductively coupled plasma dynamic reaction cell mass spectrometry for the multi-element analysis of polymers

    Science.gov (United States)

    Resano, M.; García-Ruiz, E.; Vanhaecke, F.

    2005-11-01

    In this work, the potential of laser ablation-inductively coupled plasma-mass spectrometry for the fast analysis of polymers has been explored. Different real-life samples (polyethylene shopping bags, an acrylonitrile butadiene styrene material and various plastic bricks) as well as several reference materials (VDA 001 to 004, Cd in polyethylene) have been selected for the study. Two polyethylene reference materials (ERM-EC 680 and 681), for which a reference or indicative value for the most relevant metals is available, have proved their suitability as standards for calibration. Special attention has been paid to the difficulties expected for the determination of Cr at the μg g - 1 level in this kind of materials, due to the interference of ArC + ions on the most abundant isotopes of Cr. The use of ammonia as a reaction gas in a dynamic reaction cell is shown to alleviate this problem, resulting in a limit of detection of 0.15 μg g - 1 for this element, while limiting only modestly the possibilities of the technique for simultaneous multi-element analysis. In this regard, As is the analyte most seriously affected by the use of ammonia, and its determination has to be carried out in vented mode, at the expense of measuring time. In all cases studied, accurate results could be obtained for elements ranging in content from the sub-μg g - 1 level to tens of thousands of μg g - 1 . However, the use of an element of known concentration as internal standard may be needed for materials with a matrix significantly different from that of the standard (polyethylene in this work). Precision ranged between 5% and 10% RSD for elements found at the 10 μg g - 1 level or higher, while this value could deteriorate to 20% for analytes found at the sub-μg g - 1 level. Overall, the technique evaluated presents many advantages for the fast and accurate multi-element analysis of these materials, avoiding laborious digestion procedures and minimizing the risk of analyte losses due

  10. Optimization and application of ICPMS with dynamic reaction cell for precise determination of 44Ca/40Ca isotope ratios.

    Science.gov (United States)

    Boulyga, Sergei F; Klötzli, Urs; Stingeder, Gerhard; Prohaska, Thomas

    2007-10-15

    An inductively coupled plasma mass spectrometer with dynamic reaction cell (ICP-DRC-MS) was optimized for determining (44)Ca/(40)Ca isotope ratios in aqueous solutions with respect to (i) repeatability, (ii) robustness, and (iii) stability. Ammonia as reaction gas allowed both the removal of (40)Ar+ interference on (40)Ca+ and collisional damping of ion density fluctuations of an ion beam extracted from an ICP. The effect of laboratory conditions as well as ICP-DRC-MS parameters such a nebulizer gas flow rate, rf power, lens potential, dwell time, or DRC parameters on precision and mass bias was studied. Precision (calculated using the "unbiased" or "n - 1" method) of a single isotope ratio measurement of a 60 ng g(-1) calcium solution (analysis time of 6 min) is routinely achievable in the range of 0.03-0.05%, which corresponded to the standard error of the mean value (n = 6) of 0.012-0.020%. These experimentally observed RSDs were close to theoretical precision values given by counting statistics. Accuracy of measured isotope ratios was assessed by comparative measurements of the same samples by ICP-DRC-MS and thermal ionization mass spectrometry (TIMS) by using isotope dilution with a (43)Ca-(48)Ca double spike. The analysis time in both cases was 1 h per analysis (10 blocks, each 6 min). The delta(44)Ca values measured by TIMS and ICP-DRC-MS with double-spike calibration in two samples (Ca ICP standard solution and digested NIST 1486 bone meal) coincided within the obtained precision. Although the applied isotope dilution with (43)Ca-(48)Ca double-spike compensates for time-dependent deviations of mass bias and allows achieving accurate results, this approach makes it necessary to measure an additional isotope pair, reducing the overall analysis time per isotope or increasing the total analysis time. Further development of external calibration by using a bracketing method would allow a wider use of ICP-DRC-MS for routine calcium isotopic measurements, but it

  11. Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions

    Science.gov (United States)

    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…

  12. The dynamics of p53 in single cells: physiologically based ODE and reaction-diffusion PDE models

    Science.gov (United States)

    Eliaš, Ján; Dimitrio, Luna; Clairambault, Jean; Natalini, Roberto

    2014-08-01

    The intracellular signalling network of the p53 protein plays important roles in genome protection and the control of cell cycle phase transitions. Recently observed oscillatory behaviour in single cells under stress conditions has inspired several research groups to simulate and study the dynamics of the protein with the aim of gaining a proper understanding of the physiological meanings of the oscillations. We propose compartmental ODE and PDE models of p53 activation and regulation in single cells following DNA damage and we show that the p53 oscillations can be retrieved by plainly involving p53-Mdm2 and ATM-p53-Wip1 negative feedbacks, which are sufficient for oscillations experimentally, with no further need to introduce any delays into the protein responses and without considering additional positive feedback.

  13. Selenium speciation and isotope composition in 77Se-enriched yeast using gradient elution HPLC separation and ICP-dynamic reaction cell-MS

    DEFF Research Database (Denmark)

    Larsen, Erik Huusfeldt; Sloth, Jens Jørgen; Hansen, M.

    2003-01-01

    A batch of Se-77-labelled and enriched yeast was characterised with regard to isotopic composition and content of selenium species for later use in a human absorption study based on the method of enriched stable isotopes. The abundance of the six stable selenium isotopes was determined by ICP- MS...... equipped with a dynamic reaction cell (DRC). The results showed that the Se-77 isotope was enriched to 98.5 atom-%, whereas the remaining selenium was present as the other five isotopes at low abundance. The low-molecular Se-77 containing species, which were biosynthesised by the yeast during fermentation...

  14. Determination of depleted uranium in fish: validation of a confirmatory method by dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS).

    Science.gov (United States)

    D'Ilio, S; Violante, N; Senofonte, O; Petrucci, F

    2007-08-06

    Depleted uranium (DU) is a by-product of the uranium enrichment process for nuclear fuel. According to the Commission Decision 2002/657/EC, a confirmatory method for the quantification of DU in freeze-dried fish was developed by isotope ratio dynamic reaction cell inductively coupled plasma-mass spectrometry (IR-DRC-ICP-MS). A preliminary study was performed to determine the following parameters: instrumental detection limit (IDL), isotopic ratio measurement limit (IRML), percentage of DU (P(DU)) in presence of natural uranium (NU) and limit of quantification (LoQ(DU)). The analyses were carried out by means of IR-DRC-ICP-MS. Ammonia was the reaction gas used for the dynamic reaction cell. In addition, a sector field inductively coupled plasma mass spectrometer (SF-ICP-MS) was employed to calculate the within-laboratory reproducibility. For the confirmatory method the following parameters were determined: (a) trueness; (b) precision; (c) critical concentrations alpha and beta (CC(alpha), CC(beta)); (d) specificity; (e) stability. Trueness was assessed by using the recovery tests. The recovery and within-laboratory reproducibility were determined by fortifying the blank digested solution of dogfish tissue: six aliquots were fortified at 1, 1.5 and 2 times the LOQ(DU) with 25.0, 37.5 and 50.0 ng L(-1) or 4.16, 6.24, 8.32 microg kg(-1) with a recovery of -8.2, +9.5 and +9.6%, respectively and a within-laboratory reproducibility (three analytical run) of 15.5, 8.0 and 11.0%, respectively. The results for the decision limit and the detection capability were: CC(alpha) = 11.69 ng L(-1) and CC(beta) = 19.8 ng L(-1). The digested solutions resulted to be stable during testing time (60 days) and the method can be considered highly specific as well.

  15. Lithium Cell Reactions.

    Science.gov (United States)

    1985-02-01

    runaway or venting were found by Honeywell during charging tests with 16.5 KAhr cells (46). However, Zupancic and co-workers (47) at Union Carbide found...Q -° .- REFERENCES 47. R.L. Zupancic , L.F. Urry and V.S. Alberto, Proc. 29th Power Sources Symposium, The Electrochem. Soc. 157 (1980). 48

  16. Paper analytical devices for dynamic evaluation of cell surface N-glycan expression via a bimodal biosensor based on multibranched hybridization chain reaction amplification.

    Science.gov (United States)

    Liang, Linlin; Lan, Feifei; Li, Li; Ge, Shenguang; Yu, Jinghua; Ren, Na; Liu, Haiyun; Yan, Mei

    2016-12-15

    A novel colorimetric/fluorescence bimodal lab-on-paper cyto-device was fabricated based on concanavalin A (Con A)-integrating multibranched hybridization chain reaction (mHCR). The product of mHCR was modified PtCu nanochains (colorimetric signal label) and graphene quantum dot (fluorescence signal label) for in situ and dynamically evaluating cell surface N-glycan expression. In this strategy, preliminary detection was carried out through colorimetric method, if needed, then the fluorescence method was applied for a precise determination. Au-Ag-paper devices increased the surface areas and active sites for immobilizing larger amount of aptamers, and then specifically and efficiently captured more cancer cells. Moreover, it could effectively reduce the paper background fluorescence. Due to the specific recognition of Con A with mannose and the effective signal amplification of mHCR, the proposed strategy exhibited excellent high sensitivity for the cytosensing of MCF-7 cells ranging from 100 to 1.0×10(7) and 80-5.0×10(7) cellsmL(-1) with the detection limit of 33 and 26 cellsmL(-1) for colorimetric and fluorescence, respectively. More importantly, this strategy was successfully applied to dynamically monitor cell-surface multi-glycans expression on living cells under external stimuli of inhibitors as well as for N-glycan expression inhibitor screening. These results implied that this biosensor has potential in studying complex native glycan-related biological processes and elucidating the N-glycan-related diseases in biological and physiological processes.

  17. Markovian Dynamics on Complex Reaction Networks

    CERN Document Server

    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...

  18. Dynamical Model of Weak Pion Production Reactions

    CERN Document Server

    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.

  19. Chemical Reaction Dynamics in Nanoscle Environments

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Markovian dynamics on complex reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Application of a dynamic reaction cell (DRC) ICP-MS in chromium and iron determinations in rock, soil and terrestrial water samples.

    Science.gov (United States)

    Ogawa, Yasumasa; Yamasaki, Shin-ichi; Tsuchiya, Noriyoshi

    2010-01-01

    Despite environmental and geochemical interests, Cr and Fe have been left beyond the reach of determinations by ICP-MS due to severe interferences originating from Ar. The applicability of a dynamic reaction cell (DRC)-ICP-MS has been examined for determinations in environmental and geochemical samples. The reaction with NH(3) in the DRC system provides an eligible technique to determine Cr, because of a greater improvement in the signal/noise (S/N) ratio due to an effective elimination of interferences arising from Ar (ArC, ArN and ArO), and makes it possible to analyze Cr even at sub-microg L(-1) levels. As compared to non-DRC mode analyses, the DRC technique using m/z 56 appeared to be preferable for Fe determination in most terrestrial waters because of effective suppression of (40)Ar(16)O(+). In addition, the effects of cluster ions, such as (39)K(14)N(1)H(3)(+) and (40)Ca(14)N(1)H(2)(+), on Fe determination were also negligibly small. Measurements using (54)Fe by the DRC mode are also advantageous for Ca-rich samples, such as limestone and dolomite.

  3. Mode-Specific SN2 Reaction Dynamics.

    Science.gov (United States)

    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.

  4. Exploiting dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS) for sequential determination of trace elements in blood using a dilute-and-shoot procedure.

    Science.gov (United States)

    Batista, Bruno Lemos; Rodrigues, Jairo Lisboa; Nunes, Juliana Andrade; Souza, Vanessa Cristina de Oliveira; Barbosa, Fernando

    2009-04-20

    Inductively coupled plasma mass spectrometry with quadrupole (q-ICP-MS) and dynamic reaction cell (DRC-ICP-MS) were evaluated for sequential determination of As, Cd, Co, Cr, Cu, Mn, Pb, Se, Tl, V and Zn in blood. The method requires as little as 100 microL of blood. Prior to analysis, samples (100 microL) were diluted 1:50 in a solution containing 0.01% (v/v) Triton X-100 and 0.5% (v/v) nitric acid. The use of the DRC was only mandatory for Cr, Cu, V and Zn. For the other elements the equipment may be operated in a standard mode (q-ICP-MS). Ammonia was used as reaction gas. Selection of best flow rate of ammonium gas and optimization of the quadrupole dynamic band-pass tuning parameter (RPq) were carried out, using a ovine base blood for Cr and V and a synthetic matrix solution (SMS) for Zn and Cu diluted 1:50 and spiked to contain 1 microg L(-1) of each element. Method detection limits (3 s) for (75)As, (114)Cd, (59)Co, (51)Cr, (63)Cu (55)Mn, (208)Pb, (82)Se, (205)Tl, (51)V, and (64)Zn were 14.0, 3.0, 11.0, 7.0, 280, 9.0, 3.0, 264, 0.7, 6.0 and 800 ng L(-1), respectively. Method validation was accomplished by the analysis of blood Reference Materials produced by the L'Institut National de Santé Publique du Quebec (Canada).

  5. The application of inductively coupled plasma dynamic reaction cell mass spectrometry for measurement of selenium isotopes, isotope ratios and chromatographic detection of selenoamino acids

    DEFF Research Database (Denmark)

    Sloth, Jens Jørgen; Larsen, Erik Huusfeldt

    2000-01-01

    Inductively coupled plasma dynamic reaction cell mass spectrometry (ICP-DRC-MS) was characterised for the detection of the six naturally occurring selenium isotopes. The potentially interfering argon dimers at the selenium masses m/z 74, 76, 78 and 80 were reduced in intensity by approximately five...... orders of magnitude by using methane as reactive cell gas in the DRC. By using 3% v/v methanol in water for carbon-enhanced ionisation of selenium, the sensitivity of Se-80 was 10(4) counts s(-1) per ng ml(-1) of selenium, and the estimated limit of detection was 6 pg ml(-1). The precision of the isotope...... ratios. Deuterated methane used as the DRC gas showed that hydrogen transfer from methane was not involved in the formation of SeH as SeD was absent in the mass spectrum. The almost interference-free detection of selenium by ICP-DRC-MS made the detection of the Se-80 isotope possible for detection...

  6. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Towards silicon speciation in light petroleum products using gas chromatography coupled to inductively coupled plasma mass spectrometry equipped with a dynamic reaction cell

    Energy Technology Data Exchange (ETDEWEB)

    Chainet, Fabien, E-mail: fabien.chainet@ifpen.fr [IFP Energies nouvelles, Rond-point de l' échangeur de Solaize, BP 3, 69360 Solaize (France); Lienemann, Charles-Philippe; Ponthus, Jeremie [IFP Energies nouvelles, Rond-point de l' échangeur de Solaize, BP 3, 69360 Solaize (France); Pécheyran, Christophe; Castro, Joaudimir; Tessier, Emmanuel; Donard, Olivier François Xavier [LCABIE-IPREM, UMR 5254, CNRS-UPPA, Helioparc, 2 av. Pr. Angot, 64053 Pau (France)

    2014-07-01

    Silicon speciation has recently gained interest in the oil and gas industry due to the significant poisoning problems caused by silicon on hydrotreatment catalysts. The poisoning effect clearly depends on the structure of the silicon species which must be determined and quantified. The hyphenation of gas chromatography (GC) coupled to inductively coupled plasma mass spectrometry (ICP-MS) allows a specific detection to determine the retention times of all silicon species. The aim of this work is to determine the retention indices of unknown silicon species to allow their characterization by a multi-technical approach in order to access to their chemical structure. The optimization of the dynamic reaction cell (DRC) of the ICP-MS using hydrogen as reactant gas successfully demonstrated the resolution of the interferences ({sup 14}N{sup 14}N{sup +} and {sup 12}C{sup 16}O{sup +}) initially present on {sup 28}Si. The linearity was excellent for silicon compounds and instrumental detection limits ranged from 20 to 140 μg of Si/kg depending on the response of the silicon compounds. A continuous release of silicon in the torch was observed most likely due to the use of a torch and an injector which was made of quartz. A non-universal response for silicon was observed and it was clearly necessary to use response coefficients to quantify silicon compounds. Known silicon compounds such as cyclic siloxanes (D{sub 3}–D{sub 16}) coming from PDMS degradation were confirmed. Furthermore, more than 10 new silicon species never characterized before in petroleum products were highlighted in polydimethylsiloxane (PDMS) degradation samples produced under thermal cracking of hydrocarbons. These silicon species mainly consisted of linear and cyclic structures containing reactive functions such as ethoxy, peroxide and hydroxy groups which can be able to react with the alumina surface and hence, poison the catalyst. This characterization will further allow the development of innovative

  8. Neural Networks in Chemical Reaction Dynamics

    CERN Document Server

    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

  9. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Determination of (90)Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS).

    Science.gov (United States)

    Feuerstein, J; Boulyga, S F; Galler, P; Stingeder, G; Prohaska, T

    2008-11-01

    A rapid method is reported for the determination of (90)Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of (90)Zr, which is present in soils at concentrations higher by more than six orders of magnitude than (90)Sr. Zirconium was separated from strontium in two steps to reduce the interference by (90)Zr(+) ions by a factor of more than 10(7): (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from (88)Sr on mass 90 u was found to be about 3 x 10(-9). Detection limits of 4 fg g(-1) (0.02 Bq g(-1)) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 microg g(-1) Sr and 50 ng g(-1) Zr a detection limit of 0.2 pg g(-1) soil (1 Bq g(-1) soil) was determined. (90)Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66+/-0.27, 13.48+/-0.68 and 12.9+/-1.5 pg g(-1) corresponding to specific activities of 23.7+/-1.3, 68.6+/-3.5 and 65.6+/-7.8 Bq g(-1), respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level (90)Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g(-1).

  11. Determination of {sup 90}Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS)

    Energy Technology Data Exchange (ETDEWEB)

    Feuerstein, J.; Boulyga, S.F.; Galler, P.; Stingeder, G. [Department of Chemistry, Division of Analytical Chemistry-VIRIS Laboratory, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna (Austria); Prohaska, T. [Department of Chemistry, Division of Analytical Chemistry-VIRIS Laboratory, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna (Austria)], E-mail: thomas.prohaska@boku.ac.at

    2008-11-15

    A rapid method is reported for the determination of {sup 90}Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of {sup 90}Zr, which is present in soils at concentrations higher by more than six orders of magnitude than {sup 90}Sr. Zirconium was separated from strontium in two steps to reduce the interference by {sup 90}Zr{sup +} ions by a factor of more than 10{sup 7}: (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from {sup 88}Sr on mass 90 u was found to be about 3 x 10{sup -9}. Detection limits of 4 fg g{sup -1} (0.02 Bq g{sup -1}) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 {mu}g g{sup -1} Sr and 50 ng g{sup -1} Zr a detection limit of 0.2 pg g{sup -1} soil (1 Bq g{sup -1} soil) was determined. {sup 90}Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66 {+-} 0.27, 13.48 {+-} 0.68 and 12.9 {+-} 1.5 pg g{sup -1} corresponding to specific activities of 23.7 {+-} 1.3, 68.6 {+-} 3.5 and 65.6 {+-} 7.8 Bq g{sup -1}, respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level {sup 90}Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g{sup -1}.

  12. Quantum dynamics of fast chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Condensation reaction in the bandpass reaction cell improves sensitivity for uranium, thorium, neodymium and praseodymium measurements.

    Science.gov (United States)

    Vais, Vladimir; Li, Chunsheng; Cornett, Jack

    2003-09-01

    Condensation reactions in the bandpass reaction cell or dynamic reaction cell (DRC) were used for the determination of actinides and lanthanides such as uranium, thorium, neodymium and praseodymium. These elements react with oxygen reagent gas in the dynamic reaction cell of the ELAN DRC II instrument to give mono- and/or dioxo cationic species (UO(2)+, ThO+, NdO+ and PrO+, respectively). Increasing the oxygen flow rate in the dynamic reaction cell leads to the rapid decrease of the singly charged metal ions accompanied by the fast increase in the intensity of the oxide ion. This phenomenon is used to improve considerably the sensitivity of ICP-MS instruments equipped with a dynamic reaction cell for actinides and lanthanides. Estimated detection limits (EDL) obtained in this work for uranium, thorium, neodymium-144 and praseodymium are 0.022, 1.0, 0.045, and 0.10 ng L(-1), respectively. The detection limit for uranium measured in the standard (vented) mode of an ELAN DRC II was found to be 0.22 ng L(-1), which is an order of magnitude higher compared to the pressurized mode.

  14. New methods for quantum mechanical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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 (L2) 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 H3O- system, providing information about the potential energy surface for the OH + H2 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

  15. Chemical memory reactions induced bursting dynamics in gene expression.

    Science.gov (United States)

    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.

  16. Laser ablation-inductively coupled plasma-dynamic reaction cell-mass spectrometry for the multi-element analysis of polymers

    Energy Technology Data Exchange (ETDEWEB)

    Resano, M. [Laboratory of Analytical Chemistry, Ghent University, Institute for Nuclear Sciences, Proeftuinstraat 86, B-9000 Ghent (Belgium)]. E-mail: mresano@unizar.es; Garcia-Ruiz, E. [Laboratory of Analytical Chemistry, Ghent University, Institute for Nuclear Sciences, Proeftuinstraat 86, B-9000 Ghent (Belgium); Vanhaecke, F. [Laboratory of Analytical Chemistry, Ghent University, Institute for Nuclear Sciences, Proeftuinstraat 86, B-9000 Ghent (Belgium)

    2005-11-15

    In this work, the potential of laser ablation-inductively coupled plasma-mass spectrometry for the fast analysis of polymers has been explored. Different real-life samples (polyethylene shopping bags, an acrylonitrile butadiene styrene material and various plastic bricks) as well as several reference materials (VDA 001 to 004, Cd in polyethylene) have been selected for the study. Two polyethylene reference materials (ERM-EC 680 and 681), for which a reference or indicative value for the most relevant metals is available, have proved their suitability as standards for calibration. Special attention has been paid to the difficulties expected for the determination of Cr at the {mu}g g{sup -1} level in this kind of materials, due to the interference of ArC{sup +} ions on the most abundant isotopes of Cr. The use of ammonia as a reaction gas in a dynamic reaction cell is shown to alleviate this problem, resulting in a limit of detection of 0.15 {mu}g g{sup -1} for this element, while limiting only modestly the possibilities of the technique for simultaneous multi-element analysis. In this regard, As is the analyte most seriously affected by the use of ammonia, and its determination has to be carried out in vented mode, at the expense of measuring time. In all cases studied, accurate results could be obtained for elements ranging in content from the sub-{mu}g g{sup -1} level to tens of thousands of {mu}g g{sup -1}. However, the use of an element of known concentration as internal standard may be needed for materials with a matrix significantly different from that of the standard (polyethylene in this work). Precision ranged between 5% and 10% RSD for elements found at the 10 {mu}g g{sup -1} level or higher, while this value could deteriorate to 20% for analytes found at the sub-{mu}g g{sup -1} level. Overall, the technique evaluated presents many advantages for the fast and accurate multi-element analysis of these materials, avoiding laborious digestion procedures and

  17. Multi-element analysis of urine using dynamic reaction cell inductively coupled plasma mass spectrometry (ICP-DRC-MS — A practical application

    Directory of Open Access Journals (Sweden)

    Renata Brodzka

    2013-04-01

    Full Text Available Objectives: The method for the determination of As, Al, Cd, Ni, Pb (toxic elements and Cr, Co, Cu, Fe, Mn, Zn (essential elements in human urine by the use of Inductively Coupled Plasma Mass Spectrometry (quadrupole ICP-MS DRCe Elan, Perkin Elmer with the dynamic reaction cell (DRC was developed. Materials and Methods: The method has been applied for multi-element analysis of the urine of 16 non-exposed healthy volunteers and 27 workers employed in a copper smelter. The analysis was conducted after initial 10-fold dilution of the urine samples with 0,1% nitric acid. Rhodium was used as an internal standard. The method validation parameters such as detection limit, sensitivity, precision were described for all elements. Accuracy of the method was checked by the regular use of certified reference materials ClinCheck®-Control Urine (Recipe as well as by participation of the laboratory in the German External Quality Assessment Scheme (G-EQUAS. Results: The detection limits (DL 3s of the applied method were 0.025, 0.007, 0.002, 0.004, 0.004, 0.086, 0.037, 0.009, 0.016, 0.008, 0.064 (μg/l for Al, As, Cd, Cr, Co, Cu, Fe, Mn, Ni, Pb, Zn in urine, respectively. For each element linearity with correlation coefficient of at least 0.999 was determined. Spectral interferences from some of the ions were removed using DRC-e with addition of alternative gas: methane for cobalt, copper, cadmium, chromium, iron, manganese, nickel and rhodium, and oxygen for arsenic. Conclusions: The developed method allows to determine simultaneously eleven elements in the urine with low detection limits, high sensitivity and good accuracy. Moreover, the method is appropriate for the assessment of both environmental and occupational exposure.

  18. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics.

    Science.gov (United States)

    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.

  19. Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS

    Science.gov (United States)

    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

  20. Recycling probability and dynamical properties of germinal center reactions

    CERN Document Server

    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 ...

  1. Reaction dynamics and photochemistry of divalent systems

    Energy Technology Data Exchange (ETDEWEB)

    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 + NO2. Formation of the dominant BaO(1Σ) + NO products resulted primarily from decay of long-lived Ba+NO2- collision complexes. Secondary mechanisms led to formation of forward scattered, internally excited BaO, and BaNO + O. Do(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(1S) + H2O led to BaO + H2, whereas excited state Ba(1D) + H2O reacted to form BaOH + H. Collisions between Ba and CH3OH led to BaOCH3 + H. Radical channels involve H-atom migration and are promoted by excitation of the incident Ba atom. In Chapter 3, reactions of Ba(1S) with ClO22 and O3 are discussed. Again, direct and complex mechanisms were observed. Formation of BaCl + O2 from decomposition of Ba+ClO2- accounted for 10% of total reaction crass section. Although Ba + O3 → BaO + 02 occurs primarily by direct reaction mechanisms, the secondary channel Ba + 03 → BaO2 + 0 involved decay of long lived Ba1+O3- intermediates. Do(Ba-O2) = 120 ±20 kcal/mol. Photodissociation dynamics of NO3 is explored in chapter 4. Visible excitation leads to formation of NO + 02 and NO2 + O. Wavelength dependence of branching ratios is investigated. Do(O-NO2) = 48.55 kcal/mole ;and calculate ΔHf(NO3) = 17.75 kcal/mole (298K). Chapter 5 discusses the photodissociation of OClO in a molecular beam. Although ClO(2II) + O(3P) is dominant, Cl(2P) + O2

  2. Dynamics of cell orientation

    Science.gov (United States)

    de, Rumi; Zemel, Assaf; Safran, Samuel A.

    2007-09-01

    Many physiological processes depend on the response of biological cells to mechanical forces generated by the contractile activity of the cell or by external stresses. Using a simple theoretical model that includes the forces due to both the mechanosensitivity of cells and the elasticity of the matrix, we predict the dynamics and orientation of cells in both the absence and presence of applied stresses. The model predicts many features observed in measurements of cellular forces and orientation including the increase with time of the cellular forces in the absence of applied stress and the consequent decrease of the force in the presence of quasi-static stresses. We also explain the puzzling observation of parallel alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for dynamically varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency.

  3. Development of a method based on inductively coupled plasma-dynamic reaction cell-mass spectrometry for the simultaneous determination of phosphorus, calcium and strontium in bone and dental tissue

    Energy Technology Data Exchange (ETDEWEB)

    De Muynck, David [Ghent University, Department of Analytical Chemistry, Krijgslaan 281-S12, BE-9000 Ghent (Belgium)], E-mail: David.DeMuynck@UGent.be; Vanhaecke, Frank [Ghent University, Department of Analytical Chemistry, Krijgslaan 281-S12, BE-9000 Ghent (Belgium)], E-mail: Frank.Vanhaecke@UGent.be

    2009-05-15

    A method, based on the use of a quadrupole-based inductively coupled plasma-mass spectrometry instrument equipped with a quadrupole-based collision/reaction cell (dynamic reaction cell, DRC), was developed for the simultaneous determination of phosphorus, calcium and strontium in bone and dental (enamel and dentine) tissue. The use of NH{sub 3}, introduced at a gas flow rate of 0.8 mL min{sup -1} in the dynamic reaction cell, combined with a rejection parameter q (RPq) setting of 0.65, allows interference-free determination of calcium via its low-abundant isotopes {sup 42}Ca, {sup 43}Ca and {sup 44}Ca, and of strontium via its isotopes {sup 86}Sr and {sup 88}Sr that are freed from overlap due to the occurrence of ArCa{sup +} and/or Ca{sub 2}{sup +} ions. Also the determination of phosphorus ({sup 31}P, mono-isotopic) was shown to be achievable using the same dynamic reaction cell operating conditions. The bone certified reference materials NIST SRM 1400 Bone Ash and NIST SRM 1486 Bone Meal were used for validation of the measurement protocol that was shown capable of providing accurate and reproducible results. Detection limits of P, Ca and Sr in dental tissue digests were established as 3 {mu}g L{sup -1} for P, 2 {mu}g L{sup -1} for Ca and 0.2 {mu}g L{sup -1} for Sr. This method can be used to simultaneously (i) evaluate the impact of diagenesis on the elemental and isotopic composition of buried skeletal tissue via its Ca/P ratio and (ii) determine its Sr concentration. The measurement protocol was demonstrated as fit-for-purpose by the analysis of a set of teeth of archaeological interest for their Ca/P ratio and Sr concentration.

  4. Real-Time Dynamics of Galvanic Replacement Reactions of Silver Nanocubes and Au Studied by Liquid-Cell Transmission Electron Microscopy.

    Science.gov (United States)

    Tan, Shu Fen; Lin, Guanhua; Bosman, Michel; Mirsaidov, Utkur; Nijhuis, Christian A

    2016-08-23

    We study the galvanic replacement reaction of silver nanocubes in dilute, aqueous ethylenediaminetetraacetic acid disodium salt (EDTA)-capped gold aurate solutions using in situ liquid-cell electron microscopy. Au/Ag etched nanostructures with concave faces are formed via (1) etching that starts from the faces of the nanocubes, followed by (2) the deposition of an Au layer as a result of galvanic replacement, and (3) Au deposition via particle coalescence and monomer attachment where small nanoparticles are formed during the reaction as a result of radiolysis. Analysis of the Ag removal rate and Au deposition rate provides a quantitative picture of the growth process and shows that the morphology and composition of the final product are dependent on the stoichiometric ratio between Au and Ag.

  5. Single cell dynamic phenotyping

    OpenAIRE

    Katherin Patsch; Chi-Li Chiu; Mark Engeln; Agus, David B.; Parag Mallick; Shannon M. Mumenthaler; Daniel Ruderman

    2016-01-01

    Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype track...

  6. Mechanical reaction-diffusion model for bacterial population dynamics

    CERN Document Server

    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.

  7. The molecular dynamics of atmospheric reaction

    Science.gov (United States)

    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.

  8. Electrostatic effects and the dynamics of enzyme reactions at the surface of plant cells. 3. Interplay between limited cell-wall autolysis, pectin methyl esterase activity and electrostatic effects in soybean cell walls.

    Science.gov (United States)

    Nari, J; Noat, G; Diamantidis, G; Woudstra, M; Ricard, J

    1986-02-17

    Soybean cell walls display a process of autolysis which results in the release of reducing sugars from the walls. Loosening and autolysis of cell wall are involved in the cell-wall growth process, for autolysis is maximum during both cell extension and cell-wall synthesis. Autolysis goes to completion within about 50 h and is an enzymatic process that results from the activity of cell wall exo- and endo-glycosyltransferases. The optimum pH of autolysis is about 5. Increasing the ionic strength of the bulk phase where cell-wall fragments are suspended, results in a shift of the pH profile towards low pH. This is consistent with the view that at 'low' ionic strength, the local pH in the cell wall is lower than in the bulk phase. One of the main ideas of the model proposed in a preceding paper, is that pectin methyl esterase reaction, by building up a high fixed charge density, results in proton attraction in the wall. Low pH must then activate the wall loosening enzymes involved in autolysis and cell growth. This view may be directly confirmed experimentally. The pH of a cell-wall suspension, initially equal to 5, was brought to 8 for 20 min, then back to 5. Under these conditions, the rate of cell-wall autolysis was enhanced with respect to the rate of autolysis obtained with cell-wall fragments kept at pH 5. The pH response of the multienzyme plant cell-wall system basically relies on opposite pH sensitivities of the two types of enzymes involved in the growth process. Pectin methyl esterase, which generates the cell-wall Donnan potential, is inhibited by protons, whereas the wall-loosening enzymes involved in cell growth are activated by protons.

  9. Simultaneous determination of Se, trace elements and major elements in Se-rich rice by dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS) after microwave digestion.

    Science.gov (United States)

    Wei, Yi Hua; Zhang, Jin Yan; Zhang, Da Wen; Luo, Lin Guang; Tu, Tian Hua

    2014-09-15

    A quick and accurate method was devised to determine Se, As, Ba, Ca, Cd, Cr, Cu, Fe, Mg, Mn, Ni, Pb, Sr and Zn in Se-rich rice samples by microwave digestion and inductively coupled plasma-mass spectrometry (ICP-MS). Spectral interferences on Se were eliminated using methane as a reaction gas in the dynamic reaction cell (DRC). Rhodium was used as an internal standard to compensate for sample matrix effects. A rice-certified reference material (CRM) (GBW 10010) was used to verify the accuracy of the method. The method detection limits were 0.001-0.03 mg/kg, analyte recoveries were 85-108% and precisions (RSDs) ranged from 2.1% to 5.8%. Correlation analysis showed that the Se concentrations in the Se-rich rice samples correlated well with the Cu concentrations (r=0.53, p<0.05).

  10. CONVENTIONAL RENAL CELL CARCINOMA WITH GRANULOMATOUS REACTION

    Directory of Open Access Journals (Sweden)

    Srinivas

    2014-09-01

    Full Text Available : Granulomatous inflammation is a distinctive pattern of chronic inflammatory reaction characterized by microscopic aggregation of activated macrophages which often develop epithelioid appearance and multinucleate giant cells. Granulomas are encountered in limited number of infectious and some non-infectious conditions. Granulomas have been described within the stroma of malignancies like carcinomas of the breast and colon, seminoma and Hodgkin’s lymphoma, where they represent T-cell-mediated reaction of the tumor stroma to antigens expressed by the tumor. Granulomatous reaction in association with renal cell carcinoma (RCC is uncommon, with only few published reports in the literature. We describe a case of conventional (clear cell RCC associated with epithelioid cell granulomas within the tumor parenchyma.

  11. Dynamics of B cells in germinal centres.

    Science.gov (United States)

    De Silva, Nilushi S; Klein, Ulf

    2015-03-01

    Humoral immunity depends on the germinal centre (GC) reaction during which somatically mutated high-affinity memory B cells and plasma cells are generated. Recent studies have uncovered crucial cues that are required for the formation and the maintenance of GCs and for the selection of high-affinity antibody mutants. In addition, it is now clear that these events are promoted by the dynamic movements of cells within and between GCs. These findings have resolved the complexities of the GC reaction in greater detail than ever before. This Review focuses on these recent advances and discusses their implications for the establishment of humoral immunity.

  12. Cell Division, Differentiation and Dynamic Clustering

    CERN Document Server

    Kaneko, K; Kaneko, Kunihiko; Yomo, Tetsuya

    1993-01-01

    A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to show three successive stages with the growth of the number of cells; coherent growth, dynamic clustering, and fixed cell differentiation. At the last stage, disparity in activities, germ line segregation, somatic cell differentiation, and homeochaotic stability against external perturbation are found. Our results, in consistency with the experiments of the preceding paper, imply that cell differentiation can occur without a spatial pattern. From dynamical systems viewpoint, the new concept of ``open chaos" is proposed, as a novel and general scenario for systems with growing numbers of elements, also seen in economics and sociology.A

  13. Determination of copper in coal fly ash in the presence of excess titanium by dynamic reaction cell inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Liu, Hui-Tao; Jiang, Shiuh-Jen

    2003-01-01

    Inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) was used for the accurate determination of copper in coal fly ash samples in the presence of excess titanium, using the reaction of Cu(+) ions with NH(3) in the cell. The method eliminated the effect of polyatomic isobaric interferences at m/z 63 and 65 caused by the formation of (47)Ti(16)O(+), (49)Ti(16)O(+) and (47)Ti(18)O(+) on (63)Cu(+) and (65)Cu(+) by detecting Cu(+) as the product cluster ion Cu(NH(3))(2)(+). As the signal of (63)Cu(NH(3))(2)(+) overlapped with that of (97)Mo(+) which existed in the samples, (65)Cu(NH(3))(2)(+) was detected at m/z 99. The effect of the operating conditions of DRC system was studied in order to obtain the best signal to noise ratio for Cu(NH(3))(2)(+) at m/z 99. The formation of Cu(NH(3))(2)(+) was through the clustering reaction Cu(+)+2NH(3)-->Cu(NH(3))(2)(+) which resulted in the separation of analyte from the interfering oxide. The detection limit for Cu(NH(3))(2)(+) was 0.015 ng mL(-1) as Cu. The method was applied to the determination of copper in NIST SRM 1633a and 1633b coal fly ash reference materials. The precision between sample replicates was better than 2.0% and the analysis results were in good agreement with the certified values.

  14. Determination of copper in coal fly ash in the presence of excess titanium by dynamic reaction cell inductively coupled plasma mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hui-Tao [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Jiang, Shiuh-Jen [Department of Chemistry, National Sun Yat-sen University, Kaohsiung 80424 (Taiwan)

    2003-01-01

    Inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) was used for the accurate determination of copper in coal fly ash samples in the presence of excess titanium, using the reaction of Cu{sup +} ions with NH{sub 3} in the cell. The method eliminated the effect of polyatomic isobaric interferences at m/z 63 and 65 caused by the formation of {sup 47}Ti{sup 16}O{sup +}, {sup 49}Ti{sup 16}O{sup +} and {sup 47}Ti{sup 18}O{sup +} on {sup 63}Cu{sup +} and {sup 65}Cu{sup +} by detecting Cu{sup +} as the product cluster ion Cu(NH{sub 3}){sub 2}{sup +}. As the signal of {sup 63}Cu(NH{sub 3}){sub 2}{sup +} overlapped with that of {sup 97}Mo{sup +} which existed in the samples, {sup 65}Cu(NH{sub 3}){sub 2}{sup +} was detected at m/z 99. The effect of the operating conditions of DRC system was studied in order to obtain the best signal to noise ratio for Cu(NH{sub 3}){sub 2}{sup +} at m/z 99. The formation of Cu(NH{sub 3}){sub 2}{sup +} was through the clustering reaction Cu{sup +}+2NH{sub 3}{yields}Cu(NH{sub 3}){sub 2}{sup +} which resulted in the separation of analyte from the interfering oxide. The detection limit for Cu(NH{sub 3}){sub 2}{sup +} was 0.015 ng mL{sup -1} as Cu. The method was applied to the determination of copper in NIST SRM 1633a and 1633b coal fly ash reference materials. The precision between sample replicates was better than 2.0% and the analysis results were in good agreement with the certified values. (orig.)

