Validity of the site-averaging approximation for modeling the dissociative chemisorption of H{sub 2} on Cu(111) surface: A quantum dynamics study on two potential energy surfaces

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

Liu, Tianhui; Fu, Bina, E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H., E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn

A new finding of the site-averaging approximation was recently reported on the dissociative chemisorption of the HCl/DCl+Au(111) surface reaction [T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 139, 184705 (2013); T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 140, 144701 (2014)]. Here, in order to investigate the dependence of new site-averaging approximation on the initial vibrational state of H{sub 2} as well as the PES for the dissociative chemisorption of H{sub 2} on Cu(111) surface at normal incidence, we carried out six-dimensional quantum dynamics calculations using the initial state-selected time-dependent wave packet approach, withmore » H{sub 2} initially in its ground vibrational state and the first vibrational excited state. The corresponding four-dimensional site-specific dissociation probabilities are also calculated with H{sub 2} fixed at bridge, center, and top sites. These calculations are all performed based on two different potential energy surfaces (PESs). It is found that the site-averaging dissociation probability over 15 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability for H{sub 2} (v = 0) and (v = 1) on the two PESs.« less

Activated adsorption of methane on clean and oxygen-modified Pt?111? and Pd?110?

NASA Astrophysics Data System (ADS)

Valden, M.; Pere, J.; Hirsimäki, M.; Suhonen, S.; Pessa, M.

1997-04-01

Activated adsorption of CH 4 on clean and oxygen modified Pt{111} and Pd{110} has been studied using molecular beam surface scattering. The absolute dissociation probability of CH 4 was measured as a function of the incident normal energy ( E) and the surface temperature ( Ts). The results from clean Pt{111} and Pd{110} are consistent with a direct dissociation mechanism. The dissociative chemisorption dynamics of CH 4 is addressed by using quantum mechanical and statistical models. The influence of adsorbed oxygen on the dissociative adsorption of CH 4 on both Pt{111} and Pd{110} shows that the dissociation probability decreases linearly with increasing oxygen coverage.

The Leaky Dielectric Model as a Weak Electrolyte Limit of an Electrodiffusion Model

NASA Astrophysics Data System (ADS)

Mori, Yoichiro; Young, Yuan-Nan

2017-11-01

The Taylor-Melcher (TM) model is the standard model for the electrohydrodynamics of poorly conducting leaky dielectric fluids under an electric field. The TM model treats the fluid as an ohmic conductor, without modeling ion dynamics. On the other hand, electrodiffusion models, which have been successful in describing electokinetic phenomena, incorporates ionic concentration dynamics. Mathematical reconciliation between electrodiffusion and the TM models has been a major issue for electrohydrodynamic theory. Here, we derive the TM model from an electrodiffusion model where we explicitly model the electrochemistry of ion dissociation. We introduce salt dissociation reaction in the bulk and take the limit of weak salt dissociation (corresponding to poor conductors in the TM model.) Assuming small Debye length we derive the TM model with or without the surface charge advection term depending upon the scaling of relevant dimensionless parameters. Our analysis also gives a description of the ionic concentration distribution within the Debye layer, which hints at possible scenarios for electrohydrodynamic singularity formation. In our analysis we also allow for a jump in voltage across the liquid interface which causes a drifting velocity for a liquid drop under an electric field. YM is partially supported by NSF-DMS-1516978 and NSF-DMS-1620316. YNY is partially supported by NSF-DMS-1412789 and NSF-DMS-1614863.

Molecular model for the diffusion of associating telechelic polymer networks

NASA Astrophysics Data System (ADS)

Ramirez, Jorge; Dursch, Thomas; Olsen, Bradley

Understanding the mechanisms of motion and stress relaxation of associating polymers at the molecular level is critical for advanced technological applications such as enhanced oil-recovery, self-healing materials or drug delivery. In associating polymers, the strength and rates of association/dissociation of the reversible physical crosslinks govern the dynamics of the network and therefore all the macroscopic properties, like self-diffusion and rheology. Recently, by means of forced Rayleigh scattering experiments, we have proved that associating polymers of different architectures show super-diffusive behavior when the free motion of single molecular species is slowed down by association/dissociation kinetics. Here we discuss a new molecular picture for unentangled associating telechelic polymers that considers concentration, molecular weight, number of arms of the molecules and equilibrium and rate constants of association/dissociation. The model predicts super-diffusive behavior under the right combination of values of the parameters. We discuss some of the predictions of the model using scaling arguments, show detailed results from Brownian dynamics simulations of the FRS experiments, and attempt to compare the predictions of the model to experimental data.

Quantum dynamics of water dissociative chemisorption on rigid Ni(111): An approximate nine-dimensional treatment

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

Jiang, Bin, E-mail: bjiangch@ustc.edu.cn, E-mail: hguo@unm.edu; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131; Song, Hongwei

The quantum dynamics of water dissociative chemisorption on the rigid Ni(111) surface is investigated using a recently developed nine-dimensional potential energy surface. The quantum dynamical model includes explicitly seven degrees of freedom of D{sub 2}O at fixed surface sites, and the final results were obtained with a site-averaging model. The mode specificity in the site-specific results is reported and analyzed. Finally, the approximate sticking probabilities for various vibrationally excited states of D{sub 2}O are obtained considering surface lattice effects and formally all nine degrees of freedom. The comparison with experiment reveals the inaccuracy of the density functional theory and suggestsmore » the need to improve the potential energy surface.« less

The key role of dislocation dissociation in the plastic behaviour of single crystal nickel-based superalloy with low stacking fault energy: Three-dimensional discrete dislocation dynamics modelling

NASA Astrophysics Data System (ADS)

Huang, Minsheng; Li, Zhenhuan

2013-12-01

To model the deformation of single crystal nickel based superalloys (SCNBS) with low stacking fault energy (SFE), three-dimensional discrete dislocation dynamics (3D-DDD) is extended by incorporating dislocation dissociation mechanism. The present 3D-DDD simulations show that, consistent with the existing TEM observation, the leading partial can enter the matrix channel efficiently while the trailing partial can hardly glide into it when the dislocation dissociation is taken into account. To determine whether the dislocation dissociation can occur or not, a critical percolation stress (CPS) based criterion is suggested. According to this CPS criterion, for SCNBS there exists a critical matrix channel width. When the channel width is lower than this critical value, the dislocation tends to dissociate into an extended configuration and vice versa. To clarify the influence of dislocation dissociation on CPS, the classical Orowan formula is improved by incorporating the SFE. Moreover, the present 3D-DDD simulations also show that the yielding stress of SCNBSs with low SFE may be overestimated up to 30% if the dislocation dissociation is ignored. With dislocation dissociation being considered, the size effect due to the width of γ matrix channel and the length of γ‧ precipitates on the stress-strain responses of SCNBS can be enhanced remarkably. In addition, due to the strong constraint effect by the two-phase microstructure in SCNBS, the configuration of formed junctions is quite different from that in single phase crystals such as Cu. The present results not only provide clear understanding of the two-phase microstructure levelled microplastic mechanisms in SCNBSs with low SFE, but also help to develop new continuum-levelled constitutive laws for SCNBSs.

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

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

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Ab initio state-specific N2 + O dissociation and exchange modeling for molecular simulations

NASA Astrophysics Data System (ADS)

Luo, Han; Kulakhmetov, Marat; Alexeenko, Alina

2017-02-01

Quasi-classical trajectory (QCT) calculations are used in this work to calculate state-specific N2(X1Σ ) +O(3P ) →2 N(4S ) +O(3P ) dissociation and N2(X1Σ ) +O(3P ) →NO(X2Π ) +N(4S ) exchange cross sections and rates based on the 13A″ and 13A' ab initio potential energy surface by Gamallo et al. [J. Chem. Phys. 119, 2545-2556 (2003)]. The calculations consider translational energies up to 23 eV and temperatures between 1000 K and 20 000 K. Vibrational favoring is observed for dissociation reaction at the whole range of collision energies and for exchange reaction around the dissociation limit. For the same collision energy, cross sections for v = 30 are 4 to 6 times larger than those for the ground state. The exchange reaction has an effective activation energy that is dependent on the initial rovibrational level, which is different from dissociation reaction. In addition, the exchange cross sections have a maximum when the total collision energy (TCE) approaches dissociation energy. The calculations are used to generate compact QCT-derived state-specific dissociation (QCT-SSD) and QCT-derived state-specific exchange (QCT-SSE) models, which describe over 1 × 106 cross sections with about 150 model parameters. The models can be used directly within direct simulation Monte Carlo and computational fluid dynamics simulations. Rate constants predicted by the new models are compared to the experimental measurements, direct QCT calculations and predictions by other models that include: TCE model, Bose-Candler QCT-based exchange model, Macheret-Fridman dissociation model, Macheret's exchange model, and Park's two-temperature model. The new models match QCT-calculated and experimental rates within 30% under nonequilibrium conditions while other models under predict by over an order of magnitude under vibrationally-cold conditions.

Dislocation Dissociation Strongly Influences on Frank—Read Source Nucleation and Microplasticy of Materials with Low Stacking Fault Energy

NASA Astrophysics Data System (ADS)

Huang, Min-Sheng; Zhu, Ya-Xin; Li, Zhen-Huan

2014-04-01

The influence of dislocation dissociation on the evolution of Frank—Read (F-R) sources is studied using a three-dimensional discrete dislocation dynamics simulation (3D-DDD). The classical Orowan nucleation stress and recently proposed Benzerga nucleation time models for F-R sources are improved. This work shows that it is necessary to introduce the dislocation dissociation scheme into 3D-DDD simulation, especially for simulations on micro-plasticity of small sized materials with low stacking fault energy.

Attosecond Spectroscopy Probing Electron Correlation Dynamics

NASA Astrophysics Data System (ADS)

Winney, Alexander H.

Electrons are the driving force behind every chemical reaction. The exchange, ionization, or even relaxation of electrons is behind every bond broken or formed. According to the Bohr model of the atom, it takes an electron 150 as to orbit a proton[6]. With this as a unit time scale for an electron, it is clear that a pulse duration of several femtoseconds will not be sufficient to understanding electron dynamics. Our work demonstrates both technical and scientific achievements that push the boundaries of attosecond dynamics. TDSE studies show that amplification the yield of high harmonic generation (HHG) may be possible with transverse confinement of the electron. XUV-pump-XUV-probe shows that the yield of APT train can be sufficient for 2-photon double ionization studies. A zero dead-time detection system allows for the measurement of state-resolved double ionization for the first time. Exploiting attosecond angular streaking[7] probes sequential and non-sequential double ionization via electron-electron correlations with attosecond time resolution. Finally, using recoil frame momentum correlation, the fast dissociation of CH 3I reveals important orbital ionization dynamics of non-dissociative & dissociative, single & double ionization.

Effects of surface motion and electron-hole pair excitations in CO2 dissociation and scattering on Ni(100)

NASA Astrophysics Data System (ADS)

Luo, Xuan; Zhou, Xueyao; Jiang, Bin

2018-05-01

The energy transfer between different channels is an important aspect in chemical reactions at surfaces. We investigate here in detail the energy transfer dynamics in a prototypical system, i.e., reactive and nonreactive scattering of CO2 on Ni(100), which is related to heterogeneous catalytic processes with Ni-based catalysts for CO2 reduction. On the basis of our earlier nine-dimensional potential energy surface for CO2/Ni(100), dynamical calculations have been done using the generalized Langevin oscillator (GLO) model combined with local density friction approximation (LDFA), in which the former accounts for the surface motion and the latter accounts for the low-energy electron-hole pair (EHP) excitation. In spite of its simplicity, it is found that the GLO model yields quite satisfactory results, including the significant energy loss and product energy disposal, trapping, and steering dynamics, all of which agree well with the ab initio molecular dynamics ones where many surface atoms are explicitly involved with high computational cost. However, the GLO model fails to describe the reactivity enhancement due to the lattice motion because it intrinsically does not incorporate the variance of barrier height on the surface atom displacement. On the other hand, in LDFA, the energy transferred to EHPs is found to play a minor role and barely alter the dynamics, except for slightly reducing the dissociation probabilities. In addition, vibrational state-selected dissociative sticking probabilities are calculated and previously observed strong mode specificity is confirmed. Our work suggests that further improvement of the GLO model is needed to consider the lattice-induced barrier lowering.

Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

PubMed

English, Niall J; Clarke, Elaine T

2013-09-07

Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming.

PubMed

Wallmann, Klaus; Riedel, M; Hong, W L; Patton, H; Hubbard, A; Pape, T; Hsu, C W; Schmidt, C; Johnson, J E; Torres, M E; Andreassen, K; Berndt, C; Bohrmann, G

2018-01-08

Methane seepage from the upper continental slopes of Western Svalbard has previously been attributed to gas hydrate dissociation induced by anthropogenic warming of ambient bottom waters. Here we show that sediment cores drilled off Prins Karls Foreland contain freshwater from dissociating hydrates. However, our modeling indicates that the observed pore water freshening began around 8 ka BP when the rate of isostatic uplift outpaced eustatic sea-level rise. The resultant local shallowing and lowering of hydrostatic pressure forced gas hydrate dissociation and dissolved chloride depletions consistent with our geochemical analysis. Hence, we propose that hydrate dissociation was triggered by postglacial isostatic rebound rather than anthropogenic warming. Furthermore, we show that methane fluxes from dissociating hydrates were considerably smaller than present methane seepage rates implying that gas hydrates were not a major source of methane to the oceans, but rather acted as a dynamic seal, regulating methane release from deep geological reservoirs.

Photodissociation dynamics and spectroscopy of free radical combustion intermediates

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

Osborn, David Lewis

1996-12-01

The photodissociation spectroscopy and dynamics of free radicals is studied by the technique of fast beam photofragment translational spectroscopy. Photodetachment of internally cold, mass-selected negative ions produces a clean source of radicals, which are subsequently dissociated and detected. The photofragment yield as a function of photon energy is obtained, mapping out the dissociative and predissociative electronic states of the radical. In addition, the photodissociation dynamics, product branching ratios, and bond energies are probed at fixed photon energies by measuring the translational energy, P(E T), and angular distribution of the recoiling fragments using a time- and position-sensitive detector. Ab initio calculationsmore » are combined with dynamical and statistical models to interpret the observed data. The photodissociation of three prototypical hydrocarbon combustion intermediates forms the core of this work.« less

Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering

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

Rimmerman, Dolev; Leshchev, Denis; Hsu, Darren J.