  15. Dynamic CT of tuberculous meningeal reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Electromagnetic Reactions and Few-Nucleon Dynamics

    CERN Document Server

    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.

  17. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    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

  18. Programming the dynamics of biochemical reaction networks.

    Science.gov (United States)

    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.

  19. NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics

    CERN Document Server

    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...

  20. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  1. Transverse flow reactor studies of the dynamics of radical reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

    KAUST Repository

    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.

  3. Bayesian inversion analysis of nonlinear dynamics in surface heterogeneous reactions.

    Science.gov (United States)

    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.

  4. Manual for Dynamic Triaxial Cell

    DEFF Research Database (Denmark)

    Pedersen, Thomas Schmidt; Ibsen, Lars Bo

    This report is a test report that describes the test setup for a dynamic triaxial cell at the Laboratory for Geotechnique at Aalborg University.......This report is a test report that describes the test setup for a dynamic triaxial cell at the Laboratory for Geotechnique at Aalborg University....

  5. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    Science.gov (United States)

    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.

  6. Quantum Dynamics of Radical-Ion-Pair Reactions

    OpenAIRE

    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...

  7. Dynamized Preparations in Cell Culture

    Directory of Open Access Journals (Sweden)

    Ellanzhiyil Surendran Sunila

    2009-01-01

    Full Text Available Although reports on the efficacy of homeopathic medicines in animal models are limited, there are even fewer reports on the in vitro action of these dynamized preparations. We have evaluated the cytotoxic activity of 30C and 200C potencies of ten dynamized medicines against Dalton's Lymphoma Ascites, Ehrlich's Ascites Carcinoma, lung fibroblast (L929 and Chinese Hamster Ovary (CHO cell lines and compared activity with their mother tinctures during short-term and long-term cell culture. The effect of dynamized medicines to induce apoptosis was also evaluated and we studied how dynamized medicines affected genes expressed during apoptosis. Mother tinctures as well as some dynamized medicines showed significant cytotoxicity to cells during short and long-term incubation. Potentiated alcohol control did not produce any cytotoxicity at concentrations studied. The dynamized medicines were found to inhibit CHO cell colony formation and thymidine uptake in L929 cells and those of Thuja, Hydrastis and Carcinosinum were found to induce apoptosis in DLA cells. Moreover, dynamized Carcinosinum was found to induce the expression of p53 while dynamized Thuja produced characteristic laddering pattern in agarose gel electrophoresis of DNA. These results indicate that dynamized medicines possess cytotoxic as well as apoptosis-inducing properties.

  8. Dynamical dipole mode in heavy-ion fusion reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. Dynamics of synchrotron VUV-induced intracluster reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. The hunt for the dynamical resonances in chemical reaction dynamics: a perspective on historical advances

    Directory of Open Access Journals (Sweden)

    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.

  11. Determination of glyphosate and AMPA in surface and waste water using high-performance ion chromatography coupled to inductively coupled plasma dynamic reaction cell mass spectrometry (HPIC-ICP-DRC-MS).

    Science.gov (United States)

    Popp, Maximilian; Hann, Stephan; Mentler, Axel; Fuerhacker, Maria; Stingeder, Gerhard; Koellensperger, Gunda

    2008-05-01

    A novel method employing high-performance cation chromatography in combination with inductively coupled plasma dynamic reaction cell mass spectrometry (ICP-DRC-MS) for the simultaneous determination of the herbicide glyphosate (N-phosphonomethylglycine) and its main metabolite aminomethyl phosphonic acid (AMPA) is presented. P was measured as (31)P(16)O(+) using oxygen as reaction gas. For monitoring the stringent target value of 0.1 μg L(-1) for glyphosate, applicable for drinking and surface water within the EU, a two-step enrichment procedure employing Chelex 100 and AG1-X8 resins was applied prior to HPIC-ICP-MS analysis. The presented approach was validated for surface water, revealing concentrations of 0.67 μg L(-1) glyphosate and 2.8 μg L(-1) AMPA in selected Austrian river water samples. Moreover, investigations at three waste water-treatment plants showed that elimination of the compounds at the present concentration levels was not straightforward. On the contrary, all investigated plant effluents showed significant amounts of both compounds. Concentration levels ranged from 0.5-2 μg L(-1) and 4-14 μg L(-1) for glyphosate and AMPA, respectively.

  12. Reaction Profiles and Molecular Dynamics Simulations of Cyanide Radical Reactions Relevant to Titan's Atmosphere

    Science.gov (United States)

    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

  13. Reaction Dynamics and Spectroscopy of Hydrocarbons in Plasma

    Energy Technology Data Exchange (ETDEWEB)

    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.

  14. Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

    Science.gov (United States)

    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.

  15. Potential energy surfaces and reaction dynamics of polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    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.

  17. Dynamics of anion-molecule reactions at low energy

    Energy Technology Data Exchange (ETDEWEB)

    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.)

  18. Quantum Dynamics of Radical-Ion-Pair Reactions

    CERN Document Server

    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.

  19. Roaming dynamics in ion-molecule reactions: phase space reaction pathways and geometrical interpretation

    CERN Document Server

    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...

  20. Cell reactions with biomaterials: the microscopies

    Directory of Open Access Journals (Sweden)

    Curtis A. S.G.

    2001-01-01

    Full Text Available The methods and results of optical microscopy that can be used to observe cell reactions to biomaterials are Interference Reflection Microscopy (IRM, Total Internal Reflection Fluorescence Microscopy (TIRFM, Surface Plasmon Resonance Microscopy (SPRM and Forster Resonance Energy Transfer Microscopy (FRETM and Standing Wave Fluorescence Microscopy. The last three are new developments, which have not yet been fully perfected. TIRFM and SPRM are evanescent wave methods. The physics of these methods depend upon optical phenomena at interfaces. All these methods give information on the dimensions of the gap between cell and the substratum to which it is adhering and thus are especially suited to work with biomaterials. IRM and FRETM can be used on opaque surfaces though image interpretation is especially difficult for IRM on a reflecting opaque surface. These methods are compared with several electron microscopical methods for studying cell adhesion to substrata. These methods all yield fairly consistent results and show that the cell to substratum distance on many materials is in the range 5 to 30 nm. The area of contact relative to the total projected area of the cell may vary from a few per cent to close to 100% depending on the cell type and substratum. These methods show that those discrete contact areas well known as focal contacts are frequently present. The results of FRETM suggest that the separation from the substratum even in a focal contact is about 5 nm.

  1. Quantum dynamics of the abstraction reaction of H with cyclopropane.

    Science.gov (United States)

    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.

  2. Unimolecular reaction dynamics of well characterized ionic reactions. Final report, 1993--1997

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. The photodissociation and reaction dynamics of vibrationally excited molecules

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Untangling knots via reaction-diffusion dynamics of vortex strings

    CERN Document Server

    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.

  5. Effect of Coriolis coupling in chemical reaction dynamics.

    Science.gov (United States)

    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.

  6. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    Science.gov (United States)

    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.

  7. Reaction dynamics studies for the system 7Be+58Ni

    Science.gov (United States)

    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].

  8. Dynamic signaling cascades: reversible covalent reaction-coupled molecular switches.

    Science.gov (United States)

    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.

  9. Simultaneous quantification of 17 trace elements in blood by dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS) equipped with a high-efficiency sample introduction system.

    Science.gov (United States)

    D'Ilio, S; Violante, N; Di Gregorio, M; Senofonte, O; Petrucci, F

    2006-10-10

    A quadrupole inductively coupled plasma mass spectrometer (Q-ICP-MS) equipped with a dynamic reaction cell (DRC) and coupled with a desolvating nebulization system (APEX-IR) was employed to determine 17 elements (Al, As, Ba, Cd, Co, Cr, Li, Mn, Mo, Ni, Pb, Sb, Se, Sn, Sr, V, and Zr) in blood samples. Ammonia (for Al, Cr, Mn, and V) and O2 (for As and Se) were used as reacting gases. Selection of the best flow rate of the gases and optimization of the quadrupole dynamic bandpass tuning parameter (RPq) were carried out, using digested blood diluted 1+9 with deionized water and spiked with 1 microg L(-1) of Al, Cr, Mn, V and 5 microgL(-1) of As and Se. Detection limits were determined in digested blood using the 3sigma criterion. The desolvating system allowed a sufficient sensitivity to be achieved to determine elements at levels of ng L(-1) without detriment of signal stability. The accuracy of the method was tested with the whole blood certified reference material (CRM), certified for Al, As, Cd, Co, Cr, Mn, Mo, Ni, Pb, Sb, Se, and V, and with indicative values for Ba, Li, Sn, Sr, and Zr. The addition calibration approach was chosen for analysis. In order to confirm the DRC data, samples were also analyzed by means of sector field inductively coupled plasma mass spectrometry (SF-ICP-MS), operating in medium (m/Deltam=4000) and high (m/Deltam=10,000) resolution mode and achieving a good agreement between the two techniques.

  10. A novel methodology for rapid digestion of rare earth element ores and determination by microwave plasma-atomic emission spectrometry and dynamic reaction cell-inductively coupled plasma-mass spectrometry.

    Science.gov (United States)

    Helmeczi, Erick; Wang, Yong; Brindle, Ian D

    2016-11-01

    Short-wavelength infrared radiation has been successfully applied to accelerate the acid digestion of refractory rare-earth ore samples. Determinations were achieved with microwave plasma-atomic emission spectrometry (MP-AES) and dynamic reaction cell - inductively coupled plasma-mass spectrometry (DRC-ICP-MS). The digestion method developed was able to tackle high iron-oxide and silicate matrices using only phosphoric acid in a time frame of only 8min, and did not require perchloric or hydrofluoric acid. Additionally, excellent recoveries and reproducibilities of the rare earth elements, as well as uranium and thorium, were achieved. Digestions of the certified reference materials OREAS-465 and REE-1, with radically different mineralogies, delivered results that mirror those obtained by fusion processes. For the rare-earth CRM OKA-2, whose REE data are provisional, experimental data for the rare-earth elements were generally higher than the provisional values, often exceeding z-values of +2. Determined values for Th and U in this reference material, for which certified values are available, were in excellent agreement. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics.

    Science.gov (United States)

    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.

  12. Transcription Dynamics in Living Cells.

    Science.gov (United States)

    Lenstra, Tineke L; Rodriguez, Joseph; Chen, Huimin; Larson, Daniel R

    2016-07-01

    The transcription cycle can be roughly divided into three stages: initiation, elongation, and termination. Understanding the molecular events that regulate all these stages requires a dynamic view of the underlying processes. The development of techniques to visualize and quantify transcription in single living cells has been essential in revealing the transcription kinetics. They have revealed that (a) transcription is heterogeneous between cells and (b) transcription can be discontinuous within a cell. In this review, we discuss the progress in our quantitative understanding of transcription dynamics in living cells, focusing on all parts of the transcription cycle. We present the techniques allowing for single-cell transcription measurements, review evidence from different organisms, and discuss how these experiments have broadened our mechanistic understanding of transcription regulation.

  13. Geometrical Models of the Phase Space Structures Governing Reaction Dynamics

    CERN Document Server

    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...

  14. Dynamic biochemical reaction process analysis and pathway modification predictions.

    Science.gov (United States)

    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.

  15. ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.

    Directory of Open Access Journals (Sweden)

    Johannes Schöneberg

    Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.

  16. Coriolis-coupled wave packet dynamics of H + HLi reaction.

    Science.gov (United States)

    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.

  17. Imaging the dynamics of chlorine atom reactions with alkenes

    Science.gov (United States)

    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.

  18. Molecular-dynamics study of detonation. II. The reaction mechanism

    Science.gov (United States)

    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.

  19. Crossed-beam studies of the dynamics of radical reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. The quantum dynamics of electronically nonadiabatic chemical reactions

    Science.gov (United States)

    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

  1. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    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

  2. Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics

    CERN Document Server

    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.

  3. Quasi-elastic reactions: an interplay of reaction dynamics and nuclear structure

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Incidents of chemical reactions in cell equipment

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, N.M.; Barlow, C.R. [Uranium Enrichment Organization, Oak Ridge, TN (United States)

    1991-12-31

    Strongly exothermic reactions can occur between equipment structural components and process gases under certain accident conditions in the diffusion enrichment cascades. This paper describes the conditions required for initiation of these reactions, and describes the range of such reactions experienced over nearly 50 years of equipment operation in the US uranium enrichment program. Factors are cited which can promote or limit the destructive extent of these reactions, and process operations are described which are designed to control the reactions to minimize equipment damage, downtime, and the possibility of material releases.

  5. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    Science.gov (United States)

    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.

  6. Platelet reactions to modified surfaces under dynamic conditions.

    Science.gov (United States)

    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.

  7. Systematic development of reduced reaction mechanisms for dynamic modeling

    Science.gov (United States)

    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.

  8. Measurements of Dynamical Dipole in isospin asymmetric fusion reactions

    Science.gov (United States)

    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.

  9. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics

    CERN Document Server

    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.

  11. Global dynamics of a reaction-diffusion system

    Directory of Open Access Journals (Sweden)

    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.

  12. Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics

    KAUST Repository

    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.

  13. Statistical theory for the kinetics and dynamics of roaming reactions.

    Science.gov (United States)

    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.

  14. Multi-elemental characterization of tunnel and road dusts in Houston, Texas using dynamic reaction cell-quadrupole-inductively coupled plasma-mass spectrometry: Evidence for the release of platinum group and anthropogenic metals from motor vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Spada, Nicholas; Bozlaker, Ayse [Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77204-4003 (United States); Chellam, Shankararaman, E-mail: chellam@uh.edu [Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77204-4003 (United States); Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204-4004 (United States)

    2012-07-20

    Highlights: Black-Right-Pointing-Pointer Analytical method for PGEs, main group, transition and rare earth metals developed. Black-Right-Pointing-Pointer Comprehensive characterization of road and tunnel dust samples was accomplished. Black-Right-Pointing-Pointer PGEs in dusts arise from autocatalyst attrition. Black-Right-Pointing-Pointer Mobile sources also contributed to Cu, Zn, Ga, As, Mo, Cd, Sn, Sb, Ba, W and Pb. Black-Right-Pointing-Pointer All other elements, including rare earths arose from crustal sources. - Abstract: Platinum group elements (PGEs) including Rh, Pd, and Pt are important tracers for vehicular emissions, though their measurement is often challenging and difficult to replicate in environmental campaigns. These challenges arise from sample preparation steps required for PGE quantitation, which often cause severe isobaric interferences and spectral overlaps from polyatomic species of other anthropogenically emitted metals. Consequently, most previous road dust studies have either only quantified PGEs or included a small number of anthropogenic elements. Therefore a novel analytical method was developed to simultaneously measure PGEs, lanthanoids, transition and main group elements to comprehensively characterize the elemental composition of urban road and tunnel dusts. Dust samples collected from the vicinity of high-traffic roadways and a busy underwater tunnel restricted to single-axle (predominantly gasoline-driven) vehicles in Houston, TX were analyzed for 45 metals with the newly developed method using dynamic reaction cell-quadrupole-inductively coupled plasma-mass spectrometry (DRC-q-ICP-MS). Average Rh, Pd and Pt concentrations were 152 {+-} 52, 770 {+-} 208 and 529 {+-} 130 ng g{sup -1} respectively in tunnel dusts while they varied between 6 and 8 ng g{sup -1}, 10 and 88 ng g{sup -1} and 35 and 131 ng g{sup -1} in surface road dusts. Elemental ratios and enrichment factors demonstrated that PGEs in dusts originated from autocatalyst

  15. Ring opening reaction dynamics in the reaction of hydrogen atoms with ethylene oxide

    Science.gov (United States)

    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.

  16. Crawling and turning in a minimal reaction-diffusion cell motility model: Coupling cell shape and biochemistry

    Science.gov (United States)

    Camley, Brian A.; Zhao, Yanxiang; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan

    2017-01-01

    We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.

  17. Crawling and turning in a minimal reaction-diffusion cell motility model: coupling cell shape and biochemistry

    CERN Document Server

    Camley, Brian A; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan

    2016-01-01

    We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability, and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.

  18. Copper-Catalyzed Click Reaction on/in Live Cells.

    Science.gov (United States)

    Li, Siheng; Wang, Lin; Yu, Fei; Zhu, Zhiling; Shobaki, Dema; Chen, Haoqing; Wang, Mu; Wang, Jun; Qin, Guoting; Erasquin, Uriel J; Ren, Li; Wang, Yingjun; Cai, Chengzhi

    2017-03-01

    We demonstrated that copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction could be performed inside live mammalian cells without using a chelating azide. Under optimized conditions, the reaction was performed in human ovary cancer cell line OVCAR5 in which newly synthesized proteins were metabolically modified with homopropargylglycine (HPG). This model system allowed us to estimate the efficiency of the reaction on the cell membranes and in the cytosol using mass spectrometry. We found that the reaction was greatly promoted by a tris(triazolylmethyl)amine Cu(I) ligand tethering a cell-penetrating peptide. Uptake of the ligand, copper, and a biotin-tagged azide in the cells was determined to be 69 ± 2, 163 ± 3 and 1.3 ± 0.1 µM, respectively. After 10 minutes of reaction, the product yields on the membrane and cytosolic proteins were higher than 18% and 0.8%, respectively, while 75% cells remained viable. By reducing the biothiols in the system by scraping or treatment with N-ethylmalemide, the reaction yield on the cytosolic proteins was greatly improved to ~9% and ~14%, respectively, while the yield on the membrane proteins remained unchanged. The results indicate that out of many possibilities, deactivation of the current copper catalysts by biothiols is the major reason for the low yield of CuAAC reaction in the cytosol. Overall, we have improved the efficiency for CuAAC reaction on live cells by 3-fold. Despite the low yielding inside live cells, the products that strongly bind to the intracellular targets can be detected by mass spectrometry. Hence, the in situ CuAAC reaction can be potentially used for screening of cell-specific enzyme inhibitors or biomarkers containing 1,4-substituted 1,2,3-triazoles.

  19. Case reports: delayed hemolytic transfusion reaction in sickle cell disease.

    Science.gov (United States)

    Syed, S K; Sears, D A; Werch, J B; Udden, M M; Milam, J D

    1996-10-01

    This article reports the details of delayed hemolytic transfusion reactions in four patients with sickle cell disease. These cases demonstrate the characteristics of the reactions, the significant risks involved, and the principles useful in diagnosis and treatment. Patients with sickle cell disease are at particular risk for delayed hemolytic transfusion reactions because they may be transfused at intervals over many years; they frequently form alloantibodies because of antigenic differences from the donor population; and they may receive emergency care in different hospitals where transfusion records are not available. In addition, exchange transfusions, which are often used for patients with sickle cell disease and which were given in three of these cases, raise the risks through increased exposure to foreign erythrocyte antigens and through an increased volume of erythrocytes susceptible to hemolysis. It was concluded that the hazards of these transfusion reactions justify preventive measures, such as extended erythrocyte phenotyping of patients with sickle cell disease and extended phenotypic matching of transfused cells.

  20. Mast cell subsets and neuropeptides in leprosy reactions

    Directory of Open Access Journals (Sweden)

    Antunes Sérgio Luiz Gomes

    2003-01-01

    Full Text Available The immunohistochemical identification of neuropeptides (calcitonin gene-related peptide, vasoactive intestinal polypeptide, substance P, alpha-melanocyte stimulating hormone and gamma-melanocyte stimulating hormone quantification of mast cells and their subsets (tryptase/chymase-immunoreactive mast cells = TCMC and tryptase-immunoreactive mast cells = TMC were determined in biopsies of six patients with leprosy reactions (three patients with type I reaction and three with type II. Biopsies were compared with those taken from the same body site in the remission stage of the same patient. We found a relative increase of TMC in the inflammatory infiltrate of the reactional biopsies compared to the post-reactional biopsy. Also, the total number of mast cells and the TMC/TCMC ratio in the inflammatory infiltrate was significantly higher than in the intervening dermis of the biopsies of both periods. No significant difference was found regarding neuroptide expression in the reactional and post-reactional biopsies. The relative increase of TMC in the reactional infiltrates could implicate this mast cell subset in the reported increase of the immune response in leprosy reactions.

  1. Shape dynamics of growing cell walls

    CERN Document Server

    Banerjee, Shiladitya; Dinner, Aaron R

    2015-01-01

    We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape with the dynamics of growth and constriction. The model allows us to derive constraints on cell wall mechanical energy based on the observed dynamics of cell shape. We predict that exponential growth in cell size requires a constant amount of cell wall energy to be dissipated per unit volume. We use the model to understand and contrast growth in bacteria with different shapes such as spherical, ellipsoidal, cylindrical and toroidal morphologies. Coupling growth to cell wall constriction, we predict a discontinuous shape transformation, from partial constriction to cell division, as a function of the chemical potential driving cell-wall synthesis. Our model for cell wall energy and shape dynamics relates growth kinetics with cell geometry, and provides a unified framework to d...

  2. Reaction of Np atom with H₂O in the gas phase: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    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.

  3. Motif analysis for small-number effects in chemical reaction dynamics

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-01

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  4. Motif analysis for small-number effects in chemical reaction dynamics.

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-07

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  5. Whole cell biotransformation for reductive amination reactions

    OpenAIRE

    Klatte, Stephanie; Lorenz, Elisabeth; Wendisch, Volker F.

    2013-01-01

    Whole cell biotransformation systems with enzyme cascading increasingly find application in biocatalysis to complement or replace established chemical synthetic routes for production of, e.g., fine chemicals. Recently, we established an Escherichia coli whole cell biotransformation system for reductive amination by coupling a transaminase and an amino acid dehydrogenase with glucose catabolism for cofactor recycling. Transformation of 2-keto-3-methylvalerate to l-isoleucine by E. coli cells w...

  6. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Can post-error dynamics explain sequential reaction time patterns?

    Directory of Open Access Journals (Sweden)

    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.

  8. Isospin dynamics on neck fragmentation in isotopic nuclear reactions

    CERN Document Server

    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...

  9. Whole cell biotransformation for reductive amination reactions

    Science.gov (United States)

    Klatte, Stephanie; Lorenz, Elisabeth; Wendisch, Volker F

    2014-01-01

    Whole cell biotransformation systems with enzyme cascading increasingly find application in biocatalysis to complement or replace established chemical synthetic routes for production of, e.g., fine chemicals. Recently, we established an Escherichia coli whole cell biotransformation system for reductive amination by coupling a transaminase and an amino acid dehydrogenase with glucose catabolism for cofactor recycling. Transformation of 2-keto-3-methylvalerate to l-isoleucine by E. coli cells was improved by genetic engineering of glucose metabolism for improved cofactor regeneration. Here, we compare this system with different strategies for cofactor regeneration such as cascading with alcohol dehydrogenases, with alternative production hosts such as Pseudomonas species or Corynebacterium glutamicum, and with improving whole cell biotransformation systems by metabolic engineering of NADPH regeneration. PMID:24406456

  10. Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series

    Science.gov (United States)

    Ganscha, Stefan; Claassen, Manfred

    2016-01-01

    Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants. We have assessed the structure learning capabilities of the reactionet lasso on synthetic data for the complete TRAIL induced apoptosis signaling cascade comprising 70 reactions. We find that the reactionet lasso is able to efficiently recover the structure of these reaction systems, ab initio, with high sensitivity and specificity. With only lasso is able to recover 45% of all true reactions ab initio among > 6000 possible reactions and over 102000 network topologies. In conjunction with information rich single cell technologies such as single cell RNA sequencing or mass cytometry, the reactionet lasso will enable large-scale structure learning, particularly in areas with partial network structure knowledge, such as cancer biology, and thereby enable the detection of pathological alterations of reaction networks. We provide software to allow for wide applicability of the reactionet lasso. PMID:27923064

  11. Detailed Molecular Dynamics of the Photochromic Reaction of Spiropyran: A Semiclassical Dynamics Study

    Directory of Open Access Journals (Sweden)

    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.

  12. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    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…

  13. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    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…

  14. Regulation of Germinal Center Reactions by B and T Cells

    Directory of Open Access Journals (Sweden)

    Yeonseok Chung

    2013-10-01

    Full Text Available Break of B cell tolerance to self-antigens results in the development of autoantibodies and, thus, leads to autoimmunity. How B cell tolerance is maintained during active germinal center (GC reactions is yet to be fully understood. Recent advances revealed several subsets of T cells and B cells that can positively or negatively regulate GC B cell responses in vivo. IL-21-producing CXCR5+ CD4+ T cells comprise a distinct lineage of helper T cells—termed follicular helper T cells (TFH—that can provide help for the development of GC reactions where somatic hypermutation and affinity maturation take place. Although the function of TFH cells is beneficial in generating high affinity antibodies against infectious agents, aberrant activation of TFH cell or B cell to self-antigens results in autoimmunity. At least three subsets of immune cells have been proposed as regulatory cells that can limit such antibody-mediated autoimmunity, including follicular regulatory T cells (TFR, Qa-1 restricted CD8+ regulatory T cells (CD8+TREG, and regulatory B cells (BREG. In this review, we will discuss our current understanding of GC B cell regulation with specific emphasis on the newly identified immune cell subsets involved in this process.

  15. Classical Radiation Reaction in Particle-In-Cell Simulations

    CERN Document Server

    Vranic, Marija; Fonseca, Ricardo A; Silva, Luis O

    2015-01-01

    Under the presence of ultra high intensity lasers or other intense electromagnetic fields the motion of particles in the ultrarelativistic regime can be severely affected by radiation reaction. The standard particle-in-cell (PIC) algorithms do not include radiation reaction effects. Even though this is a well known mechanism, there is not yet a definite algorithm nor a standard technique to include radiation reaction in PIC codes. We have compared several models for the calculation of the radiation reaction force, with the goal of implementing an algorithm for classical radiation reaction in the Osiris framework, a state-of-the-art PIC code. The results of the different models are compared with standard analytical results, and the relevance/advantages of each model are discussed. Numerical issues relevant to PIC codes such as resolution requirements, application of radiation reaction to macro particles and computational cost are also addressed. The Landau and Lifshitz reduced model is chosen for implementatio...

  16. Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths.

    Science.gov (United States)

    Aono, Masashi; Wakabayashi, Masamitsu

    2015-09-01

    We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], "the satisfiability problem," and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [ http://www.cs.ubc.ca/~hoos/5/benchm.html ]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate "AmoebaChem," which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.

  17. Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths

    Science.gov (United States)

    Aono, Masashi; Wakabayashi, Masamitsu

    2015-09-01

    We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], "the satisfiability problem," and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [http://www.cs.ubc.ca/~hoos/5/benchm.html]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate "AmoebaChem," which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths.

  18. Dynamical resonance in F+H2 chemical reaction and rotational excitation effect

    Institute of Scientific and Technical Information of China (English)

    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.

  19. Physical chemistry of reaction dynamics in ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Physical Chemistry of Reaction Dynamics in Ionic Liquid

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. About supramolecular systems for dynamically probing cells

    NARCIS (Netherlands)

    Brinkmann, J.; Cavatorta, E.; Sankaran, S.; Schmidt, B.; van Weerd, Jasper; Jonkheijm, Pascal

    2014-01-01

    This article reviews the state of the art in the development of strategies for generating supramolecular systems for dynamic cell studies. Dynamic systems are crucial to further our understanding of cell biology and are consequently at the heart of many medical applications. Increasing interest has

  2. Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Saria

    Science.gov (United States)

    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

  3. Reaction dynamics: The view from a transition state

    Science.gov (United States)

    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.

  4. State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

    Science.gov (United States)

    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.

  5. Dynamic Reaction Mechanisms of ClO(-) with CH3Cl: Comparison Between Direct Dynamics Trajectory Simulations and Experiment.

    Science.gov (United States)

    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).

  6. Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Proteomic analysis of cellular response induced by boron neutron capture reaction in human squamous cell carcinoma SAS cells.

    Science.gov (United States)

    Sato, Akira; Itoh, Tasuku; Imamichi, Shoji; Kikuhara, Sota; Fujimori, Hiroaki; Hirai, Takahisa; Saito, Soichiro; Sakurai, Yoshinori; Tanaka, Hiroki; Nakamura, Hiroyuki; Suzuki, Minoru; Murakami, Yasufumi; Baiseitov, Diaz; Berikkhanova, Kulzhan; Zhumadilov, Zhaxybay; Imahori, Yoshio; Itami, Jun; Ono, Koji; Masunaga, Shinichiro; Masutani, Mitsuko

    2015-12-01

    To understand the mechanism of cell death induced by boron neutron capture reaction (BNCR), we performed proteome analyses of human squamous tumor SAS cells after BNCR. Cells were irradiated with thermal neutron beam at KUR after incubation under boronophenylalanine (BPA)(+) and BPA(-) conditions. BNCR mainly induced typical apoptosis in SAS cells 24h post-irradiation. Proteomic analysis in SAS cells suggested that proteins functioning in endoplasmic reticulum, DNA repair, and RNA processing showed dynamic changes at early phase after BNCR and could be involved in the regulation of cellular response to BNCR. We found that the BNCR induces fragments of endoplasmic reticulum-localized lymphoid-restricted protein (LRMP). The fragmentation of LRMP was also observed in the rat tumor graft model 20 hours after BNCT treatment carried out at the National Nuclear Center of the Republic of Kazakhstan. These data suggest that dynamic changes of LRMP could be involved during cellular response to BNCR.

  8. Structural parameter identifiability analysis for dynamic reaction networks

    DEFF Research Database (Denmark)

    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...

  9. Direct Dynamics Study on CH2O + CH·3 → CHO + CH4 Reaction

    Institute of Scientific and Technical Information of China (English)

    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.

  10. A fractional model of a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions

    Science.gov (United States)

    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.

  11. Dynamical coupled-channels study of meson production reactions from EBAC@Jlab

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. The clinical implications of mixed lymphocyte reaction with leukemic cells.

    Science.gov (United States)

    Kim, Hee-Je; Kim, Tai-Gyu; Cho, Hyun Il; Han, Hoon; Min, Woo-Sung; Kim, Chun-Choo

    2002-11-01

    To evaluate the clinical implications of a mixed lymphocyte reaction between leukemic cells and lymphocytes from HLA-matched sibling donors, we attempted to generate donor-derived, graft-versus-leukemia-effective cells and to define their characteristics. We studied 8 patients with chronic myelogenous leukemia (CML), including 5 patients in the chronic phase (CP), 3 patients in the accelerated phase (AP), and 2 patients with acute myelogenous leukemia (AML) in their first complete remission. Cells from these patients were used as stimulators in a mixed lymphocyte reaction.The effects of natural killer (NK) cells and cytotoxic T-lymphocytes (CTLs) were separated by observing tests for cytotoxicity to target cells, including K562 cells, the patient's leukemic cells, and phytohemagglutinin (PHA) blasts. Donor-derived antileukemic CTLs againstthe patient's own leukemic cells are productive in vitro. The efficacy of generating CTLs against leukemic target cells was (in decreasing order) AML, CML-CP, and CML-AP. Cytotoxic activity against leukemic targets was prominent in 4 cases--2 CML-CP and the 2 AML cases. On the contrary, the 3 cases of CML-AP showed low CTL activity. In cases showing 1 positive result among 3 targets (K562 cells, the patient's leukemic cells, and PHA blasts), the relapse rate was significantly lower (P = .022) on follow-up (median, 33 months; 7-40 months) after hematopoietic stem cell transplantation. By a combined analysis of the cytotoxicity effects for all 3 target cells, we were able to demonstrate a correlation between leukemic relapse and the variable degree of the cytotoxicity test results. Although the total sample numbers for this study were low, we speculate that these results may come from differences in the individual characteristics of the leukemic cells that are in line with their clinical disease status.

  13. Target Turing patterns and growth dynamics in the chlorine dioxide-iodine-malonic acid reaction.

    Science.gov (United States)

    Preska Steinberg, Asher; Epstein, Irving R; Dolnik, Milos

    2014-04-03

    We study the growth dynamics of Turing patterns in the chlorine dioxide-iodine-malonic acid reaction-diffusion system in response to perturbations with visible light. We describe several mechanisms by which Turing patterns reappear after they are suppressed by illumination with a disc-shaped geometry. We observe that under specific conditions the patterns reorganize from a random configuration of spots and stripes to a set of ordered, concentric rings, which we refer to as target Turing patterns. These patterns closely resemble the unit cells of the Turing hexagonal superlattices known as black eye patterns. However, these target Turing patterns are not part of a larger superlattice structure, and they usually have a larger number of concentric rings. Numerical simulations support the experimental findings.

  14. Coarse-graining the calcium dynamics on a stochastic reaction-diffusion lattice model

    CERN Document Server

    Shen, Chuansheng

    2013-01-01

    We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo (kMC) simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion $m$, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed $m$, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size eff...

  15. Dynamical Dipole mode in heavy-ion fusion reactions in the 192Pb mass region

    Science.gov (United States)

    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.

  16. Universal signal generator for dynamic cell stimulation.

    Science.gov (United States)

    Piehler, Andreas; Ghorashian, Navid; Zhang, Ce; Tay, Savaş

    2017-06-27

    Dynamic cell stimulation is a powerful technique for probing gene networks and for applications in stem cell differentiation, immunomodulation and signaling. We developed a robust and flexible method and associated microfluidic devices to generate a wide-range of precisely formulated dynamic chemical signals to stimulate live cells and measure their dynamic response. This signal generator is capable of digital to analog conversion (DAC) through combinatoric selection of discrete input concentrations, and outperforms existing methods by both achievable resolution, dynamic range and simplicity in design. It requires no calibration, has minimal space requirements and can be easily integrated into microfluidic cell culture devices. The signal generator hardware and software we developed allows to choose the waveform, period and amplitude of chemical input signals and features addition of well-defined chemical noise to study the role of stochasticity in cellular information processing.

  17. Theoretical studies of the dynamics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Dynamics of Surface Exchange Reactions Between Au and Pt for HER and HOR

    DEFF Research Database (Denmark)

    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...

  19. Dynamic metabolic flux analysis of plant cell wall synthesis.

    Science.gov (United States)

    Chen, Xuewen; Alonso, Ana P; Shachar-Hill, Yair

    2013-07-01

    The regulation of plant cell wall synthesis pathways remains poorly understood. This has become a bottleneck in designing bioenergy crops. The goal of this study was to analyze the regulation of plant cell wall precursor metabolism using metabolic flux analysis based on dynamic labeling experiments. Arabidopsis T87 cells were cultured heterotrophically with (13)C labeled sucrose. The time course of ¹³C labeling patterns in cell wall precursors and related sugar phosphates was monitored using liquid chromatography tandem mass spectrometry until steady state labeling was reached. A kinetic model based on mass action reaction mechanisms was developed to simulate the carbon flow in the cell wall synthesis network. The kinetic parameters of the model were determined by fitting the model to the labeling time course data, cell wall composition, and synthesis rates. A metabolic control analysis was performed to predict metabolic regulations that may improve plant biomass composition for biofuel production. Our results describe the routes and rates of carbon flow from sucrose to cell wall precursors. We found that sucrose invertase is responsible for the entry of sucrose into metabolism and UDP-glucose-4-epimerase plays a dominant role in UDP-Gal synthesis in heterotrophic Aradidopsis cells under aerobic conditions. We also predicted reactions that exert strong regulatory influence over carbon flow to cell wall synthesis and its composition.

  20. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    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...

  1. Stochastic and coherent dynamics of single and coupled beta cells

    DEFF Research Database (Denmark)

    phenomenon, modeled by a slow-fast nonlinear system of ordinary differential equations (ODEs). The single cell oscillations are complex as the dynamical behavior is a result of traversing a series of saddle node and homoclinic bifurcations, controlled by the slow variable. We shall present results...... is the simplest reaction-diffusion partial differential equation....... on the burst period as function of an external applied stochastic term and use a technique for reducing the stochastic differential equations to ODEs for the average and higher order moments. The later method is approximate and we shall discuss the limits of validity. The individual beta cells are coupled...

  2. Reaction dynamics of initial O2 sticking on Pd(100).

    Science.gov (United States)

    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.

  3. Reaction dynamics of initial O2 sticking on Pd(100)

    Science.gov (United States)

    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.

  4. Resonances and reactions from mean-field dynamics

    Directory of Open Access Journals (Sweden)

    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.

  5. Classical radiation reaction in particle-in-cell simulations

    Science.gov (United States)

    Vranic, M.; Martins, J. L.; Fonseca, R. A.; Silva, L. O.

    2016-07-01

    Under the presence of ultra high intensity lasers or other intense electromagnetic fields the motion of particles in the ultrarelativistic regime can be severely affected by radiation reaction. The standard particle-in-cell (PIC) algorithms do not include radiation reaction effects. Even though this is a well known mechanism, there is not yet a definite algorithm nor a standard technique to include radiation reaction in PIC codes. We have compared several models for the calculation of the radiation reaction force, with the goal of implementing an algorithm for classical radiation reaction in the Osiris framework, a state-of-the-art PIC code. The results of the different models are compared with standard analytical results, and the relevance/advantages of each model are discussed. Numerical issues relevant to PIC codes such as resolution requirements, application of radiation reaction to macro particles and computational cost are also addressed. For parameters of interest where the classical description of the electron motion is applicable, all the models considered are shown to give comparable results. The Landau and Lifshitz reduced model is chosen for implementation as one of the candidates with the minimal overhead and no additional memory requirements.

  6. Relation Between the Cell Volume and the Cell Cycle Dynamics in Mammalian cell

    Science.gov (United States)

    Magno, A. C. G.; Oliveira, I. L.; Hauck, J. V. S.

    2016-08-01

    The main goal of this work is to add and analyze an equation that represents the volume in a dynamical model of the mammalian cell cycle proposed by Gérard and Goldbeter (2011) [1]. The cell division occurs when the cyclinB/Cdkl complex is totally degraded (Tyson and Novak, 2011)[2] and it reaches a minimum value. At this point, the cell is divided into two newborn daughter cells and each one will contain the half of the cytoplasmic content of the mother cell. The equations of our base model are only valid if the cell volume, where the reactions occur, is constant. Whether the cell volume is not constant, that is, the rate of change of its volume with respect to time is explicitly taken into account in the mathematical model, then the equations of the original model are no longer valid. Therefore, every equations were modified from the mass conservation principle for considering a volume that changes with time. Through this approach, the cell volume affects all model variables. Two different dynamic simulation methods were accomplished: deterministic and stochastic. In the stochastic simulation, the volume affects every model's parameters which have molar unit, whereas in the deterministic one, it is incorporated into the differential equations. In deterministic simulation, the biochemical species may be in concentration units, while in stochastic simulation such species must be converted to number of molecules which are directly proportional to the cell volume. In an effort to understand the influence of the new equation a stability analysis was performed. This elucidates how the growth factor impacts the stability of the model's limit cycles. In conclusion, a more precise model, in comparison to the base model, was created for the cell cycle as it now takes into consideration the cell volume variation

  7. Dynamic culture improves cell reprogramming efficiency.

    Science.gov (United States)

    Sia, Junren; Sun, Raymond; Chu, Julia; Li, Song

    2016-06-01

    Cell reprogramming to pluripotency is an inefficient process and various approaches have been devised to improve the yield of induced pluripotent stem cells. However, the effect of biophysical factors on cell reprogramming is not well understood. Here we showed that, for the first time, dynamic culture with orbital shaking significantly improved the reprogramming efficiency in adherent cells. Manipulating the viscosity of the culture medium suggested that the improved efficiency is mainly attributed to convective mixing rather than hydrodynamic shear stress. Temporal studies demonstrated that the enhancement of reprogramming efficiency required the dynamic culture in the middle but not early phase. In the early phase, fibroblasts had a high proliferation rate, but as the culture became over-confluent in the middle phase, expression of p57 was upregulated to inhibit cell proliferation and consequently, cell reprogramming. Subjecting the over confluent culture to orbital shaking prevented the upregulation of p57, thus improving reprogramming efficiency. Seeding cells at low densities to avoid over-confluency resulted in a lower efficiency, and optimal reprogramming efficiency was attained at a high seeding density with dynamic culture. Our findings provide insight into the underlying mechanisms of how dynamic culture condition regulate cell reprogramming, and will have broad impact on cell engineering for regenerative medicine and disease modeling.

  8. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    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

  9. Epigenetic dynamics across the cell cycle

    DEFF Research Database (Denmark)

    Kheir, Tony Bou; Lund, Anders H.

    2010-01-01

    Progression of the mammalian cell cycle depends on correct timing and co-ordination of a series of events, which are managed by the cellular transcriptional machinery and epigenetic mechanisms governing genome accessibility. Epigenetic chromatin modifications are dynamic across the cell cycle......, and are shown to influence and be influenced by cell-cycle progression. Chromatin modifiers regulate cell-cycle progression locally by controlling the expression of individual genes and globally by controlling chromatin condensation and chromosome segregation. The cell cycle, on the other hand, ensures...... a correct inheritance of epigenetic chromatin modifications to daughter cells. In this chapter, we summarize the current knowledge on the dynamics of epigenetic chromatin modifications during progression of the cell cycle....

  10. The dynamics of reaction of Cl atoms with tetramethylsilane.

    Science.gov (United States)

    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.

  11. Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

    Science.gov (United States)

    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.

  12. Real-time electron dynamics simulation of two-electron transfer reactions induced by nuclear motion

    Science.gov (United States)

    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.

  13. Optimal Fluxes, Reaction Replaceability, and Response to Enzymopathies in the Human Red Blood Cell

    Directory of Open Access Journals (Sweden)

    A. De Martino

    2010-01-01

    most harmful reaction knockouts. The integration of combinatorial methods with sampling techniques to explore the space of viable flux states may provide crucial insights on this issue. We assess the replaceability of every metabolic conversion in the human red blood cell by enumerating the alternative paths from substrate to product, obtaining a complete map of he potential damage of single enzymopathies. Sampling the space of optimal steady state fluxes in the healthy and in the mutated cell reveals both correlations and complementarity between topologic and dynamical aspects.

  14. Dynamical Adaptation in Terrorist Cells/Networks

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar; Ahmed, Zaki

    2010-01-01

    Typical terrorist cells/networks have dynamical structure as they evolve or adapt to changes which may occur due to capturing or killing of a member of the cell/network. Analytical measures in graph theory like degree centrality, betweenness and closeness centralities are very common and have long...

  15. Sorting cells by their dynamical properties

    Science.gov (United States)

    Henry, Ewan; Holm, Stefan H.; Zhang, Zunmin; Beech, Jason P.; Tegenfeldt, Jonas O.; Fedosov, Dmitry A.; Gompper, Gerhard

    2016-10-01

    Recent advances in cell sorting aim at the development of novel methods that are sensitive to various mechanical properties of cells. Microfluidic technologies have a great potential for cell sorting; however, the design of many micro-devices is based on theories developed for rigid spherical particles with size as a separation parameter. Clearly, most bioparticles are non-spherical and deformable and therefore exhibit a much more intricate behavior in fluid flow than rigid spheres. Here, we demonstrate the use of cells’ mechanical and dynamical properties as biomarkers for separation by employing a combination of mesoscale hydrodynamic simulations and microfluidic experiments. The dynamic behavior of red blood cells (RBCs) within deterministic lateral displacement (DLD) devices is investigated for different device geometries and viscosity contrasts between the intra-cellular fluid and suspending medium. We find that the viscosity contrast and associated cell dynamics clearly determine the RBC trajectory through a DLD device. Simulation results compare well to experiments and provide new insights into the physical mechanisms which govern the sorting of non-spherical and deformable cells in DLD devices. Finally, we discuss the implications of cell dynamics for sorting schemes based on properties other than cell size, such as mechanics and morphology.

  16. Oxygen electrode reaction in molten carbonate fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Appleby, A.J.; White, R.E.

    1992-07-07

    Molten carbonate fuel cell system is a leading candidate for the utility power generation because of its high efficiency for fuel to AC power conversion, capability for an internal reforming, and a very low environmental impact. However, the performance of the molten carbonate fuel cell is limited by the oxygen reduction reaction and the cell life time is limited by the stability of the cathode material. An elucidation of oxygen reduction reaction in molten alkali carbonate is essential because overpotential losses in the molten carbonate fuel cell are considerably greater at the oxygen cathode than at the fuel anode. Oxygen reduction on a fully-immersed gold electrode in a lithium carbonate melt was investigated by electrochemical impedance spectroscopy and cyclic voltammetry to determine electrode kinetic and mass transfer parameters. The dependences of electrode kinetic and mass transfer parameters on gas composition and temperature were examined to determine the reaction orders and the activation energies. The results showed that oxygen reduction in a pure lithium carbonate melt occurs via the peroxide mechanism. A mass transfer parameter, D{sub O}{sup 1/2}C{sub O}, estimated by the cyclic voltammetry concurred with that calculated by the EIS technique. The temperature dependence of the exchange current density and the product D{sub O}{sup 1/2}C{sub O} were examined and the apparent activation energies were determined to be about 122 and 175 kJ/ mol, respectively.

  17. Nonstatistical dynamics on potentials exhibiting reaction path bifurcations and valley-ridge inflection points

    CERN Document Server

    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.

  18. Low-energy heavy-ion reactions: a link between nuclear structure and reaction dynamics

    CERN Document Server

    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.

  19. Reaction dynamics and nuclear structure of moderately neutron-rich Ne isotopes by heavy ion reactions

    Directory of Open Access Journals (Sweden)

    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.

  20. Quantum Dynamics Study on D+OD+ Reaction: Competition between Exchange and Abstraction Channels

    Institute of Scientific and Technical Information of China (English)

    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.

  1. Effect of reaction-step-size noise on the switching dynamics of stochastic populations

    Science.gov (United States)

    Be'er, Shay; Heller-Algazi, Metar; Assaf, Michael

    2016-05-01

    In genetic circuits, when the messenger RNA lifetime is short compared to the cell cycle, proteins are produced in geometrically distributed bursts, which greatly affects the cellular switching dynamics between different metastable phenotypic states. Motivated by this scenario, we study a general problem of switching or escape in stochastic populations, where influx of particles occurs in groups or bursts, sampled from an arbitrary distribution. The fact that the step size of the influx reaction is a priori unknown and, in general, may fluctuate in time with a given correlation time and statistics, introduces an additional nondemographic reaction-step-size noise into the system. Employing the probability-generating function technique in conjunction with Hamiltonian formulation, we are able to map the problem in the leading order onto solving a stationary Hamilton-Jacobi equation. We show that compared to the "usual case" of single-step influx, bursty influx exponentially decreases the population's mean escape time from its long-lived metastable state. In particular, close to bifurcation we find a simple analytical expression for the mean escape time which solely depends on the mean and variance of the burst-size distribution. Our results are demonstrated on several realistic distributions and compare well with numerical Monte Carlo simulations.

  2. Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution from Ab Initio Potential and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    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.

  3. Closed Loop Adaptive Refinement of Dynamical Models for Complex Chemical Reactions

    Science.gov (United States)

    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

  4. Sensitivity Analysis of Centralized Dynamic Cell Selection

    DEFF Research Database (Denmark)

    Lopez, Victor Fernandez; Alvarez, Beatriz Soret; Pedersen, Klaus I.;

    2016-01-01

    mechanism and solutions involving cell switching in general. Simulation results show that such solutions can greatly benefit from the use of receivers with interference suppression capabilities and a larger number of antennas, with a maximum data rate gain of 120%. High performance gains are observed...... with two different traffic models, and it is not necessary to be able to connect to a large number of cells in order to reap most of the benefits of the centralized dynamic cell selection....

  5. Chiral dynamics in the gamma p --> p pi0 reaction

    CERN Document Server

    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.

  6. Quasi-elastic reactions: an interplay of reaction dynamics and nuclear structure

    Directory of Open Access Journals (Sweden)

    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.

  7. The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak

    Directory of Open Access Journals (Sweden)

    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.

  8. Time-resolved imaging of purely valence-electron dynamics during a chemical reaction

    DEFF Research Database (Denmark)

    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...

  9. Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics

    Science.gov (United States)

    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).

  10. ThermoData engine (TDE): software implementation of the dynamic data evaluation concept. 4. Chemical reactions.

    Science.gov (United States)

    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.

  11. Crossed molecular beam studies of unimolecular reaction dynamics. [Angular and velocity distributions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics

    Institute of Scientific and Technical Information of China (English)

    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.

  13. Dynamic/Thermochemical Balance Drives Unusual Alkyl/F Exchange Reactions in Siloxides and Analogs.

    Science.gov (United States)

    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.

  14. Spectroscopy and reaction dynamics of collision complexes containing hydroxyl radicals

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Analysis of dynamic foot pressure distribution and ground reaction forces

    Science.gov (United States)

    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.

  16. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    Science.gov (United States)

    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.

  17. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    Science.gov (United States)

    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.

  18. Dynamical resonances in the fluorine atom reaction with the hydrogen molecule.

    Science.gov (United States)

    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

  19. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Dynamic input to determine hip joint moments, power and work on the prosthetic limb of transfemoral amputees: ground reaction vs knee reaction

    OpenAIRE

    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...

  1. A review of dynamical resonances in A  +  BC chemical reactions

    Science.gov (United States)

    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.

  2. Averaging methods for stochastic dynamics of complex reaction networks: description of multi-scale couplings

    CERN Document Server

    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...

  3. Reaction dynamics of small molecules at metal surfaces

    CERN Document Server

    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...

  4. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    Science.gov (United States)

    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.

  5. Multicompartment Artificial Organelles Conducting Enzymatic Cascade Reactions inside Cells

    DEFF Research Database (Denmark)

    Gallardo, Maria Godoy; Labay, Cédric Pierre; Trikalitis, Vasileios

    2017-01-01

    Cell organelles are subcellular structures entrapping a set of enzymes to achieve a specific functionality. The incorporation of artificial organelles into cells is a novel medical paradigm which might contribute to the treatment of various cell disorders by replacing malfunctioning organelles....... In particular, artificial organelles are expected to be a powerful solution in the context of enzyme replacement therapy since enzymatic malfunction is the primary cause of organelle dysfunction. Although several attempts have been made to encapsulate enzymes within a carrier vehicle, only few intracellularly...... active artificial organelles have been reported to date and they all consist of single-compartment carriers. However, it is noted that biological organelles consist of multicompartment architectures where enzymatic reactions are executed within distinct subcompartments. Compartmentalization allows...

  6. Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. [Age-related dynamics of the motion reaction in school children].

    Science.gov (United States)

    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.

  8. Nonlinear dynamics of cell orientation

    Science.gov (United States)

    Safran, S. A.; de, Rumi

    2009-12-01

    The nonlinear dependence of cellular orientation on an external, time-varying stress field determines the distribution of orientations in the presence of noise and the characteristic time, τc , for the cell to reach its steady-state orientation. The short, local cytoskeletal relaxation time distinguishes between high-frequency (nearly perpendicular) and low-frequency (random or parallel) orientations. However, τc is determined by the much longer, orientational relaxation time. This behavior is related to experiments for which we predict the angle and characteristic time as a function of frequency.

  9. Diffusion Controlled Reactions, Fluctuation Dominated Kinetics, and Living Cell Biochemistry

    CERN Document Server

    Konkoli, Zoran

    2009-01-01

    In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging from systems biology approaches, through network analysis (motif identification) towards developing language and simulators for low level biochemical processes. Apart from simulation work, much of the efforts are directed to using mean field equations (equivalent to the equations of classical chemical kinetics) to address various problems (stability, robustness, sensitivity analysis, etc.). Rarely is the use of mean field equations questioned. This review will provide a brief overview of the situations when mean field equations fail and should not be used. These equations can be derived from the theory of diffusion controlled reactions, and emerge when assumption of perfect mixing is used.

  10. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency.

    Science.gov (United States)

    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.

  11. Influence of the leaving group on the dynamics of a gas-phase SN2 reaction

    Science.gov (United States)

    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.

  12. The oxidative burst reaction in mammalian cells depends on gravity.

    Science.gov (United States)

    Adrian, Astrid; Schoppmann, Kathrin; Sromicki, Juri; Brungs, Sonja; von der Wiesche, Melanie; Hock, Bertold; Kolanus, Waldemar; Hemmersbach, Ruth; Ullrich, Oliver

    2013-12-20

    Gravity has been a constant force throughout the Earth's evolutionary history. Thus, one of the fundamental biological questions is if and how complex cellular and molecular functions of life on Earth require gravity. In this study, we investigated the influence of gravity on the oxidative burst reaction in macrophages, one of the key elements in innate immune response and cellular signaling. An important step is the production of superoxide by the NADPH oxidase, which is rapidly converted to H2O2 by spontaneous and enzymatic dismutation. The phagozytosis-mediated oxidative burst under altered gravity conditions was studied in NR8383 rat alveolar macrophages by means of a luminol assay. Ground-based experiments in "functional weightlessness" were performed using a 2 D clinostat combined with a photomultiplier (PMT clinostat). The same technical set-up was used during the 13th DLR and 51st ESA parabolic flight campaign. Furthermore, hypergravity conditions were provided by using the Multi-Sample Incubation Centrifuge (MuSIC) and the Short Arm Human Centrifuge (SAHC). The results demonstrate that release of reactive oxygen species (ROS) during the oxidative burst reaction depends greatly on gravity conditions. ROS release is 1.) reduced in microgravity, 2.) enhanced in hypergravity and 3.) responds rapidly and reversible to altered gravity within seconds. We substantiated the effect of altered gravity on oxidative burst reaction in two independent experimental systems, parabolic flights and 2D clinostat / centrifuge experiments. Furthermore, the results obtained in simulated microgravity (2D clinorotation experiments) were proven by experiments in real microgravity as in both cases a pronounced reduction in ROS was observed. Our experiments indicate that gravity-sensitive steps are located both in the initial activation pathways and in the final oxidative burst reaction itself, which could be explained by the role of cytoskeletal dynamics in the assembly and function

  13. Dynamics and Synchrony of Pancreatic beta-cells and Islets

    DEFF Research Database (Denmark)

    Pedersen, Morten Gram

    2006-01-01

    biological hypotheses. The subjects addressed are: Quasi-steady-state approximations of enzyme reactions, the effect of noise on bursting electrical behavior, exciation wave propagation in pancreatic islets, intra- and inter-islet synchronization and pulsatile insulin secretion, and mitochondrial dynamics.......Pancreatic beta-cells secrete insulin in response to raised glucose levels. Malfunctioning of this system plays an important role in the metabolic disease diabetes. The biological steps from glucose stimulus to the final release of insulin are incompletely understood, and a more complete...

  14. Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.

    Science.gov (United States)

    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.

  15. Proceedings of the Workshop on open problems in heavy ion reaction dynamics at VIVITRON energies

    Energy Technology Data Exchange (ETDEWEB)

    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.).

  16. Dynamical theory of primary processes of charge separation in the photosynthetic reaction center.

    Science.gov (United States)

    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.

  17. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

    OpenAIRE

    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...

  18. Human T Cell Memory: A Dynamic View

    Directory of Open Access Journals (Sweden)

    Derek C. Macallan

    2017-02-01

    Full Text Available Long-term T cell-mediated protection depends upon the formation of a pool of memory cells to protect against future pathogen challenge. In this review we argue that looking at T cell memory from a dynamic viewpoint can help in understanding how memory populations are maintained following pathogen exposure or vaccination. For example, a dynamic view resolves the apparent paradox between the relatively short lifespans of individual memory cells and very long-lived immunological memory by focussing on the persistence of clonal populations, rather than individual cells. Clonal survival is achieved by balancing proliferation, death and differentiation rates within and between identifiable phenotypic pools; such pools correspond broadly to sequential stages in the linear differentiation pathway. Each pool has its own characteristic kinetics, but only when considered as a population; single cells exhibit considerable heterogeneity. In humans, we tend to concentrate on circulating cells, but memory T cells in non-lymphoid tissues and bone marrow are increasingly recognised as critical for immune defence; their kinetics, however, remain largely unexplored. Considering vaccination from this viewpoint shifts the focus from the size of the primary response to the survival of the clone and enables identification of critical system pinch-points and opportunities to improve vaccine efficacy.

  19. Collective dynamics of cell migration and cell rearrangements

    Science.gov (United States)

    Kabla, Alexandre

    Understanding multicellular processes such as embryo development or cancer metastasis requires to decipher the contributions of local cell autonomous behaviours and long range interactions with the tissue environment. A key question in this context concerns the emergence of large scale coordination in cell behaviours, a requirement for collective cell migration or convergent extension. I will present a few examples where physical and mechanical aspects play a significant role in driving tissue scale dynamics. Geometrical confinement is one of the key external factors influencing large scale coordination during collective migration. Using a combination of in vitro experiments and numerical simulations, we show that the velocity correlation length, measured in unconfined conditions, provides a convenient length scale to predict the dynamic response under confinement. The same length scale can also be used to quantify the influence range of directional cues within the cell population. Heterogeneity within motile cell populations is frequently associated with an increase in their invasive capability and appears to play an important role during cancer metastasis. Using in silico experiments, we studied the way cell invasion is influenced by both the degree of cell coordination and the amount of variability in the motile force of the invading cells. Results suggest that mechanical heterogeneity dramatically enhances the invasion rate through an emerging cooperative process between the stronger and weaker cells, accounting for a number of observed invasion phenotypes. Effective convergent extension requires on a consistent orientation of cell intercalation at the tissue scale, most often in relation with planar cell polarity mechanisms to define the primary axes of deformation. Using a novel modelling approach for cells mechanical interactions, we studied the dynamics of substrate free motile cell populations. Ongoing work shows in particular that nematic order emerges

  20. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    Science.gov (United States)

    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.

  1. Influence of Marangoni flows on the dynamics of isothermal A + B → C reaction fronts

    Science.gov (United States)

    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.

  2. RFQ Reaction Cells for AMS: Developments and Applications

    Directory of Open Access Journals (Sweden)

    Kieser William E.

    2013-12-01

    Full Text Available The use of anion-gas interactions in Radiofrequency Quadrupole (RFQ ion guide reaction cells has been shown to be very effective in the elimination of a number of atomic and molecular isobars which have caused difficulties for Accelerator Mass Spectrometry (AMS measurements [1,2]. This presentation begins with a review of the early work leading to the use of ion-gas reactions and continues with a discussion the recent measurements of the efficacy of this technique, some of which involve fluoride molecular anions. However, the transformation of the equipment used for these proof-of-principle measurements into a system suitable for routine analysis has required attention to aspects of the ion beam transport and gas handling subsystems. For example, the cross sections of the ion-gas reactions, involving both the analyte ion as well as the isobar, are critically dependent on the ion energy which has to be reduced from the ion source energy, usually between 20 and 80 keV, to energies typically in the range of several eV, a task complicated by the energy spread and divergence of beams from AMS sputter sources. With simulations using SIMION 8.1 [3] and tests of promising configurations in a laboratory system, principles for the design of the retarder optics have been developed. These are discussed, along with their planned implementation in a next generation analytical system.

  3. Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

    CERN Document Server

    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.

  4. Experimental and numerical investigation of coupled microvibration dynamics for satellite reaction wheels

    Science.gov (United States)

    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.

  5. Dynamics of Pickering Emulsions in the Presence of an Interfacial Reaction: A Simulation Study.

    Science.gov (United States)

    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.

  6. Dynamics of the Spiral Tip in a Closed Belousov-Zhabotinsky Reaction

    Institute of Scientific and Technical Information of China (English)

    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.

  7. Quantum state-resolved gas/surface reaction dynamics probed by reflection absorption infrared spectroscopy.

    Science.gov (United States)

    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.

  8. Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.

    Science.gov (United States)

    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.

  9. Dynamical Modes and Mechanisms in Ternary Reaction of 197Au+197Au

    Science.gov (United States)

    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.

  10. Dynamical Dipole mode in heavy-ion fusion reactions by using stable and radioactive beams

    Directory of Open Access Journals (Sweden)

    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.

  11. Dynamical Behavior of Core 3 He Nuclear Reaction-Diffusion Systems and Sun's Gravitational Field

    Institute of Scientific and Technical Information of China (English)

    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.

  12. Chiral Dynamics and Dubna-Mainz-Taipei Dynamical Model for Pion-Photoproduction Reaction

    CERN Document Server

    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.

  13. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

    Science.gov (United States)

    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.

  14. On the study of nonlinear dynamics of complex chemical reaction systems

    Institute of Scientific and Technical Information of China (English)

    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.

  15. Dynamic synchrony of local cell assembly.

    Science.gov (United States)

    Sakurai, Yoshio; Takahashi, Susumu

    2008-01-01

    In the present paper, we focus on the problem of the dynamic size of a cell assembly and discuss how we can detect synchronized firing of a local cell assembly consisting of closely neighboring neurons in the working brain. A local cell assembly is difficult to detect because of the problem of spike overlapping of neighboring neurons, which cannot be overcome by ordinary spike-sorting techniques. We introduce a unique technique of spike-sorting that combines independent component analysis (ICA) and an ordinary sorting method to separate individual neighboring neurons and analyze their firing synchrony in behaving animals. One of our experiments employing this method showed that some closely neighboring neurons in the monkey prefrontal cortex have dynamic and sharp synchrony of firing reflecting local cell assemblies during working-memory processes. Another experiment showed that our other method (ICSort) of novel spike-sorting by ICA using special electrodes (dodecatrodes) can distinguish firing signals from the soma and those from the dendrites of individual neurons in behaving rats and suggests that the somatic and dendritic signals have different roles in information processing. This indicates that functional connectivity among neurons may be more dynamic and complex and spikes from the soma and dendrites of individual neurons should be considered in the investigation of the activity of local cell assemblies. We finally propose that detailed and real features of a local cell assembly consisting of closely neighboring neurons should be examined further and detection of local cell assemblies could be applied to the development of neuronal prosthetic devices, that is, brain-machine interfaces (BMIs).

  16. Molecular dynamics study of phase separation in fluids with chemical reactions.

    Science.gov (United States)

    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.

  17. Nonadiabatic quantum dynamics calculations for the N + NH --> N(2) + H reaction.

    Science.gov (United States)

    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.

  18. Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Sarin

    Science.gov (United States)

    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.

  19. Unified equation for access to rate constants of first-order reactions in dynamic and on-column reaction chromatography.

    Science.gov (United States)

    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.

  20. Modeling cell dynamics under mobile phone radiation.

    Science.gov (United States)

    Minelli, Tullio Antonio; Balduzzo, Maurizio; Milone, Francesco Ferro; Nofrate, Valentina

    2007-04-01

    Perturbations by pulse-modulated microwave radiation from GSM mobile phones on neuron cell membrane gating and calcium oscillations have been suggested as a possible mechanism underlying activation of brain states and electroencephalographic epiphenomena. As the employ of UMTS phones seems to reveal other symptoms, a unified phenomenological framework is needed. In order to explain possible effects of mobile phone radiation on cell oscillations, GSM and UMTS low-frequency envelopes have been detected, recorded and used as input in cell models. Dynamical systems endowed with contiguous regular and chaotic regimes suitable to produce stochastic resonance can both account for the perturbation of the neuro-electrical activity and even for the low intensity of the signal perceived by high sensitive subjects. Neuron models of this kind can be employed as a reductionist hint for the mentioned phenomenology. The Hindmarsh-Rose model exhibits frequency enhancement and regularization phenomena induced by weak GSM and UMTS. More realistic simulations of cell membrane gating and calcium oscillations have been performed with the help of an adaptation of the Chay-Keizer dynamical system. This scheme can explain the suspected subjective sensitivity to mobile phone signals under the thermal threshold, in terms of cell calcium regularity mechanisms. Concerning the two kinds of emission, the stronger occupation of the ELF band of last generation UMTS phones is compensated by lower power emitted.

  1. Reaction mechanisms of aqueous monoethanolamine with carbon dioxide: a combined quantum chemical and molecular dynamics study.

    Science.gov (United States)

    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.

  2. Should Thermostatted Ring Polymer Molecular Dynamics be used to calculate reaction rates?

    CERN Document Server

    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...

  3. Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Analysis of dynamical process with mass distribution of fission fragmentin heavy ion reactions

    Directory of Open Access Journals (Sweden)

    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.

  5. 7Be- and 8B-reaction dynamics at Coulomb barrier energies

    Directory of Open Access Journals (Sweden)

    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.

  6. 7Be- and 8B-reaction dynamics at Coulomb barrier energies

    Science.gov (United States)

    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.

  7. Untangling the Energetics and Dynamics of Boron Monoxide Radical Reactions (11BO; X2Sigma+)

    Science.gov (United States)

    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

  8. The complex-forming dynamics of Ne + NeH(D)+ (v = 0, 1; j = 0) reactions

    Science.gov (United States)

    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.

  9. Functional changes of dendritic cells in hypersensivity reactions to amoxicillin

    Directory of Open Access Journals (Sweden)

    C.M.F. Lima

    2010-10-01

    Full Text Available A better understanding of dendritic cell (DC involvement in responses to haptenic drugs is needed, because it represents a possible approach to the development of an in vitro test, which could identify patients prone to drug allergies. There are two main DC subsets: plasmacytoid DC (pDC and myeloid DC (mDC. β-lactams form hapten-carrier conjugates and may provide a suitable model to study DC behavior in drug allergy reactions. It has been demonstrated that drugs interact differently with DC in drug allergic and non-allergic patients, but there are no studies regarding these subsets. Our aim was to assess the functional changes of mDC and pDC harvested from an amoxicillin-hypersensitive 32-year-old woman who experienced a severe maculopapular exanthema as reflected in interleukin-6 (IL-6 production after stimulation with this drug and penicillin. We also aim to demonstrate, for the first time, the feasibility of this method for dendritic cell isolation followed by in vitro stimulation for studies of drug allergy physiopathology. DC were harvested using a double Percoll density gradient, which generates a basophil-depleted cell (BDC suspension. Further, pDC were isolated by blood DC antigen 4-positive magnetic selection and gravity filtration through magnetized columns. After stimulation with amoxicillin, penicillin and positive and negative controls, IL-6 production was measured by ELISA. A positive dose-response curve for IL-6 after stimulation with amoxicillin and penicillin was observed for pDC, but not for mDC or BDC suspension. These preliminary results demonstrate the feasibility of this methodology to expand the knowledge of the effect of dendritic cell activation by drug allergens.

  10. Interdependence of conformational and chemical reaction dynamics during ion assembly in polar solvents.

    Science.gov (United States)

    Ji, Minbiao; Hartsock, Robert W; Sun, Zheng; Gaffney, Kelly J

    2011-10-01

    We have utilized time-resolved vibrational spectroscopy to study the interdependence of the conformational and chemical reaction dynamics of ion assembly in solution. We investigated the chemical interconversion dynamics of the LiNCS ion pair and the (LiNCS)(2) ion-pair dimer, as well as the spectral diffusion dynamics of these ionic assemblies. For the strongly coordinating Lewis base solvents benzonitrile, dimethyl carbonate, and ethyl acetate, we observe Li(+) coordination by both solvent molecules and NCS(-) anions, while the weak Lewis base solvent nitromethane shows no evidence for solvent coordination of Li(+) ions. The strong interaction between the ion-pair dimer structure and the Lewis base solvents leads to ion-pair dimer solvation dynamics that proceed more slowly than the ion-pair dimer dissociation. We have attributed the slow spectral diffusion dynamics to electrostatic reorganization of the solvent molecules coordinated to the Li(+) cations present in the ion-pair dimer structure and concluded that the dissociation of ion-pair dimers depends more critically on longer length scale electrostatic reorganization. This unusual inversion of the conformational and chemical reaction rates does not occur for ion-pair dimer dissociation in nitromethane or for ion pair association in any of the solvents.

  11. Equilibrium properties of the reaction H2 ⇌ 2H by classical molecular dynamics simulations.

    Science.gov (United States)

    Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe

    2014-01-21

    We have developed a classical molecular dynamics model for the hydrogen dissociation reaction, containing two- and three-particle potentials derived by Kohen, Tully and Stillinger. Two fluid densities were investigated for a wide range of temperatures, and 11 fluid densities were considered for one temperature. We report the temperature range where the degree of reaction is significant, and also where a stable molecule dominates the population in the energy landscape. The three-particle potential, which is essential for the reaction model and seldom studied, together with the two-particle interaction lead to a large effective excluded volume diameter of the molecules in the molecular fluid. The three-particle interaction was also found to give a large positive contribution to the pressure of the reacting mixture at high density and/or low temperatures. From knowledge of the dissociation constant of the reaction and the fluid pressure, we estimated the standard enthalpy of the dissociation reaction to be 430 kJ mol(-1) (ρ = 0.0695 g cm(-3)) and 380 kJ mol(-1) (ρ = 0.0191 g cm(-3)). These values are in good agreement with the experimental vaule of 436 kJ mol(-1) under ambient pressure. The model is consistent with a Lennard-Jones model of the molecular fluid, and may facilitate studies of the impact of chemical reactions on transport systems.

  12. 17O+58Ni scattering and reaction dynamics around the Coulomb barrier

    Science.gov (United States)

    Strano, E.; Torresi, D.; Mazzocco, M.; Keeley, N.; Boiano, A.; Boiano, C.; Di Meo, P.; Guglielmetti, A.; La Commara, M.; Molini, P.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Signorini, C.; Soramel, F.; Filipescu, D.; Gheorghe, A.; Glodariu, T.; Grebosz, J.; Jeong, S.; Kim, Y. H.; Lay, J. A.; Miyatake, H.; Nicoletto, M.; Pakou, A.; Rusek, K.; Sgouros, O.; Soukeras, V.; Stroe, L.; Toniolo, N.; Vitturi, A.; Watanabe, Y.; Zerva, K.

    2016-08-01

    This work aims at investigating the projectile binding energy influence on the reaction dynamics, introducing new results and new data analysis methods in order to overcome some typically encountered problems, such as the identification of reaction products differing by few mass units and the discrimination of direct reaction processes. The 17O+58Ni collision was studied at five near-barrier energies employing a compact experimental setup consisting of four double-sided silicon strip detectors (DSSSDs). Different reaction processes, namely the elastic and inelastic scattering and the 1 n stripping, were discriminated by means of a detailed analysis of the experimental energy spectra based on Monte Carlo simulations. The elastic scattering angular distributions were investigated within the framework of the optical model using Woods-Saxon and double-folding potentials. The total reaction cross sections were extracted and the reduced cross sections compared with those obtained for 17F (Sp=0.600 MeV), the mirror nucleus of 17O (Sn=4.143 MeV), and for the tightly bound 16O projectile. The 17O+58Ni total reaction cross sections were larger than those for 16O on the same target at the lowest energies studied, becoming identical, within errors, as the incident energy increased above the Coulomb barrier. This behavior was related to a strong contribution from the 1 n -stripping channel at the lowest energies.

  13. Bio-Photoelectrochemical Solar Cells Incorporating Reaction Center and Reaction Center Plus Light Harvesting Complexes

    Science.gov (United States)

    Yaghoubi, Houman

    Harvesting solar energy can potentially be a promising solution to the energy crisis now and in the future. However, material and processing costs continue to be the most important limitations for the commercial devices. A key solution to these problems might lie within the development of bio-hybrid solar cells that seeks to mimic photosynthesis to harvest solar energy and to take advantage of the low material costs, negative carbon footprint, and material abundance. The bio-photoelectrochemical cell technologies exploit biomimetic means of energy conversion by utilizing plant-derived photosystems which can be inexpensive and ultimately the most sustainable alternative. Plants and photosynthetic bacteria harvest light, through special proteins called reaction centers (RCs), with high efficiency and convert it into electrochemical energy. In theory, photosynthetic RCs can be used in a device to harvest solar energy and generate 1.1 V open circuit voltage and ~1 mA cm-2 short circuit photocurrent. Considering the nearly perfect quantum yield of photo-induced charge separation, efficiency of a protein-based solar cell might exceed 20%. In practice, the efficiency of fabricated devices has been limited mainly due to the challenges in the electron transfer between the protein complex and the device electrodes as well as limited light absorption. The overarching goal of this work is to increase the power conversion efficiency in protein-based solar cells by addressing those issues (i.e. electron transfer and light absorption). This work presents several approaches to increase the charge transfer rate between the photosynthetic RC and underlying electrode as well as increasing the light absorption to eventually enhance the external quantum efficiency (EQE) of bio-hybrid solar cells. The first approach is to decrease the electron transfer distance between one of the redox active sites in the RC and the underlying electrode by direct attachment of the of protein complex

  14. HENLE'S REACTION OF THE CHROMAFFIN CELLS IN THE ADRENALS, AND THE MICROSCOPIC TEST FOR ADRENALIN

    Science.gov (United States)

    Ogata, Tomosaburo; Ogata, Akira

    1917-01-01

    We have established the fact that the chrome reaction as well as the silver and osmium reactions are merely reductions by adrenalin. In our opinion the naming of the cells giving a positive reaction should not be based upon the reaction i.e., chromaffin cells), but on the presence of adrenalin itself. Biedl's terms, adrenal cell, adrenal organ, adrenal body, adrenal system, and also Bonnamour's term, adrenalin-producing cells, are appropriate in this respect. We propose the names adrenalin cell, adrenalin tissue, adrenalin system, thereby indicating the presence of adrenalin. PMID:19868124

  15. Characterizing motility dynamics in human RPE cells

    Science.gov (United States)

    Liu, Zhuolin; Kurokawa, Kazuhiro; Zhang, Furu; Miller, Donald T.

    2017-02-01

    Retinal pigment epithelium (RPE) cells are vital to health of the outer retina, however, are often compromised in ageing and ocular diseases that lead to blindness. Early manifestation of RPE disruption occurs at the cellular level, but while in vivo biomarkers at this scale hold considerable promise, RPE cells have proven extremely challenging to image in the living human eye. Recently we addressed this problem by using organelle motility as a novel contrast agent to enhance the RPE cell in conjunction with 3D resolution of adaptive optics-optical coherence tomography (AO-OCT) to section the RPE layer. In this study, we expand on the central novelty of our method - organelle motility - by characterizing the dynamics of the motility in individual RPE cells, important because of its direct link to RPE physiology. To do this, AO-OCT videos of the same retinal patch were acquired at approximately 1 min intervals or less, time stamped, and registered in 3D with sub-cellular accuracy. Motility was quantified by an exponential decay time constant, the time for motility to decorrelate the speckle field across an RPE cell. In two normal subjects, we found the decay time constant to be just 3 seconds, thus indicating rapid motility in normal RPE cells.

  16. Nonadiabatic quantum wave packet dynamics of the H + H2 reaction including the coriolis coupling

    Indian Academy of Sciences (India)

    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.

  17. Structural and dynamical control of the reaction rate in protein electron transfer

    Science.gov (United States)

    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.

  18. Acute effects of static and dynamic stretching on balance, agility, reaction time and movement time.

    Science.gov (United States)

    Chatzopoulos, Dimitris; Galazoulas, Christos; Patikas, Dimitrios; Kotzamanidis, Christos

    2014-05-01

    The purpose of this study was to compare the acute effects of three different stretching protocols on balance, agility, reaction time and movement time of the upper limbs. Participants were thirty one female high school athletes (age = 17.3 ± 0.5 yr.). All participants performed one of the following protocols on different days: (a) 3 min jogging followed by 7 min static stretching (SS), (b) 3 min jogging followed by 7 min dynamic stretching (DS), and (c) 3 min jogging followed by 7 min of rest (NS). After the protocols participants performed the following tests: dynamic balance, 505 agility test, reaction time (time between a sound stimulus and release of a button) and movement time (movement of the upper extremity over a 0.5 m distance). The order of stretching protocols and performance tests were counterbalanced to avoid carryover effects. Repeated measures analysis of variance revealed significant main effects for all variables except reaction time. The DS protocol compared to SS performed significantly better in balance, agility and movement time. Additionally, the DS protocol compared to NS performed significantly better in agility. According to the results of the study, a DS protocol is more appropriate than SS for activities that require balance, rapid change of running direction (agility) and movement time of the upper extremities. Key pointsStatic stretching has a negative effect on balance and agility performance compared to dynamic stretching.There was no effect of the stretching protocols on reaction time.Dynamic stretching was more effective than static stretching for increasing movement time of the upper extremities.