Biological functions frequently require protein-protein interactions that involve secondary and tertiary structural perturbation. Here we study protein-protein dissociation and reassociation dynamics in insulin, a model system for protein oligomerization. Insulin dimer dissociation into monomers was induced by a nanosecond temperature-jump (T-jump) of ~8 °C in aqueous solution, and the resulting protein and solvent dynamics were tracked by time-resolved X-ray solution scattering (TRXSS) on time scales of 10 ns to 100 ms. The protein scattering signals revealed the formation of five distinguishable transient species during the association process that deviate from simple two state kinetics. Our results show that the combinationmore » of T-jump pump coupled to TRXSS probe allows for direct tracking of structural dynamics in nonphotoactive proteins.« less

Exploring the importance of quantum effects in nucleation: The archetypical Nen case

NASA Astrophysics Data System (ADS)

Unn-Toc, Wesley; Halberstadt, Nadine; Meier, Christoph; Mella, Massimo

2012-07-01

The effect of quantum mechanics (QM) on the details of the nucleation process is explored employing Ne clusters as test cases due to their semi-quantal nature. In particular, we investigate the impact of quantum mechanics on both condensation and dissociation rates in the framework of the microcanonical ensemble. Using both classical trajectories and two semi-quantal approaches (zero point averaged dynamics, ZPAD, and Gaussian-based time dependent Hartree, G-TDH) to model cluster and collision dynamics, we simulate the dissociation and monomer capture for Ne8 as a function of the cluster internal energy, impact parameter and collision speed. The results for the capture probability Ps(b) as a function of the impact parameter suggest that classical trajectories always underestimate capture probabilities with respect to ZPAD, albeit at most by 15%-20% in the cases we studied. They also do so in some important situations when using G-TDH. More interestingly, dissociation rates kdiss are grossly overestimated by classical mechanics, at least by one order of magnitude. We interpret both behaviours as mainly due to the reduced amount of kinetic energy available to a quantum cluster for a chosen total internal energy. We also find that the decrease in monomer dissociation energy due to zero point energy effects plays a key role in defining dissociation rates. In fact, semi-quantal and classical results for kdiss seem to follow a common "corresponding states" behaviour when the proper definition of internal and dissociation energies are used in a transition state model estimation of the evaporation rate constants.

Systemic Case Formulation, Individualized Process Monitoring, and State Dynamics in a Case of Dissociative Identity Disorder.

PubMed

Schiepek, Günter K; Stöger-Schmidinger, Barbara; Aichhorn, Wolfgang; Schöller, Helmut; Aas, Benjamin

2016-01-01

Objective: The aim of this case report is to demonstrate the feasibility of a systemic procedure (synergetic process management) including modeling of the idiographic psychological system and continuous high-frequency monitoring of change dynamics in a case of dissociative identity disorder. The psychotherapy was realized in a day treatment center with a female client diagnosed with borderline personality disorder (BPD) and dissociative identity disorder. Methods: A three hour long co-creative session at the beginning of the treatment period allowed for modeling the systemic network of the client's dynamics of cognitions, emotions, and behavior. The components (variables) of this idiographic system model (ISM) were used to create items for an individualized process questionnaire for the client. The questionnaire was administered daily through an internet-based monitoring tool (Synergetic Navigation System, SNS), to capture the client's individual change process continuously throughout the therapy and after-care period. The resulting time series were reflected by therapist and client in therapeutic feedback sessions. Results: For the client it was important to see how the personality states dominating her daily life were represented by her idiographic system model and how the transitions between each state could be explained and understood by the activating and inhibiting relations between the cognitive-emotional components of that system. Continuous monitoring of her cognitions, emotions, and behavior via SNS allowed for identification of important triggers, dynamic patterns, and psychological mechanisms behind seemingly erratic state fluctuations. These insights enabled a change in management of the dynamics and an intensified trauma-focused therapy. Conclusion: By making use of the systemic case formulation technique and subsequent daily online monitoring, client and therapist continuously refer to detailed visualizations of the mental and behavioral network and its dynamics (e.g., order transitions). Effects on self-related information processing, on identity development, and toward a more pronounced autonomy in life (instead of feeling helpless against the chaoticity of state dynamics) were evident in the presented case and documented by the monitoring system.

Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel

NASA Astrophysics Data System (ADS)

Kurosaki, Yuzuru; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel

2009-07-01

Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open→cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O2+O asymptote on the O3 ground-state A1' potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O2+O dissociation channel lie at ˜0.05, ˜0.086, and ˜0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O2+O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

NASA Astrophysics Data System (ADS)

Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

2017-10-01

Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

Coupled channel effects on resonance states of positronic alkali atom

NASA Astrophysics Data System (ADS)

Yamashita, Takuma; Kino, Yasushi

2018-01-01

S-wave Feshbach resonance states belonging to dipole series in positronic alkali atoms (e+Li, e+Na, e+K, e+Rb and e+Cs) are studied by coupled-channel calculations within a three-body model. Resonance energies and widths below a dissociation threshold of alkali-ion and positronium are calculated with a complex scaling method. Extended model potentials that provide positronic pseudo-alkali-atoms are introduced to investigate the relationship between the resonance states and dissociation thresholds based on a three-body dynamics. Resonances of the dipole series below a dissociation threshold of alkali-atom and positron would have some associations with atomic energy levels that results in longer resonance lifetimes than the prediction of the analytical law derived from the ion-dipole interaction.

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

Development and testing of a numerical simulation method for thermally nonequilibrium dissociating flows in ANSYS Fluent

NASA Astrophysics Data System (ADS)

Shoev, G. V.; Bondar, Ye. A.; Oblapenko, G. P.; Kustova, E. V.

2016-03-01

Various issues of numerical simulation of supersonic gas flows with allowance for thermochemical nonequilibrium on the basis of fluid dynamic equations in the two-temperature approximation are discussed. The computational tool for modeling flows with thermochemical nonequilibrium is the commercial software package ANSYS Fluent with an additional userdefined open-code module. A comparative analysis of results obtained by various models of vibration-dissociation coupling in binary gas mixtures of nitrogen and oxygen is performed. Results of numerical simulations are compared with available experimental data.

Controlling Heterogeneous Catalysis of Water Dissociation Using Cu-Ni Bimetallic Alloy Surfaces: A Quantum Dynamics Study.

PubMed

Ray, Dhiman; Ghosh, Smita; Tiwari, Ashwani Kumar

2018-06-07

Copper-Nickel bimetallic alloys are emerging heterogeneous catalysts for water dissociation which is the rate determining step of industrially important Water Gas Shift (WGS) reaction. Yet, the detailed quantum dynamics studies of water-surface scattering in literature are limited to pure metal surfaces. We present here, a three dimensional wave-packet dynamics study of water dissociation on Cu-Ni alloy surfaces, using a pseudo diatomic model of water on a London-Eyring-Polanyi-Sato (LEPS) potential energy surface in order to study the effect of initial vibration, rotation and orientation of water molecule on reactivity. For all the chosen surfaces reactivity increases significantly with vibrational excitation. In general, for lower vibrational states the reactivity increases with increasing rotational excitation but it decreases in higher vibrational states. Molecular orientation strongly affects reactivity by helping the molecule to align along the reaction path at higher vibrational states. For different alloys, the reaction probability follows the trend of barrier heights and the surfaces having all Ni atoms in the uppermost layer are much more reactive than the ones with Cu atoms. Hence the nature of the alloy surface and initial quantum state of the incoming molecule significantly influence the reactivity in surface catalyzed water dissociation.

Simulations of dissociation constants in low pressure supercritical water

NASA Astrophysics Data System (ADS)

Halstead, S. J.; An, P.; Zhang, S.

2014-09-01

This article reports molecular dynamics simulations of the dissociation of hydrochloric acid and sodium hydroxide in water from ambient to supercritical temperatures at a fixed pressure of 250 atm. Corrosion of reaction vessels is known to be a serious problem of supercritical water, and acid/base dissociation can be a significant contributing factor to this. The SPC/e model was used in conjunction with solute models determined from density functional calculations and OPLSAA Lennard-Jones parameters. Radial distribution functions were calculated, and these show a significant increase in solute-solvent ordering upon forming the product ions at all temperatures. For both dissociations, rapidly decreasing entropy of reaction was found to be the controlling thermodynamic factor, and this is thought to arise due to the ions produced from dissociation maintaining a relatively high density and ordered solvation shell compared to the reactants. The change in entropy of reaction reaches a minimum at the critical temperature. The values of pKa and pKb were calculated and both increased with temperature, in qualitative agreement with other work, until a maximum value at 748 K, after which there was a slight decrease.

Ab initio multiple spawning dynamics study of dimethylnitramine and dimethylnitramine-Fe complex to model their ultrafast nonadiabatic chemistry

NASA Astrophysics Data System (ADS)

Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu

2017-07-01

Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.

Six-dimensional quantum dynamics study for the dissociative adsorption of DCl on Au(111) surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Fu, Bina; Zhang, Dong H.

2014-04-01

We carried out six-dimensional quantum dynamics calculations for the dissociative adsorption of deuterium chloride (DCl) on Au(111) surface using the initial state-selected time-dependent wave packet approach. The four-dimensional dissociation probabilities are also obtained with the center of mass of DCl fixed at various sites. These calculations were all performed based on an accurate potential energy surface recently constructed by neural network fitting to density function theory energy points. The origin of the extremely small dissociation probability for DCl/HCl (v = 0, j = 0) fixed at the top site compared to other fixed sites is elucidated in this study. The influence of vibrational excitation and rotational orientation of DCl on the reactivity was investigated by calculating six-dimensional dissociation probabilities. The vibrational excitation of DCl enhances the reactivity substantially and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. The site-averaged dissociation probability over 25 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability.

Six-dimensional quantum dynamics study for the dissociative adsorption of DCl on Au(111) surface

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

Liu, Tianhui; Fu, Bina, E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H., E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn

We carried out six-dimensional quantum dynamics calculations for the dissociative adsorption of deuterium chloride (DCl) on Au(111) surface using the initial state-selected time-dependent wave packet approach. The four-dimensional dissociation probabilities are also obtained with the center of mass of DCl fixed at various sites. These calculations were all performed based on an accurate potential energy surface recently constructed by neural network fitting to density function theory energy points. The origin of the extremely small dissociation probability for DCl/HCl (v = 0, j = 0) fixed at the top site compared to other fixed sites is elucidated in this study. The influence of vibrational excitationmore » and rotational orientation of DCl on the reactivity was investigated by calculating six-dimensional dissociation probabilities. The vibrational excitation of DCl enhances the reactivity substantially and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. The site-averaged dissociation probability over 25 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability.« less

Correlated electron-nuclear dissociation dynamics: classical versus quantum motion

NASA Astrophysics Data System (ADS)

Schaupp, Thomas; Albert, Julian; Engel, Volker

2017-01-01

We investigate the coupled electron-nuclear dynamics in a model system which undergoes dissociation. In choosing different initial conditions, the cases of adiabatic and non-adiabatic dissociation are realized. We treat the coupled electronic and nuclear motion in the complete configuration space so that classically, no surface hopping procedures have to be incorporated in the case that more than a single adiabatic electronic state is populated during the fragmentation. Due to the anharmonic interaction potential, it is expected that classical mechanics substantially deviate from quantum mechanics. However, we provide examples where the densities and fragmentation yields obtained from the two treatments are in astonishingly strong agreement in the case that one starts in the electronic ground state initially. As expected, larger deviations are found if one starts in electronically excited states where trajectories are sampled from the more spatially extended electronic wave function. In that case, higher initial energies are accessed, and the motion proceeds in regions with increasing degree of anharmonicity. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

School Shock: A Psychodynamic View of Learning Disability.

ERIC Educational Resources Information Center

Zitani, E. Alfredo

Learning disability is seen to be a dissociative disorder (school shock) similar to shell shock in wartime. The shell shock model is explained to focus diagnosis and treatment of learning disabilities around the dynamics of the predisposing unconscious conflict, the dynamics in the environment, the mechanism which allows these two conditions to…

Description and control of dissociation channels in gas-phase protein complexes

NASA Astrophysics Data System (ADS)

Thachuk, Mark; Fegan, Sarah K.; Raheem, Nigare

2016-08-01

Using molecular dynamics simulations of a coarse-grained model of the charged apo-hemoglobin protein complex, this work expands upon our initial report [S. K. Fegan and M. Thachuk, J. Am. Soc. Mass Spectrom. 25, 722-728 (2014)] about control of dissociation channels in the gas phase using specially designed charge tags. Employing a charge hopping algorithm and a range of temperatures, a variety of dissociation channels are found for activated gas-phase protein complexes. At low temperatures, a single monomer unfolds and becomes charge enriched. At higher temperatures, two additional channels open: (i) two monomers unfold and charge enrich and (ii) two monomers compete for unfolding with one eventually dominating and the other reattaching to the complex. At even higher temperatures, other more complex dissociation channels open with three or more monomers competing for unfolding. A model charge tag with five sites is specially designed to either attract or exclude charges. By attaching this tag to the N-terminus of specific monomers, the unfolding of those monomers can be decidedly enhanced or suppressed. In other words, using charge tags to direct the motion of charges in a protein complex provides a mechanism for controlling dissociation. This technique could be used in mass spectrometry experiments to direct forces at specific attachment points in a protein complex, and hence increase the diversity of product channels available for quantitative analysis. In turn, this could provide insight into the function of the protein complex in its native biological environment. From a dynamics perspective, this system provides an interesting example of cooperative behaviour involving motions with differing time scales.

Predicting the effect of angular momentum on the dissociation dynamics of highly rotationally excited radical intermediates.