  19. Dynamics of small autocatalytic reaction network; 2, replication, mutation and catalysis

    CERN Document Server

    Stadler, P F; Först, C J; Schuster, P; Stadler, Peter F; Schnabl, Wolfgang; Forst, Christian V; Schuster, Peter; Biotechnology, Molecuar

    1994-01-01

    Mutation is introduced into autocatalytic reaction networks. Examples of low dimensional dynamical systems --- n = 2, 3 and 4 --- are discussed and complete qualitative analysis is presented. Error thresholds known from simple replication-mutation kinetics with frequency independent replication rates occur here as well. Instead of cooperative transitions or higher order phase transistions the thresholds appear here as supercritical or subcritical bifurcations being analogous to first order phase transitions.

  20. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Theory and Practical Applications

    CERN Document Server

    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.

  1. Reaction dynamics and statistical theory for the growth of hydrogen bonding clusters

    Institute of Scientific and Technical Information of China (English)

    WANG; Haijun; BA; Xinwu(巴信武); ZHAO; Min(赵敏)

    2002-01-01

    The similarities between the formation of hydrogen bonds and polycondensation reactions are stated from the statistical viewpoint, and then taking the hydrogen bonding system of AaDd type as an example, the growing process of hydrogen bonding clusters is investigated in terms of the theory of reaction dynamics and statistical theory for polymeric reactions. The two methods lead to the same conclusions, stating that the statistical theory for polymerization is applicable to the hydrogen bonding systems. Based on this consideration, the explicit relationship between the conversions of proton-donors and proton-acceptors and the Gibbs free energy of the system under study is given. Furthermore, the sol-gel phase transition is predicted to take place in some hydrogen bonding systems, and the corresponding generalized scaling laws describing this kind of phase transition are obtained.

  2. Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications.

    Science.gov (United States)

    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.

  3. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Science.gov (United States)

    Zobač, Vladmír; Lewis, James P.; Jelínek, Pavel

    2016-07-01

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

  4. ARTICLE Crossed Beams Study on the Dynamics of F Atom Reaction with 1,2-Butadiene

    Science.gov (United States)

    Xiao, Chong-fa; Shen, Guan-lin; Wang, Xiu-yan; Yang, Xue-ming

    2010-12-01

    We have investigated the dynamics of the F+C4H6 reaction using the universal crossed molecular beam method. The C4H5F+H reaction channel was observed in this experiment. Angular resolved time-of-flight spectra have been measured for the C4H5F product. Product angular distributions as well as kinetic energy distributions were determined for this product channel. Experimental results show that the C4H5F product is largely backward scattered with considerable forward scattering signal, relative to the F atom beam direction. This suggests that the reaction channel mainly proceeds via a long-lived complex formation mechanism, with possible contribution from a direct SN2 type mechanism.

  5. Quantum and quasiclassical dynamics of the multi-channel H + H2S reaction

    Science.gov (United States)

    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.

  6. Dynamic behaviour of reactive distillation tray columns described with a non-equilibrium cell model

    NARCIS (Netherlands)

    Baur, R.; Taylor, R.; Krishna, R.

    2001-01-01

    In this paper we develop a generic, dynamic, nonequilibrium (NEQ) cell model for reactive distillation (RD) tray columns. The features of our model are (1) the use of Maxwell–Stefan equations for describing mass transfer between fluid phases, (2) the reaction is assumed to take place in the liquid

  7. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

    Science.gov (United States)

    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

  8. Study of dynamics of glucose-glucose oxidase-ferricyanide reaction

    Science.gov (United States)

    Nováková, A.; Schreiberová, L.; Schreiber, I.

    2011-12-01

    This work is focused on dynamics of the glucose-glucose oxidase-ferricyanide enzymatic reaction with or without sodium hydroxide in a continuous-flow stirred tank reactor (CSTR) and in a batch reactor. This reaction exhibits pH-variations having autocatalytic character and is reported to provide nonlinear dynamic behavior (bistability, excitability). The dynamical behavior of the reaction was examined within a wide range of inlet parameters. The main inlet parameters were the ratio of concentrations of sodium hydroxide and ferricyanide and the flow rate. In a batch reactor we observed an autocatalytic drop of pH from slightly basic to medium acidic values. In a CSTR our aim was to find bistability in the presence of sodium hydroxide. However, only a basic steady state was found. In order to reach an acidic steady state, we investigated the system in the absence of sodium hydroxide. Under these conditions the transition from the basic to the acidic steady state was observed when inlet glucose concentration was increased.

  9. Dynamics of gecko locomotion: a force-measuring array to measure 3D reaction forces.

    Science.gov (United States)

    Dai, Zhendong; Wang, Zhouyi; Ji, Aihong

    2011-03-01

    Measuring the interaction between each foot of an animal and the substrate is one of the most effective ways to understand the dynamics of legged locomotion. Here, a new facility - the force-measuring array (FMA) - was developed and applied to measure 3D reaction forces of geckos on different slope surfaces. The FMA consists of 16 3D sensors with resolution to the mN level. At the same time the locomotion behaviour of geckos freely moving on the FMA was recorded by high speed camera. The reaction forces acting on the gecko's individual feet measured by the FMA and correlated with locomotion behaviour provided enough information to reveal the mechanical and dynamic secrets of gecko locomotion. Moreover, dynamic forces were also measured by a force platform and correlated with locomotion behaviour. The difference between the forces measured by the two methods is discussed. From the results we conclude that FMA is the best way to obtain true reaction forces acting on the gecko's individual feet.

  10. Microscopic dynamics simulations of heavy-ion fusion reactions induced by neutron-rich nuclei

    CERN Document Server

    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 ...

  11. Heavy ion collision dynamics of 10,11B+10,11B reactions

    Directory of Open Access Journals (Sweden)

    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.

  12. Theory of the reaction dynamics of small molecules on metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Bret [Univ. of Massachusetts, Amherst, MA (United States)

    2016-09-09

    The objective of this project has been to develop realistic theoretical models for gas-surface interactions, with a focus on processes important in heterogeneous catalysis. The dissociative chemisorption of a molecule on a metal is a key step in many catalyzed reactions, and is often the rate-limiting step. We have explored the dissociative chemisorption of H2, H2O and CH4 on a variety of metal surfaces. Most recently, our extensive studies of methane dissociation on Ni and Pt surfaces have fully elucidated its dependence on translational energy, vibrational state and surface temperature, providing the first accurate comparisons with experimental data. We have explored Eley-Rideal and hot atom reactions of H atoms with H- and C-covered metal surfaces. H atom interactions with graphite have also been explored, including both sticking and Eley-Rideal recombination processes. Again, our methods made it possible to explain several experiments studying these reactions. The sticking of atoms on metal surfaces has also been studied. To help elucidate the experiments that study these processes, we examine how the reaction dynamics depend upon the nature of the molecule-metal interaction, as well as experimental variables such as substrate temperature, beam energy, angle of impact, and the internal states of the molecules. Electronic structure methods based on Density Functional Theory are used to compute each molecule-metal potential energy surface. Both time-dependent quantum scattering techniques and quasi-classical methods are used to examine the reaction or scattering dynamics. Much of our effort has been directed towards developing improved quantum methods that can accurately describe reactions, as well as include the effects of substrate temperature (lattice vibration).

  13. Fast and stable redox reactions of MnO₂/CNT hybrid electrodes for dynamically stretchable pseudocapacitors.

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-21

    Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid electrodes. The extremely small relaxation time constant of less than 0.15 s indicates a fast redox reaction at the MnO2/CNT hybrid electrodes, securing a stable electrochemical performance for the dynamically stretchable pseudocapacitors. This finding and the fundamental understanding gained from the pseudo-capacitive behavior coupled with mechanical deformation under a dynamic stretching mode would provide guidance to further improve their overall performance including a higher power density than LIBs, a higher energy density than EDLCs, and a long-life cycling stability. Most importantly, these results will potentially accelerate the applications of stretchable pseudocapacitors for flexible and biomedical electronics.

  14. Dynamical Dipole and Equation of State in N/Z Asymmetric Fusion Reactions

    Directory of Open Access Journals (Sweden)

    Giaz Agnese

    2014-03-01

    Full Text Available In heavy ion reactions, in the case of N/Z asymmetry between projectile and target, the process leading to complete fusion is expected to produce pre-equilibrium dipole γ-ray emission. It is generated during the charge equilibration process and it is known as Dynamical Dipole. A new measurement of the dynamical dipole emission was performed by studying 16O + 116Sn at 12 MeV/u. These data, together with those measured at 8.1 MeV/u and 15.6 MeV/u for the same reaction, provide the dependence on the Dynamical Dipole total emission yield with beam energy and they can be compared with theoretical expectations. The experimental results show a weak increase of the Dynamical Dipole total yield with beam energies and are in agreement with the prediction of a theoretical model based on the Boltzmann–Nordheim–Vlasov (BNV approach. The measured trend with beam energy does not confirm the rise and fall behavior previously reported for the same fused compound but with a much higher dipole moment.

  15. Role of rotational energy component in the dynamics of 16O+198Pt reaction

    Directory of Open Access Journals (Sweden)

    Sharma Manoj K.

    2017-01-01

    Full Text Available The role of rotational energy is investigated in reference to the dynamics of 16O+198Pt →214Rn∗ reaction using the sticking (IS and the non-sticking (INS limits of moment of inertia within the framework of dynamical cluster decay model. The decay barrier height and barrier position get significantly modified for the use of sticking or non-sticking choice, which in turn reproduce the evaporation residue and the fusion-fission cross-sections nicely by the IS approach, while the INS approach provides feasible addressal of data only for evaporation residue channel. Moreover, the fragmentation path of decaying fragments of 214Rn∗ compound nucleus gets influenced for different choices of moment of inertia. Beside this, the role of nuclear deformations i.e. static, dynamic quadurpole (β2 and higher order static deformation up to β4 are duly investigated for both choices of the moment of inertia.

  16. Dynamic path bifurcation in the Beckmann reaction: support from kinetic analyses.

    Science.gov (United States)

    Yamamoto, Yutaro; Hasegawa, Hiroto; Yamataka, Hiroshi

    2011-06-03

    The reactions of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles when the migrating groups have reasonable stability as cations. The reactions of oxime sulfonates of 1-substituted-phenyl-2-propanone derivatives (7-X) and related substrates (8-X, 9a-X) in aqueous CH(3)CN gave both rearrangement products (amides) and fragmentation products (alcohols), the ratio of which depends on the system; the reactions of 7-X gave amides predominantly, whereas 9a-X yielded alcohols as the major product. The logk-logk plots between the systems gave excellent linear correlations with slopes of near unity. The results support the occurrence of path bifurcation after the rate-determining TS of the Beckmann rearrangement/fragmentation reaction, which has previously been proposed on the basis of molecular dynamics simulations. It was concluded that path-bifurcation phenomenon could be more common than thought and that a reactivity-selectivity argument based on the traditional TS theory may not always be applicable even to a well-known textbook organic reaction.

  17. A ring polymer molecular dynamics study of the Cl + O3 reaction.

    Science.gov (United States)

    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.

  18. A method for efficient calculation of diffusion and reactions of lipophilic compounds in complex cell geometry.

    Science.gov (United States)

    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.

  19. A method for efficient calculation of diffusion and reactions of lipophilic compounds in complex cell geometry.

    Directory of Open Access Journals (Sweden)

    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.

  20. Acceleration of convective dissolution by chemical reaction in a Hele-Shaw cell.

    Science.gov (United States)

    Cherezov, Ilia; Cardoso, Silvana S S

    2016-09-14

    New laboratory experiments quantify the destabilising effect of a second-order chemical reaction on the fingering instability of a diffusive boundary layer in a Hele-Shaw cell. We show that, for a given chemical system, the dynamics of such a reactive boundary layer is fully determined by two dimensionless groups, Da/Ra(2), which measures the timescale for convection compared to those for reaction and diffusion, and CBo', which reflects the excess of the environmental reactant species relative to the diffusing solute. Results of a systematic study varying CBo' in the range 0-0.1 are presented. It is shown that the chemical reaction increases the growth rate of a perturbation and favours small wavelengths compared to the inert system. A higher concentration of CBo' not only accelerates the onset of convection, but crucially also increases the transport of the solute by up to 150% compared to the inert system. This increase in solute transfer has important practical implications, such as in the storage of carbon dioxide in saline aquifers.

  1. Properties of Si Nanowires Synthesized by Galvanic Cell Reaction

    Science.gov (United States)

    Yasushi Kobayashi,; Sadao Adachi,

    2010-07-01

    A galvanic cell reaction is used to synthesize Si nanowires (SiNWs) in AgNO3/HF solution at 30 °C for 60 min. The AgNO3 concentration ise varied from M=0.0001 to 0.6 mol/L in aqueous HF solution (5 mol/L). Vertically well-aligned SiNW arrays are found to be formed in the limited AgNO3 concentration range of M˜ 0.02--0.08 mol/L. The maximum nanowire length is ˜35 μm (M˜ 0.05 mol/L). The photoluminescence (PL) spectra of the SiNWs exhibit a broad peak centered at ˜1.8 eV. Below M˜ 0.02 or above ˜0.08 mol/L, the solutions produce only roughened surfaces. No PL emission is observed from such surfaces. Passive HF etching of the SiNWs leads to the removal of the surface oxide overlayer and changes the wettability from highly hydrophilic (˜5°) to superhydrophobic (˜135°). Optical absorption and Fourier-transform infrared spectroscopy show that the SiNWs have an extremely large optical absorbability not only in the interband-transition region but also in the far-infrared spectral region.

  2. Mechanosensing Dynamics of Red blood Cells

    Science.gov (United States)

    Wan, Jiandi

    2015-11-01

    Mechanical stress-induced deformation of human red blood cells (RBCs) plays important physiopathological roles in oxygen delivery, blood rheology, transfusion, and malaria. Recent studies demonstrate that, in response to mechanical deformation, RBCs release adenosine-5'-triphosphate (ATP), suggesting the existence of mechanotransductive pathways in RBCs. Most importantly, the released ATP from RBCs regulates vascular tone and impaired release of ATP from RBCs has been linked to diseases such as type II diabetes and cystic fibrosis. To date, however, the mechanisms of mechanotransductive release of ATP from RBCs remain unclear. Given that RBCs experience shear stresses continuously during the circulation cycle and the released ATP plays a central role in vascular physiopathology, understanding the mechanotransductive release of ATP from RBCs will provide not only fundamental insights to the role of RBCs in vascular homeostasis but also novel therapeutic strategies for red cell dysfunction and vascular disease. This talk describes the main research in my group on integrating microfluidic-based approaches to study the mechanosensing dynamics of RBCs. Specifically, I will introduce a micro?uidic approach that can probe the dynamics of shear-induced ATP release from RBCs with millisecond resolution and provide quantitative understandings of the mechanosensitive ATP release processes in RBCs. Furthermore, I will also describe our recent findings about the roles of the Piezo1 channel, a newly discovered mechanosensitive cation channel in the mechanotransductive ATP release in RBCs. Last, possible functions of RBCs in the regulation of cerebral blood flow will be discussed.

  3. Galectin-9: From cell biology to complex disease dynamics.

    Science.gov (United States)

    John, Sebastian; Mishra, Rashmi

    2016-09-01

    Galectins is a family of non-classically secreted, beta-galactoside-binding proteins that has recently received considerable attention in the spatio-temporal regulation of surface 'signal lattice' organization, membrane dynamics, cell-adhesion and disease therapeutics. Galectin-9 is a unique member of this family, with two non-homologous carbohydrate recognition domains joined by a linker peptide sequence of variable lengths, generating isoforms with distinct properties and functions in both physiological and pathological settings, such as during development, immune reaction, neoplastic transformations and metastasis. In this review, we summarize the latest knowledge on the structure, receptors, cellular targets, trafficking pathways and functional properties of galectin-9 and discuss how galectin-9-mediated signalling cascades can be exploited in cancers and immunotherapies.

  4. Sperm Cell Dynamics in Shallow Chambers

    Science.gov (United States)

    Condat, Carlos; Marconi, Veronica; Guidobaldi, Alejandro; Giojalas, Laura; Silhanek, Alejandro; Jeyaram, Yogesh; Moshchalkov, Victor

    2015-03-01

    Self-propelled microorganisms are attracted to surfaces. This makes their dynamic behavior in restricted geometries very different from that observed in the bulk. Here we analyze the motion of spermatozoids confined to shallow chambers, investigating the nature of the cell trajectories and their accumulation near the side boundaries. Observed cell trajectories are composed of a succession of quasi-circular and quasi-linear segments. This suggests that the cells follow a path of intermittent trappings near the top and down surfaces separated by stretches of quasi-free motion near the center of the gap. Use of microstructured petal-shaped edges limits accumulation near the borders and contributes to increase the concentration in the chamber interior. System stabilization occurs over times of the order of minutes, which agrees well with a theoretical estimate that assumes that the cell mean-square displacement is largely due to the quasi-linear segments. Pure quasi-circular trajectories would require several hours to stabilize. Our estimates also indicate that stabilization proceeds 2.5 times faster in the rosette geometries than in the smooth-edged chambers, which is another practical reason to prefer the former.

  5. Quantum molecular dynamics simulations of hydrogen production and solar cells

    Science.gov (United States)

    Mou, Weiwei

    The global energy crisis presents two major challenges for scientists around the world: Producing cleaner energy which is sustainable for the environment; And improving the efficiency of energy production as well as consumption. It is crucial and yet elusive to understand the atomistic mechanisms and electronic properties, which are needed in order to tackle those challenges. Quantum molecular dynamics simulations and nonadiabatic quantum molecular dynamics are two of the dominant methods used to address the atomistic and electronic properties in various energy studies. This dissertation is an ensemble of three studies in energy research: (1) Hydrogen production from the reaction of aluminum clusters with water to provide a renewable energy cycle; (2) The photo-excited charge transfer and recombination at a quaterthiophene/zinc oxide interface to improve the power conversion efficiency of hybrid poly(3-hexylthiophene) (P3HT) /ZnO solar cells; and (3) the charge transfer at a rubrene/C60 interface to understand why phenyl groups in rubrene improve the performance of rubrene/C60 solar cells.

  6. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    Science.gov (United States)

    Stingaciu, Laura-Roxana; O'Neill, Hugh; Liberton, Michelle; Urban, Volker S.; Pakrasi, Himadri B.; Ohl, Michael

    2016-01-01

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.

  7. Molecular Network Dynamics of Cell Cycle Control: Periodicity of Start and Finish.

    Science.gov (United States)

    Palmisano, Alida; Zámborszky, Judit; Oguz, Cihan; Csikász-Nagy, Attila

    2017-01-01

    The cell division cycle is controlled by a complex regulatory network which ensures that the phases of the cell cycle are executed in the right order. This regulatory network receives signals from the environment, monitors the state of the DNA, and decides timings of cell cycle events. The underlying transcriptional and post-translational regulatory interactions lead to complex dynamical responses, such as the oscillations in the levels of cell cycle proteins driven by intertwined biochemical reactions. A cell moves between different phases of its cycle similar to a dynamical system switching between its steady states. The complex molecular network driving these phases has been investigated in previous computational systems biology studies. Here, we review the critical physiological and molecular transitions that occur in the cell cycle and discuss the role of mathematical modeling in elucidating these transitions and understand cell cycle synchronization.

  8. Reaction dynamics. Extremely short-lived reaction resonances in Cl + HD (v = 1) → DCl + H due to chemical bond softening.

    Science.gov (United States)

    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.

  9. Interface reactions in CdTe solar cell processing

    Energy Technology Data Exchange (ETDEWEB)

    Albin, D.; Dhere, R.; Swartzlander-Guest, A. [National Renewable Energy Lab., Golden, CO (United States)] [and others

    1998-12-31

    Currently, the best performing CdS/CdTe solar cells use a superstrate structure in which CdTe is deposited on a heated CdS/SnO{sub 2}/Glass substrate. In the close-spaced-sublimation (CSS) process, substrate temperatures in the range 550 C to 620 C are common. Understanding how these high processing temperatures impact reactions at the CdS/CdTe interface in addition to reactions between previously deposited layers is critical. At the SnO{sub 2}/CdS interface the authors have determined that SnO{sub 2} can be susceptible to reduction, particularly in H{sub 2} ambients. Room-temperature sputtered SnO{sub 2} shows the most susceptibility. In contrast, higher growth temperature chemical vapor deposited (CVD) SnO{sub 2} appears to be much more stable. Elimination of unstable SnO{sub 2} layers, and the substitution of thermal treatments for H{sub 2} anneals has produced total-area solar conversion efficiencies of 13.6% using non-optimized SnO{sub 2} substrates and chemical-bath deposited (CBD) CdS. Alloying and interdiffusion at the CdS/CdTe interface was studied using a new lift-off approach which allows enhanced compositional and structural analysis at the interface. Small-grained CdS, grown by a low-temperature CBD process, results in more CdTe{sub 1{minus}x}S{sub x} alloying (x = 12--13%) relative to larger-grained CdS grown by high-temperature CSS (x{approximately}2--3%). Interdiffusion of S and Te at the interface, measured with lift-off samples, appears to be inversely proportional to the amount of oxygen used during the CSS CdTe deposition. The highest efficiency to date using CSS-grown CdS is 10.7% and was accomplished by eliminating oxygen during the CdTe deposition.

  10. Excitation of the dynamical dipole in the charge asymmetric reaction 16O + 116Sn

    Science.gov (United States)

    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.

  11. Excitation of the dynamical dipole in the charge asymmetric reaction {sup 16}O + {sup 116}Sn

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Acute Effects of Static and Dynamic Stretching on Balance, Agility, Reaction Time and Movement Time

    Directory of Open Access Journals (Sweden)

    Dimitris Chatzopoulos

    2014-06-01

    Full Text Available The purpose of this study was to compare the acute effects of three different stretching protocols on balance, agility, reaction time and movement time of the upper limbs. Participants were thirty one female high school athletes (age = 17.3 ± 0.5 yr.. All participants performed one of the following protocols on different days: (a 3 min jogging followed by 7 min static stretching (SS, (b 3 min jogging followed by 7 min dynamic stretching (DS, and (c 3 min jogging followed by 7 min of rest (NS. After the protocols participants performed the following tests: dynamic balance, 505 agility test, reaction time (time between a sound stimulus and release of a button and movement time (movement of the upper extremity over a 0.5 m distance. The order of stretching protocols and performance tests were counterbalanced to avoid carryover effects. Repeated measures analysis of variance revealed significant main effects for all variables except reaction time. The DS protocol compared to SS performed significantly better in balance, agility and movement time. Additionally, the DS protocol compared to NS performed significantly better in agility. According to the results of the study, a DS protocol is more appropriate than SS for activities that require balance, rapid change of running direction (agility and movement time of the upper extremities.

  13. Complex integrated method of dynamic meditation with Buddhists’ breathing in case of neurotic reactions

    Directory of Open Access Journals (Sweden)

    Omelyanenko V.I.

    2014-02-01

    Full Text Available Purpose: to elaborate complex integrated method of psychological influence upon sport dancers in time of training on base of Buddhists’ meditation “conscious breathing” for neurotic reactions elimination, professional skill improvement and psycho emotional stability advance. Material : twenty dancers at the age of 40-50 with neurotic reactions participated in the research. At the first stage of the research all the subjects’ ability to focus attention at breathing during sports dancing performance was examined. At the second stage training in method of dynamic meditation applied for martial arts of the experimental group of 10 subjects was conducted. Both individual and group training sessions were held. At the third stage the experimental group joined dynamic meditation and breathing at dance performance. At the fourth stage the experimental group’s results were compared with the control group’s results. Results : at the first stage of the research all the subjects noted difficulties in focusing attention on Buddhists’ nasal breathing and dance technique come-down. 3-5 sessions of training in method of dynamic meditation were necessary for the subjects of the experimental group at the second stage of the research. At the third stage of the research all the subjects of the experimental group could control their nasal breathing at dance performance without dance technique come-down. At the fourth stage the comparative evaluation of the results of the experimental and control groups revealed that it was necessary 3-7 sport dance practice sessions for elimination of the neurotic reactions. No such effect was observed in the control group. Conclusions : The results of the research prove that Buddhists’ meditation “conscious breathing” may be joined with dynamic meditation successfully. It’s impossible to focus attention continuously on breathing at time of sport dance performance. The elaborated technique of the integration of

  14. A study of Hodgkin/Reed-Sternberg cells using single cell polymerase chain reaction.

    Science.gov (United States)

    Deng, F; Liao, L; Lü, G; Li, G; Yang, G

    2000-01-01

    To investigate the characteristics of Hodgkin/Reed-Stemberg (H/R-S) cells found in patients with various types of Hodgkin's disease (HD). H/R-S cells were micropicked from frozen sections of tissues affected by HD. The DNA from these cells was amplified by polymerase chain reaction (PCR) using immunoglobulin heavy chain gene FR III a/JH primers and light chain gene family-specific primers. A total of 52/135 (35.8%) isolated cells showed the specific products in the reactions. IgH and V kappa 4 rearrangements were repeatedly found in many cells from a lymphocyte predominance type sample; repeated V kappa 4 and individual IgH/V kappa 2,4 rearrangements and individual IgH, V lambda 3/ V kappa 4 rearrangements were found in two different cases of the nodular sclerosis type; repeated IgH/ V lambda 3 and individual V lambda 2,4 rearrangements, repeated V kappa 2,4 rearrangements, repeated V kappa 4 and individual IgH/ V kappa 3 rearrangements, repeated IgH and individual V kappa 3/ V lambda 4 rearrangements were detected in 3 cases of the mixed cellularity type. Repeated and individual IgH rearrangements were found in other 2 cases. The H/R-S cells isolated from the lymphocyte predominance subtypes of HD have IgH and V lambda 4 gene rearrangements. This suggests that the lymphocyte predominance type is a proliferation of neoplastic B cells. The cells isolated from the mixed cellularity and nodular sclerosis types derive from B lineage cells at various stages of differentiation because of the presence of their IgH, kappa and/or lambda gene rearrangements. To our knowledge, this is the first time that the lambda gene rearrangement was detected in H/R-S cells.

  15. In situ transmission electron microscopy of ionic conductivity and reaction mechanisms in ultrathin solid oxide fuel cells.

    Science.gov (United States)

    Tavabi, Amir H; Arai, Shigeo; Muto, Shunsuke; Tanji, Takayoshi; Dunin-Borkowski, Rafal E

    2014-12-01

    Solid oxide fuel cells (SOFCs) are promising candidates for use in alternative energy technologies. A full understanding of the reaction mechanisms in these dynamic material systems is required to optimize device performance and overcome present limitations. Here, we show that in situ transmission electron microscopy (TEM) can be used to study redox reactions and ionic conductivity in SOFCs in a gas environment at elevated temperature. We examine model ultrathin half and complete cells in two environmental TEMs using off-axis electron holography and electron energy-loss spectroscopy. Our results from the model cells provide insight into the essential phenomena that are important for the operation of commercial devices. Changes in the activities of dopant cations in the solid electrolyte are detected during oxygen anion conduction, demonstrating the key role of dopants in electrolyte architecture in SOFCs.

  16. Comparative Static and Dynamic Study of a Prototype SN2 Reaction.

    Science.gov (United States)

    Joubert, Laurent; Pavone, Michele; Barone, Vincenzo; Adamo, Carlo

    2006-09-01

    Ab initio molecular-dynamic simulations, using density functional theory (DFT) and the recent atom-centered density-matrix propagation method (ADMP), were used to study the bond formation process in a prototypical SN2 reaction, namely the Walden inversion. Using the real space partition schemes of both electronic density and electron localization function gradient fields, we analyzed different quantum chemical topology (QCT) properties along the ADMP trajectory. In particular, atomic charges derived from the Bader's atoms-in-molecules (AIM) theory were used to analyze intra- and intermolecular charge transfers between atoms, while the electronic population of the forming bonding basin obtained from the electron localization function (ELF) gradient field was employed to describe the bond formation process. These results were compared to the corresponding QCT properties issuing from a static approach based on the intrinsic reaction path (IRP). Although similar features are found for both static and dynamic approaches, the dynamic QCT analysis provides some explanation of the differences observed during the formation of the ion-molecule complex. In particular, it suggests a stronger electron exchange leading to an effective maximization of both covalent and noncovalent interactions.

  17. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

    Science.gov (United States)

    Wales, D. J.

    2015-04-01

    This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of "friction" effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

  18. A molecular dynamics study of bond exchange reactions in covalent adaptable networks.

    Science.gov (United States)

    Yang, Hua; Yu, Kai; Mu, Xiaoming; Shi, Xinghua; Wei, Yujie; Guo, Yafang; Qi, H Jerry

    2015-08-21

    Covalent adaptable networks are polymers that can alter the arrangement of network connections by bond exchange reactions where an active unit attaches to an existing bond then kicks off its pre-existing peer to form a new bond. When the polymer is stretched, bond exchange reactions lead to stress relaxation and plastic deformation, or the so-called reforming. In addition, two pieces of polymers can be rejoined together without introducing additional monomers or chemicals on the interface, enabling welding and reprocessing. Although covalent adaptable networks have been researched extensively in the past, knowledge about the macromolecular level network alternations is limited. In this study, molecular dynamics simulations are used to investigate the macromolecular details of bond exchange reactions in a recently reported epoxy system. An algorithm for bond exchange reactions is first developed and applied to study a crosslinking network formed by epoxy resin DGEBA with the crosslinking agent tricarballylic acid. The trace of the active units is tracked to show the migration of these units within the network. Network properties, such as the distance between two neighboring crosslink sites, the chain angle, and the initial modulus, are examined after each iteration of the bond exchange reactions to provide detailed information about how material behaviors and macromolecular structure evolve. Stress relaxation simulations are also conducted. It is found that even though bond exchange reactions change the macroscopic shape of the network, microscopic network characteristic features, such as the distance between two neighboring crosslink sites and the chain angle, relax back to the unstretched isotropic state. Comparison with a recent scaling theory also shows good agreement.

  19. Comparative dynamics of the two channels of the reaction of D + MuH.

    Science.gov (United States)

    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

  20. Computational modeling of transport and electrochemical reactions in proton-exchange membrane fuel cells

    Science.gov (United States)

    Um, Sukkee

    A comprehensive, multi-physics computational fuel cell dynamics (CFCD) model integrating electrochemical kinetics, charge transport, mass transport (particularly water transport), and flow dynamics is developed in this thesis. The numerical model is validated against published experimental data and utilized to generate results that reveal the internal operation of a PEM fuel cell. A number of model applications are demonstrated in the present work. First, the CFCD model is applied to explore hydrogen dilution effects in the anode feed. Detailed two-dimensional electrochemical and flow/transport simulations are provided to examine substantial anode concentration polarization due to hydrogen depletion at the reaction sites. A transient simulation of the cell current response to a step change in cell voltage is also attempted to elucidate characteristics of the dynamic response of a fuel cell for the first time. After the two-dimensional computational study, the CFCD model is applied to illustrate three-dimensional interactions between mass transfer and electrochemical kinetics. Emphasis is placed on obtaining a fundamental understanding of fully three-dimensional flow in the air cathode with interdigitated flowfield design and how it impacts the transport and electrochemical reaction processes. The innovative design concept for enhanced oxygen transport to, and effective water removal from the cathode, is explored numerically. Next, an analytical study of water transport is performed to investigate various water transport regimes of practical interest. The axial locations characteristic of anode water loss and cathode flooding are predicted theoretically and compared with numerical results. A continuous stirred fuel cell reactor (CSFCR) model is also proposed for the limiting situation where the anode and cathode sides reach equilibrium in water concentration with a thin ionomer membrane in between. In addition to the analytical solutions, a detailed water transport

  1. Ultrafast chemical reactions in shocked nitromethane probed with dynamic ellipsometry and transient absorption spectroscopy.

    Science.gov (United States)

    Brown, Kathryn E; McGrane, Shawn D; Bolme, Cynthia A; Moore, David S

    2014-04-10

    Initiation of the shock driven chemical reactions and detonation of nitromethane (NM) can be sensitized by the addition of a weak base; however, the chemical mechanism by which sensitization occurs remains unclear. We investigated the shock driven chemical reaction in NM and in NM sensitized with diethylenetriamine (DETA), using a sustained 300 ps shock driven by a chirped Ti:sapphire laser. We measured the solutions' visible transient absorption spectra and measured interface particle and shock velocities of the nitromethane solutions using ultrafast dynamic ellipsometry. We found there to be a volume-increasing reaction that takes place around interface particle velocity up = 2.4 km/s and up = 2.2 km/s for neat NM and NM with 5% DETA, respectively. The rate at which transient absorption increases is similar in all mixtures, but with decreasing induction times for solutions with increasing DETA concentrations. This result supports the hypothesis that the chemical reaction mechanisms for shocked NM and NM with DETA are the same. Data from shocked NM are compared to literature experimental and theoretical data.

  2. Investigation of Coal-biomass Catalytic Gasification using Experiments, Reaction Kinetics and Computational Fluid Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Investigation of Coal-biomass Catalytic Gasification using Experiments, Reaction Kinetics and Computational Fluid Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Dynamic cell culture system (7-IML-1)

    Science.gov (United States)

    Cogoli, Augusto

    1992-01-01

    This experiment is one of the Biorack experiments being flown on the International Microgravity Laboratory 1 (MIL-1) mission as part of an investigation studying cell proliferation and performance in space. One of the objectives of this investigation is to assess the potential benefits of bioprocessing in space with the ultimate goal of developing a bioreactor for continuous cell cultures in space. This experiment will test the operation of an automated culture chamber that was designed for use in a Bioreactor in space. The device to be tested is called the Dynamic Cell Culture System (DCCS). It is a simple device in which media are renewed or chemicals are injected automatically, by means of osmotic pumps. This experiment uses four Type I/O experiment containers. One DCCS unit, which contains a culture chamber with renewal of medium and a second chamber without a medium supply fits in each container. Two DCCS units are maintained under zero gravity conditions during the on-orbit period. The other two units are maintained under 1 gh conditions in a 1 g centrifuge. The schedule for incubator transfer is given.

  5. Total Reaction Cross Section in an Isospin-Dependent Quantum Molecular Dynamics Model

    Institute of Scientific and Technical Information of China (English)

    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.

  6. Parity violation and dynamical relativistic effects in $(\\vec{e},e'N)$ reactions

    CERN Document Server

    González-Jiménez, R; Donnelly, T W

    2015-01-01

    It is well known that coincidence quasielastic $(\\vec{e},e'N)$ reactions are not appropriate to analyze effects linked to parity violation due the presence of the fifth electromagnetic (EM) response $R^{TL'}$. Nevertheless, in this work we develop a fully relativistic approach to be applied to parity-violating (PV) quasielastic $(\\vec{e},e'N)$ processes. This is of importance as a preliminary step in the subsequent study of inclusive quasielastic PV $(\\vec{e},e')$ reactions. Moreover, our present analysis allows us to disentangle effects associated with the off-shell character of nucleons in nuclei, gauge ambiguities and the role played by the lower components in the nucleon wave functions, i.e., dynamical relativistic effects. This study can help in getting clear information on PV effects. Particular attention is paid to the relativistic plane-wave impulse approximation where the explicit expressions for the PV single-nucleon responses are shown for the first time.

  7. Communication: Mode specific quantum dynamics of the F + CHD3 → HF + CD3 reaction.

    Science.gov (United States)

    Qi, Ji; Song, Hongwei; Yang, Minghui; Palma, Juliana; Manthe, Uwe; Guo, Hua

    2016-05-01

    The mode specific reactivity of the F + CHD3 → HF + CD3 reaction is investigated using an eight-dimensional quantum dynamical model on a recently developed ab initio based full-dimensional potential energy surface. Our results indicate prominent resonance structures at low collision energies and absence of an energy threshold in reaction probabilities. It was also found that excitation of the C-D stretching or CD3 umbrella mode has a relatively small impact on reactivity. On the other hand, the excitation of the C-H vibration (v1) in CHD3 is shown to significantly increase the reactivity, which, like several recent quasi-classical trajectory studies, is at odds with the available experimental data. Possible sources of the disagreement are discussed.

  8. Efficient Light Harvester Layer Prepared by Solid/Mist Interface Reaction for Perovskite Solar Cells.

    Science.gov (United States)

    Xia, Xiang; Li, Hongcui; Wu, Wenyi; Li, Yanhua; Fei, Dehou; Gao, Chunxiao; Liu, Xizhe

    2015-08-12

    A solid/mist reaction method is developed to produce well-crystallized light harvester layers without pinhole defects for perovskite solar cells. The reaction based on mist precursor can be facilely operated with low process temperature. And it can effectively control the volume of CH3NH3I solution and the reaction temperature, which affect the quality of perovskite harvester layers and the performance of perovskite solar cells remarkably. Under optimized condition, the efficiencies of devices reach 16.2% with the average efficiency of 14.9%. The solid/mist reaction is also used to fabricate planar junction solar cells and a PCE of 14.9% is obtained.

  9. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    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.

  10. Static and dynamical critical behavior of the monomer-monomer reaction model with desorption

    Science.gov (United States)

    da Costa, E. C.; Rusch, Flávio Roberto

    2016-06-01

    We studied in this work the monomer-monomer reaction model on a linear chain. The model is described by the following reaction: A + B → AB, where A and B are two monomers that arrive at the surface with probabilities yA and yB, respectively, and we have considered desorption of the monomer B with probability α. The model is studied in the adsorption controlled limit where the reaction rate is infinitely larger than the adsorption rate. We employ site and pair mean-field approximations as well as static and dynamical Monte Carlo simulations. We show that the model exhibits a continuous phase transition between an active steady state and an A-absorbing state, when the parameter yA is varied through a critical value, which depends on the value of α. Monte Carlo simulations and finite-size scaling analysis near the critical point are used to determine the static critical exponents β and ν⊥ and the dynamical critical exponents ν∥ and z. The results found for the monomer-monomer reaction model with B desorption, in the linear chain, are different from those found by E. V. Albano (Albano, 1992) and are in accordance with the values obtained by Jun Zhuo and Sidney Redner (Zhuo and Redner, 1993), and endorse the conjecture of Grassberger, which states that any system undergoing a continuous phase transition from an active steady state to a single absorbing state, exhibits the same critical behavior of the directed percolation universality class.