PubMed

Brynteson, Matthew D; Butler, Laurie J

2015-02-07

We present a model which accurately predicts the net speed distributions of products resulting from the unimolecular decomposition of rotationally excited radicals. The radicals are produced photolytically from a halogenated precursor under collision-free conditions so they are not in a thermal distribution of rotational states. The accuracy relies on the radical dissociating with negligible energetic barrier beyond the endoergicity. We test the model predictions using previous velocity map imaging and crossed laser-molecular beam scattering experiments that photolytically generated rotationally excited CD2CD2OH and C3H6OH radicals from brominated precursors; some of those radicals then undergo further dissociation to CD2CD2 + OH and C3H6 + OH, respectively. We model the rotational trajectories of these radicals, with high vibrational and rotational energy, first near their equilibrium geometry, and then by projecting each point during the rotation to the transition state (continuing the rotational dynamics at that geometry). This allows us to accurately predict the recoil velocity imparted in the subsequent dissociation of the radical by calculating the tangential velocities of the CD2CD2/C3H6 and OH fragments at the transition state. The model also gives a prediction for the distribution of angles between the dissociation fragments' velocity vectors and the initial radical's velocity vector. These results are used to generate fits to the previously measured time-of-flight distributions of the dissociation fragments; the fits are excellent. The results demonstrate the importance of considering the precession of the angular velocity vector for a rotating radical. We also show that if the initial angular momentum of the rotating radical lies nearly parallel to a principal axis, the very narrow range of tangential velocities predicted by this model must be convoluted with a J = 0 recoil velocity distribution to achieve a good result. The model relies on measuring the kinetic energy release when the halogenated precursor is photodissociated via a repulsive excited state but does not include any adjustable parameters. Even when different conformers of the photolytic precursor are populated, weighting the prediction by a thermal conformer population gives an accurate prediction for the relative velocity vectors of the fragments from the highly rotationally excited radical intermediates.

Surface-induced dissociation: a unique tool for studying energetics and kinetics of the gas-phase fragmentation of large ions

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

Laskin, Julia

2015-01-01

Surface-induced dissociation (SID) is valuable tool for investigating activation and dissociation of large ions in tandem mass spectrometry. This account summarizes key findings from studies of the energetics and mechanisms of complex ion dissociation, in which SID experiments were combined with Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental data. These studies used time- and collision-energy-resolved SID experiments and SID combined with resonant ejection of selected fragment ions on a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Fast ion activation by collision with a surface combined with the long and variable timescale of a FT-ICR MS is perfectlymore » suited for studying the energetics and dynamics of complex ion dissociation in the gas phase. Modeling of time- and collision-energy-resolved SID enables accurate determination of energy and entropy effects in the dissociation process. It has been demonstrated that entropy effects play an important role in determining the dissociation rates of both covalent and non-covalent bonds in large gaseous ions. SID studies have provided important insights on the competition between charge-directed and charge-remote fragmentation in even-electron peptide ions and the role of charge and radical site on the energetics of the dissociation of odd-electron peptide ions. Furthermore, this work examined factors that affect the strength of non-covalent binding, as well as the competition between covalent and non-covalent bond cleavages and between proton and electron transfer in model systems. Finally, SID studies have been used to understand the factors affecting nucleation and growth of clusters in solution and the gas phase.« less

Six-dimensional quantum dynamics study for the dissociative adsorption of HCl on Au(111) surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Fu, Bina; Zhang, Dong H.

2013-11-01

The six-dimensional quantum dynamics calculations for the dissociative chemisorption of HCl on Au(111) are carried out using the time-dependent wave-packet approach, based on an accurate PES which was recently developed by neural network fitting to density functional theory energy points. The influence of vibrational excitation and rotational orientation of HCl on the reactivity is investigated by calculating the exact six-dimensional dissociation probabilities, as well as the four-dimensional fixed-site dissociation probabilities. The vibrational excitation of HCl enhances the reactivity and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. A new interesting site-averaged effect is found for the title molecule-surface system that one can essentially reproduce the six-dimensional dissociation probability by averaging the four-dimensional dissociation probabilities over 25 fixed sites.

Potential energy surfaces and reaction dynamics of polyatomic molecules

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

Chang, Yan-Tyng

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 hydrogenmore » 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.« less

Statistical mechanical models for dissociative adsorption of O2 on metal(100) surfaces with blocking, steering, and funneling

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

Evans, James W.; Liu, Da-Jiang

We develop statistical mechanical models amenable to analytic treatment for the dissociative adsorption of O2 at hollow sites on fcc(100) metal surfaces. The models incorporate exclusion of nearest-neighbor pairs of adsorbed O. However, corresponding simple site-blocking models, where adsorption requires a large ensemble of available sites, exhibit an anomalously fast initial decrease in sticking. Thus, in addition to blocking, our models also incorporate more facile adsorption via orientational steering and funneling dynamics (features supported by ab initio Molecular Dynamics studies). Behavior for equilibrated adlayers is distinct from those with finite adspecies mobility. We focus on the low-temperature limited-mobility regime wheremore » analysis of the associated master equations readily produces exact results for both short- and long-time behavior. Kinetic Monte Carlo simulation is also utilized to provide a more complete picture of behavior. These models capture both the initial decrease and the saturation of the experimentally observed sticking versus coverage, as well as features of non-equilibrium adlayer ordering as assessed by surface-sensitive diffraction.« less

Statistical mechanical models for dissociative adsorption of O{sub 2} on metal(100) surfaces with blocking, steering, and funneling

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

Evans, James W.; Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011; Liu, Da-Jiang

We develop statistical mechanical models amenable to analytic treatment for the dissociative adsorption of O{sub 2} at hollow sites on fcc(100) metal surfaces. The models incorporate exclusion of nearest-neighbor pairs of adsorbed O. However, corresponding simple site-blocking models, where adsorption requires a large ensemble of available sites, exhibit an anomalously fast initial decrease in sticking. Thus, in addition to blocking, our models also incorporate more facile adsorption via orientational steering and funneling dynamics (features supported by ab initio Molecular Dynamics studies). Behavior for equilibrated adlayers is distinct from those with finite adspecies mobility. We focus on the low-temperature limited-mobility regimemore » where analysis of the associated master equations readily produces exact results for both short- and long-time behavior. Kinetic Monte Carlo simulation is also utilized to provide a more complete picture of behavior. These models capture both the initial decrease and the saturation of the experimentally observed sticking versus coverage, as well as features of non-equilibrium adlayer ordering as assessed by surface-sensitive diffraction.« less

Nascent energy distribution of the Criegee intermediate CH2OO from direct dynamics calculations of primary ozonide dissociation.

PubMed

Pfeifle, Mark; Ma, Yong-Tao; Jasper, Ahren W; Harding, Lawrence B; Hase, William L; Klippenstein, Stephen J

2018-05-07

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C 2 H 4 O 3 , the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H 2 COO) and formaldehyde (H 2 CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (∼30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Nascent energy distribution of the Criegee intermediate CH2OO from direct dynamics calculations of primary ozonide dissociation

NASA Astrophysics Data System (ADS)

Pfeifle, Mark; Ma, Yong-Tao; Jasper, Ahren W.; Harding, Lawrence B.; Hase, William L.; Klippenstein, Stephen J.

2018-05-01

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C2H4O3, the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H2COO) and formaldehyde (H2CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (˜30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Mapping the Complete Reaction Path of a Complex Photochemical Reaction.

PubMed

Smith, Adam D; Warne, Emily M; Bellshaw, Darren; Horke, Daniel A; Tudorovskya, Maria; Springate, Emma; Jones, Alfred J H; Cacho, Cephise; Chapman, Richard T; Kirrander, Adam; Minns, Russell S

2018-05-04

We probe the dynamics of dissociating CS_{2} molecules across the entire reaction pathway upon excitation. Photoelectron spectroscopy measurements using laboratory-generated femtosecond extreme ultraviolet pulses monitor the competing dissociation, internal conversion, and intersystem crossing dynamics. Dissociation occurs either in the initially excited singlet manifold or, via intersystem crossing, in the triplet manifold. Both product channels are monitored and show that, despite being more rapid, the singlet dissociation is the minor product and that triplet state products dominate the final yield. We explain this by a consideration of accurate potential energy curves for both the singlet and triplet states. We propose that rapid internal conversion stabilizes the singlet population dynamically, allowing for singlet-triplet relaxation via intersystem crossing and the efficient formation of spin-forbidden dissociation products on longer timescales. The study demonstrates the importance of measuring the full reaction pathway for defining accurate reaction mechanisms.

Mapping the Complete Reaction Path of a Complex Photochemical Reaction

NASA Astrophysics Data System (ADS)

Smith, Adam D.; Warne, Emily M.; Bellshaw, Darren; Horke, Daniel A.; Tudorovskya, Maria; Springate, Emma; Jones, Alfred J. H.; Cacho, Cephise; Chapman, Richard T.; Kirrander, Adam; Minns, Russell S.

2018-05-01

We probe the dynamics of dissociating CS2 molecules across the entire reaction pathway upon excitation. Photoelectron spectroscopy measurements using laboratory-generated femtosecond extreme ultraviolet pulses monitor the competing dissociation, internal conversion, and intersystem crossing dynamics. Dissociation occurs either in the initially excited singlet manifold or, via intersystem crossing, in the triplet manifold. Both product channels are monitored and show that, despite being more rapid, the singlet dissociation is the minor product and that triplet state products dominate the final yield. We explain this by a consideration of accurate potential energy curves for both the singlet and triplet states. We propose that rapid internal conversion stabilizes the singlet population dynamically, allowing for singlet-triplet relaxation via intersystem crossing and the efficient formation of spin-forbidden dissociation products on longer timescales. The study demonstrates the importance of measuring the full reaction pathway for defining accurate reaction mechanisms.

The Dual Role of Disorder on the Dissociation of Interfacial Charge Transfer Excitons

NASA Astrophysics Data System (ADS)

Shi, Liang; Lee, Chee-Kong; Willard, Adam

In organic-based photovoltaics (OPV), dissociation of neutral photo-excitations (i.e., Frenkel excitons) into free charge carriers requires the excitons to overcome binding energy that can significantly exceed thermal energies. The inability of bound charges to overcome this large binding energy has been implicated as a primary source of efficiency loss in OPVs. Despite the potential impact on the performance of organic solar cells much remains to be understood about the microscopic mechanism of exciton dissociation in OPV materials. Here we explore the role of static molecular disorder in mediating this charge dissociation process. Using a simple lattice model of exciton dynamics we demonstrate that random spatial variations in the energetic landscape can mitigate the effects of the exciton binding energy by lowering the free energy barrier. By considering the competition between this thermodynamic effect and the disorder-induced slowing of dissociation kinetics we demonstrate that exciton dissociation yields are expected to depend non-monotonically on the degree of static disorder. We conclude that a certain amount of molecular-scale disorder is desirable in order to optimize the performance of organic photovoltaic materials.

Six-dimensional quantum dynamics study for the dissociative adsorption of HCl on Au(111) surface

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

Liu, Tianhui; Fu, Bina; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn

The six-dimensional quantum dynamics calculations for the dissociative chemisorption of HCl on Au(111) are carried out using the time-dependent wave-packet approach, based on an accurate PES which was recently developed by neural network fitting to density functional theory energy points. The influence of vibrational excitation and rotational orientation of HCl on the reactivity is investigated by calculating the exact six-dimensional dissociation probabilities, as well as the four-dimensional fixed-site dissociation probabilities. The vibrational excitation of HCl enhances the reactivity and the helicopter orientation yields higher dissociation probability than the cartwheel orientation. A new interesting site-averaged effect is found for the titlemore » molecule-surface system that one can essentially reproduce the six-dimensional dissociation probability by averaging the four-dimensional dissociation probabilities over 25 fixed sites.« less

Functional connectivity and dynamics of cortical-thalamic networks co-cultured in a dual compartment device

NASA Astrophysics Data System (ADS)

Kanagasabapathi, Thirukumaran T.; Massobrio, Paolo; Barone, Rocco Andrea; Tedesco, Mariateresa; Martinoia, Sergio; Wadman, Wytse J.; Decré, Michel M. J.

2012-06-01

Co-cultures containing dissociated cortical and thalamic cells may provide a unique model for understanding the pathophysiology in the respective neuronal sub-circuitry. In addition, developing an in vitro dissociated co-culture model offers the possibility of studying the system without influence from other neuronal sub-populations. Here we demonstrate a dual compartment system coupled to microelectrode arrays (MEAs) for co-culturing and recording spontaneous activities from neuronal sub-populations. Propagation of electrical activities between cortical and thalamic regions and their interdependence in connectivity is verified by means of a cross-correlation algorithm. We found that burst events originate in the cortical region and drive the entire cortical-thalamic network bursting behavior while mutually weak thalamic connections play a relevant role in sustaining longer burst events in cortical cells. To support these experimental findings, a neuronal network model was developed and used to investigate the interplay between network dynamics and connectivity in the cortical-thalamic system.

THE DYNAMICS OF MERGING CLUSTERS: A MONTE CARLO SOLUTION APPLIED TO THE BULLET AND MUSKET BALL CLUSTERS

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

Dawson, William A., E-mail: wadawson@ucdavis.edu

2013-08-01

Merging galaxy clusters have become one of the most important probes of dark matter, providing evidence for dark matter over modified gravity and even constraints on the dark matter self-interaction cross-section. To properly constrain the dark matter cross-section it is necessary to understand the dynamics of the merger, as the inferred cross-section is a function of both the velocity of the collision and the observed time since collision. While the best understanding of merging system dynamics comes from N-body simulations, these are computationally intensive and often explore only a limited volume of the merger phase space allowed by observed parametermore » uncertainty. Simple analytic models exist but the assumptions of these methods invalidate their results near the collision time, plus error propagation of the highly correlated merger parameters is unfeasible. To address these weaknesses I develop a Monte Carlo method to discern the properties of dissociative mergers and propagate the uncertainty of the measured cluster parameters in an accurate and Bayesian manner. I introduce this method, verify it against an existing hydrodynamic N-body simulation, and apply it to two known dissociative mergers: 1ES 0657-558 (Bullet Cluster) and DLSCL J0916.2+2951 (Musket Ball Cluster). I find that this method surpasses existing analytic models-providing accurate (10% level) dynamic parameter and uncertainty estimates throughout the merger history. This, coupled with minimal required a priori information (subcluster mass, redshift, and projected separation) and relatively fast computation ({approx}6 CPU hours), makes this method ideal for large samples of dissociative merging clusters.« less

Control of photodissociation and photoionization of the NaI molecule by dynamic Stark effect.

PubMed

Han, Yong-Chang; Yuan, Kai-Jun; Hu, Wen-Hui; Cong, Shu-Lin

2009-01-28

The diabatic photodissociation and photoionization processes of the NaI molecule are studied theoretically using the quantum wave packet method. A pump laser pulse is used to prepare a dissociation wave packet that propagates through both the ionic channel (NaI-->Na(+)+I(-)) and the covalent channel (NaI-->Na+I). A Stark pulse is used to control the diabatic dissociation dynamics and a probe pulse is employed to ionize the products from the two channels. Based on the first order nonresonant nonperturbative dynamic Stark effect, the dissociation probabilities and the branching ratio of the products from the two channels can be controlled. Moreover the final photoelectron kinetic energy distribution can also be affected by the Stark pulse. The influences of the delay time, intensity, frequency, and carrier-envelope phase of the Stark pulse on the dissociation and ionization dynamics of the NaI molecule are discussed in detail.

The Palestinian/Israeli Conflict: a geopolitical identity disorder.

PubMed

Brenner, Ira

2009-03-01

In this paper, the author considers that the large-group dynamics in certain war-torn, hot spots throughout the world are symptoms of a "geopolitical identity disorder." He extrapolates from the model of the severely traumatized psyche in dissociative identity disorder in which there is so much intolerable emotion, destructive aggression and conflict that different selves with different identities develop which are unable to recognize how interdependent and related they actually are. In the most extreme cases, one dissociated self tries to kill off "the other" in order to gain exclusive control of the body and make it comply with his or her wishes and vision. In actuality, however, such an attempt is a dissociated suicide plan with lethal implications. This model is applied to the Palestinian/Israeli situation where there is a deadly battle over the land. A clinical vignette is offered to illustrate these ideas and offer possibilities for help.

Real-time tracking of dissociation of hyperpolarized 89Y-DTPA: a model for degradation of open-chain Gd3+ MRI contrast agents

NASA Astrophysics Data System (ADS)

Ferguson, Sarah; Niedbalski, Peter; Parish, Christopher; Kiswandhi, Andhika; Kovacs, Zoltan; Lumata, Lloyd

Gadolinium (Gd) complexes are widely used relaxation-based clinical contrast agents in magnetic resonance imaging (MRI). Gd-based MRI contrast agents with open-chain ligand such as Gd-DTPA, commercially known as magnevist, are less stable compared to Gd complexes with macrocyclic ligands such as GdDOTA (Dotarem). The dissociation of Gd-DPTA into Gd ion and DTPA ligand under certain biological conditions such as high zinc levels can potentially cause kidney damage. Since Gd is paramagnetic, direct NMR detection of the Gd-DTPA dissociation is quite challenging due to ultra-short relaxation times. In this work, we have investigated Y-DTPA as a model for Gd-DPTA dissociation under high zinc content solutions. Using dissolution dynamic nuclear polarization (DNP), the 89Y NMR signal is amplified by several thousand-fold. Due to the the relatively long T1 relaxation time of 89Y which translates to hyperpolarization lifetime of several minutes, the dissociation of Y-DTPA can be tracked in real-time by hyperpolarized 89Y NMR spectroscopy. Dissociation kinetic rates and implications on the degradation of open-chain Gd3+ MRI contrast agents will be discussed. This work was supported by the U.S. Department of Defense Award Number W81XWH-14-1-0048 and by the Robert A. Welch Foundation research Grant Number AT-1877.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

NASA Astrophysics Data System (ADS)

Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

2016-07-01

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Vibrational excitation and dissociative attachment of a triatomic molecule: CO/sub 2/ in the collinear approximation

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

Wong, C.F.; Light, J.C.

1986-02-01

The effective R-matrix model and the R-matrix propagative method applied earlier to elec- tron--diatomic-molecule scattering are extended to treat dissociative attachment of collinear triatomic molecules. To describe the vibrational excitation and dissociative attachment of CO/sub 2/ in the 4-eV region, the nuclear dynamics is solved on a Wall-Porter potential-energy surface. A hybrid approach is developed in which the L/sup 2/ and R-matrix propagation methods are combined to evaluate the global R matrix. Our calculations show that it is easier to excite the symmetric mode vibrations than the asymmetric mode vibrations. Our results also show that the observed structures in themore » energy dependence of the dissociative attachment cross sections are due to the vibrational states of the negative ion (CO/sub 2/ /sup -/) and not to the vibrational states of the CO fragment.« less

First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface

NASA Astrophysics Data System (ADS)

Yang, Yu; Zhang, Ping

2015-05-01

Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.

Momentum-imaging apparatus for the study of dissociative electron attachment dynamics

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

Moradmand, A.; Williams, J. B.; Landers, A. L.

An ion-momentum spectrometer is used to study the dissociative dynamics of electron attachment to molecules. A skimmed, supersonic gas jet is crossed with a pulsed beam of low-energy electrons, and the resulting negative ions are extracted toward a time- and position-sensitive detector. Calculations of the momentum in three dimensions may be used to determine the angular dependence of dissociative attachment as well as the energetics of the reaction.

Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

PubMed

Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

2016-02-23

The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in that it initially involves transitions to surfaces with fewer, less favorable contacts compared with those seen in the fully formed complex. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Kinetics of CH4 and CO2 hydrate dissociation and gas bubble evolution via MD simulation.

PubMed

Uddin, M; Coombe, D

2014-03-20

Molecular dynamics simulations of gas hydrate dissociation comparing the behavior of CH4 and CO2 hydrates are presented. These simulations were based on a structurally correct theoretical gas hydrate crystal, coexisting with water. The MD system was first initialized and stabilized via a thorough energy minimization, constant volume-temperature ensemble and constant volume-energy ensemble simulations before proceeding to constant pressure-temperature simulations for targeted dissociation pressure and temperature responses. Gas bubble evolution mechanisms are demonstrated as well as key investigative properties such as system volume, density, energy, mean square displacements of the guest molecules, radial distribution functions, H2O order parameter, and statistics of hydrogen bonds. These simulations have established the essential similarities between CH4 and CO2 hydrate dissociation. The limiting behaviors at lower temperature (no dissociation) and higher temperature (complete melting and formation of a gas bubble) have been illustrated for both hydrates. Due to the shift in the known hydrate stability curves between guest molecules caused by the choice of water model as noted by other authors, the intermediate behavior (e.g., 260 K) showed distinct differences however. Also, because of the more hydrogen-bonding capability of CO2 in water, as reflected in its molecular parameters, higher solubility of dissociated CO2 in water was observed with a consequence of a smaller size of gas bubble formation. Additionally, a novel method for analyzing hydrate dissociation based on H-bond breakage has been proposed and used to quantify the dissociation behaviors of both CH4 and CO2 hydrates. Activation energies Ea values from our MD studies were obtained and evaluated against several other published laboratory and MD values. Intrinsic rate constants were estimated and upscaled. A kinetic reaction model consistent with macroscale fitted kinetic models has been proposed to indicate the macroscopic consequences of this analysis.

Water dissociating on rigid Ni(100): A quantum dynamics study on a full-dimensional potential energy surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Chen, Jun; Zhang, Zhaojun; Shen, Xiangjian; Fu, Bina; Zhang, Dong H.

2018-04-01

We constructed a nine-dimensional (9D) potential energy surface (PES) for the dissociative chemisorption of H2O on a rigid Ni(100) surface using the neural network method based on roughly 110 000 energies obtained from extensive density functional theory (DFT) calculations. The resulting PES is accurate and smooth, based on the small fitting errors and the good agreement between the fitted PES and the direct DFT calculations. Time dependent wave packet calculations also showed that the PES is very well converged with respect to the fitting procedure. The dissociation probabilities of H2O initially in the ground rovibrational state from 9D quantum dynamics calculations are quite different from the site-specific results from the seven-dimensional (7D) calculations, indicating the importance of full-dimensional quantum dynamics to quantitatively characterize this gas-surface reaction. It is found that the validity of the site-averaging approximation with exact potential holds well, where the site-averaging dissociation probability over 15 fixed impact sites obtained from 7D quantum dynamics calculations can accurately approximate the 9D dissociation probability for H2O in the ground rovibrational state.

Dissociation of I II in chemical oxygen-iodine lasers: experiment, modeling, and pre-dissociation by electrical discharge

NASA Astrophysics Data System (ADS)

Katz, A.; Waichman, K.; Dahan, Z.; Rybalkin, V.; Barmashenko, B. D.; Rosenwaks, S.

2007-06-01

The dissociation of I II molecules at the optical axis of a supersonic chemical oxygen-iodine laser (COIL) was studied via detailed measurements and three dimensional computational fluid dynamics calculations. Comparing the measurements and the calculations enabled critical examination of previously proposed dissociation mechanisms and suggestion of a mechanism consistent with the experimental and theoretical results obtained in a supersonic COIL for the gain, temperature and I II dissociation fraction at the optical axis. The suggested mechanism combines the recent scheme of Azyazov and Heaven (AIAA J. 44, 1593 (2006)), where I II(A' 3Π 2u), I II(A 3Π 1u) and O II(a1Δ g, v) are significant dissociation intermediates, with the "standard" chain branching mechanism of Heidner et al. (J. Phys. Chem. 87, 2348 (1983)), involving I(2P 1/2) and I II(X1Σ + g, v). In addition, we examined a new method for enhancement of the gain and power in a COIL by applying DC corona/glow discharge in the transonic section of the secondary flow in the supersonic nozzle, dissociating I II prior to its mixing with O II(1Δ). The loss of O II(1Δ) consumed for dissociation was thus reduced and the consequent dissociation rate downstream of the discharge increased, resulting in up to 80% power enhancement. The implication of this method for COILs operating beyond the specific conditions reported here is assessed.

Structure and Mobility of Dissociated Vacancies at Twist Grain Boundaries and Screw Dislocations in Ionic Rocksalt Compounds

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

Kolluri, Kedarnath; Martinez Saez, Enrique; Uberuaga, Blas Pedro

Interfaces, grain boundaries, and dislocations are known to have significant impact on the transport properties of materials. Even so, it is still not clear how the structure of interfaces influences the mobility and concentration of carriers that are responsible for transport. Using low angle twist grain boundaries in MgO as a model system, we examine the structural and kinetic properties of vacancies. These boundaries are characterized by a network of screw dislocations. Vacancies of both types, Mg and O, are strongly attracted to the dislocation network, residing preferentially at the misfit dislocation intersections (MDIs). However, the vacancies can lower theirmore » energy by splitting into two parts, which then repel each other along the dislocation line between two MDIs, further lowering their energy. This dissociated structure has important consequences for transport, as the free energy of the dissociated vacancies decreases with decreasing twist angle, leading to an increase in the net migration barrier for diffusion as revealed by molecular dynamics simulations. Similar behavior is observed in BaO and NaCl, highlighting the generality of the behavior. Finally, we analyze the structure of the dissociated vacancies as a pair of jogs on the dislocation and construct a model containing electrostatic and elastic contributions that qualitatively describe the energetics of the dissociated vacancy. Our results represent the first validation of a mechanism for vacancy dissociation on screw dislocations in ionic materials first discussed by Thomson and Balluffi in 1962.« less

Structure and Mobility of Dissociated Vacancies at Twist Grain Boundaries and Screw Dislocations in Ionic Rocksalt Compounds

DOE PAGES

Kolluri, Kedarnath; Martinez Saez, Enrique; Uberuaga, Blas Pedro

2018-03-05

Interfaces, grain boundaries, and dislocations are known to have significant impact on the transport properties of materials. Even so, it is still not clear how the structure of interfaces influences the mobility and concentration of carriers that are responsible for transport. Using low angle twist grain boundaries in MgO as a model system, we examine the structural and kinetic properties of vacancies. These boundaries are characterized by a network of screw dislocations. Vacancies of both types, Mg and O, are strongly attracted to the dislocation network, residing preferentially at the misfit dislocation intersections (MDIs). However, the vacancies can lower theirmore » energy by splitting into two parts, which then repel each other along the dislocation line between two MDIs, further lowering their energy. This dissociated structure has important consequences for transport, as the free energy of the dissociated vacancies decreases with decreasing twist angle, leading to an increase in the net migration barrier for diffusion as revealed by molecular dynamics simulations. Similar behavior is observed in BaO and NaCl, highlighting the generality of the behavior. Finally, we analyze the structure of the dissociated vacancies as a pair of jogs on the dislocation and construct a model containing electrostatic and elastic contributions that qualitatively describe the energetics of the dissociated vacancy. Our results represent the first validation of a mechanism for vacancy dissociation on screw dislocations in ionic materials first discussed by Thomson and Balluffi in 1962.« less

Temperature-dependent subunit exchange and chaperone-like activities of Hsp16.3, a small heat shock protein from Mycobacterium tuberculosis.

PubMed

Fu, Xinmiao; Chang, Zengyi

2004-04-02

Small heat shock proteins (sHsps) usually exist as oligomers that undergo dynamic oligomeric dissociation/re-association, with the dissociated oligomers as active forms to bind substrate proteins under heat shock conditions. In this study, however, we found that Hsp16.3, one sHsp from Mycobacterium tuberculosis, is able to sensitively modulate its chaperone-like activity in a range of physiological temperatures (from 25 to 37.5 degrees C) while its native oligomeric size is still maintained. Further analysis demonstrated that Hsp16.3 exposes higher hydrophobic surfaces upon temperatures increasing and that a large soluble complex between Hsp16.3 and substrate is formed only in the condition of heating temperature up to 35 and 37.5 degrees C. Structural analysis by fluorescence anisotropy showed that Hsp16.3 nonameric structure becomes more dynamic and variable at elevated temperatures. Moreover, subunit exchange between Hsp16.3 oligomers was found to occur faster upon temperatures increasing as revealed by fluorescence energy resonance transfer. These observations indicate that Hsp16.3 is able to modulate its chaperone activity by adjusting the dynamics of oligomeric dissociation/re-association process while maintaining its static oligomeric size unchangeable. A kinetic model is therefore proposed to explain the mechanism of sHsps-binding substrate proteins through oligomeric dissociation. The present study also implied that Hsp16.3 is at least capable of binding non-native proteins in vivo while expressing in the host organism that survives at 37 degrees C.

Dynamics of dissociative electron attachment to ammonia

DOE PAGES

Rescigno, T. N.; Trevisan, C. S.; Orel, A. E.; ...

2016-05-12

We present that ab initio theoretical studies and momentum-imaging experiments are combined to provide a consistent picture of the dynamics of dissociative electron attachment to ammonia through its 5.5- and 10.5-eV resonance channels. The present study clarifies the character and symmetry of the anion states involved and the dynamics that leads to the observed fragment-ion channels, their branching ratios, and angular distributions.

Dynamics of dissociative electron attachment to ammonia

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

Rescigno, T. N.; Trevisan, C. S.; Orel, A. E.

We present that ab initio theoretical studies and momentum-imaging experiments are combined to provide a consistent picture of the dynamics of dissociative electron attachment to ammonia through its 5.5- and 10.5-eV resonance channels. The present study clarifies the character and symmetry of the anion states involved and the dynamics that leads to the observed fragment-ion channels, their branching ratios, and angular distributions.