  11. Ultrafast ring-closing reaction dynamics of a photochromic furan-based difurylethene

    Science.gov (United States)

    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.

  12. Improved Quantum Molecular Dynamics Model and its Application to Fusion Reaction Near Barrier

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An improved quantum molecular dynamics model is proposed. By using this model, the properties of ground state of nuclei from 6Li to 208Pb can be described very well with one set of parameters. The fusion reactions for 40Ca+90Zr, 40Ca+96Zr and 48Ca+90Zr at the energy near the barrier are studied by this model. The experimental data of the fusion cross sections for 40Ca+90,96Zr at the energy near the barrier can be reproduced remarkably well without introducing any new parameters. The mechanism

  13. Quantum trajectory tests of radical-pair quantum dynamics in CIDNP measurements of photosynthetic reaction centers

    CERN Document Server

    Tsampourakis, K

    2015-01-01

    Chemically induced dynamic nuclear polarization is a ubiquitous phenomenon in photosynthetic reaction centers. The relevant nuclear spin observables are a direct manifestation of the radical-pair mechanism. We here use quantum trajectories to describe the time evolution of radical-pairs, and compare their prediction of nuclear spin observables to the one derived from the radical-pair master equation. We unravel a major inconsistency within the Haberkorn approach, while our approach provides a consistent description. These results further challenge the traditional understanding of the radical-pair mechanism as well as the understanding of CIDNP experiments within Haberkorn's approach.

  14. Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions.

    Directory of Open Access Journals (Sweden)

    Niamh M C Connolly

    Full Text Available Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK, re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult.

  15. The dynamics of nonlinear reaction-diffusion equations with small Lévy noise

    CERN Document Server

    Debussche, Arnaud; Imkeller, Peter

    2013-01-01

    This work considers a small random perturbation of alpha-stable jump type nonlinear reaction-diffusion equations with Dirichlet boundary conditions over an interval. It has two stable points whose domains of attraction meet in a separating manifold with several saddle points. Extending a method developed by Imkeller and Pavlyukevich it proves that in contrast to a Gaussian perturbation, the expected exit and transition times between the domains of attraction depend polynomially on the noise intensity in the small intensity limit. Moreover the solution exhibits metastable behavior: there is a polynomial time scale along which the solution dynamics correspond asymptotically to the dynamic behavior of a finite-state Markov chain switching between the stable states.

  16. Dynamics of the induced acrosome reaction in boar sperm evaluated by flow cytometry

    DEFF Research Database (Denmark)

    Birck, Anders; Labouriau, Rodrigo; Christensen, Preben

    2009-01-01

    The present study investigated the dynamics of the in vitro induced acrosome reaction (AR) in boar sperm in response to medium composition, incubation time and ionophore concentration. The AR is a prerequisite for normal sperm fertilizing capability and can be studied in vitro following induction...... induced AR. A detailed description of the dynamics of sperm viability and acrosomal status of boar sperm following in vitro induction of the AR has to our knowledge not previously been conducted. In the present study, a triple color flow cytometric detection technique was used, which gave simultaneous...... information on sperm viability and acrosomal status. The ionophore induced AR was dependent on extracellular Ca2+, but could be easily induced in boar sperm without capacitation. Capacitation-associated plasma membrane phospholipid scrambling was assessed and a medium specific ability to induce these membrane...

  17. Energy momentum pseudo-tensor of high frequency gravitational waves and their dynamical back-reaction

    Institute of Scientific and Technical Information of China (English)

    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.

  18. Angular momentum dependence of quasifission dynamics in the reaction 48Ca+244Pu

    Science.gov (United States)

    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.

  19. Beta cell dynamics: beta cell replenishment, beta cell compensation and diabetes.

    Science.gov (United States)

    Cerf, Marlon E

    2013-10-01

    Type 2 diabetes, characterized by persistent hyperglycemia, arises mostly from beta cell dysfunction and insulin resistance and remains a highly complex metabolic disease due to various stages in its pathogenesis. Glucose homeostasis is primarily regulated by insulin secretion from the beta cells in response to prevailing glycemia. Beta cell populations are dynamic as they respond to fluctuating insulin demand. Beta cell replenishment and death primarily regulate beta cell populations. Beta cells, pancreatic cells, and extra-pancreatic cells represent the three tiers for replenishing beta cells. In rodents, beta cell self-replenishment appears to be the dominant source for new beta cells supported by pancreatic cells (non-beta islet cells, acinar cells, and duct cells) and extra-pancreatic cells (liver, neural, and stem/progenitor cells). In humans, beta cell neogenesis from non-beta cells appears to be the dominant source of beta cell replenishment as limited beta cell self-replenishment occurs particularly in adulthood. Metabolic states of increased insulin demand trigger increased insulin synthesis and secretion from beta cells. Beta cells, therefore, adapt to support their physiology. Maintaining physiological beta cell populations is a strategy for targeting metabolic states of persistently increased insulin demand as in diabetes.

  20. Excited state dynamics in photosynthetic reaction center and light harvesting complex 1

    Science.gov (United States)

    Strümpfer, Johan; Schulten, Klaus

    2012-08-01

    Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC.

  1. Dynamic reaction coordinate in thermally fluctuating environment in the framework of the multidimensional generalized Langevin equations.

    Science.gov (United States)

    Kawai, Shinnosuke; Komatsuzaki, Tamiki

    2010-12-21

    A framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in a multidimensional Langevin equation is extended to the generalized Langevin equations without a priori assumption of the forms of the potential (in general, nonlinearly coupled systems) and the friction kernel. The equation of motion with memory effect can be transformed into an equation without memory at the cost of an increase in the dimensionality of the system, and hence the theoretical framework developed for the (nonlinear) Langevin formulation can be generalized to the non-Markovian process with colored noise. It is found that the increased dimension can be physically interpreted as effective modes of the fluctuating environment. As an illustrative example, we apply this theory to a multidimensional generalized Langevin equation for motion on the Müller-Brown potential surface with an exponential friction kernel. Numerical simulations find a boundary between the highly reactive region and the less reactive region in the space of initial conditions. The location of the boundary is found to depend significantly on both the memory kernel and the nonlinear couplings. The theory extracts a reaction coordinate whose sign determines the fate of the reaction taking into account thermally fluctuating environments, memory effect, and nonlinearities. It is found that the location of the boundary of reactivity is satisfactorily reproduced as the zero of the statistical average of the new reaction coordinate, which is an analytical functional of both the original position coordinates and velocities of the system, and of the properties of the environment.

  2. Dynamic imaging of cell-free and cell-associated viral capture in mature dendritic cells.

    Science.gov (United States)

    Izquierdo-Useros, Nuria; Esteban, Olga; Rodriguez-Plata, Maria T; Erkizia, Itziar; Prado, Julia G; Blanco, Julià; García-Parajo, Maria F; Martinez-Picado, Javier

    2011-12-01

    Dendritic cells (DCs) capture human immunodeficiency virus (HIV) through a non-fusogenic mechanism that enables viral transmission to CD4(+) T cells, contributing to in vivo viral dissemination. Although previous studies have provided important clues to cell-free viral capture by mature DCs (mDCs), dynamic and kinetic insight on this process is still missing. Here, we used three-dimensional video microscopy and single-particle tracking approaches to dynamically dissect both cell-free and cell-associated viral capture by living mDCs. We show that cell-free virus capture by mDCs operates through three sequential phases: virus binding through specific determinants expressed in the viral particle, polarized or directional movements toward concrete regions of the cell membrane and virus accumulation in a sac-like structure where trapped viral particles display a hindered diffusive behavior. Moreover, real-time imaging of cell-associated viral transfer to mDCs showed a similar dynamics to that exhibited by cell-free virus endocytosis leading to viral accumulation in compartments. However, cell-associated HIV type 1 transfer to mDCs was the most effective pathway, boosted throughout enhanced cellular contacts with infected CD4(+) T cells. Our results suggest that in lymphoid tissues, mDC viral uptake could occur either by encountering cell-free or cell-associated virus produced by infected cells generating the perfect scenario to promote HIV pathogenesis and impact disease progression.

  3. Mitochondrial dynamics and the cell cycle

    Directory of Open Access Journals (Sweden)

    Penny M.A. Kianian

    2014-05-01

    Full Text Available Nuclear-mitochondrial (NM communication impacts many aspects of plant development including vigor, sterility and viability. Dynamic changes in mitochondrial number, shape, size, and cellular location takes place during the cell cycle possibly impacting the process itself and leading to distribution of this organelle into daughter cells. The genes that underlie these changes are beginning to be identified in model plants such as Arabidopsis. In animals disruption of the drp1 gene, a homolog to the plant drp3A and drp3B, delays mitochondrial division. This mutation results in increased aneuploidy due to chromosome mis-segregation. It remains to be discovered if a similar outcome is observed in plants. Alloplasmic lines provide an opportunity to understand the communication between the cytoplasmic organelles and the nucleus. Examples of studies in these lines, especially from the extensive collection in wheat, point to the role of mitochondria in chromosome movement, pollen fertility and other aspects of development. Genes involved in NM interaction also are believed to play a critical role in evolution of species and interspecific cross incompatibilities.

  4. The reaction of the building structure with window unit to the explosiveimpact on the basis of dynamic equation solution

    Directory of Open Access Journals (Sweden)

    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.

  5. Analytic Solution of the Three-Variable Dynamical Equations of Oscillation Phenomena in B-Z Reaction

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The dynamical behaviour of the inorganic bromate oscillator catalyzed by manganese ions in the B-Z reaction is discussed, a three-variable nonlinear dynamical equations of the oscillation phenomena have been obtained, and an analytic solution and numerical results of the equations are given.

  6. Coupled effects of dehydration reaction, dilatant strengthening and shear heating on dynamic fault slip

    Science.gov (United States)

    Yamashita, T.

    2012-12-01

    It is believed that dynamic fault slip is affected by thermal pressurization. However, dilatant strengthening and dehydration reaction may significantly affect the degree of thermal pressurization. In addition, it is not clear how such effects influence the fault slip as a whole. We theoretically study how dilatant strengthening, frictional heating and dehydration reaction are coupled and how they affect dynamic slip assuming a fault in a thermoporoelastic medium saturated with fluid. After mathematical analysis is carried out for 1D model, the behavior of 2D fault model is studied numerically. The porosity is assumed to increase with increasing fault slip following Suzuki and Yamashita (2008). Our mathematical formulation of dehydration reaction is based on Brantut et al.(2010); the dehydration reaction is assumed to be endothermic. In addition, starting from the temperature Ts, all the frictional energy is assumed to be absorbed by the dehydration reaction rather than converted into heat. Although Brantut et al.(2010) assumed a constant slip velocity, we consider the temporal evolution of slip assuming the Coulomb law of friction on the fault. We first make the analysis assuming adiabatic and undrained conditions for the 1D model. We find that three nondimensional parameters Su, P0 and G0 determine the system behavior if the initial temperature T0 and dehydration starting temperature Ts are given, where Su (>0) is a parameter proportional to the pore creation rate, P0 (>0) is the initial nondimensional frictional stress and G0 (>0) is a parameter proportional to the mass fraction of fluid released per unit of total rock mass divided by the energy change per unit volume of the slip zone. The nondimensional frictional stress P is defined by the Coulomb frictional stress divided by the initial shear stress, which suggests the relation 0Ts, where Te is the temperature. We find for Te>Ts that the evolution of P is described by the equation dP/dT=(1-P)(Su-G0*P), where

  7. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, Benjamin Joel [Univ. of California, Berkeley, CA (United States)

    1992-11-01

    The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in ~240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH2I2 and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a ~350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.

  8. Body-Fitted Detonation Shock Dynamics and the Pseudo-Reaction-Zone Energy Release Model

    Science.gov (United States)

    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.

  9. Note: CO₂-mineral dissolution experiments using a rocking autoclave and a novel titanium reaction cell.

    Science.gov (United States)

    Purser, Gemma; Rochelle, Christopher A; Wallis, Humphrey C; Rosenqvist, Jörgen; Kilpatrick, Andrew D; Yardley, Bruce W D

    2014-08-01

    A novel titanium reaction cell has been constructed for the study of water-rock-CO2 reactions. The reaction cell has been used within a direct-sampling rocking autoclave and offers certain advantages over traditional "flexible gold/titanium cell" approaches. The main advantage is robustness, as flexible cells are prone to rupture on depressurisation during gas-rich experiments. The reaction cell was tested in experiments during an inter-laboratory comparison study, in which mineral kinetic data were determined. The cell performed well during experiments up to 130 °C and 300 bars pressure. The data obtained were similar to those of other laboratories participating in the study, and also to previously published data.

  10. Dynamic Monte Carlo simulation of the NO+H reaction on Pt(100): TPR spectra

    Science.gov (United States)

    Álvarez-Falcón, L.; Alas, S. J.; Vicente, L.

    2011-11-01

    The catalytic reduction of nitric oxide by hydrogen over a Pt surface is studied using a dynamic Monte Carlo (MC) method on a square lattice under low pressure conditions. Using a Langmuir-Hinshelwood reaction mechanism, a simplified model with only four adsorbed species (NO, H, O, and N) is constructed. The effect on the NO dissociation rate, the limiting step in the whole reaction, is inhibited by co-adsorbed NO and H 2 molecules and is enhanced both by the presence of empty sites and adsorbed N atoms at nearest neighbors. In these simulations, several experimental parameter values are included, such as: adsorption, desorption and diffusion of the reactants. The phenomenon is studied while varying the temperature over the 300-550 K range. The model reproduces well-observed TPD and TPR experimental results. For the whole NO+H 2 reaction, the phenomena of “surface explosion” is observed and can be explained as the result of the abrupt production of N 2 due to both the autocatalytic NO decomposition favored by the presence of vacant sites and the development of inhomogeneous fluctuations. MA simulations also allow a visualization of the spatial development of the surface explosion as heating proceeds.

  11. Site and bond-specific dynamics of reactions at the gas-liquid interface.

    Science.gov (United States)

    Tesa-Serrate, Maria A; King, Kerry L; Paterson, Grant; Costen, Matthew L; McKendrick, Kenneth G

    2014-01-01

    The dynamics of the interfacial reactions of O((3)P) with the hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene) have been studied experimentally. Laser-induced fluorescence (LIF) was used to detect the nascent gas-phase OH products. The O((3)P) atoms are acutely sensitive to the chemical differences of the squalane and squalene surfaces. The larger exothermicity of abstraction from allylic C-H sites in squalene is reflected in markedly hotter OH rotational and vibrational distributions. There is a more modest increase in translational energy release. A larger fraction of the available energy is deposited in the liquid for squalene than for squalane, consistent with a more extensive geometry change on formation of the allylic radical co-product. Although the dominant reaction mechanism is direct, impulsive scattering, there is some evidence for OH being accommodated at both liquid surfaces, resulting in thermalised translation and rotational distributions. Despite the H-abstraction reaction being strongly favoured energetically for squalene, the yield of OH is substantially lower than for squalane. This is very likely due to competitive addition of O((3)P) to the unsaturated sites in squalene, implying that double bonds are extensively exposed at the liquid surface.

  12. Dynamics of interfacial reactions between O(3 P) atoms and long-chain liquid hydrocarbons

    Science.gov (United States)

    Allan, Mhairi; Bagot, Paul A. J.; Köhler, Sven P. K.; Reed, Stewart K.; Westacott, Robin E.; Costen, Matthew L.; McKendrick, Kenneth G.

    2007-09-01

    Recent progress that has been made towards understanding the dynamics of collisions at the gas-liquid interface is summarized briefly. We describe in this context a promising new approach to the experimental study of gas-liquid interfacial reactions that we have introduced. This is based on laser-photolytic production of reactive gas-phase atoms above the liquid surface and laser-spectroscopic probing of the resulting nascent products. This technique is illustrated for reaction of O(3P) atoms at the surface of the long-chain liquid hydrocarbon squalane (2,6,10,15,19,23-hexamethyltetracosane). Laser-induced fluorescence detection of the nascent OH has revealed mechanistically diagnostic correlations between its internal and translational energy distributions. Vibrationally excited OH molecules are able to escape the surface. At least two contributions to the product rotational distributions are identified, confirming and extending previous hypotheses of the participation of both direct and trapping-desorption mechanisms. We speculate briefly on future experimental and theoretical developments that might be necessary to address the many currently unanswered mechanistic questions for this, and other, classes of gas-liquid interfacial reaction.

  13. N-dimensional switch function for energy conservation in multiprocess reaction dynamics.

    Science.gov (United States)

    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.

  14. Reaction dynamics of Cl + butanol isomers by crossed-beam sliced ion imaging.

    Science.gov (United States)

    Estillore, Armando D; Visger-Kiefer, Laura M; Suits, Arthur G

    2012-01-01

    Butanol is now prominent among the prototype renewable biofuels. We have studied oxidation of a variety of butanol isomers under single collision conditions using chlorine atom as the oxidizing agent to gain detailed insight into the energetics and dynamics of these reactions. The interaction of chlorine atom radicals with butanol isomers: n-butanol, iso-butanol, sec-butanol, and tert-butanol have been studied by crossed-beam dc slice ion imaging techniques. The hydroxybutyl radicals generated from the H-abstraction processes were probed by single photon ionization using an F2 excimer laser. After background subtraction and density-to-flux correction of the raw images, translational energy distribution and product angular distributions were generated. At low collision energy, the hydroxyalkyl products are backscattered with respect to the alcohol beam and the scattering shifts to the forward direction as the collision energy is increased. The translational energy distributions are reminiscent to that of Cl + pentane reactions we studied earlier, i.e. a sharp forward peak -80% of the collision energy appears at the high collision energy. Isomer-specific details of the reactions will be discussed.

  15. Towards a nonequilibrium Green's function description of nuclear reactions: one-dimensional mean-field dynamics

    CERN Document Server

    Rios, Arnau; Buchler, Mark; Danielewicz, Pawel

    2010-01-01

    Nonequilibrium Green's function methods allow for an intrinsically consistent description of the evolution of quantal many-body body systems, with inclusion of different types of correlations. In this paper, we focus on the practical developments needed to build a Green's function methodology for nuclear reactions. We start out by considering symmetric collisions of slabs in one dimension within the mean-field approximation. We concentrate on two issues of importance for actual reaction simulations. First, the preparation of the initial state within the same methodology as for the reaction dynamics is demonstrated by an adiabatic switching on of the mean-field interaction, which leads to the mean-field ground state. Second, the importance of the Green's function matrix-elements far away from the spatial diagonal is analyzed by a suitable suppression process that does not significantly affect the evolution of the elements close to the diagonal. The relative lack of importance of the far-away elements is tied t...

  16. Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data

    Directory of Open Access Journals (Sweden)

    Kansuporn eSriyudthsak

    2016-05-01

    Full Text Available The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.

  17. The type of seeder cells determines the efficiency of germinal center reactions

    CERN Document Server

    Meyer-Hermann, M; Meyer-Hermann, Michael; Beyer, Tilo

    2002-01-01

    We discuss the origin of two classes of germinal centers that have been observed during humoral immune responses: Some germinal centers develop very well and give rise to a large number of high affinity antibody producing plasma cells. Other germinal center reaction are very weak and the output production is practically absent. We propose an explanation for this nearly all-or-none behavior of germinal center reactions: The affinity of the seeder B-cells to the antigen is the critical parameter that determines the fate of the germinal center reaction. This hypothesis is verified in the framework of a space-time simulation of germinal center reactions.

  18. Chemical reaction dynamics of PeCB and TCDD decomposition: A tight-binding quantum chemical molecular dynamics study with first-principles parameterization

    Science.gov (United States)

    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.

  19. Dynamical Cluster-decay Model (DCM) applied to 9Li+208Pb reaction

    Science.gov (United States)

    Kaur, Arshdeep; Hemdeep; Kaushal, Pooja; Behera, Bivash R.; Gupta, Raj K.

    2017-10-01

    The decay mechanism of 217At* formed in 9Li+208Pb reaction is studied within the dynamical cluster-decay model (DCM) at various center-of-mass energies. The aim is to see the behavior of a light neutron-rich radioactive beam on a doubly-magic target nucleus for the (total) fusion cross section σfus and the individual decay channel cross sections. Experimentally, only the isotopic yield of heavy mass residues 211-214At * [equivalently, the light-particles (LPs) evaporation residue cross sections σxn for x = 3- 6 neutrons emission] are measured, with the fusion-fission (ff) component σff taken zero. For a fixed neck-length parameter ΔR, the only parameter in the DCM, we are able to fit σfus =∑x=16σxn almost exactly for 9Li on 208Pb at all E c . m .'s. However, the observed individual decay channels (3n-6n) are very poorly fitted, with unobserved channels (1n, 2n) and σff strongly over-estimated. Different ΔR values, meaning thereby different reaction time scales, are required to fit individually both the observed and unobserved evaporation residue channels (1n-6n) and σff, but then the compound nucleus (CN) contribution σCN is very small (< 1%), and the non-compound nucleus (nCN) decay cross section σnCN contributes the most towards total σfus (=σCN +σnCN). Thus, the 9Li induced reaction on doubly-magic 208Pb is more of a quasi-fission-like nCN decay, which is further analyzed in terms of the statistical CN formation probability PCN and CN survival probability Psurv. For the reaction under study, PCN < < 1 and Psurv → 1, in particular at above barrier energies.

  20. Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering

    CERN Document Server

    Drescher, Knut; Cisneros, Luis H; Ganguly, Sujoy; Goldstein, Raymond E; 10.1073/pnas.1019079108

    2011-01-01

    Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli both far from and near to a solid surface. These experiments allowed us to examine the relative importance of fluid dynamics and rotational diffusion for bacteria. For cell-cell interactions it is shown that thermal and intrinsic stochasticity drown the effects of long-range fluid dynamics, implying that physical interactions between bacteria are determined by steric collisions and near-field lubrication forces. This dom...

  1. Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

    Energy Technology Data Exchange (ETDEWEB)

    Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.

    2015-07-07

    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 DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

  2. Ultrafast infrared studies of chemical reaction dynamics in room-temperature liquids

    Energy Technology Data Exchange (ETDEWEB)

    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 η3-Tp*Rh(CO), silane Si–H bond activation by η5-CpMn(CO)2 and η5-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 HSiR3 (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

  3. Discharging dynamics in an electrolytic cell

    Science.gov (United States)

    Feicht, Sarah E.; Frankel, Alexandra E.; Khair, Aditya S.

    2016-07-01

    We analyze the dynamics of a discharging electrolytic cell comprised of a binary symmetric electrolyte between two planar, parallel blocking electrodes. When a voltage is initially applied, ions in the electrolyte migrate towards the electrodes, forming electrical double layers. After the system reaches steady state and the external current decays to zero, the applied voltage is switched off and the cell discharges, with the ions eventually returning to a uniform spatial concentration. At voltages on the order of the thermal voltage VT=kBT /q ≃25 mV, where kB is Boltzmann's constant, T is temperature, and q is the charge of a proton, experiments on surfactant-doped nonpolar fluids observe that the temporal evolution of the external current during charging and discharging is not symmetric [V. Novotny and M. A. Hopper, J. Electrochem. Soc. 126, 925 (1979), 10.1149/1.2129195; P. Kornilovitch and Y. Jeon, J. Appl. Phys. 109, 064509 (2011), 10.1063/1.3554445]. In fact, at sufficiently large voltages (several VT), the current during discharging is no longer monotonic: it displays a "reverse peak" before decaying in magnitude to zero. We analyze the dynamics of discharging by solving the Poisson-Nernst-Planck equations governing ion transport via asymptotic and numerical techniques in three regimes. First, in the "linear regime" when the applied voltage V is formally much less than VT, the charging and discharging currents are antisymmetric in time; however, the potential and charge density profiles during charging and discharging are asymmetric. The current evolution is on the R C timescale of the cell, λDL /D , where L is the width of the cell, D is the diffusivity of ions, and λD is the Debye length. Second, in the (experimentally relevant) thin-double-layer limit ɛ =λD/L ≪1 , there is a "weakly nonlinear" regime defined by VT≲V ≲VTln(1 /ɛ ) , where the bulk salt concentration is uniform; thus the R C timescale of the evolution of the current magnitude

  4. Kinetics and thermodynamics of chemical reactions in Li/SOCl2 cells

    Science.gov (United States)

    Hansen, Lee D.; Frank, Harvey

    1987-01-01

    Work is described that was designed to determine the kinetic constants necessary to extrapolate kinetic data on Li/SOCl2 cells over the temperature range from 25 to 75 C. A second objective was to characterize as far as possible the chemical reactions that occur in the cells since these reactions may be important in understanding the potential hazards of these cells. The kinetics of the corrosion processes in undischarged Li/SOCl2 cells were determined and separated according to their occurrence at the anode and cathode; the effects that switching the current on and off has on the corrosion reactions was determined; and the effects of discharge state on the kinetics of the corrosion process were found. A thermodynamic analysis of the current-producing reactions in the cell was done and is included.

  5. Kinetics and thermodynamics of chemical reactions in Li/SOCl2 cells

    Science.gov (United States)

    Hansen, Lee D.; Frank, Harvey

    1987-01-01

    Work is described that was designed to determine the kinetic constants necessary to extrapolate kinetic data on Li/SOCl2 cells over the temperature range from 25 to 75 C. A second objective was to characterize as far as possible the chemical reactions that occur in the cells since these reactions may be important in understanding the potential hazards of these cells. The kinetics of the corrosion processes in undischarged Li/SOCl2 cells were determined and separated according to their occurrence at the anode and cathode; the effects that switching the current on and off has on the corrosion reactions was determined; and the effects of discharge state on the kinetics of the corrosion process were found. A thermodynamic analysis of the current-producing reactions in the cell was done and is included.

  6. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  7. Hysteresis in the solid oxide fuel cell cathode reaction

    DEFF Research Database (Denmark)

    Jacobsen, Torben; Zachau-Christiansen, Birgit; Bay, Lasse

    2001-01-01

    The oxygen electrode reaction at the Pt/yttria-stabilised zirconia (YSZ) interface is investigated at 1000degreesC on Pt point electrodes on YSZ and YSZ point contacts on Pt. Linear potential sweeps show a pronounced non-linear current-voltage relation and inductive hysteresis, in particular at l...

  8. Dynamic behaviour of human neuroepithelial cells in the developing forebrain

    Science.gov (United States)

    Subramanian, Lakshmi; Bershteyn, Marina; Paredes, Mercedes F.; Kriegstein, Arnold R.

    2017-01-01

    To understand how diverse progenitor cells contribute to human neocortex development, we examined forebrain progenitor behaviour using timelapse imaging. Here we find that cell cycle dynamics of human neuroepithelial (NE) cells differ from radial glial (RG) cells in both primary tissue and in stem cell-derived organoids. NE cells undergoing proliferative, symmetric divisions retract their basal processes, and both daughter cells regrow a new process following cytokinesis. The mitotic retraction of the basal process is recapitulated by NE cells in cerebral organoids generated from human-induced pluripotent stem cells. In contrast, RG cells undergoing vertical cleavage retain their basal fibres throughout mitosis, both in primary tissue and in older organoids. Our findings highlight developmentally regulated changes in mitotic behaviour that may relate to the role of RG cells to provide a stable scaffold for neuronal migration, and suggest that the transition in mitotic dynamics can be studied in organoid models. PMID:28139695

  9. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

    Science.gov (United States)

    Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

    2015-07-01

    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 and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

  10. The Lower Extremities Exoskeleton Actuator Dynamics Research Taking into Account Support Reaction

    Directory of Open Access Journals (Sweden)

    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

  11. Numerical simulation of a direct internal reforming solid oxide fuel cell using computational fluid dynamics methodas

    Institute of Scientific and Technical Information of China (English)

    Jun LI; Ying-wei KANG; Guang-yi CAO; Xin-jian ZHU; Heng-yong TU; Jian LI

    2008-01-01

    A detailed mathematical model of a direct internal reforming solid oxide fuel cell (DIR-SOFC) incorporating with simulation of chemical and physical processes in the fuel cell is presented. The model is developed based on the reforming and electrochemical reaction mechanisms, mass and energy conservation, and heat transfer. A computational fluid dynamics (CFD) method is used for solving the complicated multiple partial differential equations (PDEs) to obtain the numerical approximations.The resulting distributions of chemical species concentrations, temperature and current density in a cross-flow DIR-SOFC are given and analyzed in detail. Further, the influence between distributions of chemical species concentrations, temperature and current density during the simulation is illustrated and discussed. The heat and mass transfer, and the kinetics of reforming and electrochemical reactions have significant effects on the parameter distributions within the cell. The results show the particularchar acteristics of the DIR-SOFC among fuel cells, and can aid in stack design and control.

  12. STUDY OF THE REACTION DYNAMICS OF Li + HF, HCl BY THE CROSSED MOLECULAR BEAMS METHOD

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Christopher H.; Casavecchia, Piergiorgio; Tiedemann, Peter W.; Valentini, James J.; Lee, Yuan T.

    1980-05-01

    }) are evaluated by integrating the product distributions in the c.m. frame and using small angle nonreactive scattering of Li as an absolute calibrant. Values of {sigma}{sub R} are: for LiF formation {sigma}{sub R} ~ 0.8 {Angstrom}{sup 2} and 0.94 {Angstrom}{sup 2} at E{sub c} = 3 and 8.7 kcal/mole, while for LiCl formation {sigma}{sub R} = 27 {Angstrom}{sup 2} and 42 {Angstrom}{sup 2} at E{sub c} = 2.9 and 9.2 kcal/mole, with estimated absolute and relative uncertainties of a factor of 2, and 30%, respectively. Average opacities for reaction have been estimated from the reaction cross sections and the extent of rotational excitation of products to be about 0.1 for reaction (I) and 1 for reaction (II), for L values allowed to react. These results are discussed in some detail with regard to the kinematic constraints, reaction dynamics and potential energy surfaces for these two reactions, and related experimental and theoretical work are noted. In addition, angular distributions of nonreactive scattering of Li off HF and HCl are measured at 4 different E{sub c} each. Rainbow structure is observed at low E{sub c} and the angular distributions are fit by a spherically symmetric piecewise analytic potential. The resulting values of the potential's well depth ({epsilon}) and minimum position (r{sub m} ) are: for Li + HF {epsilon} = 0.46 kcal/mole and r{sub m} = 4.34 {Angstrom} and for Li + HCl {epsilon} = 0.32 kcal/mole and r{sub m} = 4.7 {Angstrom}. These results differ significantly from some earlier estimates based on the measurements of integral scattering cross sections.

  13. Dynamic reaction design of enzymic biotransformations in organic media: equilibrium-controlled synthesis of antibiotics by penicillin G acylase.

    Science.gov (United States)

    Fernandez-Lafuente, R; Rosell, C M; Guisan, J M

    1996-10-01

    Parameters relevant to the thermodynamically controlled synthesis of cephalothin utilizing highly active stabilized penicillin G acylase derivatives were studied. These included solubility/stability of substrates, enzyme derivative activity/stability, reaction course and synthetic yields. These parameters were altered by varying the pH, dimethylformamide concentration and temperature. Simultaneous optimization of the selected parameters could not be achieved with a single set of conditions. However, continuous adjustment of conditions throughout the reaction course allowed each parameter to be optimized (dynamic reaction design). This strategy works by optimizing those parameters that are critical to the overall reaction at a given point, whilst leaving others sub-optimal when their contribution to the total is minimal. This strategy has achieved a 90% transformation of antibiotic nucleus to cephalothin at a final concentration of 20 g/l, high enzyme and reactant stability, with a reaction period of 3 h (using 1 ml of derivative/40 ml of reaction solution).

  14. Stochastic dynamics of complexation reaction in the limit of small numbers.

    Science.gov (United States)

    Ghosh, Kingshuk

    2011-05-21

    We study stochastic dynamics of the non-linear bimolecular reaction A + B↔AB. These reactions are common in several bio-molecular systems such as binding, complexation, protein multimerization to name a few. We use master equation to compute the full distribution of several stochastic equilibrium properties such as number of complexes formed (N(c)), equilibrium constant (K). We provide exact analytical and simpler approximate expression for equilibrium fluctuation quantities to quickly estimate the amount of noise as a function of reactant molecules and rates. We construct the phase diagram for a fluctuational quantity f, defined as the ratio of standard deviation to average (f=√(ΔN(c))(2)/N(c)), as a function of different number of reactant molecules and reaction rates. One of the striking result is, it is possible to have f as high as 45% or higher in significant regions of the phase diagram even when number of reactants involved are around 20-40, typical in biology. Our finding indicates studying averages alone using mass action law needs careful scrutiny. We also outline possible application of our findings in gene expression. Furthermore, we compute average and fluctuation properties of time dependent quantities and derive equations of motion for different moments such as N(c)(t) and N(c)(t)(2). While mean-field mass action law fails to reproduce the exact time dependence, approximate solutions of coupled equations of motions for different moments, capturing fluctuation, is in good agreement with exact results. This may be a way to compute time development of averages and fluctuations in such non-linear systems where mass action law breaks down. Moreover, for this reaction, we outline connection to variational principle of maximum caliber and other more traditional approaches such as chemical Langevin equation. We derive noise statistics for the equivalent Langevin equation and show possible departure from Gaussian white noise. We believe quantitative

  15. Designer cells for stereocomplementary de novo enzymatic cascade reactions based on laboratory evolution.

    Science.gov (United States)

    Agudo, Rubén; Reetz, Manfred T

    2013-12-04

    Designer cells for a synthetic cascade reaction harnessing selective redox reactions were devised, featuring two successive regioselective P450-catalyzed CH-activating oxidations of 1-cyclohexene carboxylic acid methyl ester followed by stereoselective olefin-reduction catalysed by (R)- or (S)-selective mutants of an enoate reductase.

  16. Benchmarking Pt-based electrocatalysts for low temperature fuel cell reactions with the rotating disk electrode

    DEFF Research Database (Denmark)

    Pedersen, Christoffer Mølleskov; Escribano, Maria Escudero; Velazquez-Palenzuela, Amado Andres

    2015-01-01

    We present up-to-date benchmarking methods for testing electrocatalysts for polymer exchange membrane fuel cells (PEMFC), using the rotating disk electrode (RDE) method. We focus on the oxygen reduction reaction (ORR) and the hydrogen oxidation reaction (HOR) in the presence of CO. We have chosen...

  17. Dynamic Deuterium Enrichment in Cometary Water via Eley–Rideal Reactions

    Science.gov (United States)

    Yao, Yunxi; Giapis, Konstantinos P.

    2017-01-01

    The deuterium-to-hydrogen ratio (D/H) in water found in the coma of Jupiter family comet (JFC) 67P/Churyumov–Gerasimenko was reported to be (5.3 ± 0.7) × 10‑4, the highest among comets and three times the value for other JFCs with an ocean-like ratio. This discrepancy suggests the diverse origins of JFCs and clouds the issue of the origin of Earth’s oceanic water. Here we demonstrate that Eley–Rideal reactions between accelerated water ions and deuterated cometary surface analogs can lead to instantaneous deuterium enrichment in water scattered from the surface. The reaction proceeds with H2O+ abstracting adsorbed D atoms, forming an excited H2DO* state, which dissociates subsequently to produce energetic HDO. Hydronium ions are also produced readily by the abstraction of H atoms, consistent with H3O+ detection and abundance in various comets. Experiments with water isotopologs and kinematic analysis on deuterated platinum surfaces confirmed the dynamic abstraction mechanism. The instantaneous fractionation process is independent of the surface temperature and may operate on the surface of cometary nuclei or dust grains, composed of deuterium-rich silicates and carbonaceous chondrites. The requisite energetic water ions have been detected in the coma of 67P in two populations. This dynamic fractionation process may temporarily increase the water D/H ratio, especially as the comet gets closer to the Sun. The magnitude of the effect depends on the water ion energy-flux and the deuterium content of the exposed cometary surfaces.

  18. Hybrid direct carbon fuel cells and their reaction mechanisms - a review

    DEFF Research Database (Denmark)

    Deleebeeck, Lisa; Kammer Hansen, Kent

    2014-01-01

    with carbon capture and storage (CCS) due to the high purity of CO2 emitted in the exhaust gas. Direct carbon (or coal) fuel cells (DCFCs) are directly fed with solid carbon to the anode chamber. The fuel cell converts the carbon at the anode and the oxygen at the cathode into electricity, heat and reaction...... is discussed on the fuel cell stack and system levels. The range of DCFC types can be roughly broken down into four fuel cell types: aqueous hydroxide, molten hydroxide, molten carbonate and solid oxide fuel cells. Emphasis is placed on the electrochemical reactions occurring at the anode and the proposed...... mechanism(s) of these reactions for molten carbonate, solid oxide and hybrid direct carbon fuel cells. Additionally, the criteria of choosing the ‘best’ DCFC technology is explored, including system design (continuous supply of solid fuel), performance (power density, efficiency), environmental burden...

  19. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    Science.gov (United States)

    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.

  20. Dynamical coupled-channel model of meson production reactions in the nucleon resonance region

    CERN Document Server

    Matsuyama, A; Sato, T

    2006-01-01

    A dynamical coupled-channel model is presented for investigating the nucleon resonances in the meson production reactions induced by pions and photons. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method. By applying the projection operator techniques,we derive a set of coupled-channel equations which satisfy the unitarity conditions within the channel space spanned by the considered two-particle meson-baryon states and the three-particle $\\pi\\pi N$ state. We present and explain in detail a numerical method based on a spline-function expansion for solving the resulting coupled-channel equations which contain logarithmically divergent one-particle-exchange driving terms resulted from the $\\pi\\pi N$ unitarity cut. We show that this driving term can generate rapidly varying structure in the reaction amplitudes associated with the unstable particle channels. It also has large effects in determining the two-pion production cros...