Improvement of the model for surface process of tritium release from lithium oxide

NASA Astrophysics Data System (ADS)

Yamaki, Daiju; Iwamoto, Akira; Jitsukawa, Shiro

2000-12-01

Among the various tritium transport processes in lithium ceramics, the importance and the detailed mechanism of surface reactions remain to be elucidated. The dynamic adsorption and desorption model for tritium desorption from lithium ceramics, especially Li 2O was constructed. From the experimental results, it was considered that both H 2 and H 2O are dissociatively adsorbed on Li 2O and generate OH - on the surface. In the first model developed in 1994, it was assumed that either the dissociative adsorption of H 2 or H 2O on Li 2O generates two OH - on the surface. However, recent calculation results show that the generation of one OH - and one H - is more stable than that of two OH -s by the dissociative adsorption of H 2. Therefore, assumption of H 2 adsorption and desorption in the first model is improved and the tritium release behavior from Li 2O surface is evaluated again by using the improved model. The tritium residence time on the Li 2O surface is calculated using the improved model, and the results are compared with the experimental results. The calculation results using the improved model agree well with the experimental results than those using the first model.

Thermospheric production of O(1S) by dissociative recombination of vibrationally excited O2(+)

NASA Technical Reports Server (NTRS)

Yee, Jeng-Hwa; Killeen, T. L.

1986-01-01

High spectral resolution line profiles at 5577 A of the nighttime, F-region O(1S) emission measured by the Fabry-Perot interferometer on board the Dynamics Explorer satellite are analyzed using a continuous O(1S) relaxation model. The model is an improvement over the previous model of Killeen and Hays (1981) in that energy loss via elastic collision is considered in addition to the single collision, excitation exchange thermalization process. The results show that the active channel for O(1S) production is capture into the 1Sigma(+)u repulsive state of O2 and that the main contributor to its production is the dissociative recombination of O2(+) ions in vibrational levels v = 1 and 2 in agreement with the quantal calculations of Guberman (1983).

Dissociative electron attachments to ethanol and acetaldehyde: A combined experimental and simulation study

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

Wang, Xu-Dong; Xuan, Chuan-Jin; Feng, Wen-Ling

Dissociation dynamics of the temporary negative ions of ethanol and acetaldehyde formed by the low-energy electron attachments is investigated by using the anion velocity map imaging technique and ab initio molecular dynamics simulations. The momentum images of the dominant fragments O{sup −}/OH{sup −} and CH{sub 3}{sup −} are recorded, indicating the low kinetic energies of O{sup −}/OH{sup −} for ethanol while the low and high kinetic energy distributions of O{sup −} ions for acetaldehyde. The CH{sub 3}{sup −} image for acetaldehyde also shows the low kinetic energy. With help of the dynamics simulations, the fragmentation processes are qualitatively clarified. Amore » new cascade dissociation pathway to produce the slow O{sup −} ion via the dehydrogenated intermediate, CH{sub 3}CHO{sup −} (acetaldehyde anion), is proposed for the dissociative electron attachment to ethanol. After the electron attachment to acetaldehyde molecule, the slow CH{sub 3}{sup −} is produced quickly in the two-body dissociation with the internal energy redistributions in different aspects before bond cleavages.« less

Stability and dissociation dynamics of N{sub 2}{sup ++} ions following core ionization studied by an Auger-electron–photoion coincidence method

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

Iwayama, H.; Shigemasa, E.; SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki 444-8585

An Auger-electron–photoion coincidence (AEPICO) method has been applied to study the stability and dissociation dynamics of dicationic states after the N K-shell photoionization of nitrogen molecules. From time-of-flight and kinetic energy analyses of the product ions, we have obtained coincident Auger spectra associated with metastable states of N{sub 2}{sup ++} ions and dissociative states leading to N{sub 2}{sup ++} → N{sup +} + N{sup +} and N{sup ++} + N. To investigate the production of dissociative states, we present two-dimensional AEPICO maps which reveal the correlations between the binding energies of the Auger final states and the ion kinetic energymore » release. These correlations have been used to determine the dissociation limits of individual Auger final states.« less

Substrate binding interferes with active site conformational dynamics in endoglucanase Cel5A from Thermobifida fusca.

PubMed

Jiang, Xukai; Wang, Yuying; Xu, Limei; Chen, Guanjun; Wang, Lushan

2017-09-09

The role of protein dynamics in enzyme catalysis is one of the most active areas in current enzymological research. Here, using endoglucanase Cel5A from Thermobifida fusca (TfCel5A) as a model, we applied molecular dynamics simulations to explore the dynamic behavior of the enzyme upon substrate binding. The collective motions of the active site revealed that the mechanism of TfCel5A substrate binding can likely be described by the conformational-selection model; however, we observed that the conformations of active site residues changed differently along with substrate binding. Although most active site residues retained their native conformational ensemble, some (Tyr163 and Glu355) generated newly induced conformations, whereas others (Phe162 and Tyr189) exhibited shifts in the equilibration of their conformational distributions. These results showed that TfCel5A substrate binding relied on a hybrid mechanism involving induced fit and conformational selection. Interestingly, we found that TfCel5A active site could only partly rebalance its conformational dynamics upon substrate dissociation within the same simulation time, which implies that the conformational rebalance upon substrate dissociation is likely more difficult than the conformational selection upon substrate binding at least in the view of the time required. Our findings offer new insight into enzyme catalysis and potential applications for future protein engineering. Copyright © 2017 Elsevier Inc. All rights reserved.

Photodissociation dynamics of nitromethane and methyl nitrite by infrared multiphoton dissociation imaging with quasiclassical trajectory calculations: signatures of the roaming pathway.

PubMed

Dey, Arghya; Fernando, Ravin; Abeysekera, Chamara; Homayoon, Zahra; Bowman, Joel M; Suits, Arthur G

2014-02-07

We combine the techniques of infrared multiphoton dissociation (IRMPD) with state selective ion imaging to probe roaming dynamics in the unimolecular dissociation of nitromethane and methyl nitrite. Recent theoretical calculations suggest a "roaming-mediated isomerization" pathway of nitromethane to methyl nitrite prior to decomposition. State-resolved imaging of the NO product coupled with infrared multiphoton dissociation was carried out to examine this unimolecular decomposition near threshold. The IRMPD images for the NO product from nitromethane are consistent with the earlier IRMPD studies that first suggested the importance of an isomerization pathway. A significant Λ-doublet propensity is seen in nitromethane IRMPD but not methyl nitrite. The experimental observations are augmented by quasiclassical trajectory calculations for nitromethane and methyl nitrite near threshold for each dissociation pathway. The observation of distinct methoxy vibrational excitation for trajectories from nitromethane and methyl nitrite dissociation at the same total energy show that the nitromethane dissociation bears a nonstatistical signature of the roaming isomerization pathway, and this is possibly responsible for the nitromethane Λ-doublet propensity as well.

Bipolaron assisted Bloch-like oscillations in organic lattices

NASA Astrophysics Data System (ADS)

Ribeiro, Luiz Antonio; Ferreira da Cunha, Wiliam; Magela e Silva, Geraldo

2017-06-01

The transport of a dissociated bipolaron in organic one-dimensional lattices is theoretically investigated in the scope of a tight-binding model that includes electron-lattice interactions and an external electric field. Remarkably, the results point to a physical picture in which the dissociated bipolaron propagates as a combined state of two free-like electrons that coherently perform spatial Bloch oscillations (BO) above a critical field strength. It was also obtained that the BO's trajectory presents a net forward motion in the direction of the applied electric field. The impact of dynamical disorder in the formation of electronic BOs is determined.

Dislocation dynamics in hexagonal close-packed crystals

DOE PAGES

Aubry, S.; Rhee, M.; Hommes, G.; ...

2016-04-14

Extensions of the dislocation dynamics methodology necessary to enable accurate simulations of crystal plasticity in hexagonal close-packed (HCP) metals are presented. They concern the introduction of dislocation motion in HCP crystals through linear and non-linear mobility laws, as well as the treatment of composite dislocation physics. Formation, stability and dissociation of and other dislocations with large Burgers vectors defined as composite dislocations are examined and a new topological operation is proposed to enable their dissociation. Furthermore, the results of our simulations suggest that composite dislocations are omnipresent and may play important roles both in specific dislocation mechanisms and in bulkmore » crystal plasticity in HCP materials. While fully microscopic, our bulk DD simulations provide wealth of data that can be used to develop and parameterize constitutive models of crystal plasticity at the mesoscale.« less

Use of a single trajectory to study product energy partitioning in unimolecular dissociation: mass effects for halogenated alkanes.

PubMed

Sun, Lipeng; Park, Kyoyeon; Song, Kihyung; Setser, Donald W; Hase, William L

2006-02-14

A single trajectory (ST) direct dynamics approach is compared with quasiclassical trajectory (QCT) direct dynamics calculations for determining product energy partitioning in unimolecular dissociation. Three comparisons are made by simulating C(2)H(5)F-->HF + C(2)H(4) product energy partitioning for the MP26-31G(*) and MP26-311 + + G(**) potential energy surfaces (PESs) and using the MP26-31G(*) PES for C(2)H(5)F dissociation as a model to simulate CHCl(2)CCl(3)-->HCl + C(2)Cl(4) dissociation and its product energy partitioning. The trajectories are initiated at the transition state with fixed energy in reaction-coordinate translation E(t) (double dagger). The QCT simulations have zero-point energy (ZPE) in the vibrational modes orthogonal to the reaction coordinate, while there is no ZPE for the STs. A semiquantitative agreement is obtained between the ST and QCT average percent product energy partitionings. The ST approach is used to study mass effects for product energy partitioning in HX(X = F or Cl) elimination from halogenated alkanes by using the MP26-31G(*) PES for C(2)H(5)F dissociation and varying the masses of the C, H, and F atoms. There is, at most, only a small mass effect for partitioning of energy to HX vibration and rotation. In contrast, there are substantial mass effects for partitioning to relative translation and the polyatomic product's vibration and rotation. If the center of mass of the polyatomic product is located away from the C atom from which HX recoils, the polyatomic has substantial rotation energy. Polyatomic products, with heavy atoms such as Cl atoms replacing the H atoms, receive substantial vibration energy that is primarily transferred to the wag-bend motions. For E(t) (double dagger) of 1.0 kcalmol, the ST calculations give average percent partitionings to relative translation, polyatomic vibration, polyatomic rotation, HX vibration, and HX rotation of 74.9%, 6.8%, 1.5%, 14.4%, and 2.4% for C(2)H(5)F dissociation and 39.7%, 38.1%, 0.2%, 16.1%, and 5.9% for a model of CHCl(2)CCl(3) dissociation.

Dissociation Energetics and Mechanisms of Leucine Enkephalin (M + H)+ and (2M + X)+ Ions (X = H, Li, Na, K, and Rb) Measured by Blackbody Infrared Radiative Dissociation

PubMed Central

Schnier, Paul D.; Price, William D.; Strittmatter, Eric F.; Williams, Evan R.

2005-01-01

The dissociation kinetics of protonated leucine enkephalin and its proton and alkali metal bound dimers were investigated by blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Protonated leucine enkephalin dissociates to form b4 and (M−H2O)+ ions with an average activation energy (Ea) of 1.1 eV and an A factor of 1010.5 s−1. The value of the A factor indicates that these dissociation processes are rearrangements. The b4 ions subsequently dissociate to form a4 ions via a process with a relatively high activation energy (1.3 eV), but one that is entropically favored. For the cationized dimers, the thermal stability decreases with increasing cation size, consistent with a simple electrostatic interaction in these noncovalent ion–molecule complexes. The Ea and A factors are indistinguishable within experimental error with values of ~1.5 eV and 1017 s−1, respectively. Although not conclusive, results from master equation modeling indicate that all these BIRD processes, except for b4 → a4, are in the rapid energy exchange limit. In this limit, the internal energy of the precursor ion population is given by a Boltzmann distribution and information about the energetics and dynamics of the reaction are obtained directly from the measured Arrhenius parameters. PMID:16554908

Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Nagaya, Kiyonobu; Shimojo, Fuyuki; Yao, Makoto

2015-08-01

The dynamic properties of liquid B2O3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B2O3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8).

Photodissociation Studies of Polyatomic Free Radicals

DTIC Science & Technology

1993-08-01

photofragment, that varies with vibrational level, and appears to have a strong J dependence. We are currently in the process of modelling these effects, as well...have also begun to study the photodissociation dynamics of thionyl halides, The photodissociation of thionyl chloride (C12SO) is of interest as a model ...concerted three-body fragmentation mechanism as the primary dissociation channel. A Franck- Condon/golden rule model elucidates the geometry prior to

Electronic State Decomposition of Energetic Materials and Model Systems

DTIC Science & Technology

2010-11-17

Nitromethane at 226 nm and 271 nm at both Nanosecond and Femtosecond Temporal Scales," J. Phys. Chem. A 113, 85 (2009). Y. Q. Guo, A. Bhattacharya and E...less "energetic". 8. Photodissociation Dynamics of Nitromethane at 226 and 271 nm at Both Nanosecond and Femtosecond Time Scales Photodissociation...of nitromethane has been investigated for decades both theoretically and experimentally; however, as a whole picture, the dissociation dynamics for

Effects of molecular dissociation on the hydrogen equation of state

NASA Astrophysics Data System (ADS)

Bonev, Stanimir; Schwegler, Eric; Galli, Giulia; Gygi, Francois

2002-03-01

It has been suggested recently(François Gygi and G. Galli, submitted to Phys. Rev. Lett.) that the physical mechanism behind the larger compressibility of liquid deuterium observed in laser shock experiments as compared to ab initio simulations may be related to shock-induced electronic excitations. A possible result of such non-adiabatic processes is hindering of the molecular dissociation. This has motivated us to study the importance of molecular dissociation on the hydrogen equation of state. To this end, we have carried out ab initio molecular dynamics simulations of liquid deuterium where intramolecular dissociation is prevented by the use of bond length contraints. Simulations at both fixed thermodynamic conditions and dynamical simulations of shocked deuterium will be discussed.

A molecular dynamics study of melting and dissociation of tungsten nanoparticles

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

Li, Min; Wang, Jun; Fu, Baoqin

2015-12-15

Molecular dynamics simulations were conducted to study the melting and dissociation of free tungsten nanoparticles. For the various interatomic potentials applied, the melting points of the tungsten nanoparticles increased with increasing nanoparticle diameter. Combining these results with the melting point of bulk tungsten in the experiment, the melting point of nanoparticles with diameters ranging from 4 to 12 nm could be determined. As the temperature increases, free nanoparticles are subject to dissociation phenomena. The dissociation rate was observed to follow Arrhenius behavior, and the Meyer–Neldel rule was obeyed. These results are useful in understanding the behavior of tungsten dust generatedmore » in nuclear fusion devices as well as for the preparation, formation, and application of tungsten powders.« less

Ultrafast dynamics of the lowest-lying neutral states in carbon dioxide

DOE PAGES

Wright, Travis W.; Champenois, Elio G.; Cryan, James P.; ...