  1. Dynamical coupled-channels study of pi N --> pi pi N reactions

    CERN Document Server

    Kamano, H; Lee, T -S H; Matsuyama, A; Sato, T

    2008-01-01

    As a step toward performing a complete coupled-channels analysis of the world data of pi N, gamma^* N --> pi N, eta N, pi pi N reactions, the pi N --> pi pi N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C76, 065201 (2007). The channels included are pi N, eta N, and pi pi N which has pi Delta, rho N, and sigma N resonant components. The non-resonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16 bare excited nucleon (N^*) states which are dressed by the non-resonant interactions as constrained by the unitarity condition. The available total cross section data of pi^+ p --> pi^+ pi^+ n, pi^+ pi^0p and pi^- p --> pi^+ pi^- n, pi^- pi^0 n, pi^0 pi^0 n can be reproduced to a very large extent both in magnitudes and energy-dependence. Possible improvements of the model are investigated, in particular on the role of the n...

  2. Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.

    Science.gov (United States)

    Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi

    2014-04-11

    Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming

  3. Characterization and Dynamics of Substituted Ruthenacyclobutanes Relevant to the Olefin Cross-Metathesis Reaction

    Science.gov (United States)

    Blake, Garrett; VanderVelde, David G.; Grubbs, Robert H.

    2011-01-01

    The reaction of the phosphonium alkylidene [(H2IMes)RuCl2=CHP(Cy)3)]+ BF4– with propene, 1-butene, and 1-hexene at –45 °C affords various substituted, metathesis-active ruthenacycles. These metallacycles were found to equilibrate over extended reaction times in response to decreases in ethylene concentrations, which favored increased populations of α-monosubstituted and α,α’-disubstituted (both cis and trans) ruthenacycles. On an NMR timescale, rapid chemical exchange was found to preferentially occur between the β-hydrogens of the cis and trans stereoisomers prior to olefin exchange. Exchange on an NMR timescale was also observed between the α- and β-methylene groups of the monosubstituted ruthenacycle (H2IMes)Cl2Ru(CHRCH2CH2) (R = CH3, CH2CH3, (CH2)3CH3). EXSY NMR experiments at –87 °C were used to determine the activation energies for both of these exchange processes. In addition, new methods have been developed for the direct preparation of metathesis-active ruthenacyclobutanes via the protonolysis of dichloro(1,3-bis(2,4,6-trimethylphenyl)-2-imidazolidinylidene)(benzylidene) bis(pyridine)ruthenium(II) and its 3-bromopyridine analog. Using either trifluoroacetic acid or silica-bound toluenesulfonic acid as the proton source, the ethylene-derived ruthenacyclobutane (H2IMes)Cl2Ru(CH2CH2CH2) was observed in up to 98% yield via NMR at –40 °C. On the basis of these studies, mechanisms accounting for the positional and stereochemical exchange within ruthenacyclobutanes are proposed, as well as the implications of these dynamics towards olefin metathesis catalyst and reaction design are described. PMID:21452876

  4. Analysis of dynamical behavior of reactions associated with 118,120,122Xe* isotopes

    Science.gov (United States)

    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.

  5. Diverse spatio-temporal dynamical patterns of p53 and cell fate decisions

    Science.gov (United States)

    Clairambault, Jean; Eliaš, Ján

    2016-06-01

    The protein p53 as a tumour suppressor protein accumulates in cells in response to DNA damage and transactivates a large variety of genes involved in apoptosis, cell cycle regulation and numerous other processes. Recent biological observations suggest that specific spatio-temporal dynamical patterns of p53 may be associated with specific cellular response, and thus the spatio-temporal heterogeneity of the p53 dynamics contributes to the overall complexity of p53 signalling. Reaction-diffusion equations taking into account spatial representation of the cell and motion of the species inside the cell can be used to model p53 protein network and could be thus of some help to biologists and pharmacologists in anticancer treatment.

  6. Nonequilibrium population dynamics of phenotype conversion of cancer cells.

    Directory of Open Access Journals (Sweden)

    Joseph Xu Zhou

    Full Text Available Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant. We derived the condition that different cancer cell types can maintain distinctive subpopulations and we also explain why there always exists a stable fixed ratio after cell sorting based on putative surface markers. The cell fraction ratio can be shifted by changing either the growth rates of the subpopulations (Darwinism selection or by environment-instructed transitions (Lamarckism induction. This insight can help us to understand the dynamics of the heterogeneity of cancer cells and lead us to new strategies to overcome cancer drug resistance.

  7. A case of delayed hemolytic transfusion reaction in sickle cell disease patient

    Science.gov (United States)

    Dogra, Ashu; Sidhu, Meena

    2016-01-01

    Sickle cell disease (SCD) is autosomal recessive, genetically transmitted hemoglobinopathy responsible for considerable morbidity and mortality. It is prevalent in many parts of India including Central India, where the prevalence in different communities has ranged from 9.4% to 22%. Perioperative management may include transfusion of red blood cells. Hemolytic transfusion reactions can occur, and these can be either acute or delayed. We present a case of delayed hemolytic transfusion reaction in a patient with SCD. PMID:27605854

  8. Complementarity between Quantum and Classical Mechanics in Chemical Modeling. The H + HeH+ → H2 + + He Reaction: A Rigourous Test for Reaction Dynamics Methods.

    Science.gov (United States)

    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+.

  9. Cell mechanics and stress: from molecular details to the 'universal cell reaction' and hormesis.

    Science.gov (United States)

    Agutter, Paul S

    2007-04-01

    The 'universal cell reaction' (UCR), a coordinated biphasic response to external (noxious and other) stimuli observed in all living cells, was described by Nasonov and his colleagues in the mid-20th century. This work has received no attention from cell biologists in the West, but the UCR merits serious consideration. Although it is non-specific, it is likely to be underpinned by precise mechanisms and, if these mechanisms were characterized and their relationship to the UCR elucidated, then our understanding of the integration of cellular function could be improved. As a step towards identifying such mechanisms, I review some recent advances in understanding cell mechanics and the stress response and I suggest potentially testable hypotheses. There is a particular need for time-course studies of cellular responses to different stimulus doses or intensities. I also suggest a correspondence with hormesis; re-investigation of the UCR using modern biophysical and molecular-biological techniques might throw light on this much-discussed phenomenon.

  10. The unified equation for the evaluation of degenerated first-order reactions in dynamic electrophoresis.

    Science.gov (United States)

    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.

  11. Modeling of advection-diffusion-reaction processes using transport dissipative particle dynamics

    Science.gov (United States)

    Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

    2015-11-01

    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. In particular, the transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of Lagrangian particles. To validate the proposed tDPD model and the boundary conditions, three benchmark simulations of one-dimensional diffusion with different boundary conditions are performed, and the results show excellent agreement with the theoretical solutions. Also, two-dimensional simulations of ADR systems are performed and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, an application of tDPD to the spatio-temporal dynamics of blood coagulation involving twenty-five reacting species is performed to demonstrate the promising biological applications of the tDPD model. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.

  12. Initial dynamics of the Norrish Type I reaction in acetone: probing wave packet motion.

    Science.gov (United States)

    Brogaard, Rasmus Y; Sølling, Theis I; Møller, Klaus B

    2011-02-10

    The Norrish Type I reaction in the S(1) (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels toward the S(1) minimum in less than 30 fs and stays there for more than 100 picoseconds [Chem. Phys. Lett.2008, 461, 193]. In this work we present simulated TRMS and TRPES signals based on ab initio multiple spawning simulations of the dynamics during the first 200 fs after excitation, getting quite good agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S(1) minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics simulations in interpreting experimental results.

  13. Bifurcations of Normally Hyperbolic Invariant Manifolds and Consequences for Reaction Dynamics

    CERN Document Server

    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...

  14. A protein dynamics study of photosystem II: the effects of protein conformation on reaction center function.

    Science.gov (United States)

    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.

  15. Formations of Bacteria-like Textures by dynamic reactions in Meteorite and Syntheses

    Science.gov (United States)

    Miura, Y.

    2009-05-01

    1. Introduction Spherule texture can be formed in dynamic reaction during meteoritic impact in air. However, there are no reports on nano-bacteria-like (i.e. spherule-chained) textures with iron (and Nickel) oxides (with chlorine) in composition and micro-texture with 100nm order [1] in meteorite and synthetic experiment. The purpose of the present study is to elucidate spherule-chained texture with micro-texture of 100nm in order found in the Kuga iron meteorite, Iwakuni, Yamaguchi, Japan, and its first artificial synthesis in laboratory. 2. Two textures in the Kuga meteorite: The Kuga iron meteorite found in Kuga, Iwakuni, Yamaguchi, Japan reveals spherule-chained texture with Fe, Ni-rich composition with 10μm in size, where each spherule contained "long micro-texture in 100nm in size"[1,2]. The complex texture of flow and chained shapes can be found only in the fusion crust of the meteorite formed by quenched and random processes with vapor-melting process in air of the Earth. The FE-ASEM with EDX analyses by an in-situ observation indicate that the matrix of the spherule-chained texture with Fe, Ni, O-rich (with minor Cl) composition is carbon-rich composition formed by impact reactions in air. 3. Comparison with Martian meteorite Remnant of life in ocean can be found by mineralized fossil, which can be found in the Martian meteorite ALH84001 as bacteria-like chained texture of magnetite in composition (in 100nm order) around carbonate spherules [3]. Similarity of bacteria-like texture of the ALH84001 compared with the Kuga meteorites in this study are composition of Fe-rich, C-bearing, and chained texture of small size replaced by Fe and O-rich composition in air. Major difference of these textures is no carbonates minerals in the Kuga meteorite at dynamic reaction in air [1, 2, 3]. 4. First synthesis of bacteria- like akaganeite: A bacteria-like texture with Fe oxides (with minor chlorine as akaganeite-like compositions) is synthesized by chlorine and water

  16. Kinematic chain reactions on trunk and dynamic postural steadiness in subjects with recurrent low back pain.

    Science.gov (United States)

    Sung, Paul S; Maxwell, Michael J

    2017-07-05

    Although subjects with recurrent low back pain (LBP) demonstrate altered trunk control, the kinematic and kinetic responses of the trunk have not been carefully investigated. This study was conducted to compare the standing time, spine range of motion (ROM), and dynamic postural steadiness index (DPSI) based on visual condition between subjects with and without recurrent LBP during upright one leg standing. Sixty-three individuals participated in the study, including 34 control subjects and 29 subjects with recurrent LBP. The DPSI was a composite of the medio-lateral (MLSI), anterior-posterior (APSI), and vertical steadiness indices (VSI) on a force platform. The control group demonstrated longer standing time (s) during the eyes-open condition than the LBP group (26.82±6.03 vs. 19.87±9.36; t=2.96, p=0.01). Regarding spine ROM, visual condition was significantly different between groups (F=7.09, p=0.01) and demonstrated interactions with spine region and group (F=5.53, p=0.02). For the kinetic measures, there was a significant interaction between visual conditions and indices (F=25.30, p=0.001). In the LBP group, the DPSI was significantly correlated with the MLSI (r=0.59, p=0.002), APSI (r=0.44, p=0.03), and VSI (r=0.98, p=0.01) in the eyes-closed condition. Overall, the results of this study indicated that the LBP group decreased thorax and lumbar spine rotations during the eyes-closed condition. The LBP group also demonstrated positive correlations with the kinetic indices, enhancing dynamic postural steadiness in the eyes-closed condition in order to possibly avoid pain or further injury. This dynamic postural steadiness strategy is necessary to improve kinetic and kinematic chain reactions in the LBP group. This compensatory pattern supports the development of optimal postural correction strategies to prevent LBP recurrence and might represent a chain reaction to protect trunk control without visual input. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Desmosome dynamics in migrating epithelial cells requires the actin cytoskeleton

    Science.gov (United States)

    Roberts, Brett J.; Pashaj, Anjeza; Johnson, Keith R.; Wahl, James K.

    2011-01-01

    Re-modeling of epithelial tissues requires that the cells in the tissue rearrange their adhesive contacts in order to allow cells to migrate relative to neighboring cells. Desmosomes are prominent adhesive structures found in a variety of epithelial tissues that are believed to inhibit cell migration and invasion. Mechanisms regulating desmosome assembly and stability in migrating cells are largely unknown. In this study we established a cell culture model to examine the fate of desmosomal components during scratch wound migration. Desmosomes are rapidly assembled between epithelial cells at the lateral edges of migrating cells and structures are transported in a retrograde fashion while the structures become larger and mature. Desmosome assembly and dynamics in this system are dependent on the actin cytoskeleton prior to being associated with the keratin intermediate filament cytoskeleton. These studies extend our understanding of desmosome assembly and provide a system to examine desmosome assembly and dynamics during epithelial cell migration. PMID:21945137

  18. Multispectral fingerprinting for improved in vivo cell dynamics analysis

    Directory of Open Access Journals (Sweden)

    Cooper Cameron HJ

    2010-09-01

    Full Text Available Abstract Background Tracing cell dynamics in the embryo becomes tremendously difficult when cell trajectories cross in space and time and tissue density obscure individual cell borders. Here, we used the chick neural crest (NC as a model to test multicolor cell labeling and multispectral confocal imaging strategies to overcome these roadblocks. Results We found that multicolor nuclear cell labeling and multispectral imaging led to improved resolution of in vivo NC cell identification by providing a unique spectral identity for each cell. NC cell spectral identity allowed for more accurate cell tracking and was consistent during short term time-lapse imaging sessions. Computer model simulations predicted significantly better object counting for increasing cell densities in 3-color compared to 1-color nuclear cell labeling. To better resolve cell contacts, we show that a combination of 2-color membrane and 1-color nuclear cell labeling dramatically improved the semi-automated analysis of NC cell interactions, yet preserved the ability to track cell movements. We also found channel versus lambda scanning of multicolor labeled embryos significantly reduced the time and effort of image acquisition and analysis of large 3D volume data sets. Conclusions Our results reveal that multicolor cell labeling and multispectral imaging provide a cellular fingerprint that may uniquely determine a cell's position within the embryo. Together, these methods offer a spectral toolbox to resolve in vivo cell dynamics in unprecedented detail.

  19. Predicting rare events in chemical reactions: Application to skin cell proliferation.

    Science.gov (United States)

    Lee, Chiu Fan

    2010-08-01

    In a well-stirred system undergoing chemical reactions, fluctuations in the reaction propensities are approximately captured by the corresponding chemical Langevin equation. Within this context, we discuss in this work how the Kramers escape theory can be used to predict rare events in chemical reactions. As an example, we apply our approach to a recently proposed model on cell proliferation with relevance to skin cancer [P. B. Warren, Phys. Rev. E 80, 030903 (2009)]. In particular, we provide an analytical explanation for the form of the exponential exponent observed in the onset rate of uncontrolled cell proliferation.

  20. Chemical reaction model of cathode failure in large prebaked anode aluminum reduction cells

    Institute of Scientific and Technical Information of China (English)

    赵群; 谢雁丽; 高炳亮; 邱竹贤; 赵无畏

    2002-01-01

    By partial and general dissection of large prebaked alumina electrolysis cells, the macro appearance, chemical composition and phase variations were studied employing actual observations and measurements on the cells together with X-ray diffraction phase analysis and scanning electron microscopy of samples from different locations. According to the practical production, a chemical reaction model of aluminum reduction cell failure was set up in order to reduce the incidence of cell failure and extend pot service life.

  1. The functional role of protein dynamics in photosynthetic reaction centers investigated by elastic and quasielastic neutron scattering

    Directory of Open Access Journals (Sweden)

    Pieper Jörg

    2015-01-01

    Full Text Available This short review summarizes our current knowledge about the functional relevance of protein dynamics in photosynthetic reaction centers. In the case of Photosystem II membrane fragments, elastic and quasielastic neutron scattering experiments reveal a dynamical transition at about 240 K corresponding to the activation of picosecond molecular motions. Likewise, a “freezing” of molecular dynamics is observed upon dehydration. Intriguingly, these effects correlate with the pronounced temperature- and hydration-dependence of specific electron transfer steps in Photosystem II indicating that molecular dynamics is an indispensable prerequisite for its function. Thus, electron transfer in Photosystem II appears to be a prototypical example for a dynamics-function correlation. Finally, the laser-neutron pump-probe technique is shown to permit in-situ monitoring of molecular dynamics in specific functional states of a protein in real time.

  2. Development and dynamics of cell polarity at a glance.

    Science.gov (United States)

    Campanale, Joseph P; Sun, Thomas Y; Montell, Denise J

    2017-04-01

    Cells exhibit morphological and molecular asymmetries that are broadly categorized as cell polarity. The cell polarity established in early embryos prefigures the macroscopic anatomical asymmetries characteristic of adult animals. For example, eggs and early embryos have polarized distributions of RNAs and proteins that generate global anterior/posterior and dorsal/ventral axes. The molecular programs that polarize embryos are subsequently reused in multiple contexts. Epithelial cells require apical/basal polarity to establish their barrier function. Migrating cells polarize in the direction of movement, creating distinct leading and trailing structures. Asymmetrically dividing stem cells partition different molecules between themselves and their daughter cells. Cell polarity can develop de novo, be maintained through rounds of cell division and be dynamically remodeled. In this Cell Science at a Glance review and poster, we describe molecular asymmetries that underlie cell polarity in several cellular contexts. We highlight multiple developmental systems that first establish cell/developmental polarity, and then maintain it. Our poster showcases repeated use of the Par, Scribble and Crumbs polarity complexes, which drive the development of cell polarity in many cell types and organisms. We then briefly discuss the diverse and dynamic changes in cell polarity that occur during cell migration, asymmetric cell division and in planar polarized tissues.

  3. Charge carrier dynamics in thin film solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Strothkaemper, Christian

    2013-06-24

    This work investigates the charge carrier dynamics in three different technological approaches within the class of thin film solar cells: radial heterojunctions, the dye solar cell, and microcrystalline CuInSe{sub 2}, focusing on charge transport and separation at the electrode, and the relaxation of photogenerated charge carriers due to recombination and energy dissipation to the phonon system. This work relies mostly on optical-pump terahertz-probe (OPTP) spectroscopy, followed by transient absorption (TA) and two-photon photoemission (2PPE). The charge separation in ZnO-electrode/In{sub 2}S{sub 3}-absorber core/shell nanorods, which represent a model system of a radial heterojunction, is analyzed by OPTP. It is concluded, that the dynamics in the absorber are determined by multiple trapping, which leads to a dispersive charge transport to the electrode that lasts over hundreds of picoseconds. The high trap density on the order of 10{sup 19}/cm{sup 3} is detrimental for the injection yield, which exhibits a decrease with increasing shell thickness. The heterogeneous electron transfer from a series of model dyes into ZnO proceeds on a time-scale of 200 fs. However, the photoconductivity builds up just on a 2-10 ps timescale, and 2PPE reveals that injected electrons are meanwhile localized spatially and energetically at the interface. It is concluded that the injection proceeds through adsorbate induced interface states. This is an important result because the back reaction from long lived interface states can be expected to be much faster than from bulk states. While the charge transport in stoichiometric CuInSe{sub 2} thin films is indicative of free charge carriers, CuInSe{sub 2} with a solar cell grade composition (Cu-poor) exhibits signs of carrier localization. This detrimental effect is attributed to a high density of charged defects and a high degree of compensation, which together create a spatially fluctuating potential that inhibits charge transport. On

  4. Development of a reaction cell for in-situ/operando studies of surface of a catalyst under a reaction condition and during catalysis.

    Science.gov (United States)

    Nguyen, Luan; Tao, Franklin Feng

    2016-06-01

    Tracking surface chemistry of a catalyst during catalysis is significant for fundamental understanding of catalytic performance of the catalyst since it allows for establishing an intrinsic correlation between surface chemistry of a catalyst at its working status and its corresponding catalytic performance. Ambient pressure X-ray photoelectron spectroscopy can be used for in-situ studies of surfaces of different materials or devices in a gas. To simulate the gaseous environment of a catalyst in a fixed-bed a flowing gaseous environment of reactants around the catalyst is necessary. Here, we report the development of a new flowing reaction cell for simulating in-situ study of a catalyst surface under a reaction condition in gas of one reactant or during catalysis in a mixture of reactants of a catalytic reaction. The homemade reaction cell is installed in a high vacuum (HV) or ultrahigh vacuum (UHV) environment of a chamber. The flowing gas in the reaction cell is separated from the HV or UHV environment through well sealings at three interfaces between the reaction cell and X-ray window, sample door and aperture of front cone of an energy analyzer. Catalyst in the cell is heated through infrared laser beam introduced through a fiber optics interfaced with the reaction cell through a homemade feedthrough. The highly localized heating on the sample holder and Au-passivated internal surface of the reaction cell effectively minimizes any unwanted reactions potentially catalyzed by the reaction cell. The incorporated laser heating allows a fast heating and a high thermal stability of the sample at a high temperature. With this cell, a catalyst at 800 °C in a flowing gas can be tracked readily.

  5. Modeling and simulation of the dynamic behavior of portable proton exchange membrane fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Ziegler, C.

    2005-07-01

    In order to analyze the operational behavior, a mathematical model of planar self-breathing fuel cells is developed and validated in Chapter 3 of this thesis. The multicomponent transport of the species is considered as well as the couplings between the transport processes of heat, charge, and mass and the electrochemical reactions. Furthermore, to explain the oxygen mass transport limitation in the porous electrode of the cathode side an agglomerate model for the oxygen reduction reaction is developed. In Chapter 4 the important issue of liquid water generation and transport in PEMFCs is addressed. One of the major tasks when operating this type of fuel cell is avoiding the complete flooding of the PEMFC during operation. A one-dimensional and isothermal model is developed that is based on a coupled system of partial differential equations. The model contains a dynamic and two-phase description of the proton exchange membrane fuel cell. The mass transport in the gas phase and in the liquid phase is considered as well as the phase transition between liquid water and water vapor. The transport of charges and the electrochemical reactions are part of the model. Flooding effects that are caused by liquid water accumulation are described by this model. Moreover, the model contains a time-dependent description of the membrane that accounts for Schroeder's paradox. The model is applied to simulate cyclic voltammograms. Chapter 5 is focused on the dynamic investigation of PEMFC stacks. Understanding the dynamic behavior of fuel cell stacks is important for the operation and control of fuel cell stacks. Using the single cell model of Chapter 3 and the dynamic model of Chapter 4 as basis, a mathematical model of a PEMFC stack is developed. However, due to the complexity of a fuel cell stack, the spatial resolution and dynamic description of the liquid water transport are not accounted for. These restrictions allow for direct comparison between the solution variables of

  6. Exploring Neural Cell Dynamics with Digital Holographic Microscopy

    KAUST Repository

    Marquet, Pierre

    2013-04-21

    In this talk, I will present how digital holographic microscopy, as a powerful quantitative phase technique, can non-invasively measure cell dynamics and especially resolve local neuronal network activity through simultaneous multiple site optical recording.

  7. Protein dynamics in individual human cells: experiment and theory.

    Directory of Open Access Journals (Sweden)

    Ariel Aharon Cohen

    Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

  8. Dynamic 3D cell culture via a chemoselective photoactuated ligand.

    Science.gov (United States)

    Westcott, Nathan P; Luo, Wei; Goldstein, Jeffrey; Yousaf, Muhammad N

    2014-09-01

    A new strategy to create a dynamic scaffold for three-dimensional (3D) cell experiments based on a photo-activated cell adhesive peptide ligand is described. After polymerization, the inert matrix becomes cell adhesive by chemoselective modification through the conjugation of oxyamine-terminated ligands. Furthermore, spatial and temporal control of cell culture within the 3D matrix was achieved by the use of a biospecific photoprotected peptide and visualized by confocal microscopy.

  9. Dynamics of cell degradation. [nickel cadmium batteries

    Science.gov (United States)

    Mcdermott, P. P.

    1978-01-01

    The use of chemical and physical data as a supplement to linear regression models in the prediction of cell failure is discussed. Principal factors to be considered are the positive thickness and weight, and the negative thickness. A model for cell degradation and failure in accelerated life test cells is presented and predictions based on a teardown analysis are included.

  10. Proton-transfer reaction dynamics and energetics in calcification and decalcification.

    Science.gov (United States)

    Suwa, Ryota; Hatta, Masayuki; Ichikawa, Kazuhiko

    2014-10-13

    CaCO3 -saturated saline waters at pH values below 8.5 are characterized by two stationary equilibrium states: reversible chemical calcification/decalcification associated with acid dissociation, Ca(2+) +HCO3 (-) ⇌CaCO3 +H(+) ; and reversible static physical precipitation/dissolution, Ca(2+) +CO3 (2-) ⇌CaCO3 . The former reversible reaction was determined using a strong base and acid titration. The saturation state described by the pH/PCO2 -independent solubility product, [Ca(2+) ][CO3 (2-) ], may not be observed at pH below 8.5 because [Ca(2+) ][CO3 (2-) ]/([Ca(2+) ][HCO3 (-) ]) ≪1. Since proton transfer dynamics controls all reversible acid dissociation reactions in saline waters, the concentrations of calcium ion and dissolved inorganic carbon (DIC) were expressed as a function of dual variables, pH and PCO2 . The negative impact of ocean acidification on marine calcifying organisms was confirmed by applying the experimental culture data of each PCO2 /pH-dependent coral polyp skeleton weight (Wskel) to the proton transfer idea. The skeleton formation of each coral polyp was performed in microspaces beneath its aboral ectoderm. This resulted in a decalcification of 14 weight %, a normalized CaCO3 saturation state Λ of 1.3 at PCO2 ≈400 ppm and pH ≈8.0, and serious decalcification of 45 % and Λ 2.5 at PCO2 ≈1000 ppm and pH ≈7.8.

  11. Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches.

    Science.gov (United States)

    Schluttig, Jakob; Alamanova, Denitsa; Helms, Volkhard; Schwarz, Ulrich S

    2008-10-21

    We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric, and thermal forces. As three model systems with distinctly different properties we consider the pairs barnase:barstar, cytochrome c-cytochrome c peroxidase, and p53:MDM2. In each case, proteins are modeled either as spherical particles, as dipolar spheres, or as collection of several small beads with one dipole. Spherical reaction patches are placed on the model proteins according to the known experimental structures of the protein complexes. In the computer simulations, concentration is varied by changing box size. Encounter is defined as overlap of the reaction patches and the corresponding first passage times are recorded together with the number of unsuccessful contacts before encounter. We find that encounter frequency scales linearly with protein concentration, thus proving that our microscopic model results in a well-defined macroscopic encounter rate. The number of unsuccessful contacts before encounter decreases with increasing encounter rate and ranges from 20 to 9000. For all three models, encounter rates are obtained within one order of magnitude of the experimentally measured association rates. Electrostatic steering enhances association up to 50-fold. If diffusional encounter is dominant (p53:MDM2) or similarly important as electrostatic steering (barnase:barstar), then encounter rate decreases with decreasing patch radius. More detailed modeling of protein shapes decreases encounter rates by 5%-95%. Our study shows how generic principles of protein-protein association are modulated by molecular features of the systems under consideration. Moreover it allows us to assess different coarse-graining strategies for the future modeling of the dynamics of large protein complexes.

  12. Effect of the geometric phase on the dynamics of the hydrogen-exchange reaction.

    Science.gov (United States)

    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.

  13. Dynamic Influences of Non-Stationary Liquid Flows in Fluid Drives of Heavy Metallurgical Machines on System Dynamics and Reaction for Surroundings

    Directory of Open Access Journals (Sweden)

    Michalczyk J.

    2015-04-01

    Full Text Available The influence of liquids contained in hydraulic pipes of drives of heavy metallurgical machines, e.g. forging hammers and presses, on reduced mass and system dynamics and forces and moments of reaction for surroundings, was investigated in the paper.

  14. Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism.

    Science.gov (United States)

    Zhao, Zhiqiang; Zhang, Zhaojun; Liu, Shu; Zhang, Dong H

    2017-02-22

    Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.

  15. Adaptive and innate immune reactions regulating mast cell activation: from receptor-mediated signaling to responses

    DEFF Research Database (Denmark)

    Tkaczyk, Christine; Jensen, Bettina M; Iwaki, Shoko

    2006-01-01

    In this article, we have described studies that have demonstrated that mast cells can be activated as a consequence of adaptive and innate immune reactions and that these responses can be modified by ligands for other receptors expressed on the surface of mast cells. These various stimuli...

  16. Studies of solvent effects on reaction dynamics using ultrafast transient absorption spectroscopy

    Science.gov (United States)

    Harris, Don Ahmasi

    Ultrafast transient absorption spectroscopy was used to investigate the solvent dependent reaction dynamics of two prototypical chemical systems: (1) The ring-opening reaction of 1,3-cyclohexadiene, the isolated chromophore in Provitamin D, and (2) The photolysis of various Vitamin B12 cofactors. We investigated the influence of solvent polarity on the ground state conformational relaxation of 1,3,5-cis hexatriene subsequent to the ring opening of 1,3-cyclohexadiene in methanol and 1-propanol solvents. Comparisons to the conformational relaxation in alkane solvents studied earlier demonstrated a surprising influence of solvent polarity on single bond isomerization. Temperature dependent transient absorption measurements were performed on 1,3,5-cis hexatriene in cyclohexane and 1-propanol to determine the effect of solvent polarity on the activation energy barrier for ground state single bond isomerization. These measurements conclude that the polar solvent lowers the energy barrier for single bond isomerization allowing conformational relaxation to proceed faster in alcohol solvents compared to alkane solvents. With no perceived polar transition state for single bond isomerization, this result disagrees with the conventional view of solvation and differentiates the single bond isomerization dynamics of polyenes from alkanes. Transient absorption spectroscopy was also utilized to study the solvent effects in the photolysis of various B12 cofactors in different environments. We investigated the solvent dependent photolysis of adenosylcobalamin, methylcobalamin, and cyanocobalamin in water and ethylene glycol as a function of solvent temperature. In comparing the radical cage escape of adenosylcobalamin and cyanocobalamin, we determined a larger than expected hydrodynamic radii for the diffusing radicals in water compared to ethylene glycol, thus making necessary a revised perspective of solvent interaction with the diffusing radical. In addition, we investigated the

  17. Femtosecond Dynamics of Fundamental Reaction Processes in Liquids: Proton Transfer, Geminate Recombination, Isomerization and Vibrational Relaxation.

    Science.gov (United States)

    Schwartz, Benjamin Joel

    Femtosecond and picosecond transient absorption spectroscopy are used to probe several fundamental aspects of chemical reactivity in the condensed phase including proton transfer, germinate recombination, isomerization and vibrational relaxation. The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured for the first time, and the effects of external hydrogen-bonding interactions on the proton transfer are studied in detail. The proton transfer takes place in ~240 fsec in non-polar environments, but becomes faster than the instrumental resolution of 110 fsec in methanol solutions. A simple model is proposed to explain these results. The dynamics following photodissociation of CH _2I_2 and other small molecules provide the first direct observations of germinate recombination. The recombination of many different photodissociating species occurs on a ~350 fsec time scale. Results also show that recombination yields but not rates depend on the molecular details of the solvent environment and suggest that recombination kinetics are dominated by a single collision with the surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. The data show no simple correlation between the hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes. This strongly implies that the isomerization of these systems does not provide a suitable testing ground for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in the photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial

  18. Dynamics of dye release from nanocarriers of different types in model cell membranes and living cells

    Directory of Open Access Journals (Sweden)

    Tkacheva T. N.

    2014-07-01

    Full Text Available Aim. To study the dynamics of lipophilic content release from nanocarriers of different types, organic molecular ensembles and inorganic nanoparticles (NPs in vitro experiments. Methods. Two-channel ratiometric fluorescence detection method based on Forster Resonance Energy Transfer, fluorescent spectroscopy and micro-spectroscopy have been used. Results. It has been found that the profiles of lipophilic dyes release from organic nanocarriers (PC liposomes and SDS micelles and inorganic ones (GdYVO4:Eu3+ and CeO2 NPs are well fitted by the first-order reaction kinetics in both model cell membranes and living cells (rat hepatocytes. The dye release constants (K and half-lives (t1/2 were analyzed. Conclusions. GdYVO4:Eu3+ and CeO2 NPs have been shown to provide faster lipophilic content release in model cell membranes as compared to PC liposomes. Negatively charged or lipophilic compounds added into nanocarriers can decrease the rate of lipophilic dyes release. Specific interaction of GdYVO4:Eu3+ NPs with rat hepatocytes has been observed.

  19. Development of a new molecular dynamics method for tribochemical reaction and its application to formation dynamics of MoS 2 tribofilm

    Science.gov (United States)

    Morita, Yusuke; Onodera, Tasuku; Suzuki, Ai; Sahnoun, Riadh; Koyama, Michihisa; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A.; Shin-yoshi, Takatoshi; Nishino, Noriaki; Suzuki, Atsushi; Miyamoto, Akira

    2008-09-01

    Recently we have developed a novel molecular dynamics program NEW-RYUDO-CR, which can deal with chemical reactions. The developed method has been applied to the study of tribochemical reaction dynamics of MoS 2 tribofilm on iron surface. The initially amorphous MoS 2 layer self-organized its structure as result of the tribochemical reactions and formed layered MoS 2 tribofilm. The friction coefficient significantly decreased as the MoS 2 tribofilm was formed. Besides, sliding was observed between sulfur layers of MoS 2 tribofilms which occurred due to repulsive Coulombic interaction forces between sulfur atoms. This indicates that the formation of the layered MoS 2 tribofilm is important to achieve better lubrication properties.

  20. Dynamics of the gas-liquid interfacial reaction of O(1D) with a liquid hydrocarbon.

    Science.gov (United States)

    Waring, Carla; King, Kerry L; Costen, Matthew L; McKendrick, Kenneth G

    2011-06-30

    The dynamics of the gas-liquid interfacial reaction of the first electronically excited state of the oxygen atom, O((1)D), with the surface of a liquid hydrocarbon, squalane (C(30)H(62); 2,6,10,15,19,23-hexamethyltetracosane) has been studied experimentally. Translationally hot O((1)D) atoms were generated by 193 nm photolysis of a low pressure (nominally 1 mTorr) of N(2)O a short distance (mean = 6 mm) above a continually refreshed liquid squalane surface. Nascent OH (X(2)Π, v' = 0) reaction products were detected by laser-induced fluorescence (LIF) on the OH A(2)Σ(+)-X(2)Π (1,0) band at the same distance above the surface. The speed distribution of the recoiling OH was characterized by measuring the appearance profiles as a function of photolysis-probe delay for selected rotational levels, N'. The rotational (and, partially, fine-structure) state distributions were also measured by recording LIF excitation spectra at selected photolysis-probe delays. The OH v' = 0 rotational distribution is bimodal and can be empirically decomposed into near thermal (~300 K) and much hotter (~6000 K) Boltzmann-temperature components. There is a strong positive correlation between rotational excitation and translation energy. However, the colder rotational component still represents a significant fraction (~30%) of the fastest products, which have substantially superthermal speeds. We estimate an approximate upper limit of 3% for the quantum yield of OH per O((1)D) atom that collides with the surface. By comparison with established mechanisms for the corresponding reactions in the gas phase, we conclude that the rotationally and translationally hot products are formed via a nonstatistical insertion mechanism. The rotationally cold but translationally hot component is most likely produced by direct abstraction. Secondary collisions at the liquid surface of products of either of the previous two mechanisms are most likely responsible for the rotationally and translationally cold

  1. Mitochondrial dynamics and morphology in beta-cells.

    Science.gov (United States)

    Stiles, Linsey; Shirihai, Orian S

    2012-12-01

    Mitochondrial dynamics contribute to the regulation of mitochondrial shape as well as various mitochondrial functions and quality control. This is of particular interest in the beta-cell because of the key role mitochondria play in the regulation of beta-cell insulin secretion function. Moreover, mitochondrial dysfunction has been suggested to contribute to the development of Type 2 Diabetes. Genetic tools that shift the balance of mitochondrial fusion and fission result in alterations to beta-cell function and viability. Additionally, conditions that induce beta-cell dysfunction, such as exposure to a high nutrient environment, disrupt mitochondrial morphology and dynamics. While it has been shown that mitochondria display a fragmented morphology in islets of diabetic patients and animal models, the mechanism behind this is currently unknown. Here, we review the current literature on mitochondrial morphology and dynamics in the beta-cell as well as some of the unanswered question in this field.

  2. Cell shape dynamics: from waves to migration.

    Directory of Open Access Journals (Sweden)

    Meghan K Driscoll

    Full Text Available We observe and quantify wave-like characteristics of amoeboid migration. Using the amoeba Dictyostelium discoideum, a model system for the study of chemotaxis, we demonstrate that cell shape changes in a wave-like manner. Cells have regions of high boundary curvature that propagate from the leading edge toward the back, usually along alternating sides of the cell. Curvature waves are easily seen in cells that do not adhere to a surface, such as cells that are electrostatically repelled from surfaces or cells that extend over the edge of micro-fabricated cliffs. Without surface contact, curvature waves travel from the leading edge to the back of a cell at -35 µm/min. Non-adherent myosin II null cells do not exhibit these curvature waves. At the leading edge of adherent cells, curvature waves are associated with protrusive activity. Like regions of high curvature, protrusive activity travels along the boundary in a wave-like manner. Upon contact with a surface, the protrusions stop moving relative to the surface, and the boundary shape thus reflects the history of protrusive motion. The wave-like character of protrusions provides a plausible mechanism for the zig-zagging of pseudopods and for the ability of cells both to swim in viscous fluids and to navigate complex three dimensional topography.

  3. Coherent-states dynamics of the H + + HF reaction at ELab = 30 eV: A complete electron nuclear dynamics investigation

    Science.gov (United States)

    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.

  4. Analysis of free energy and entropy changes for half-cell reactions

    Science.gov (United States)

    Lampinen, Markku J.; Fomino, Marina

    1993-12-01

    A comprehensive study of different entropy scales used in chemical thermodynamics is presented, and a semi-absolute entropy scale is introduced, by which problems involving noncharged and charge species can be considered correctly and further, the heat generation of half-cell reactions can be calculated. In this context, the entropy of an electron in a metal is derived. The entropy changes for electrode reactions are calculated, and the heat distribution among the electrodes of the cell is solved. The correlation of the zeros of the energy scales for H2(g), H'(aq), and e(exp MIN) (vacuum) is studied, and the value of chemical potential of electron in metal and gas phase is derived. An estimation for the free-enthalpy changes for the half-cell reaction H2(g) yields 2H(exp PLU)(aq) + 2e(exp MIN) (Pt electrode) is presented. The Galvanic potential differences for half cells are calculated, and tables of Delta H, Delta S, and Delta H are presented. An example of the use of half-cell reaction entropies and free-energy changes for a fuel cell is presented. With this method we can establish how the total heat generated in the fuel cell is distributed between the cathode and the anode of the cell. This method gives new basic information on electrochemical cells, which can be applied to mathematical models of single electrodes. The physical meaning of Delta G for half-cell reactions is illustrated by Poynting's vector.

  5. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B.

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  6. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions.

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  7. The Reaction Dynamics of the Reactions Ba+CmH2m+1Br(m=1,2,3,4,5)

    Institute of Scientific and Technical Information of China (English)

    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.

  8. Self-propagating exothermic reaction analysis in Ti/Al reactive films using experiments and computational fluid dynamics simulation

    Science.gov (United States)

    Sen, Seema; Lake, Markus; Kroppen, Norman; Farber, Peter; Wilden, Johannes; Schaaf, Peter

    2017-02-01

    This study describes the self-propagating exothermic reaction in Ti/Al reactive multilayer foils by using experiments and computational fluid dynamics simulation. The Ti/Al foils with different molar ratios of 1Ti/1Al, 1Ti/2Al and 1Ti/3Al were fabricated by magnetron sputtering method. Microstructural characteristics of the unreacted and reacted foils were analyzed by using electronic and atomic force microscopes. After an electrical ignition, the influence of ignition potentials on reaction propagation has been experimentally investigated. The reaction front propagates with a velocity of minimum 0.68 ± 0.4 m/s and maximum 2.57 ± 0.6 m/s depending on the input ignition potentials and the chemical compositions. Here, the 1Ti/3Al reactive foil exhibits both steady state and unsteady wavelike reaction propagation. Moreover, the numerical computational fluid dynamics (CFD) simulation shows the time dependent temperature flow and atomic mixing in a nanoscale reaction zone. The CFD simulation also indicates the potentiality for simulating exothermic reaction in the nanoscale Ti/Al foil.

  9. Coriolis coupling effects in the dynamics of deep well reactions: application to the H(+) + D2 reaction.

    Science.gov (United States)

    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.

  10. Red light-induced redox reactions in cells observed with TEMPO.

    Science.gov (United States)

    Eichler, Maor; Lavi, Ronit; Friedmann, Harry; Shainberg, Asher; Lubart, Rachel

    2007-06-01

    The aim of this study was to determine the wavelength dependence of light-induced redox reactions in cells, particularly whether there is any contribution by red wavelengths. An additional aim was to assess the potential of 2,2,6,6-tetramethyl piperidine-N-oxyl (TEMPO) as a tool for measuring these redox reactions. Visible light has been shown to affect cells, and redox reactions, which have been detected previously using spin traps, have been proposed as a mechanism. However, there is little evidence that red light, which is used in most such experiments, is redox active in cells. Redox activity was observed by measuring the decay of the electron paramagnetic resonance signal of TEMPO that occurs in the presence of illuminated cells. Color filters were used to generate blue, green, and red light, and the decay resulting from these wavelengths was compared to the decay caused by white light. Shorter wavelengths have a considerably stronger effect than longer wavelengths, although red light has some effect. Creation of reactive oxygen species by red light was confirmed with the spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). Red light can induce redox reactions in illuminated cells. However, shorter wavelengths are more efficient in this regard. In addition, TEMPO was found to be a more sensitive probe than DMPO for detecting light-induced cellular redox reactions.

  11. Investigating the phase-dependent photochemical reaction dynamics of chlorine dioxide using resonance Raman spectroscopy

    Science.gov (United States)

    Hayes, Sophia C.; Wallace, Paul M.; Bolinger, Josh C.; Reid, Philip J.

    Recent progress in understanding the phase-dependent reactivity demonstrated by halooxides is outlined. Specifically, resonance Raman intensity analysis (RRIA) and time-resolved resonance Raman (TRRR) studies of chlorine dioxide (OClO) photochemistry in solution are presented. Using RRIA, it has been determined that the excited-state structural evolution that occurs along the asymmetric-stretch coordinate in the gas phase is restricted in solution. The absence of evolution along this coordinate results in the preservation of groundstate symmetry in the excited state. The role of symmetry in defining the reaction coordinate and the solvent-solute interactions responsible for modification of the excited-state potential energy surface are discussed. TRRR studies are presented which demonstrate that geminate recombination of the primary photoproducts resulting in the reformation of ground-state OClO is a central feature of OClO photochemistry in solution. These studies also demonstrate that a fraction of photoexcited OClO undergoes photoisomerization to form ClOO, with the ground-state thermal decomposition of this species resulting in Cl production on the subnanosecond timescale. Finally, time-resolved anti-Stokes experiments are presented which demonstrate that the OClO vibrational-relaxation dynamics are solvent dependent. The current picture of OClO photochemistry derived from these studies is discussed, and future directions for study are outlined.

  12. The unified equation for the evaluation of first order reactions in dynamic electrophoresis.

    Science.gov (United States)

    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.

  13. Fragment production in 16O + 80Br reaction within dynamical microscopic theory

    Indian Academy of Sciences (India)

    Rajeev K Puri; Jaivir Singh; Suneel Kumar

    2002-07-01

    We analyze the formation of fragments in O+Br reaction at different incident energies between / = 50 MeV and 200 MeV. This study is carried out within the quantum molecular dynamics (QMD) model coupled with recently advanced simulated annealing clusterization algorithm (SACA). For comparison, we also use the conventional minimum spanning tree (MST) method. Our detailed study shows that the SACA can detect the final stable fragment configuration as early as 60 fm/c which is marked by a dip in the heaviest fragment. On the other hand, the MST method needs several hundred fm/c to identify the final stable distribution. A comparison of the charge distribution with experimental data shows that the SACA is able to reproduce the data very nicely whereas (as reported earlier) the MST method fails to break the spectator matter into intermediate mass fragments. Furthermore, our results with SACA method indicate the onset of multi-fragmentation around 75 MeV/A which is again in good agreement with experimental findings.

  14. Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics.

    Science.gov (United States)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

    2014-03-14

    In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

  15. Fission dynamics of 240Cf* formed in 34,36S induced reactions

    Directory of Open Access Journals (Sweden)

    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.

  16. Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

    Directory of Open Access Journals (Sweden)

    Saera Hihara

    2012-12-01

    Full Text Available Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (∼50 nm movement/30 ms, which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information.

  17. A diabatic representation including both valence nonadiabatic interactions and spin-orbit effects for reaction dynamics.

    Science.gov (United States)

    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

  18. Fluids as Dynamic Templates for Cytoskeletal Proteins in Plant Cells

    CERN Document Server

    Lofthouse, J T

    2008-01-01

    The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external fibres observed during growth and tropic responses

  19. Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics

    CERN Document Server

    Qian, Hong

    2016-01-01

    We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume $V$, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesoscopic scale. We introduce notions such as open, driven chemical systems, entropy production, free energy dissipation, etc. Then in the macroscopic limit, we illustrate how two new "laws", in terms of a generalized free energy of the mesoscopic stochastic dynamics, emerge. Detailed balance and complex balance are two special classes of "simple" nonlinear kinetics. Phase transition is intrinsically related to multi-stability...

  20. Regulatory effects on the population dynamics and wave propagation in a cell lineage model.

    Science.gov (United States)

    Wang, Mao-Xiang; Ma, Yu-Qiang; Lai, Pik-Yin

    2016-03-21

    We consider the interplay of cell proliferation, cell differentiation (and de-differentiation), cell movement, and the effect of feedback regulations on the population and propagation dynamics of different cell types in a cell lineage model. Cells are assumed to secrete and respond to negative feedback molecules which act as a control on the cell lineage. The cell densities are described by coupled reaction-diffusion partial differential equations, and the propagating wave front solutions in one dimension are investigated analytically and by numerical solutions. In particular, wavefront propagation speeds are obtained analytically and verified by numerical solutions of the equations. The emphasis is on the effects of the feedback regulations on different stages in the cell lineage. It is found that when the progenitor cell is negatively regulated, the populations of the cell lineage are strongly down-regulated with the steady growth rate of the progenitor cell being driven to zero beyond a critical regulatory strength. An analytic expression for the critical regulation strength in terms of the model parameters is derived and verified by numerical solutions. On the other hand, if the inhibition is acting on the differentiated cells, the change in the population dynamics and wave propagation speed is small. In addition, it is found that only the propagating speed of the progenitor cells is affected by the regulation when the diffusion of the differentiated cells is large. In the presence of de-differentiation, the effect on down-regulating the progenitor population is weakened and there is no effect on the propagation speed due to regulation, suggesting that the effect of regulatory control is diminished by de-differentiation pathways.

  1. Material balance studies on animal cell metabolism using a stoichiometrically based reaction network.

    Science.gov (United States)

    Xie, L; Wang, D I

    1996-12-05

    A detailed reaction network of mammalian cell metabolism contains hundreds of enzymatic reactions. By grouping serial reactions into single overall reactions and separating overlapped pathways into independent reactions, the total number of reactions of the network is significantly reduced. This strategy of manipulating the reaction network avoids the manipulations of a large number of reactions otherwise needed to determine the reaction extents. A stoichiometric material balance model is developed based on the stoichiometry of the simplified reaction network. Closures of material balances on glucose and each of the 20 amino acids are achieved using experimental data from three controlled fed-batch and one-batch hybridoma cultures. Results show that the critical role of essential amino acids, except glutamine, is to provide precursors for protein synthesis. The catabolism of some of the essential amino acids, particularly isoleucine and leucine, is observed when an excess amount of these amino acids is available in the culture medium. It was found that the reduction of glutamine utilization (for reducing ammonia production) is accompanied by an increase in the uptake of nonessential amino acids (NAAs) from the culture medium. This suggests that NAAs are necessary even though they are not essential for cell growth. A glutamine balance shows that less than 20% of the glutamine nitrogen is utilized for essential roles, such as protein and nucleotide syntheses. A relatively constant percentage (about 45%) of the glutamine nitrogen is utilized for NAA biosynthesis, despite the fact that the absolute amount varies among the four experiments. As to the carbon skeleton of glutamine, a significant portion enters the tricarboxylic acid (TCA) cycle. A material balance on glucose shows that most of the glucose (81%) is converted into lactate when glucose is in excess. On the other hand, when glucose is limited, lactate production is considerably reduced, while a major portion

  2. Proton and charge transfer reactions dynamics of a hydroxyflavone derivative in a polar solvent and in a cyclodextrin nanocavity

    Energy Technology Data Exchange (ETDEWEB)

    Sanz, M.; Organero, J.A. [Departamento de Quimica Fisica, Seccion de Quimicas, Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III, S.N., 45071 Toledo (Spain); Douhal, A. [Departamento de Quimica Fisica, Seccion de Quimicas, Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, Avda. Carlos III, S.N., 45071 Toledo (Spain)], E-mail: Abderrazzak.douhal@uclm.es

    2007-09-25

    In this work, we report on the observation of ultrafast intramolecular charge- and proton-transfer reactions of 4'-dimethylaminoflavonol (DMAF) in N,N-dimethyl formamide and in {gamma}-cyclodextrin ({gamma}-CD) solution. Upon femtosecond excitation an intramolecular charge transfer (ICT) reaction takes place to produce an ICT structure in {approx}200 fs. This structure may undergo a proton transfer reaction to generate a zwitterionic (Z) form in 2-3 ps, or relaxes in its potential energy well, to later equilibrate with that of Z in hundreds of ps. Addition of {gamma}-CD does not significantly affect the fast dynamics of the formed anion. The fs-emission signals of the parent molecule, 3-hydroxyflavone, indicate that the dimethyl amino group in DMAF enhances the rate constant of intermolecular proton-transfer and intramolecular charge-transfer reactions.

  3. Fusion and quasifission dynamics in the reactions $^{48}$Ca+$^{249}$Bk and $^{50}$Ti+$^{249}$Bk using TDHF

    CERN Document Server

    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...

  4. Background defining during the imine formation reaction in FT-IR liquid cell

    Science.gov (United States)

    Namli, Hilmi; Turhan, Onur

    2006-05-01

    Imine formation is a very important chemical reaction because of its relevance to biological process. Therefore, it is crucial to follow whole reaction process in detail. The current work performed to monitor the whole imination reaction in real time in liquid cell by FT-IR spectroscopy. The complex spectral futures due to solvent, unreacted reagents, acid catalysis and other additives are eliminated by defining a background at the beginning or at any time during the reaction. This procedure also makes it possible to monitor the changes in the concentration of each component in the liquid cell. The consumption of the functional groups of the reagents results in absorbance due to the direct difference spectra while the appearance of functional groups is monitored as percentage transmittance. The concentration changes in the cell arising from the reaction gives the product spectra without having to isolate it from the mixture. It is also possible to see the intermediates appearing and disappearing during the reaction. This report also illustrates a brief application of the technique by time dependence of the peak highs in absorption (ABS) mode.

  5. Modelling of CO poisoning and its dynamics in HTPEM fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Bergmann, A.; Gerteisen, D.; Kurz, T. [Fraunhofer Institute for Solar Energy Systems ISE, Freiburg (Germany)

    2010-04-15

    In this work, a dynamic, 2-dimensional, non-isothermal model of a PBI-based HTPEM fuel cell has been developed. The model consists of a five-layer geometry with gas channels, gas diffusion layers (GDL) and membrane. The catalyst layers are taken into account as infinitesimal thin reaction layers between GDL and membrane. The overall cell behaviour is simulated considering conservation of mass, momentum, species, charge and energy. The model is focussed on CO poisoning of the anode in steady state as well as in dynamic operation. Therefore, a temperature and time-dependent approach of adsorption/desorption of CO and H{sub 2} on the catalyst sites and the electrochemical reactions of the adsorbed species is applied. The temperature dependency of the fuel cell performance is investigated in a temperature range between 125 and 160 C at pure hydrogen operation. CO poisoning of the anode is analysed with polarisation curves for different CO concentrations as well as the dynamic response during a CO pulse. The model results are validated by experimental data of in-house measurements. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  6. Macromolecular Dynamics in Red Blood Cells Investigated Using Neutron Spectroscopy

    CERN Document Server

    Stadler, Andreas Maximilian; Demmel, Franz; Artmann, Gerhard; 10.1098/rsif.2010.0306

    2011-01-01

    We present neutron scattering measurements on the dynamics of hemoglobin (Hb) in human red blood cells in vivo. Global and internal Hb dynamics were measured in the ps to ns time- and {\\AA} length-scale using quasielastic neutron backscattering spectroscopy. We observed the cross-over from global Hb short-time to long-time self-diffusion. Both short- and long-time diffusion coefficients agree quantitatively with predicted values from hydrodynamic theory of non-charged hard-sphere suspensions when a bound water fraction of around 0.23g H2O/ g Hb is taken into account. The higher amount of water in the cells facilitates internal protein fluctuations in the ps time-scale when compared to fully hydrated Hb powder. Slower internal dynamics of Hb in red blood cells in the ns time-range were found to be rather similar to results obtained with fully hydrated protein powders, solutions and E. coli cells.

  7. Direct dynamics simulations of the product channels and atomistic mechanisms for the OH(-) + CH3I reaction. Comparison with experiment.

    Science.gov (United States)

    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

  8. Comparative multiparametric analysis of HeLa and RD cell culture reactions to solcoseryl.

    Science.gov (United States)

    Magakian, Yu A; Karalyan, Z A; Karalova, E M; Abroyan, L O; Akopyan, L A; Gasparyan, M H; Jaghacpanyan, N G; Semerjyan, Z B; Ter-Pogossyan, Z R

    2009-10-01

    Reactions of continuous HeLa and RD cell cultures and their nuclear and nucleolar apparatus to addition of solcoseryl into the medium were studied. The monolayer density, proliferation activity, percentage of dead cells, RNA and DNA content in the nuclei and nucleoli, number of nucleoli in the nuclei, cell distribution in the population by the number of nucleoli in the nuclei, volume and complete surface area of the nuclei and nucleoli, and the nucleolar/nuclear ratio were evaluated. The cultures differently reacted to solcoseryl in the medium at the population and cellular levels of their organization. By the results of multiparametric analysis of the reactions of cells and their nuclear and nucleolar apparatus, solcoseryl can be referred to bioactive substances with characteristics of a factor regulating cell population growth.

  9. Spatial stochastic dynamics enable robust cell polarization.

    Directory of Open Access Journals (Sweden)

    Michael J Lawson

    Full Text Available Although cell polarity is an essential feature of living cells, it is far from being well-understood. Using a combination of computational modeling and biological experiments we closely examine an important prototype of cell polarity: the pheromone-induced formation of the yeast polarisome. Focusing on the role of noise and spatial heterogeneity, we develop and investigate two mechanistic spatial models of polarisome formation, one deterministic and the other stochastic, and compare the contrasting predictions of these two models against experimental phenotypes of wild-type and mutant cells. We find that the stochastic model can more robustly reproduce two fundamental characteristics observed in wild-type cells: a highly polarized phenotype via a mechanism that we refer to as spatial stochastic amplification, and the ability of the polarisome to track a moving pheromone input. Moreover, we find that only the stochastic model can simultaneously reproduce these characteristics of the wild-type phenotype and the multi-polarisome phenotype of a deletion mutant of the scaffolding protein Spa2. Significantly, our analysis also demonstrates that higher levels of stochastic noise results in increased robustness of polarization to parameter variation. Furthermore, our work suggests a novel role for a polarisome protein in the stabilization of actin cables. These findings elucidate the intricate role of spatial stochastic effects in cell polarity, giving support to a cellular model where noise and spatial heterogeneity combine to achieve robust biological function.

  10. Collective Calcium Dynamics in Networks of Communicating Cells

    Science.gov (United States)

    Byrd, Tommy; Potter, Garrett; Sun, Bo; Mugler, Andrew

    Cells can sense and encode information about their environment with remarkable precision. These properties have been studied extensively for single cells, but intercellular communication is known to be important for both single- and multicellular organisms. Here, we examine calcium dynamics of fibroblast cells exposed to external ATP stimuli, and the effects of communication and stimulus strength on cells' response. Experimental results show that increasing communication strength induces a greater fraction of cells to exhibit oscillatory calcium dynamics, but the frequencies of oscillation do not systematically shift with ATP strength. We developed a model of calcium signaling by adding noise, communication, and cell-to-cell variability to the model of Tang and Othmer. This model reproduces cells' increased tendency to oscillate as a function of communication strength, and frequency encoding is nearly removed at the global level. Our model therefore suggests that the propensity of cells to oscillate, rather than frequency encoding, determines the response to external ATP. These results suggest that the system lies near a critical boundary separating non-oscillatory and oscillatory calcium dynamics.

  11. SN2 and SN2' reaction dynamics of cyclopropenyl chloride with halide ion : A direct ab initio molecular dynamics (MD) study

    OpenAIRE

    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...

  12. Quantum dynamics calculation of reaction probability for H+Cl2→HCl+Cl

    Institute of Scientific and Technical Information of China (English)

    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.

  13. Quantum dynamics calculation of reaction probability for H+Cl2→HC1+Cl

    Institute of Scientific and Technical Information of China (English)

    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.

  14. Entrainment of cell division in phytoplankton with dynamic energy budgets

    Science.gov (United States)

    Muller, Erik B.; Ananthasubramaniam, Bharath; Klanjšček, Tin; Nisbet, Roger M.

    2011-11-01

    We explore the entrainment behavior of cell division in phytoplankton in the context of Dynamic Energy Budget (DEB) theory. In particular, we explore the range of DEB and environmental parameter values within which a cell divides at regular intervals in a periodic light environment with abundant nutrients and investigate the impact of parameter values on the phase of cell division. We consider three types of cells that differ in the evolution of surface area to volume ratio during the cell cycle: cells with a constant shape (isomorphs), cells with a constant surface area (V0-morphs) and cells with a constant surface area to volume ratio (V1-morphs), the latter being the default choice in studies on the population dynamics of unicellular organisms because of its desirable mathematical implications. Only in isomorphs and V0-morphs, however, cell division can be entrained to a periodic light. Regular cell division in V1 is purely coincidental, as it depends on exact choices for parameter values. We attribute this to the fact that V1-morphs lack the negative feedback of size on the dynamics of reserves in V0-morphs and isomorphs. Because entrained isomorphs and V0-morphs divide during the dark hours in our simulations, these two shapes can represent the division behavior of phytoplankton species that complete the cell cycle during the night, such as dinoflagellates and coccolithophores. A description of the division behavior of species completing the cell cycle during the day, such as silicon dependent diatoms and cyanobacteria, requires a more complex model than used in this paper. Furthermore, we explore the robustness of our findings by randomizing model parameters and introducing unevenness in biomass separation between daughter cells during cell division. We conclude that especially the entrainment in V0-morphs is relatively insensitive to perturbations.

  15. Identifying Enclosed Chemical Reaction and Dynamics at the Molecular Level Using Shell-Isolated Miniaturized Plasmonic Liquid Marble.

    Science.gov (United States)

    Han, Xuemei; Lee, Hiang Kwee; Lee, Yih Hong; Hao, Wei; Liu, Yejing; Phang, In Yee; Li, Shuzhou; Ling, Xing Yi

    2016-04-21

    Current microscale tracking of chemical kinetics is limited to destructive ex situ methods. Here we utilize Ag nanocube-based plasmonic liquid marble (PLM) microreactor for in situ molecular-level identification of reaction dynamics. We exploit the ultrasensitive surface-enhanced Raman scattering (SERS) capability imparted by the plasmonic shell to unravel the mechanism and kinetics of aryl-diazonium surface grafting reaction in situ, using just a 2-μL reaction droplet. This reaction is a robust approach to generate covalently functionalized metallic surfaces, yet its kinetics remain unknown to date. Experiments and simulations jointly uncover a two-step sequential grafting process. An initial Langmuir chemisorption of sulfonicbenzene diazonium (dSB) salt onto Ag surfaces forms an intermediate sulfonicbenzene monolayer (Ag-SB), followed by subsequent autocatalytic multilayer growth of Ag-SB3. Kinetic rate constants reveal 19-fold faster chemisorption than multilayer growth. Our ability to precisely decipher molecular-level reaction dynamics creates opportunities to develop more efficient processes in synthetic chemistry and nanotechnology.

  16. Viscoelastic and dynamic properties of embryonic stem cells

    DEFF Research Database (Denmark)

    Ritter, Christine

    ofthe cells themselves. In this thesis, the viscoelastic properties of mouse embryonic stem cells primedeither toward the epiblast (Epi) or the primitive endoderm (PrE) lineage were investigated.Optical tweezers were used to measure the fluctuations of endogenous lipid granules and therebydraw......Stem cells are often referred to as the ‘holy grail’ of regenerative medicine, because they possessthe ability to develop into any cell type. The use of stem cells within medicine is currently limited bythe effectivity of differentiation and cell reprogramming protocols, making it therefore...... imperative tounderstand stem cells’ differentiation mechanisms better. Studies have shown that mechanical cuescan have an influence on stem cell fate decision. However, in order to understand the reaction of stemcells to mechanical input, one should first investigate and understand the mechanical properties...

  17. Viscoelastic and dynamic properties of embryonic stem cells

    DEFF Research Database (Denmark)

    Ritter, Christine

    Stem cells are often referred to as the ‘holy grail’ of regenerative medicine, because they possessthe ability to develop into any cell type. The use of stem cells within medicine is currently limited bythe effectivity of differentiation and cell reprogramming protocols, making it therefore...... imperative tounderstand stem cells’ differentiation mechanisms better. Studies have shown that mechanical cuescan have an influence on stem cell fate decision. However, in order to understand the reaction of stemcells to mechanical input, one should first investigate and understand the mechanical properties...... ofthe cells themselves. In this thesis, the viscoelastic properties of mouse embryonic stem cells primedeither toward the epiblast (Epi) or the primitive endoderm (PrE) lineage were investigated.Optical tweezers were used to measure the fluctuations of endogenous lipid granules and therebydraw...

  18. Radiation reaction dynamics in an electromagnetic wave and constant electric field

    Science.gov (United States)

    Atlee Jackson, E.

    1984-05-01

    The relativistic motion of a charged particle is studied when it is acted on simultaneously by a constant electric field and a plane electromagnetic wave, propagating in the direction of the electric field (x axis). The dynamics includes the radiation reaction (self-force) on the particle through a standard approximation of the Lorentz-Dirac equation. The interest is to determine the result of the competition between the average acceleration due to the electromagnetic wave (``radiation pressure'') and the acceleration due to the constant force of the static field. Each of these actions alone of course produce an unbounded particle energy asymptotically in time. However, it is proved first that, when the ``forces'' are in opposite directions, the particle can never accelerate (on the average) indefinitely in the x direction, regardless how weak the electric field (E0) is compared to the amplitude of the wave (A). It is then proved that all solutions converge to a region of zero area in a suitable velocity phase space and, if there exists a periodic solution [in the phase ξ=ω (t-x/c)] in a specified region of this phase space, then all solutions must converge to this solution asymptotically (ξ→+∞). In the case when (E0A2/ω2) has a specified bound (ω: wave frequency), an iterative method is developed which explicitly yields such a periodic solution, showing that the energy remains bounded. The direction of the average drift is determined in terms of (A,E0,ω). When the parameter (E0A2/ω2) is above this bound, a combination of numerical and analytic results are obtained which indicate that this periodic solution persists. These results indicate that all motions tend to states with bounded energy, regardless of the field strengths.

  19. Reaction dynamics induced by the radioactive ion beam 7Be on medium-mass and heavy targets

    Science.gov (United States)

    Mazzocco, M.; Boiano, A.; Boiano, C.; La Commara, M.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Stefanini, C.; Strano, E.; Torresi, D.; Acosta, L.; Di Meo, P.; Fernandez-Garcia, J. P.; Glodariu, T.; Grebosz, J.; Guglielmetti, A.; Keeley, N.; Lay, J. A.; Marquinez-Duran, G.; Martel, I.; Mazzocchi, C.; Molini, P.; Nicoletto, M.; Pakou, A.; Parkar, V. V.; Rusek, K.; Sánchez-Benítez, A. M.; Sandoli, M.; Sava, T.; Sgouros, O.; Signorini, C.; Silvestri, R.; Soramel, F.; Soukeras, V.; Stiliaris, E.; Stroe, L.; Toniolo, N.; Zerva, K.

    2015-10-01

    We studied the reaction dynamics induced at Coulomb barrier energies by the weakly-bound Radioactive Ion Beam 7Be (Sα = 1.586 MeV) on medium-mass (58Ni) and heavy (208Pb) targets. The experiments were performed at INFN-LNL (Italy), where a 2-3×105 pps 7Be secondary beam was produced with the RIB in-flight facility EXOTIC. Charged reaction products were detected by means of high-granularity silicon detectors in rather wide angular ranges. The contribution presents an up-to-date status of the data analysis and theoretical interpretation for both systems.

  20. Growth dynamics and composition of tubular structures in a reaction-precipitation system

    Science.gov (United States)

    Pagano, Jason John

    Self-organization in reaction precipitation systems occurs in many physical, chemical, biological, and geological systems. In particular, chemical reactions provide a wealth of examples for this intriguing process. Permanent tubular structures arise from the interplay of chemical and transport phenomena such as diffusion and fluid flow. These astonishing tubular structures are prevalent throughout nature. Examples include black smokers at hydrothermal vents, silica tubes in setting cement, soda-straw stalactites in caves, and biological structures such as the outer skeleton of certain algae. In this work, the aim is to establish and understand a laboratory scale model by examining the, seemingly simple, precipitation reaction between sodium silicate and copper sulfate as well as zinc sulfate. The tubular precipitation structures in so-called silica gardens are known to many scientists and non-scientists alike. However, little is known regarding their growth dynamics and chemical composition. We devised an injection technique which provides control over parameters that are not accessible in the classic silica garden system. For the example of cupric sulfate injection into waterglass solution, we identify three distinct growth regimes (jetting, popping, and budding) and study their concentration dependent transitions. Here we describe the composition and morphology of the tube material using techniques such as electron microscopy and vibrational spectroscopy. Specifically, we find that the tube wall consists of metal hydroxide that is stabilized by a thin, exterior silica layer. After synthesis the tubes can be further modified by using chemical and/or physical means. A second study aims to understand tubule formation under "reverse" conditions. More specifically, waterglass is being injected into lighter cupric sulfate solution. In these experiments, single, downward growing precipitation tubes are created. Four distinct growth regimes are observed and their

  1. Reaction-Diffusion in the NEURON Simulator

    Directory of Open Access Journals (Sweden)

    Robert A. McDougal

    2013-11-01

    Full Text Available In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics on the dynamics of neuronal response in health and disease, NEURON has developed a Reaction-Diffusion (rxd module in Python which provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy’s sparse linear algebra library.

  2. Reaction-diffusion in the NEURON simulator.

    Science.gov (United States)

    McDougal, Robert A; Hines, Michael L; Lytton, William W

    2013-01-01

    In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library.

  3. Oscillations and multiscale dynamics in a closed chemical reaction system: second law of thermodynamics and temporal complexity.

    Science.gov (United States)

    Li, Yongfeng; Qian, Hong; Yi, Yingfei

    2008-10-21

    We investigate the oscillatory reaction dynamics in a closed isothermal chemical system: the reversible Lotka-Volterra model. The second law of thermodynamics dictates that the system ultimately reaches an equilibrium. Quasistationary oscillations are analyzed while the free energy of the system serves as a global Lyapunov function of the dissipative dynamics. A natural distinction between regions near and far from equilibrium in terms of the free energy can be established. The dynamics is analogous to a nonlinear mechanical system with time-dependent increasing damping. Near equilibrium, no oscillation is possible as dictated by Onsager's reciprocal symmetry relation. We observe that while the free energy decreases in the closed system's dynamics, it does not follow the steepest descending path.

  4. Inhibitory effects of atractylone on mast cell-mediated allergic reactions.

    Science.gov (United States)

    Han, Na-Ra; Moon, Phil-Dong; Nam, Sun-Young; Ryu, Ka-Jung; Yoou, Myoung-Schook; Choi, Jung-Hye; Hwang, Sung-Yeoun; Kim, Hyung-Min; Jeong, Hyun-Ja

    2016-10-25

    This study investigated a salutary effect of atractylone (Atr) which is an active constituent of Pyeongwee-San (KMP6) on mast cell-mediated allergic reactions. Our previous report indicated that KMP6 regulated allergic reactions. Thus, this study sought to determine the potential of Atr in vitro models, compound 48/80-stimulated rat peritoneal mast cells (RPMCs), phorbol 12-myristate 13-acetate (PMA) plus A23187-stimulated human mast cell line (HMC-1) cells, and stem cell factor (SCF)-stimulated RPMCs as well as in vivo models, IgE-mediated passive cutaneous anaphylaxis (PCA), compound 48/80-induced systemic anaphylaxis, and compound 48/80-induced ear swelling. The results showed that Atr inhibited compound 48/80-induced RPMCs degranulation, intracellular calcium level, tryptase release, and histamine release. Atr inhibited the up-regulation of p56(lck) tyrosine kinase activity by compound 48/80. And Atr reduced tryptase and histamine releases from PMA plus A23187-stimulated HMC-1 cells. In addition, Atr decreased histidine decarboxylase activity and expression in the activated HMC-1 cells. Atr inhibited SCF-induced morphological alteration and filamentous actin formation in RPMCs. Atr improved IgE-induced PCA reaction by decreasing the levels of histamine, IgE, interleukin (IL)-4, IL-5, IL-6, vascular endothelial growth factor, and IL-13 in the serum of PCA-induced mice. Furthermore, Atr mitigated compound 48/80-induced systemic anaphylaxis and ear swelling. Taken together, these results of this study indicate that Atr regulates the degranulation of mast cell, proving its potential in the treatment of mast cell-mediated allergic reactions.

  5. Inverse problem of HIV cell dynamics using Genetic Algorithms

    Science.gov (United States)

    González, J. A.; Guzmán, F. S.

    2017-01-01

    In order to describe the cell dynamics of T-cells in a patient infected with HIV, we use a flavour of Perelson's model. This is a non-linear system of Ordinary Differential Equations that describes the evolution of healthy, latently infected, infected T-cell concentrations and the free viral cells. Different parameters in the equations give different dynamics. Considering the concentration of these types of cells is known for a particular patient, the inverse problem consists in estimating the parameters in the model. We solve this inverse problem using a Genetic Algorithm (GA) that minimizes the error between the solutions of the model and the data from the patient. These errors depend on the parameters of the GA, like mutation rate and population, although a detailed analysis of this dependence will be described elsewhere.

  6. Intergenerational continuity of cell shape dynamics in Caulobacter crescentus

    Science.gov (United States)

    Wright, Charles S.; Banerjee, Shiladitya; Iyer-Biswas, Srividya; Crosson, Sean; Dinner, Aaron R.; Scherer, Norbert F.

    2015-03-01

    We investigate the intergenerational shape dynamics of single Caulobacter crescentus cells using a novel combination of imaging techniques and theoretical modeling. We determine the dynamics of cell pole-to-pole lengths, cross-sectional widths, and medial curvatures from high accuracy measurements of cell contours. Moreover, these shape parameters are determined for over 250 cells across approximately 10000 total generations, which affords high statistical precision. Our data and model show that constriction is initiated early in the cell cycle and that its dynamics are controlled by the time scale of exponential longitudinal growth. Based on our extensive and detailed growth and contour data, we develop a minimal mechanical model that quantitatively accounts for the cell shape dynamics and suggests that the asymmetric location of the division plane reflects the distinct mechanical properties of the stalked and swarmer poles. Furthermore, we find that the asymmetry in the division plane location is inherited from the previous generation. We interpret these results in terms of the current molecular understanding of shape, growth, and division of C. crescentus.

  7. GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics

    CERN Document Server

    Blumers, Ansel L; Li, Zhen; Li, Xuejin; Karniadakis, George E

    2016-01-01

    Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 c...

  8. Allosteric effects on oxidative and nitrosative reactions of cell-free hemoglobins.

    Science.gov (United States)

    Bonaventura, Celia; Henkens, Robert; Alayash, Abdu I; Crumbliss, Alvin L

    2007-01-01

    A review of the oxidative and nitrosative reactions of cell-free hemoglobin-based oxygen carriers (HBOCs) shows that these reactions are intimately linked and are subject to allosteric control. Cross-linking reactions used to produce HBOCs introduce conformational constraints and result in Hbs with reduced responses to heterotropic and homotropic allosteric effectors. The Nernst plots of heme oxidation of cross-linked HBOCs are shifted to higher potentials relative to unmodified Hb in the absence of allosteric effectors, in accord with their T-state stabilization and right-shifted Hill plots of O(2) binding. They exhibit enhanced rates of autoxidation and nitrite-induced oxidation, features that appear due to their having more solvent-accessible heme pockets. The stability of their NO-Hb derivatives varies as a result of allosteric effects on the extent of formation of pentacoordinate NO-heme geometry by alpha chains and subsequent oxidation of partner beta chains. The physiological implications of these findings on the safety, efficacy and design of second generation HBOCs are discussed in the framework of a reaction scheme showing linkages between Hb-mediated redox reactions. These redox reactions can drive formation of SNO-Hb and other reactive species and are of significance for the use of cell-free Hbs in vivo.

  9. Ion-neutral gas reactions in a collision/reaction cell in inductively coupled plasma mass spectrometry: Correlation of ion signal decrease to kinetic rate constants

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Patrick J. [Trace Element Research Laboratory, School of Earth Sciences, The Ohio State University, 125 S. Oval Mall, Columbus, OH 43210 (United States); Department of Chemistry, The Ohio State University, 120 18th Avenue, Columbus, OH 43210 (United States); Olesik, John W., E-mail: olesik.2@osu.edu [Trace Element Research Laboratory, School of Earth Sciences, The Ohio State University, 125 S. Oval Mall, Columbus, OH 43210 (United States)

    2015-03-01

    Reaction gas flow rate dependent Ar{sub 2}{sup +} and Ar{sup +} signals are correlated to fundamental kinetic rate coefficients. A simple calculation, assuming that gas exits the reaction cell due only to effusion, is described to estimate the gas pressure in the reaction cell. The value of the product of the kinetic rate constant and the ion residence time in the reaction cell can be determined from experimental measurement of the decrease in an ion signal as a function of reaction gas flow rate. New kinetic rate constants are determined for the reaction of CH{sub 3}F with Ar{sup +} and Ar{sub 2}{sup +}. - Highlights: • How to determine pressure and the product of the kinetic rate constant times the ion residence time in reaction cell • Relate measured ICP-DRC-MS signals versus gas flow rate to kinetic rate constants measured previously using SIFT-MS • Describe how to determine previously unmeasured kinetic rate constants using ICP-DRC-MS.

  10. Phosphorylation site dynamics of early T-cell receptor signaling

    DEFF Research Database (Denmark)

    Chylek, Lily A; Akimov, Vyacheslav; Dengjel, Jörn

    2014-01-01

    a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found...... that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites...

  11. Multiple cathodic reaction mechanisms in seawater cathodic biofilms operating in sediment microbial fuel cells.

    Science.gov (United States)

    Babauta, Jerome T; Hsu, Lewis; Atci, Erhan; Kagan, Jeff; Chadwick, Bart; Beyenal, Haluk

    2014-10-01

    In this study, multiple reaction mechanisms in cathodes of sediment microbial fuel cells (SMFCs) were characterized by using cyclic voltammetry and microelectrode measurements of dissolved oxygen and pH. The cathodes were acclimated in SMFCs with sediment and seawater from San Diego Bay. Two limiting current regions were observed with onset potentials of approximately +400 mVAg/AgCl for limiting current I and -120 mVAg/AgCl for limiting current II. The appearance of two catalytic waves suggests that multiple cathodic reaction mechanisms influence cathodic performance. Microscale oxygen concentration measurements showed a zero surface concentration at the electrode surface for limiting current II but not for limiting current I, which allowed us to distinguish limiting current II as the conventional oxygen reduction reaction and limiting current I as a currently unidentified cathodic reaction mechanism. Microscale pH measurements further confirmed these results.

  12. Quantum dynamics of the Walden inversion reaction Cl - +CH3Cl --> ClCH3+Cl -

    Science.gov (United States)

    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.