2017-02-17

Here, we present a study of the ultrafast dissociation dynamics of the lowest-lying electronic excited states in CO 2 by using ultraviolet (UV) and extreme-ultraviolet (XUV) pulses from high-order harmonic generation. We observe two primary dissociation channels: a direct dissociation channel along the 1Π g electronically excited manifold, and a second channel which results from the mixing of electronic states. The direct dissociation channel is found to have a lifetime which is shorter than our experimental resolution, whereas the second channel has a significantly longer lifetime of nearly 200 fs. In this long-lived channel we observe a beating of themore » vibrational populations with a period of ~133 fs.« less

On the role of electronic friction for dissociative adsorption and scattering of hydrogen molecules at a Ru(0001) surface.

PubMed

Füchsel, Gernot; Schimka, Selina; Saalfrank, Peter

2013-09-12

The role of electronic friction and, more generally, of nonadiabatic effects during dynamical processes at the gas/metal surface interface is still a matter of discussion. In particular, it is not clear if electronic nonadiabaticity has an effect under "mild" conditions, when molecules in low rovibrational states interact with a metal surface. In this paper, we investigate the role of electronic friction on the dissociative sticking and (inelastic) scattering of vibrationally and rotationally cold H2 molecules at a Ru(0001) surface theoretically. For this purpose, classical molecular dynamics with electronic friction (MDEF) calculations are performed and compared to MD simulations without friction. The two H atoms move on a six-dimensional potential energy surface generated from gradient-corrected density functional theory (DFT), that is, all molecular degrees of freedom are accounted for. Electronic friction is included via atomic friction coefficients obtained from an embedded atom, free electron gas (FEG) model, with embedding densities taken from gradient-corrected DFT. We find that within this model, dissociative sticking probabilities as a function of impact kinetic energies and impact angles are hardly affected by nonadiabatic effects. If one accounts for a possibly enhanced electronic friction near the dissociation barrier, on the other hand, reduced sticking probabilities are observed, in particular, at high impact energies. Further, there is always an influence on inelastic scattering, in particular, as far as the translational and internal energy distribution of the reflected molecules is concerned. Additionally, our results shed light on the role played by the velocity distribution of the incident molecular beam for adsorption probabilities, where, in particular, at higher impact energies, large effects are found.

Effects of membrane deformability and bond formation/dissociation rates on adhesion dynamics of a spherical capsule in shear flow.

PubMed

Zhang, Ziying; Du, Jun; Wei, Zhengying; Wang, Zhen; Li, Minghui

2018-02-01

Cellular adhesion plays a critical role in biological systems and biomedical applications. Cell deformation and biophysical properties of adhesion molecules are of significance for the adhesion behavior. In the present work, dynamic adhesion of a deformable capsule to a planar substrate, in a linear shear flow, is numerically simulated to investigate the combined influence of membrane deformability (quantified by the capillary number) and bond formation/dissociation rates on the adhesion behavior. The computational model is based on the immersed boundary-lattice Boltzmann method for the capsule-fluid interaction and a probabilistic adhesion model for the capsule-substrate interaction. Three distinct adhesion states, detachment, rolling adhesion and firm adhesion, are identified and presented in a state diagram as a function of capillary number and bond dissociation rate. The impact of bond formation rate on the state diagram is further investigated. Results show that the critical bond dissociation rate for the transition of rolling or firm adhesion to detachment is strongly related to the capsule deformability. At the rolling-adhesion state, smaller off rates are needed for larger capillary number to increase the rolling velocity and detach the capsule. In contrast, the critical off rate for firm-to-detach transition slightly increases with the capillary number. With smaller on rate, the effect of capsule deformability on the critical off rates is more pronounced and capsules with moderate deformability are prone to detach by the shear flow. Further increasing of on rate leads to large expansion of both rolling-adhesion and firm-adhesion regions. Even capsules with relatively large deformability can maintain stable rolling adhesion at certain off rate.

The dissociation mechanism and thermodynamic properties of HCl(aq) in hydrothermal fluids (to 700 °C, 60 kbar) by ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mei, Yuan; Liu, Weihua; Brugger, Joël; Sherman, David M.; Gale, Julian D.

2018-04-01

HCl is one of the most significant volatiles in the Earth's crust. It is well established that chloride activity and acidity (pH) play important roles in controlling the solubility of metals in aqueous hydrothermal fluids. Thus, quantifying the dissociation of HCl in aqueous solutions over a wide range of temperature and pressure is crucial for the understanding and numerical modeling of element mobility in hydrothermal fluids. Here we have conducted ab initio molecular dynamics (MD) simulations to investigate the mechanism of HCl(aq) dissociation and to calculate the thermodynamic properties for the dissociation reaction at 25-700 °C, 1 bar to 60 kbar, i.e. including high temperature and pressure conditions that are geologically important, but difficult to investigate via experiments. Our results predict that HCl(aq) tends to associate with increasing temperature, and dissociate with increasing pressure. In particular, HCl(aq) is highly dissociated at extremely high pressures, even at high temperatures (e.g., 60 kbar, 600-700 °C). At 25 °C, the calculated logKd values (6.79 ± 0.81) are close to the value (7.0) recommended by IUPAC (International Union of Pure and Applied Chemistry) and some previous experimental and theoretical studies (Simonson et al.., 1990; Sulpizi and Sprik, 2008, 2010). The MD simulations indicate full dissociation of HCl at low temperature; in contrast, some experiments were interpreted assuming significant association at high HCl concentrations (≥1 m HCltot) even at room T (logKd ∼0.7; e.g., Ruaya and Seward, 1987; Sretenskaya, 1992; review in Tagirov et al., 1997). This discrepancy is most likely the result of difficulties in the experimental determination of minor (if any) concentration of associated HCl(aq) under ambient conditions, and thus reflects differences in the activity models used for the interpretation of the experiments. With increasing temperature, the discrepancy between our MD results and previous experimental studies, and between different studies, becomes smaller as the degree of HCl association increases. The MD simulations and available experimental studies show consistent results at hydrothermal conditions (300-700 °C, up to 5 kbar). The new thermodynamic properties based on the MD results provide an independent check of the dissociation constants for HCl(aq), and the first dataset on HCl dissociation in high P-T fluids (up to 60 kbar, 700 °C) beyond available experimental conditions. Our results will enable prediction of the role of HCl in controlling element mobility in deep earth hydrothermal systems, including fluids associated with ultra-high pressure metasomatism in subduction zones.

First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

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

Varghese, Jithin J.; Mushrif, Samir H., E-mail: shmushrif@ntu.edu.sg

Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cu{sub n} where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barriermore » for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH{sub 3} and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CH{sub x} (x = 1–3) species and recombination of H with CH{sub x} have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.« less

Dynamic Colloidal Molecules Maneuvered by Light-Controlled Janus Micromotors.

PubMed

Gao, Yirong; Mou, Fangzhi; Feng, Yizheng; Che, Shengping; Li, Wei; Xu, Leilei; Guan, Jianguo

2017-07-12

In this work, we propose and demonstrate a dynamic colloidal molecule that is capable of moving autonomously and performing swift, reversible, and in-place assembly dissociation in a high accuracy by manipulating a TiO 2 /Pt Janus micromotor with light irradiation. Due to the efficient motion of the TiO 2 /Pt Janus motor and the light-switchable electrostatic interactions between the micromotor and colloidal particles, the colloidal particles can be captured and assembled one by one on the fly, subsequently forming into swimming colloidal molecules by mimicking space-filling models of simple molecules with central atoms. The as-demonstrated dynamic colloidal molecules have a configuration accurately controlled and stabilized by regulating the time-dependent intensity of UV light, which controls the stop-and-go motion of the colloidal molecules. The dynamic colloidal molecules are dissociated when the light irradiation is turned off due to the disappearance of light-switchable electrostatic interaction between the motor and the colloidal particles. The strategy for the assembly of dynamic colloidal molecules is applicable to various charged colloidal particles. The simulated optical properties of a dynamic colloidal molecule imply that the results here may provide a novel approach for in-place building functional microdevices, such as microlens arrays, in a swift and reversible manner.

From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

NASA Astrophysics Data System (ADS)

Liang, Wenkel

This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the characteristics of ultrafast dynamics in photoexcited fullerene derivatives, and aids in the rational design for pre-dissociative exciton in the intramolecular CT process in organic solar cells.

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

PubMed

Tiwary, Pratyush

2017-12-07

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during dissociation and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the dissociation process. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacokinetics. An improved understanding of biotin-streptavidin dissociation dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

Trauma-induced dissociative amnesia in World War I combat soldiers.

PubMed

van der Hart, O; Brown, P; Graafland, M

1999-02-01

This study relates trauma-induced dissociative amnesia reported in World War I (WW I) studies of war trauma to contemporary findings of dissociative amnesia in victims of childhood sexual abuse. Key diagnostic studies of post-traumatic amnesia in WW I combatants are surveyed. These cover phenomenology and the psychological dynamics of dissociation vis-à-vis repression. Descriptive evidence is cited for war trauma-induced dissociative amnesia. Posttraumatic amnesia extends beyond the experience of sexual and combat trauma and is a protean symptom, which reflects responses to the gamut of traumatic events.

Ab initio studies on the photodissociation dynamics of the 1,1-difluoroethyl radical

NASA Astrophysics Data System (ADS)

Fritsche, Lukas; Bach, Andreas; Chen, Peter

2018-02-01

Born-Oppenheimer molecular dynamics trajectory calculations at the HCTH147/6-31G** level of theory simulate the dissociation dynamics of photolytically excited 1,1-difluoroethyl radicals. EOMCCSD/AUG-cc-pVDZ calculations show that an excitation energy of 94.82 kcal/mol is necessary to initiate photodissociation reactions. In contrast to photodissociation dynamics of ethyl radicals where a large discrepancy between actual dissociation rates and rates that are predicted by statistical rate theories, we find reaction rates of 5.1 × 1011 s-1 for the dissociation of an H atom, which is in perfect accord with what is predicted by Rice-Ramsperger-Kassel-Marcus (RRKM) calculations and there is no indication of any nonstatistical effects. However, our trajectory calculations show a much larger fraction of C-C bond breakage reaction of 56% occurring than that expected by RRKM (only 16%).

Ab initio studies on the photodissociation dynamics of the 1,1-difluoroethyl radical.

PubMed

Fritsche, Lukas; Bach, Andreas; Chen, Peter

2018-02-28

Born-Oppenheimer molecular dynamics trajectory calculations at the HCTH147/6-31G** level of theory simulate the dissociation dynamics of photolytically excited 1,1-difluoroethyl radicals. EOMCCSD/AUG-cc-pVDZ calculations show that an excitation energy of 94.82 kcal/mol is necessary to initiate photodissociation reactions. In contrast to photodissociation dynamics of ethyl radicals where a large discrepancy between actual dissociation rates and rates that are predicted by statistical rate theories, we find reaction rates of 5.1 × 10 11 s -1 for the dissociation of an H atom, which is in perfect accord with what is predicted by Rice-Ramsperger-Kassel-Marcus (RRKM) calculations and there is no indication of any nonstatistical effects. However, our trajectory calculations show a much larger fraction of C-C bond breakage reaction of 56% occurring than that expected by RRKM (only 16%).

Dissociative recombination of the CH+ molecular ion at low energy

NASA Astrophysics Data System (ADS)

Chakrabarti, K.; Mezei, J. Zs; Motapon, O.; Faure, A.; Dulieu, O.; Hassouni, K.; Schneider, I. F.

2018-05-01

The reactive collision of the CH+ molecular ion with an electron is studied in the framework of the multichannel quantum defect theory, taking into account the contribution of the core-excited Rydberg states. In addition to the X 1Σ+ ground state of the ion, we also consider the contribution to the dynamics of the a 3Π and A 1Π excited states of CH+. Our results—in the case of the dissociative recombination in good agreement with the storage ring measurements—rely on decisive improvements—complete account of the ionisation channels and accurate evaluation of the reaction matrix—of a previously used model.

Dissociation energetics and mechanisms of leucine enkephalin (M + H)+ and (2M + X)+ ions (X = H, Li, Na, K, and Rb) measured by blackbody infrared radiative dissociation.

PubMed

Schnier, P D; Price, W D; Strittmatter, E F; Williams, E R

1997-08-01

The dissociation kinetics of protonated leucine enkephalin and its proton and alkali metal bound dimers were investigated by blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Protonated leucine enkephalin dissociates to form b(4) and (M-H(2)O)(+) ions with an average activation energy (E(a)) of 1.1 eV and an A factor of 10(10.5) s(-1). The value of the A factor indicates that these dissociation processes are rearrangements. The b(4) ions subsequently dissociate to form a(4) ions via a process with a relatively high activation energy (1.3 eV), but one that is entropically favored. For the cationized dimers, the thermal stability decreases with increasing cation size, consistent with a simple electrostatic interaction in these noncovalent ion-molecule complexes. The E(a) and A factors are indistinguishable within experimental error with values of approximately 1.5 eV and 10(17) s(-1), respectively. Although not conclusive, results from master equation modeling indicate that all these BIRD processes, except for b(4) --> a(4), are in the rapid energy exchange limit. In this limit, the internal energy of the precursor ion population is given by a Boltzmann distribution and information about the energetics and dynamics of the reaction are obtained directly from the measured Arrhenius parameters.

Photodissociation dynamics of the simplest alkyl peroxy radicals, CH 3OO and C 2H 5OO, at 248 nm

DOE PAGES

Sullivan, Erin N.; Nichols, Bethan; Neumark, Daniel M.