  13. Fast and stable redox reactions of MnO2/CNT hybrid electrodes for dynamically stretchable pseudocapacitors

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-01

    Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid electrodes. The extremely small relaxation time constant of less than 0.15 s indicates a fast redox reaction at the MnO2/CNT hybrid electrodes, securing a stable electrochemical performance for the dynamically stretchable pseudocapacitors. This finding and the fundamental understanding gained from the pseudo-capacitive behavior coupled with mechanical deformation under a dynamic stretching mode would provide guidance to further improve their overall performance including a higher power density than LIBs, a higher energy density than EDLCs, and a long-life cycling stability. Most importantly, these results will potentially accelerate the applications of stretchable pseudocapacitors for flexible and biomedical electronics.Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid

  14. Matrix photochemistry of small molecules: Influencing reaction dynamics on electronically excited hypersurfaces

    Energy Technology Data Exchange (ETDEWEB)

    Laursen, S.L.

    1990-01-01

    Investigations of chemical reactions on electronically excited reaction surfaces are presented. The role of excited-surface multiplicity is of particular interest, as are chemical reactivity and energy transfer in systems in which photochemistry is initiated through a metal atom sensitizer.'' Two approaches are employed: A heavy-atom matrix affords access to forbidden triplet reaction surfaces, eliminating the need for a potentially reactive sensitizer. Later, the role of the metal atom in the photosensitization process is examined directly.

  15. In situ liquid-cell electron microscopy of silver-palladium galvanic replacement reactions on silver nanoparticles

    National Research Council Canada - National Science Library

    Sutter, E; Jungjohann, K; Bliznakov, S; Courty, A; Maisonhaute, E; Tenney, S; Sutter, P

    2014-01-01

    .... In situ observations by liquid-cell electron microscopy can provide insight into mechanisms, rates and possible modifications of galvanic replacement reactions in the native solution environment...

  16. Long term charge retention dynamics of SONOS cells

    Science.gov (United States)

    Arreghini, A.; Akil, N.; Driussi, F.; Esseni, D.; Selmi, L.; van Duuren, M. J.

    2008-09-01

    We present a model for charge retention dynamics in SONOS non volatile memory cells which accounts for the space and energy distributions of the trapped charge in the silicon nitride, self consistently with the potential. Long term retention measurements (beyond 106 s) versus temperature allowed us to decouple two charge loss mechanisms, to calibrate the model parameters and then to reproduce a large set of measurements on devices featuring different gate stacks, initial threshold voltages (including negative ones) and operation temperatures. A detailed analysis has been also carried out to compare the retention dynamics of cells featuring thin or thick tunnel oxide barriers.

  17. Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

    Science.gov (United States)

    García-Meseguer, Rafael; Martí, Sergio; Ruiz-Pernía, J. Javier; Moliner, Vicent; Tuñón, Iñaki

    2013-07-01

    Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.

  18. Intermediate filaments: a dynamic network that controls cell mechanics.

    Science.gov (United States)

    Gruenbaum, Yosef; Aebi, Ueli

    2014-01-01

    In humans the superfamily of intermediate filament (IF) proteins is encoded by more than 70 different genes, which are expressed in a cell- and tissue-specific manner. IFs assemble into approximately 10 nm-wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. They are also required for organizing the microtubule and microfilament networks. In this review, we focus on the dynamics of IFs and how modifications regulate it. We also discuss the role of nuclear IF organization in determining nuclear mechanics as well as that of cytoplasmic IFs organization in maintaining cell stiffness, formation of lamellipodia, regulation of cell migration, and permitting cell adhesion.

  19. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. A Coupled Dynamical Model of Redox Flow Battery Based on Chemical Reaction, Fluid Flow, and Electrical Circuit

    OpenAIRE

    Li, Minghua; Hikihara, Takashi

    2008-01-01

    The redox (Reduction-Oxidation) flow battery is one of the most promising rechargeable batteries due to its ability to average loads and output of power sources. The transient characteristics are well known as the remarkable feature of the battery. Then it can also compensate for a sudden voltage drop. The dynamics are governed by the chemical reactions, fluid flow, and electrical circuit of its structure. This causes the difficulty of the analysis at transient state. This paper discusses the...

  1. Automated live cell imaging systems reveal dynamic cell behavior.

    Science.gov (United States)

    Chirieleison, Steven M; Bissell, Taylor A; Scelfo, Christopher C; Anderson, Jordan E; Li, Yong; Koebler, Doug J; Deasy, Bridget M

    2011-07-01

    Automated time-lapsed microscopy provides unique research opportunities to visualize cells and subcellular components in experiments with time-dependent parameters. As accessibility to these systems is increasing, we review here their use in cell science with a focus on stem cell research. Although the use of time-lapsed imaging to answer biological questions dates back nearly 150 years, only recently have the use of an environmentally controlled chamber and robotic stage controllers allowed for high-throughput continuous imaging over long periods at the cell and subcellular levels. Numerous automated imaging systems are now available from both companies that specialize in live cell imaging and from major microscope manufacturers. We discuss the key components of robots used for time-lapsed live microscopic imaging, and the unique data that can be obtained from image analysis. We show how automated features enhance experimentation by providing examples of uniquely quantified proliferation and migration live cell imaging data. In addition to providing an efficient system that drastically reduces man-hours and consumes fewer laboratory resources, this technology greatly enhances cell science by providing a unique dataset of temporal changes in cell activity. Copyright © 2011 American Institute of Chemical Engineers (AIChE).

  2. Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damk\\"ohler numbers

    CERN Document Server

    Bandopadhyay, Aditya; Méheust, Yves; Dentz, Marco

    2016-01-01

    Mixing fronts, where fluids of different chemical compositions mix with each other, are typically subjected to velocity gradients, ranging from the pore scale to the catchment scale due to permeability variations and flow line geometries. A common trait of these processes is that the mixing interface is strained by shear. Depending on the P\\'eclet number $Pe$, which represents the ratio of the characteristic diffusion time to the characteristic advection time, and the Damk\\"ohler number $Da$, which represents the ratio of the characteristic diffusion time to the characteristic reaction time, the local reaction rates can be strongly impacted by the dynamics of the mixing interface. This impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either very low or very high $Da$. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damk\\"ohler numbers, for a bimolecular reaction and an initial interface with separated reactants....

  3. Dynamics of activity free radical oxidation reactions in students with cerebral palsy results over the course of the educational process

    Directory of Open Access Journals (Sweden)

    Makarova E.V.

    2012-12-01

    Full Text Available The dynamics of changes activity of reactions is studied freely radical oxidize for students with the consequences of child's cerebral paralysis. 20 students took part in an experiment. Found that the course of study they have more active free radical oxidation reactions and decreases the activity of antiradical protection. Given the use of additional physical activity in aerobic training indicators intracellular antioxidant defense system increased, decreased content of reaction products of lipid peroxidation. However, increased rates of maximum oxygen consumption and increased tolerance of students with cerebral palsy to the consequences of physical activity. It is set that the pathological changes of metabolism for students ground the necessity of application of the differentiated physical loadings. The optimum forms of physical rehabilitation of the aerobic training is the dosed walking, medical swimming, dosed after distance, sometimes and by the corner of getting up pedestrian ascents. Loading is increased due to a volume, but not intensity of exercises.

  4. Stereo-dynamics of the exchange reaction Ha+LiHb→LiHa+Hb and its isotopic variants

    Institute of Scientific and Technical Information of China (English)

    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.

  5. Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

    Science.gov (United States)

    Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2014-03-01

    In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

  6. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations

    Science.gov (United States)

    La Rosa, Carmelo; Scalisi, Silvia; Lolicato, Fabio; Pannuzzo, Martina; Raudino, Antonio

    2016-05-01

    The protein transport inside a cell is a complex phenomenon that goes through several difficult steps. The facilitated transport requires sophisticated machineries involving protein assemblies. In this work, we developed a diffusion-reaction model to simulate co-transport kinetics of proteins and lipids. We assume the following: (a) there is always a small lipid concentration of order of the Critical Micellar Concentration (CMC) in equilibrium with the membrane; (b) the binding of lipids to proteins modulates the hydrophobicity of the complexes and, therefore, their ability to interact and merge with the bilayer; and (c) some lipids leave the bilayer to replenish those bound to proteins. The model leads to a pair of integral equations for the time-evolution of the adsorbed proteins in the lipid bilayer. Relationships between transport kinetics, CMC, and lipid-protein binding constants were found. Under particular conditions, a perturbation analysis suggests the onset of kinks in the protein adsorption kinetics. To validate our model, we performed leakage measurements of vesicles composed by either high or low CMC lipids interacting with Islet Amyloid PolyPeptide (IAPP) and Aβ (1-40) used as sample proteins. Since the lipid-protein complex stoichiometry is not easily accessible, molecular dynamics simulations were performed using monomeric IAPP interacting with an increasing number of phospholipids. Main results are the following: (a) 1:1 lipid-protein complexes generally show a faster insertion rate proportional to the complex hydrophobicity and inversely related to lipid CMC; (b) on increasing the number of bound lipids, the protein insertion rate decreases; and (c) at slow lipids desorption rate, the lipid-assisted proteins transport might exhibit a discontinuous behavior and does non-linearly depend on protein concentration.

  7. A quantitative and dynamic model for plant stem cell regulation.

    Directory of Open Access Journals (Sweden)

    Florian Geier

    Full Text Available Plants maintain pools of totipotent stem cells throughout their entire life. These stem cells are embedded within specialized tissues called meristems, which form the growing points of the organism. The shoot apical meristem of the reference plant Arabidopsis thaliana is subdivided into several distinct domains, which execute diverse biological functions, such as tissue organization, cell-proliferation and differentiation. The number of cells required for growth and organ formation changes over the course of a plants life, while the structure of the meristem remains remarkably constant. Thus, regulatory systems must be in place, which allow for an adaptation of cell proliferation within the shoot apical meristem, while maintaining the organization at the tissue level. To advance our understanding of this dynamic tissue behavior, we measured domain sizes as well as cell division rates of the shoot apical meristem under various environmental conditions, which cause adaptations in meristem size. Based on our results we developed a mathematical model to explain the observed changes by a cell pool size dependent regulation of cell proliferation and differentiation, which is able to correctly predict CLV3 and WUS over-expression phenotypes. While the model shows stem cell homeostasis under constant growth conditions, it predicts a variation in stem cell number under changing conditions. Consistent with our experimental data this behavior is correlated with variations in cell proliferation. Therefore, we investigate different signaling mechanisms, which could stabilize stem cell number despite variations in cell proliferation. Our results shed light onto the dynamic constraints of stem cell pool maintenance in the shoot apical meristem of Arabidopsis in different environmental conditions and developmental states.

  8. DYNAMIC MATHEMATICAL MODELLING OF REACTION KINETICS FOR CYCLODEXTRINS PRODUCTION FROM DIFFERENT STARCH SOURCES USING BACILLUS MACERANS CYCLODEXTRIN GLUCANOTRANSFERASE

    Directory of Open Access Journals (Sweden)

    Syahinaz Shahrazi

    2013-01-01

    Full Text Available This study relates to the mathematical modelling of enzymatic production of Cyclodextrins (CDs by Cyclodextrin Glucanotransferase (CGTase from Bacillus macerans. The experiments were carried out in batch mode using different starch sources and the results were used to estimate unknown parameters using linearization and dynamic simulation methods. α- and β-CD produced from tapioca were found to give the highest Michaelis-Menten constant, KM,i of 58.23 and 54.07 g L-1, respectively and maximum velocity, Vmax,i of 3.45 and 2.76 g L-1.min, respectively, while sago resulted in the highest KM,i and Vmax,i values of 342.35 g L-1 and 5.97 g L-1.min, respectively, for γ-CD obtained by the linearization method. Value of product inhibition, K1,i and CD degradation coefficient rate, δCD,i, were estimated using dynamic simulation, indicating that exponential reaction kinetics could be fitted better with the experimental data. Sensitivity analysis revealed that the product inhibition parameter in the exponential reaction kinetic equation is more significant in the process. For validation, the production of CDs by fed batch method was undertaken and starch and enzyme were added into the reaction medium. Then, the predicted profiles generated by simulation were compared with the experimental values. The proposed exponential reaction kinetics shows good fitting with the experimental data.

  9. Preparation of cell lines for single-cell analysis of transcriptional activation dynamics.

    Science.gov (United States)

    Rafalska-Metcalf, Ilona U; Janicki, Susan M

    2013-01-01

    Imaging molecularly defined regions of chromatin in single living cells during transcriptional activation has the potential to provide new insight into gene regulatory mechanisms. Here, we describe a method for isolating cell lines with multi-copy arrays of reporter transgenes, which can be used for real-time high-resolution imaging of transcriptional activation dynamics in single cells.

  10. Slow desensitization of imatinib-induced nonimmediate reactions and dynamic changes of drug-specific CD4(+)CD25(+)CD134(+) lymphocytes.

    Science.gov (United States)

    Klaewsongkram, Jettanong; Thantiworasit, Pattarawat; Sodsai, Pimpayao; Buranapraditkun, Supranee; Mongkolpathumrat, Pungjai

    2016-11-01

    Imatinib is a tyrosine kinase inhibitor indicated for the treatment of gastrointestinal stromal tumors (GISTs) and certain neoplastic diseases; however, nonimmediate adverse reactions are common. To describe the process of imatinib slow desensitization in patients who experienced nonimmediate reactions to imatinib and the dynamic change in drug-specific CD4(+)CD25(+)CD134(+) T-lymphocyte percentages. Five patients diagnosed as having GISTs and with a recent history of imatinib-induced nonimmediate reactions (maculopapular exanthema with eosinophilia, exfoliative dermatitis, palmar-plantar erythrodysesthesia, and drug rash with eosinophilia and systemic symptoms) were desensitized using a slow desensitization protocol. The reintroduced imatinib dosage was stepped up every week starting from 10 mg/d and increasing to 25, 50, 75, 100, 150, 200, and 300 mg/d until the target dose of 400 mg/d was achieved. Prednisolone of up to 30 mg/d was allowed if allergic reactions recurred. The percentages of CD4(+)CD25(+)CD134(+) T cells present after incubating peripheral blood mononuclear cells with imatinib, at baseline and after successful desensitization, were analyzed using flow cytometric analysis. By using a slow desensitization technique, all patients were able to receive 400 mg/d of imatinib, and prednisolone was gradually tapered off. The percentages of imatinib-induced CD4(+)CD25(+)CD134(+) T cells decreased from a mean (SD) of 11.3% (6.5%) and 13.4% (7.3%) at baseline to 3.2% (0.7%) and 3.0% (1.1%) after successful desensitization, when stimulating peripheral blood mononuclear cells with 1 and 2 μM of imatinib, respectively. Slow desensitization is a helpful procedure in treating patients with imatinib-induced nonimmediate reactions other than simple maculopapular exanthema. The reduced percentages of imatinib-induced CD4(+)CD25(+)CD134(+) T cells in these patients may be associated with immune tolerance. Copyright © 2016 American College of Allergy, Asthma

  11. NATO Advanced Research Workshop on The Theory of Chemical Reaction Dynamics

    CERN Document Server

    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...

  12. Dynamic modeling of a three-stage low-temperature ethanol reformer for fuel cell application

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, Vanesa M.; Serra, Maria [Institut de Robotica i Informatica Industrial (CSIC-UPC), Llorens i Artigas 4-6, 08028 Barcelona (Spain); Lopez, Eduardo; Llorca, Jordi [Institut de Tecniques Energetiques, Universitat Politecnica de Catalunya, Diagonal 647, ed. ETSEIB, 08028 Barcelona (Spain)

    2009-07-01

    A low-temperature ethanol reformer based on a cobalt catalyst for the production of hydrogen has been designed aiming the feed of a fuel cell for an autonomous low-scale power production unit. The reformer comprises three stages: ethanol dehydrogenation to acetaldehyde and hydrogen over SnO{sub 2} followed by acetaldehyde steam reforming over Co(Fe)/ZnO catalyst and water gas shift reaction. Kinetic data have been obtained under different experimental conditions and a dynamic model has been developed for a tubular reformer loaded with catalytic monoliths for the production of the hydrogen required to feed a 1 kW PEMFC. (author)

  13. Revealing dynamic processes of materials in liquids using liquid cell transmission electron microscopy.

    Science.gov (United States)

    Niu, Kai-Yang; Liao, Hong-Gang; Zheng, Haimei

    2012-12-20

    The recent development for in situ transmission electron microscopy, which allows imaging through liquids with high spatial resolution, has attracted significant interests across the research fields of materials science, physics, chemistry and biology. The key enabling technology is a liquid cell. We fabricate liquid cells with thin viewing windows through a sequential microfabrication process, including silicon nitride membrane deposition, photolithographic patterning, wafer etching, cell bonding, etc. A liquid cell with the dimensions of a regular TEM grid can fit in any standard TEM sample holder. About 100 nanoliters reaction solution is loaded into the reservoirs and about 30 picoliters liquid is drawn into the viewing windows by capillary force. Subsequently, the cell is sealed and loaded into a microscope for in situ imaging. Inside the TEM, the electron beam goes through the thin liquid layer sandwiched between two silicon nitride membranes. Dynamic processes of nanoparticles in liquids, such as nucleation and growth of nanocrystals, diffusion and assembly of nanoparticles, etc., have been imaged in real time with sub-nanometer resolution. We have also applied this method to other research areas, e.g., imaging proteins in water. Liquid cell TEM is poised to play a major role in revealing dynamic processes of materials in their working environments. It may also bring high impact in the study of biological processes in their native environment.

  14. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

    Science.gov (United States)

    Cannon, William R.; Baker, Scott E.

    2017-10-01

    Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

  15. Reactions of the Carbon Anode in Alternative Battery and Fuel Cell Configurations

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, J F; Krueger, R

    2003-10-01

    A model is formulated by combining carbonate dissociation with pre-existing anode mechanisms involving heterogeneous reaction kinetics. The proposed model accounts for both the observed preponderance of CO{sub 2} evolution and dependence of rate on carbon anode microstructure. Implications of the model for the design of carbon batteries and fuel cells are discussed, and the laboratory cells used in earlier research are described. High coulombic efficiencies for the net reaction C + O{sub 2} = CO{sub 2} require severely limiting the thickness of paste anodes in powder-fed fuel cells while the unreacting surfaces of solid prismatic anodes must be isolated from the CO{sub 2} product atmosphere to prevent Boudouard corrosion, according to C + CO{sub 2} = 2CO.

  16. Effect of disodium cromoglycate on mast cell-mediated immediate-type allergic reactions.

    Science.gov (United States)

    Shin, Hye-Young; Kim, Jung-Sook; An, Nyeon-Hyoung; Park, Rae-Kil; Kim, Hyung-Min

    2004-04-23

    We investigated the effect of disodium cromoglycate (DSCG) on mast cell-mediated immediate-type hypersensitivity. DSCG inhibited systemic allergic reaction induced by compound 48/80 dose-dependently. Passive cutaneous anaphylaxis was inhibited by 71.6% by oral administration of DSCG (1 g/kg). When DSCG was pretreated at concentration rang from 0.01-1000 g/kg, the serum histamine levels were reduced in a dose dependent manner. DSCG also significantly inhibited histamine release from rat peritoneal mast cell (RPMC) by compound 48/80. We confirmed that DSCG inhibited compound 48/80-induced degranulation of RPMC by alcian blue/nuclear fast red staining. In addition, DSCG showed a significant inhibitory effect on anti-dinitrophenyl IgE-mediated tumor necrosis factor-alpha production. These results indicate that DSCG inhibits mast cell-mediated immediate-type allergic reaction.

  17. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Zero Point Energy Conservation in Mu + H2 → MuH + H.

    Science.gov (United States)

    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.

  18. Molecular beam studies of unimolecular and bimolecular chemical reaction dynamics using VUV synchrotron radiation as a product probe

    Energy Technology Data Exchange (ETDEWEB)

    Blank, David Andrew [Univ. of California, Berkeley, CA (United States)

    1997-08-01

    This dissertation describes the use of a new molecular beam apparatus designed to use tunable VUV synchrotron radiation for photoionization of the products from scattering experiments. The apparatus was built at the recently constructed Advanced Light Source at Lawrence Berkeley National Laboratory, a third generation 1-2 GeV synchrotron radiation source. The new apparatus is applied to investigations of the dynamics of unimolecular reactions, photodissociation experiments, and bimolecular reactions, crossed molecular beam experiments. The first chapter describes the new apparatus and the VUV radiation used for photoionization. This is followed by a number of examples of the many advantages provided by using VUV photoionization in comparison with the traditional technique of electron bombardment ionization. At the end of the chapter there is a discussion of the data analysis employed in these scattering experiments. The remaining four chapters are complete investigations of the dynamics of four chemical systems using the new apparatus and provide numerous additional examples of the advantages provided by VUV photoionizaiton of the products. Chapters 2-4 are photofragment translational spectroscopy studies of the photodissociation dynamics of dimethyl sulfoxide, acrylonitrile, and vinyl chloride following absorption at 193 mn. All of these systems have multiple dissociation channels and provide good examples of the ability of the new apparatus to unravel the complex UV photodissociation dynamics that can arise in small polyatomic molecules.

  19. Dynamic heterogeneity and DNA methylation in embryonic stem cells.

    KAUST Repository

    Singer, Zakary S

    2014-07-01

    Cell populations can be strikingly heterogeneous, composed of multiple cellular states, each exhibiting stochastic noise in its gene expression. A major challenge is to disentangle these two types of variability and to understand the dynamic processes and mechanisms that control them. Embryonic stem cells (ESCs) provide an ideal model system to address this issue because they exhibit heterogeneous and dynamic expression of functionally important regulatory factors. We analyzed gene expression in individual ESCs using single-molecule RNA-FISH and quantitative time-lapse movies. These data discriminated stochastic switching between two coherent (correlated) gene expression states and burst-like transcriptional noise. We further showed that the "2i" signaling pathway inhibitors modulate both types of variation. Finally, we found that DNA methylation plays a key role in maintaining these metastable states. Together, these results show how ESC gene expression states and dynamics arise from a combination of intrinsic noise, coherent cellular states, and epigenetic regulation.

  20. Sperm cell surface dynamics during activation and fertilization

    NARCIS (Netherlands)

    Boerke, A.

    2013-01-01

    Before the sperm cell can reach the oocyte it needs to be activated and to undergo a series of preparative steps. The sperm surface dynamics was studied in relation to this activation process and the modifications and removal of sperm surface components havebeen investigated. Bicarbonate-induced rad

  1. Molecular dynamics simulation of gas-phase ozone reactions with sabinene and benzene.

    Science.gov (United States)

    Ridgway, H F; Mohan, B; Cui, X; Chua, K J; Islam, M R

    2017-06-01

    Gas-phase reactions of ozone (O3) with volatile organic compounds were investigated both by experiment and molecular simulations. From our experiments, it was found ozone readily reacts with VOC pure components and reduces it effectively. By introducing ozone intermittently, the reaction between VOC and ozone is markedly enhanced. In order to understand the relationship between intermediate reactions and end products, ozone reaction with benzene and alicyclic monoterpene sabinene were simulated via a novel hybrid quantum mechanical/molecular mechanics (QM/MM) algorithm that forced repeated bimolecular collisions. Molecular orbital (MO) rearrangements (manifested as bond dissociation or formation), resulting from the collisions, were computed by semi-empirical unrestricted Hartree-Fock methods (e.g., RM1). A minimum of 975 collisions between ozone and targeted organic species were performed to generate a distribution of reaction products. Results indicated that benzene and sabinene reacted with ozone to produce a range of stable products and intermediates, including carbocations, ring-scission products, as well as peroxy (HO2 and HO3) and hydroxyl (OH) radicals. Among the stable sabinene products observed included formaldehyde and sabina-ketone, which have been experimentally demonstrated in gas-phase ozonation reactions. Among the benzene ozonation products detected composed of oxygen mono-substituted aromatic C6H5O, which may undergo further transformation or rearrangement to phenol, benzene oxide or 2,4-cyclohexadienone; a phenomenon which has been experimentally observed in vapor-phase photocatalytic ozonation reactions. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Dynamic simulation of a direct carbonate fuel cell power plant

    Energy Technology Data Exchange (ETDEWEB)

    Ernest, J.B. [Fluor Daniel, Inc., Irvine, CA (United States); Ghezel-Ayagh, H.; Kush, A.K. [Fuel Cell Engineering, Danbury, CT (United States)

    1996-12-31

    Fuel Cell Engineering Corporation (FCE) is commercializing a 2.85 MW Direct carbonate Fuel Cell (DFC) power plant. The commercialization sequence has already progressed through construction and operation of the first commercial-scale DFC power plant on a U.S. electric utility, the 2 MW Santa Clara Demonstration Project (SCDP), and the completion of the early phases of a Commercial Plant design. A 400 kW fuel cell stack Test Facility is being built at Energy Research Corporation (ERC), FCE`s parent company, which will be capable of testing commercial-sized fuel cell stacks in an integrated plant configuration. Fluor Daniel, Inc. provided engineering, procurement, and construction services for SCDP and has jointly developed the Commercial Plant design with FCE, focusing on the balance-of-plant (BOP) equipment outside of the fuel cell modules. This paper provides a brief orientation to the dynamic simulation of a fuel cell power plant and the benefits offered.

  3. A chirped-pulse Fourier-transform microwave/pulsed uniform flow spectrometer. II. Performance and applications for reaction dynamics.

    Science.gov (United States)

    Abeysekera, Chamara; Zack, Lindsay N; Park, G Barratt; Joalland, Baptiste; Oldham, James M; Prozument, Kirill; Ariyasingha, Nuwandi M; Sims, Ian R; Field, Robert W; Suits, Arthur G

    2014-12-01

    This second paper in a series of two reports on the performance of a new instrument for studying chemical reaction dynamics and kinetics at low temperatures. Our approach employs chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy to probe photolysis and bimolecular reaction products that are thermalized in pulsed uniform flows. Here we detail the development and testing of a new K(a)-band CP-FTMW spectrometer in combination with the pulsed flow system described in Paper I [J. M. Oldham, C. Abeysekera, B. Joalland, L. N. Zack, K. Prozument, I. R. Sims, G. B. Park, R. W. Field, and A. G. Suits, J. Chem. Phys. 141, 154202 (2014)]. This combination delivers broadband spectra with MHz resolution and allows monitoring, on the μs timescale, of the appearance of transient reaction products. Two benchmark reactive systems are used to illustrate and characterize the performance of this new apparatus: the photodissociation of SO2 at 193 nm, for which the vibrational populations of the SO product are monitored, and the reaction between CN and C2H2, for which the HCCCN product is detected in its vibrational ground state. The results show that the combination of these two well-matched techniques, which we refer to as chirped-pulse in uniform flow, also provides insight into the vibrational and rotational relaxation kinetics of the nascent reaction products. Future directions are discussed, with an emphasis on exploring the low temperature chemistry of complex polyatomic systems.

  4. A full-dimensional quantum dynamics study of the mode specificity in the H + HOD abstraction reaction

    Science.gov (United States)

    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.

  5. Issues associated with modelling of proton exchange membrane fuel cell by computational fluid dynamics

    Science.gov (United States)

    Bednarek, Tomasz; Tsotridis, Georgios

    2017-03-01

    The objective of the current study is to highlight possible limitations and difficulties associated with Computational Fluid Dynamics in PEM single fuel cell modelling. It is shown that an appropriate convergence methodology should be applied for steady-state solutions, due to inherent numerical instabilities. A single channel fuel cell model has been taken as numerical example. Results are evaluated for quantitative as well qualitative points of view. The contribution to the polarization curve of the different fuel cell components such as bi-polar plates, gas diffusion layers, catalyst layers and membrane was investigated via their effects on the overpotentials. Furthermore, the potential losses corresponding to reaction kinetics, due to ohmic and mas transport limitations and the effect of the exchange current density and open circuit voltage, were also investigated. It is highlighted that the lack of reliable and robust input data is one of the issues for obtaining accurate results.

  6. Stochastic dynamics of interacting haematopoietic stem cell niche lineages.

    Directory of Open Access Journals (Sweden)

    Tamás Székely

    2014-09-01

    Full Text Available Since we still know very little about stem cells in their natural environment, it is useful to explore their dynamics through modelling and simulation, as well as experimentally. Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell populations. This is not appropriate at the level of individual cells and niches, when randomness is more likely to affect dynamics. In this paper, we introduce a fast stochastic method for simulating a metapopulation of stem cell niche lineages, that is, many sub-populations that together form a heterogeneous metapopulation, over time. By selecting the common limiting timestep, our method ensures that the entire metapopulation is simulated synchronously. This is important, as it allows us to introduce interactions between separate niche lineages, which would otherwise be impossible. We expand our method to enable the coupling of many lineages into niche groups, where differentiated cells are pooled within each niche group. Using this method, we explore the dynamics of the haematopoietic system from a demand control system perspective. We find that coupling together niche lineages allows the organism to regulate blood cell numbers as closely as possible to the homeostatic optimum. Furthermore, coupled lineages respond better than uncoupled ones to random perturbations, here the loss of some myeloid cells. This could imply that it is advantageous for an organism to connect together its niche lineages into groups. Our results suggest that a potential fruitful empirical direction will be to understand how stem cell descendants communicate with the niche and how cancer may arise as a result of a failure of such communication.

  7. A dynamic plug flow reactor model for a vanadium redox flow battery cell

    Science.gov (United States)

    Li, Yifeng; Skyllas-Kazacos, Maria; Bao, Jie

    2016-04-01

    A dynamic plug flow reactor model for a single cell VRB system is developed based on material balance, and the Nernst equation is employed to calculate cell voltage with consideration of activation and concentration overpotentials. Simulation studies were conducted under various conditions to investigate the effects of several key operation variables including electrolyte flow rate, upper SOC limit and input current magnitude on the cell charging performance. The results show that all three variables have a great impact on performance, particularly on the possibility of gassing during charging at high SOCs or inadequate flow rates. Simulations were also carried out to study the effects of electrolyte imbalance during long term charging and discharging cycling. The results show the minimum electrolyte flow rate needed for operation within a particular SOC range in order to avoid gassing side reactions during charging. The model also allows scheduling of partial electrolyte remixing operations to restore capacity and also avoid possible gassing side reactions during charging. Simulation results also suggest the proper placement for cell voltage monitoring and highlight potential problems associated with setting the upper charging cut-off limit based on the inlet SOC calculated from the open-circuit cell voltage measurement.

  8. Theoretical Study on the Dynamics of the Reaction of HNO((1)A') with HO2((2)A″).

    Science.gov (United States)

    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.

  9. Temperature dependence of the OH(-) + CH3I reaction kinetics. experimental and simulation studies and atomic-level dynamics.

    Science.gov (United States)

    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

  10. Topological defects control collective dynamics in neural progenitor cell cultures

    Science.gov (United States)

    Kawaguchi, Kyogo; Kageyama, Ryoichiro; Sano, Masaki

    2017-04-01

    Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.

  11. Dynamically constrained pipeline for tracking neural progenitor cells

    DEFF Research Database (Denmark)

    Vestergaard, Jacob Schack; Dahl, Anders; Holm, Peter

    2013-01-01

    . A mitosis detector constructed from empirical observations of cells in a pre-mitotic state interacts with the graph formulation to dynamically allow for cell mitosis when appropriate. Track consistency is ensured by introducing pragmatic constraints and the notion of blob states. We validate the proposed...... tracking methods are fundamental building blocks of setting up multi purpose pipelines. Segmentation by discriminative dictionary learning and a graph formulated tracking method constraining the allowed topology changes are combined here to accommodate for highly irregular cell shapes and movement patterns...

  12. Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Schnell, Sondre K. [Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft (Netherlands); Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720 (United States); Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim (Norway); Skorpa, Ragnhild; Bedeaux, Dick [Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim (Norway); Kjelstrup, Signe [Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim (Norway); Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft (Netherlands); Vlugt, Thijs J. H. [Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft (Netherlands); Simon, Jean-Marc, E-mail: jmsimon@u-bourgogne.fr [Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS-Université de Bourgogne, 9, av. Savary, 21000 Dijon (France)

    2014-10-14

    We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtained with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.

  13. Mechanobiology of cell migration in the context of dynamic two-way cell-matrix interactions.

    Science.gov (United States)

    Kurniawan, Nicholas A; Chaudhuri, Parthiv Kant; Lim, Chwee Teck

    2016-05-24

    Migration of cells is integral in various physiological processes in all facets of life. These range from embryonic development, morphogenesis, and wound healing, to disease pathology such as cancer metastasis. While cell migratory behavior has been traditionally studied using simple assays on culture dishes, in recent years it has been increasingly realized that the physical, mechanical, and chemical aspects of the matrix are key determinants of the migration mechanism. In this paper, we will describe the mechanobiological changes that accompany the dynamic cell-matrix interactions during cell migration. Furthermore, we will review what is to date known about how these changes feed back to the dynamics and biomechanical properties of the cell and the matrix. Elucidating the role of these intimate cell-matrix interactions will provide not only a better multi-scale understanding of cell motility in its physiological context, but also a more holistic perspective for designing approaches to regulate cell behavior.

  14. Nonlinear Dynamic Theory of Acute Cell Injuries and Brain Ischemia

    Science.gov (United States)

    Taha, Doaa; Anggraini, Fika; Degracia, Donald; Huang, Zhi-Feng

    2015-03-01

    Cerebral ischemia in the form of stroke and cardiac arrest brain damage affect over 1 million people per year in the USA alone. In spite of close to 200 clinical trials and decades of research, there are no treatments to stop post-ischemic neuron death. We have argued that a major weakness of current brain ischemia research is lack of a deductive theoretical framework of acute cell injury to guide empirical studies. A previously published autonomous model based on the concept of nonlinear dynamic network was shown to capture important facets of cell injury, linking the concept of therapeutic to bistable dynamics. Here we present an improved, non-autonomous formulation of the nonlinear dynamic model of cell injury that allows multiple acute injuries over time, thereby allowing simulations of both therapeutic treatment and preconditioning. Our results are connected to the experimental data of gene expression and proteomics of neuron cells. Importantly, this new model may be construed as a novel approach to pharmacodynamics of acute cell injury. The model makes explicit that any pro-survival therapy is always a form of sub-lethal injury. This insight is expected to widely influence treatment of acute injury conditions that have defied successful treatment to date. This work is supported by NIH NINDS (NS081347) and Wayne State University President's Research Enhancement Award.

  15. Probing the role of Skyrme interactions on the fission dynamics of the 6Li + 238U reaction

    Science.gov (United States)

    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.

  16. Oxygen electrode reaction in molten carbonate fuel cells. Final report, September 15, 1987--September 14, 1990

    Energy Technology Data Exchange (ETDEWEB)

    Dave, Bhasker B. [Texas A & M Univ., College Station, TX (United States)

    1992-07-07

    Molten carbonate fuel cell system is a leading candidate for the utility power generation because of its high efficiency for fuel to AC power conversion, capability for an internal reforming, and a very low environmental impact. However, the performance of the molten carbonate fuel cell is limited by the oxygen reduction reaction and the cell life time is limited by the stability of the cathode material. An elucidation of oxygen reduction reaction in molten alkali carbonate is essential because overpotential losses in the molten carbonate fuel cell are considerably greater at the oxygen cathode than at the fuel anode. Oxygen reduction on a fully-immersed gold electrode in a lithium carbonate melt was investigated by electrochemical impedance spectroscopy and cyclic voltammetry to determine electrode kinetic and mass transfer parameters. The dependences of electrode kinetic and mass transfer parameters on gas composition and temperature were examined to determine the reaction orders and the activation energies. The results showed that oxygen reduction in a pure lithium carbonate melt occurs via the peroxide mechanism. A mass transfer parameter, DO1/2CO, estimated by the cyclic voltammetry concurred with that calculated by the EIS technique. The temperature dependence of the exchange current density and the product DO1/2CO were examined and the apparent activation energies were determined to be about 122 and 175 kJ/ mol, respectively.

  17. Mapping the dynamics of adverse drug reactions in subsequent time periods using INDSCAL

    NARCIS (Netherlands)

    Rikken, F.; Kiers, H.A.L.; Vos, R.

    1995-01-01

    In this study we have focused on the problem of mapping the dynamics of co-word-matrices from subsequent time periods. Methods for mapping dynamics are important for following trends in research. We have explored the possibilities of a three way multidimensional scaling method, INDSCAL. We are espec

  18. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2015-12-01

    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  19. Modeling dynamics of HIV infected cells using stochastic cellular automaton

    Science.gov (United States)

    Precharattana, Monamorn; Triampo, Wannapong

    2014-08-01

    Ever since HIV was first diagnosed in human, a great number of scientific works have been undertaken to explore the biological mechanisms involved in the infection and progression of the disease. Several cellular automata (CA) models have been introduced to gain insights into the dynamics of the disease progression but none of them has taken into account effects of certain immune cells such as the dendritic cells (DCs) and the CD8+ T lymphocytes (CD8+ T cells). In this work, we present a CA model, which incorporates effects of the HIV specific immune response focusing on the cell-mediated immunities, and investigate the interaction between the host immune response and the HIV infected cells in the lymph nodes. The aim of our work is to propose a model more realistic than the one in Precharattana et al. (2010) [10], by incorporating roles of the DCs, the CD4+ T cells, and the CD8+ T cells into the model so that it would reproduce the HIV infection dynamics during the primary phase of HIV infection.

  20. An Endothelial Planar Cell Model for Imaging Immunological Synapse Dynamics.

    Science.gov (United States)

    Martinelli, Roberta; Carman, Christopher V

    2015-12-24

    Adaptive immunity is regulated by dynamic interactions between T cells and antigen presenting cells ('APCs') referred to as 'immunological synapses'. Within these intimate cell-cell interfaces discrete sub-cellular clusters of MHC/Ag-TCR, F-actin, adhesion and signaling molecules form and remodel rapidly. These dynamics are thought to be critical determinants of both the efficiency and quality of the immune responses that develop and therefore of protective versus pathologic immunity. Current understanding of immunological synapses with physiologic APCs is limited by the inadequacy of the obtainable imaging resolution. Though artificial substrate models (e.g., planar lipid bilayers) offer excellent resolution and have been extremely valuable tools, they are inherently non-physiologic and oversimplified. Vascular and lymphatic endothelial cells have emerged as an important peripheral tissue (or stromal) compartment of 'semi-professional APCs'. These APCs (which express most of the molecular machinery of professional APCs) have the unique feature of forming virtually planar cell surface and are readily transfectable (e.g., with fluorescent protein reporters). Herein a basic approach to implement endothelial cells as a novel and physiologic 'planar cellular APC model' for improved imaging and interrogation of fundamental antigenic signaling processes will be described.