2018-01-28

The photodissociation dynamics of the simplest alkyl peroxy radicals, methyl peroxy (CH 3OO) and ethyl peroxy C 2H 5OO , are investigated using fast beam photofragment translational spectroscopy. A fast beam of CH3OO- or C2H5OO- anions is photodetached to generate neutral radicals that are subsequently dissociated using 248 nm photons. The coincident detection of the photofragment positions and arrival times allows for the determination of mass, translational energy, and angular distributions for both two-body and three-body dissociation events. CH3OO exhibits repulsive O loss resulting in the formation of O(1D) + CH3O with high translational energy release. Minor two-body channels leadingmore » to OH + CH2O and CH3O + O(3P) formation are also detected. In addition, small amounts of H + O(3P) + CH2O are observed and attributed to O loss followed by CH3O dissociation. C2H5OO exhibits more complex dissociation dynamics, in which O loss and OH loss occur in roughly equivalent amounts with O(1D) formed as the dominant O atom electronic state via dissociation on a repulsive surface. Minor two-body channels leading to the formation of O2 + C2H5 and HO2 + C2H4 are also observed and attributed to a ground state dissociation pathway following internal conversion. Additionally, C2H5OO dissociation yields a three-body product channel, CH3 + O(3P) + CH2O, for which the proposed mechanism is repulsive O loss followed by the dissociation of C2H5O over a barrier. These results are compared to a recent study of tert-butyl peroxy (t-BuOO) in which 248 nm excitation results in three-body dissociatio n and ground state two-body dissociation but no O(1D) production.« less

Photodissociation dynamics of the simplest alkyl peroxy radicals, CH 3OO and C 2H 5OO, at 248 nm

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

Sullivan, Erin N.; Nichols, Bethan; Neumark, Daniel M.

The photodissociation dynamics of the simplest alkyl peroxy radicals, methyl peroxy (CH 3OO) and ethyl peroxy C 2H 5OO , are investigated using fast beam photofragment translational spectroscopy. A fast beam of CH3OO- or C2H5OO- anions is photodetached to generate neutral radicals that are subsequently dissociated using 248 nm photons. The coincident detection of the photofragment positions and arrival times allows for the determination of mass, translational energy, and angular distributions for both two-body and three-body dissociation events. CH3OO exhibits repulsive O loss resulting in the formation of O(1D) + CH3O with high translational energy release. Minor two-body channels leadingmore » to OH + CH2O and CH3O + O(3P) formation are also detected. In addition, small amounts of H + O(3P) + CH2O are observed and attributed to O loss followed by CH3O dissociation. C2H5OO exhibits more complex dissociation dynamics, in which O loss and OH loss occur in roughly equivalent amounts with O(1D) formed as the dominant O atom electronic state via dissociation on a repulsive surface. Minor two-body channels leading to the formation of O2 + C2H5 and HO2 + C2H4 are also observed and attributed to a ground state dissociation pathway following internal conversion. Additionally, C2H5OO dissociation yields a three-body product channel, CH3 + O(3P) + CH2O, for which the proposed mechanism is repulsive O loss followed by the dissociation of C2H5O over a barrier. These results are compared to a recent study of tert-butyl peroxy (t-BuOO) in which 248 nm excitation results in three-body dissociatio n and ground state two-body dissociation but no O(1D) production.« less

Changes in the physical properties of the dynamic layer and its correlation with permeate quality in a self-forming dynamic membrane bioreactor.

PubMed

Guan, Dao; Dai, Ji; Watanabe, Yoshimasa; Chen, Guanghao

2018-09-01

The self-forming dynamic membrane bioreactor (SFDMBR) is a biological wastewater treatment technology based on the conventional membrane bioreactor (MBR) with membrane material modification to a large pore size (30-100 μm). This modification requires a dynamic layer formed by activated sludge to provide effective filtration function for high-quality permeate production. The properties of the dynamic layer are therefore important for permeate quality in SFDMBRs. The interaction between the structure of the dynamic layer and the performance of SFDMBRs is little known but understandably complex. To elucidate the interaction, a lab-scale SFDMBR system coupled with a nylon woven mesh as the supporting material was operated. After development of a mature dynamic layer, excellent solid-liquid separation was achieved, as evidenced by a low permeate turbidity of less than 2 NTU. The permeate turbidity stayed below this level for nearly 80 days. In the fouling phase, the dynamic layer was compressed with an increase in the trans-membrane pressure and the quality of the permeate kept deteriorating until the turbidity exceeded 10 NTU. The investigation revealed that the majority of permeate particles were dissociated from the dynamic layer on the back surface of the supporting material, which is caused by the compression, breakdown, and dissociation of the dynamic layer. This phenomenon was observed directly in experiment instead of model prediction or conjecture for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Dissociative Subtype of Posttraumatic Stress Disorder (PTSD) Among Adolescents: Co-Occurring PTSD, Depersonalization/Derealization, and Other Dissociation Symptoms.

PubMed

Choi, Kristen R; Seng, Julia S; Briggs, Ernestine C; Munro-Kramer, Michelle L; Graham-Bermann, Sandra A; Lee, Robert C; Ford, Julian D

2017-12-01

The purpose of this study was to examine the co-occurrence of posttraumatic stress disorder (PTSD) and dissociation in a clinical sample of trauma-exposed adolescents by evaluating evidence for the depersonalization/derealization dissociative subtype of PTSD as defined by the DSM-5 and then examining a broader set of dissociation symptoms. A sample of treatment-seeking, trauma-exposed adolescents 12 to 16 years old (N = 3,081) from the National Child Traumatic Stress Network Core Data Set was used to meet the study objectives. Two models of PTSD/dissociation co-occurrence were estimated using latent class analysis, one with 2 dissociation symptoms and the other with 10 dissociation symptoms. After model selection, groups within each model were compared on demographics, trauma characteristics, and psychopathology. Model A, the depersonalization/derealization model, had 5 classes: dissociative subtype/high PTSD; high PTSD; anxious arousal; dysphoric arousal; and a low symptom/reference class. Model B, the expanded dissociation model, identified an additional class characterized by dissociative amnesia and detached arousal. These 2 models provide new information about the specific ways PTSD and dissociation co-occur and illuminate some differences between adult and adolescent trauma symptom expression. A dissociative subtype of PTSD can be distinguished from PTSD alone in adolescents, but assessing a wider range of dissociative symptoms is needed to fully characterize adolescent traumatic stress responses. Copyright © 2017 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

PubMed

Ghaani, Mohammad Reza; English, Niall J

2018-03-21

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis

NASA Astrophysics Data System (ADS)

Ghaani, Mohammad Reza; English, Niall J.

2018-03-01

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

Three cases of dissociative identity disorder and co-occurring borderline personality disorder treated with dynamic deconstructive psychotherapy.

PubMed

Chlebowski, Susan M; Gregory, Robert J

2012-01-01

Dissociative Identity Disorder (DID) is an under-researched entity and there are no clinical trials employing manual-based therapies and validated outcome measures. There is evidence that borderline personality disorder (BPD) commonly co-occurs with DID and can worsen its course. The authors report three cases of DID with co-occurring BPD that we successfully treated with a manual-based treatment, Dynamic Deconstructive Psychotherapy (DDP). Each of the three clients achieved a 34% to 79% reduction in their Dissociative Experiences Scale scores within 12 months of initiating therapy. Dynamic Deconstructive Psychotherapy was developed for treatment refractory BPD and differs in some respects from expert consensus treatment of DID. It may be a promising modality for DID complicated by co-occurring BPD.

Classical and ab-initio simulations of hydrogen in the dissociating regime

NASA Astrophysics Data System (ADS)

Clerouin, Jean; Blottiau, Patrick; Bernard, Stephane; Dufreche, Jean-Francois

1999-11-01

Recent experiments on shock compressed hydrogen ( L. B. Da Silva, P. Cellires, G. W. Collins., et al., Physical Review Letters 78, 483-486 (1997).) have motivated a large number of theoretical studies to try to reproduce the experimental Hugoniot data. In spite of the simplicity of the hydrogen molecule, a precise description of its dissociation under pressure and temperature is still missing. Here, we compare three different approaches: the empirical Ross model (M. Ross, Physical Review B 58, 669-677 (1998).) which reproduces the experimental data, a classical molecular dynamics model, which allows for the computation of transport coefficients such as the viscosity footnote J. F. Dufreche and J. Clerouin, Physical Review E , submitted (1999). and ab initio simulations for a detailed description of the dissociation process. This comparison reveals that in the region [0.1 g/cm^3< ρ< 1g/cm^3, 2000K

Photoisomerization and photodissociation dynamics of reactive free radicals

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

Bise, Ryan T.

2000-08-01

The photofragmentation pathways of chemically reactive free radicals have been examined using the technique of fast beam photofragment translational spectroscopy. Measurements of the photodissociation cross-sections, product branching ratios, product state energy distributions, and angular distributions provide insight into the excited state potential energy surfaces and nonadiabatic processes involved in the dissociation mechanisms. Photodissociation spectroscopy and dynamics of the predissociativemore » $$\\tilde{A}$$ 2A 1 and $$\\tilde{B}$$ 2A 2 states of CH 3S have been investigated. At all photon energies, CH 3 + S( 3P j), was the main reaction channel. The translational energy distributions reveal resolved structure corresponding to vibrational excitation of the CH 3 umbrella mode and the S( 3P j) fine-structure distribution from which the nature of the coupled repulsive surfaces is inferred. Dissociation rates are deduced from the photofragment angular distributions, which depend intimately on the degree of vibrational excitation in the C-S stretch. Nitrogen combustion radicals, NCN, CNN and HNCN have also been studied. For all three radicals, the elimination of molecular nitrogen is the primary reaction channel. Excitation to linear excited triplet and singlet electronic states of the NCN radical generates resolved vibrational structure of the N 2 photofragment. The relatively low fragment rotational excitation suggests dissociation via a symmetric C 2V transition state. Resolved vibrational structure of the N 2 photofragment is also observed in the photodissociation of the HNCN radical. The fragment vibrational and rotational distributions broaden with increased excitation energy. Simple dissociation models suggest that the HNCN radical isomerizes to a cyclic intermediate (c-HCNN) which then dissociates via a tight cyclic transition state. In contrast to the radicals mentioned above, resolved vibrational structure was not observed for the ICNN radical due to extensive fragment rotational excitation, suggesting that intermediate bent states are strongly coupled along the dissociation pathway. The measurements performed in this Thesis have additionally refined the heats of formation and bond dissociation energies of these radicals and have unambiguously confirmed and added to the known electronic spectroscopy.« less

Ionization dynamics of the water trimer: A direct ab initio MD study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto; Takada, Tomoya

2013-03-01

Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ˜15 fs after the ionization). In complex channel, an ion-radical contact pair (H3O+-OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50-100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.

Is the dissociative adult suggestible? A test of the trauma and fantasy models of dissociation.

PubMed

Kluemper, Nicole S; Dalenberg, Constance

2014-01-01

Psychologists have long assumed a connection between traumatic experience and psychological dissociation. This hypothesis is referred to as the trauma model of dissociation. In the past decade, a series of papers have been published that question this traditional causal link, proposing an alternative fantasy model of dissociation. In the present research, the relationship among dissociation, suggestibility, and fantasy proneness was examined. Suggestibility was measured through the Gudjonsson Scale of Interrogative Suggestibility (GSS) as well as an autobiographically based version of this measure based on the events of September 11, 2001. Consistent with prior research and with the trauma model, dissociation correlated positively with trauma severity (r = .32, p < .01) and fantasy proneness (r = .60, p < .01). Inconsistent with the fantasy model, dissociation did not correlate with the neutral form of the GSS and correlated negatively (r = -.24, p < .05) with the trauma-focused form of this suggestibility measure. Although some participants did become quite emotional during the procedure, the risk/benefit ratio was perceived by almost all participants to be positive, with more reactive individuals evaluating the procedure more positively. The results consistently support the trauma model of dissociation and fail to support the fantasy model of dissociation.

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study.

PubMed

Martínez, Leandro; Malliavin, Thérèse E; Blondel, Arnaud

2011-05-01

The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.

Dynamics of light-field control of molecular dissociation at the few-cycle limit.

PubMed

Tong, X M; Lin, C D

2007-03-23

We studied the laser-molecule interaction dynamics that leads to the asymmetric D+ ion ejection in the dissociative ionization of D2 molecules observed recently in Kling et al. [Science 312, 246 (2006)10.1126/science.1126259]. By changing the carrier-envelope phase, we showed that the asymmetry is a consequence of manipulating the initial ionization and the rescattering of the electrons within one optical cycle of the laser. The result illustrates the feasibility of coherent control of reaction dynamics at the attosecond time scale.

Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study.

PubMed

Harada, Ryuhei; Mashiko, Takako; Tachikawa, Masanori; Hiraoka, Shuichi; Shigeta, Yasuteru

2018-04-04

Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube, 16) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations. Our MD study unveiled that programed dynamic ordering exists in the dissociation processes of 16. According to the dissociation processes, it is proposed that triple π-stacking among three 3-pyridyl groups and other weak molecular interactions such as CH-π and van der Waals interactions, some of which arise from the solvophobic effect, were sequentially formed in stable and transient oligomeric states in the self-organization processes, i.e.12, 13, 14, and 15. By subsequent analyses on structural stabilities, it was found that 13 and 14 are stable intermediate oligomers, whereas 12 and 15 are transient ones. Thus, the formation of 13 from three monomers and of 16 from 14 and two monomers via corresponding transients is time consuming in the self-assembly process.

Prediction of Rate Constant for Supramolecular Systems with Multiconfigurations.

PubMed

Guo, Tao; Li, Haiyan; Wu, Li; Guo, Zhen; Yin, Xianzhen; Wang, Caifen; Sun, Lixin; Shao, Qun; Gu, Jingkai; York, Peter; Zhang, Jiwen

2016-02-25

The control of supramolecular systems requires a thorough understanding of their dynamics, especially on a molecular level. It is extremely difficult to determine the thermokinetic parameters of supramolecular systems, such as drug-cyclodextrin complexes with fast association/dissociation processes by experimental techniques. In this paper, molecular modeling combined with novel mathematical relationships integrating the thermodynamic/thermokinetic parameters of a series of isomeric multiconfigurations to predict the overall parameters in a range of pH values have been employed to study supramolecular dynamics at the molecular level. A suitable form of Eyring's equation was derived and a two-stage model was introduced. The new approach enabled accurate prediction of the apparent dissociation/association (k(off)/k(on)) and unbinding/binding (k-r/kr) rate constants of the ubiquitous multiconfiguration complexes of the supramolecular system. The pyronine Y (PY) was used as a model system for the validation of the presented method. Interestingly, the predicted k(off) value ((40 ± 1) × 10(5) s(-1), 298 K) of PY is largely in agreement with that previously determined by fluorescence correlation spectroscopy ((5 ± 3) × 10(5) s(-1), 298 K). Moreover, the k(off)/k(on) and k-r/kr for flurbiprofen-β-cylcodextrin and ibuprofen-β-cyclodextrin systems were also predicted and suggested that the association processes are diffusion-controlled. The methodology is considered to be especially useful in the design and selection of excipients for a supramolecular system with preferred association and dissociation rate constants and understanding their mechanisms. It is believed that this new approach could be applicable to a wide range of ligand-receptor supramolecular systems and will surely help in understanding their complex mechanism.

Molecular Basis of Ligand Dissociation from G Protein-Coupled Receptors and Predicting Residence Time.

PubMed

Guo, Dong; IJzerman, Adriaan P

2018-01-01

G protein-coupled receptors (GPCRs) are integral membrane proteins and represent the largest class of drug targets. During the past decades progress in structural biology has enabled the crystallographic elucidation of the architecture of these important macromolecules. It also provided atomic-level visualization of ligand-receptor interactions, dramatically boosting the impact of structure-based approaches in drug discovery. However, knowledge obtained through crystallography is limited to static structural information. Less information is available showing how a ligand associates with or dissociates from a given receptor, whose importance is in fact increasingly recognized by the drug research community. Owing to recent advances in computer power and algorithms, molecular dynamics stimulations have become feasible that help in analyzing the kinetics of the ligand binding process. Here, we review what is currently known about the dynamics of GPCRs in the context of ligand association and dissociation, as determined through both crystallography and computer simulations. We particularly focus on the molecular basis of ligand dissociation from GPCRs and provide case studies that predict ligand dissociation pathways and residence time.

State selectivity and dynamics in dissociative electron attachment to CF₃I revealed through velocity slice imaging.

PubMed

Ómarsson, Frímann H; Mason, Nigel J; Krishnakumar, E; Ingólfsson, Oddur

2014-11-03

In light of its substantially more environmentally friendly nature, CF3I is currently being considered as a replacement for the highly potent global-warming gas CF4, which is used extensively in plasma processing. In this context, we have studied the electron-driven dissociation of CF3I to form CF3(-) and I, and we compare this process to the corresponding photolysis channel. By using the velocity slice imaging (VSI) technique we can visualize the complete dynamics of this process and show that electron-driven dissociation proceeds from the same initial parent state as the corresponding photolysis process. However, in contrast to photolysis, which leads nearly exclusively to the (2)P(1/2) excited state of iodine, electron-induced dissociation leads predominantly to the (2)P(3/2) ground state. We believe that the changed spin state of the negative ion allows an adiabatic dissociation through a conical intersection, whereas this path is efficiently repressed by a required spin flip in the photolysis process. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The molecular dynamics of adsorption and dissociation of O{sub 2} on Pt(553)

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

Jacobse, Leon, E-mail: l.jacobse@chem.leidenuniv.nl; Dunnen, Angela den; Juurlink, Ludo B. F.

2015-07-07

Molecular adsorption and dissociation of O{sub 2} on the stepped Pt(553) surface have been investigated using supersonic molecular beam techniques and temperature programmed desorption. The initial and coverage-dependent sticking probability was determined with the King and Wells technique for various combinations of incident kinetic energy, surface temperature, incident angle, and surface coverage. A comparison with similar data for Pt(533) and Pt(110)(1 × 2) shows quantitatively the same high step-induced sticking at low incident energies compared to Pt(111). The enhancement is therefore insensitive to the exact arrangement of atoms forming surface corrugation. We consider energy transfer and electronic effects to explainmore » the enhanced sticking. On the other hand, dissociation dynamics at higher incident kinetic energies are strongly dependent on step type. The Pt(553) and Pt(533) surfaces are more reactive than Pt(111), but the (100) step shows higher sticking than the (110) step. We relate this difference to a variation in the effective lowering of the barrier to dissociation from molecularly adsorbed states into atomic states. Our findings are in line with results from experimental desorption studies and theoretical studies of atomic binding energies. We discuss the influence of the different step types on sticking and dissociation dynamics with a one-dimensional potential energy surface.« less

Mode Specific Electronic Friction in Dissociative Chemisorption on Metal Surfaces: H2 on Ag(111)

NASA Astrophysics Data System (ADS)

Maurer, Reinhard J.; Jiang, Bin; Guo, Hua; Tully, John C.

2017-06-01

Electronic friction and the ensuing nonadiabatic energy loss play an important role in chemical reaction dynamics at metal surfaces. Using molecular dynamics with electronic friction evaluated on the fly from density functional theory, we find strong mode dependence and a dominance of nonadiabatic energy loss along the bond stretch coordinate for scattering and dissociative chemisorption of H2 on the Ag(111) surface. Exemplary trajectories with varying initial conditions indicate that this mode specificity translates into modulated energy loss during a dissociative chemisorption event. Despite minor nonadiabatic energy loss of about 5%, the directionality of friction forces induces dynamical steering that affects individual reaction outcomes, specifically for low-incidence energies and vibrationally excited molecules. Mode-specific friction induces enhanced loss of rovibrational rather than translational energy and will be most visible in its effect on final energy distributions in molecular scattering experiments.

Jung's dissociable psyche and the ec-static self.

PubMed

Austin, Sue

2009-11-01

Much of Jung's later work assumes that the self is an a priori phenomenon in which centripetal dynamics dominate. There is, however, another current in Jung's writings which recognizes the self to be an emergent phenomenon. This view is increasingly prevalent in post-Jungian discourse, and Louis Zinkin's exploration of a post-Jungian-constructivist model of the self can be seen as part of this tendency. My paper privileges an emergent understanding of the self by focusing on the 'unravelling', 'de-centring', centrifugal experiences of otherness in the psyche. It offers a post-Jungian reading of a number of writers who have been influenced by the psychoanalyst Jean Laplanche and proposes a model of the self which focuses on our fantasies, terrors and longings about coming undone and bringing others undone. This model is then linked to Judith Butler's understanding of the self as an ec-static phenomenon, in which the self is, of necessity, outside itself, such that 'there is no final moment in which my return to myself takes place'. I suggest that Jung's early clinical researches into the dissociability of the psyche and the clinical tools which he developed as a result of this work are especially suitable for engaging with these emergent, centrifugal dynamics.

Modeling Photochemical Dynamics in Optically Active Energetic Materials

NASA Astrophysics Data System (ADS)

Nelson, Tammie; Bjorgaard, Josiah; Greenfield, Margo; Bolme, Cindy; Brown, Katie; McGrane, Shawn; Scharff, R. Jason; Tretiak, Sergei

Most high explosives (HEs) absorb in the UV range, making it difficult to develop HEs that can be excited with standard lasers. The conventional optical initiation mechanisms require high laser intensity and occur via indirect thermal or shock processes. A photochemical initiation mechanism could allow control over the chemistry contributing to decomposition leading to initiation. We combine UV femtosecond transient absorption (TA) spectroscopy and excited state femtosecond stimulated Raman spectroscopy (FSRS) with Nonadiabatic Excited State Molecular Dynamics (NA-ESMD) to model the photochemical pathways in nitromethane (NM), a low sensitivity HE known to undergo UV photolysis. We investigate the ultrafast photodecomposition of NM from the nπ* state excited at 266 nm. The FSRS photoproduct spectrum points to methyl nitrite formation as the dominant photoproduct. A total photolysis quantum yield of 0.27 and an nπ* state lifetime of 20 fs were predicted from simulations. Predicted time scales reveal that NO2 dissociation occurs in 81 +/-4 fs and methyl nitrite formation is much slower at 452 +/-9 fs corresponding to the absorption feature in the TA spectrum. The relative time scales are consistent with isomerization by NO2 dissociation and ONO rebinding.

Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

PubMed

Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

2015-08-20

The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

Energetics and dynamics through time-resolved measurements in mass spectrometry

NASA Astrophysics Data System (ADS)

Lifshitz, Chava

Results of recent work on time-resolved photoionization and electron ionization mass spectrometry carried out in Jerusalem are reviewed. Time-resolved photoionization mass spectrometry in the vacuum ultraviolet is applied to polycyclic aromatic hydrocarbons, for example naphthalene, pyrene and fluoranthene as well as to some bromo derivatives (bromonaphthalene and bromoanthracene). Time-resolved photoionization efficiency curves are modelled by Rice-Ramsperger-Kassel-Marcus QET rate-energy k ( E ) dependences of the unimolecular dissociative processes and by the rate process infrared radiative relaxation k . Experimental results are augmented by time-resolved photorad dissociation data for the same species, whenever available. Kinetic shifts, conventional and intrinsic (due to competition between dissociative and radiative decay), are evaluated. Activation parameters (activation energies and entropies) are deduced. Thermochemical information is obtained including bond energies and ionic heats of formation. Fullerenes, notably C , are studied by time-resolved electron ionization and a large intrinsic shift, due to competition with black-bodylike radiative decay in the visible is discussed.

Li+ solvation and kinetics of Li+-BF4-/PF6- ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

NASA Astrophysics Data System (ADS)

Chang, Tsun-Mei; Dang, Liem X.

2017-10-01

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found that the residence times of EC around Li+ ions varied from 60 to 450 ps, depending on the correction method used. We found that the relaxation times changed significantly from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influences the dissociation kinetics of ion pairing.

Using a model comparison approach to describe the assembly pathway for histone H1

PubMed Central

Contreras, Carlos; Villasana, Minaya; Hendzel, Michael J.

2018-01-01

Histones H1 or linker histones are highly dynamic proteins that diffuse throughout the cell nucleus and associate with chromatin (DNA and associated proteins). This binding interaction of histone H1 with the chromatin is thought to regulate chromatin organization and DNA accessibility to transcription factors and has been proven to involve a kinetic process characterized by a population that associates weakly with chromatin and rapidly dissociates and another population that resides at a binding site for up to several minutes before dissociating. When considering differences between these two classes of interactions in a mathematical model for the purpose of describing and quantifying the dynamics of histone H1, it becomes apparent that there could be several assembly pathways that explain the kinetic data obtained in living cells. In this work, we model these different pathways using systems of reaction-diffusion equations and carry out a model comparison analysis using FRAP (fluorescence recovery after photobleaching) experimental data from different histone H1 variants to determine the most feasible mechanism to explain histone H1 binding to chromatin. The analysis favors four different chromatin assembly pathways for histone H1 which share common features and provide meaningful biological information on histone H1 dynamics. We show, using perturbation analysis, that the explicit consideration of high- and low-affinity associations of histone H1 with chromatin in the favored assembly pathways improves the interpretation of histone H1 experimental FRAP data. To illustrate the results, we use one of the favored models to assess the kinetic changes of histone H1 after core histone hyperacetylation, and conclude that this post-transcriptional modification does not affect significantly the transition of histone H1 from a weakly bound state to a tightly bound state. PMID:29352283

Semiclassical Calculation of Reaction Rate Constants for Homolytical Dissociations

NASA Technical Reports Server (NTRS)

Cardelino, Beatriz H.

2002-01-01

There is growing interest in extending organometallic chemical vapor deposition (OMCVD) to III-V materials that exhibit large thermal decomposition at their optimum growth temperature, such as indium nitride. The group III nitrides are candidate materials for light-emitting diodes and semiconductor lasers operating into the blue and ultraviolet regions. To overcome decomposition of the deposited compound, the reaction must be conducted at high pressures, which causes problems of uniformity. Microgravity may provide the venue for maintaining conditions of laminar flow under high pressure. Since the selection of optimized parameters becomes crucial when performing experiments in microgravity, efforts are presently geared to the development of computational OMCVD models that will couple the reactor fluid dynamics with its chemical kinetics. In the present study, we developed a method to calculate reaction rate constants for the homolytic dissociation of III-V compounds for modeling OMCVD. The method is validated by comparing calculations with experimental reaction rate constants.

Solvent-coordinate free-energy landscape view of water-mediated ion-pair dissociation

NASA Astrophysics Data System (ADS)

Yonetani, Yoshiteru

2017-12-01

Water-mediated ion-pair dissociation is studied by molecular dynamics simulations of NaCl in water. Multidimensional free-energy analysis clarifies the relation between two essential solvent coordinates: the water coordination number and water-bridge formation. These two are related in a complex way. Both are necessary to describe ion-pair dissociation. The mechanism constructed with both solvent variables clearly shows the individual roles. The water coordination number is critical for starting ion-pair dissociation. Water-bridge formation is also important because it increases the likelihood of ion-pair dissociation by reducing the dissociation free-energy barrier. Additional Ca-Cl and NH4-Cl calculations show that these conclusions are unaffected by changes in the ion charge and shape. The present results will contribute to future explorations of many other molecular events such as surface water exchange and protein-ligand dissociation because the same mechanism is involved in such events.

Dissociative adsorption of CH{sub 3}X (X = Br and Cl) on a silicon(100) surface revisited by density functional theory

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

Wang, Chen-Guang; Lash Miller Chemical Laboratories, Department of Chemistry and Institute of Optical Sciences, University of Toronto, Toronto, Ontario M5S 3H6; Huang, Kai, E-mail: khuang@chem.utoronto.ca, E-mail: wji@ruc.edu.cn

During the dissociative adsorption on a solid surface, the substrate usually participates in a passive manner to accommodate fragments produced upon the cleavage of the internal bond(s) of a (transient) molecular adsorbate. This simple picture, however, neglects the flexibility of surface atoms. Here, we report a Density Functional Theory study to revisit our early studies of the dissociative adsorption of CH{sub 3}X (X = Br and Cl) on Si(100). We have identified a new reaction pathway, which involves a flip of a silicon dimer; this new pathway agrees better with experiments. For our main exemplar of CH{sub 3}Br, insights havemore » been gained using a simple model that involves a three-atom reactive center, Br-C-Si. When the silicon dimer flips, the interaction between C and Si in the Br-C-Si center is enhanced, evident in the increased energy-split of the frontier orbitals. We also examine how the dissociation dynamics of CH{sub 3}Br is altered on a heterodimer (Si-Al, Si-P, and Si-Ge) in a Si(100) surface. In each case, we conclude, on the basis of computed reaction pathways, that no heterodimer flipping is involved before the system transverses the transition state to dissociative adsorption.« less

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

Ion-momentum imaging of dissociative attachment of electrons to molecules

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

Slaughter, D. S.; Belkacem, A.; McCurdy, C. W.

Here, we present an overview of experiments and theory relevant to dissociative electron attachment studied by momentum imaging. We describe several key examples of characteristic transient anion dynamics in the form of small polyatomic electron-molecule systems. In each of these examples the so-called axial recoil approximation is found to break down due to correlation of the electronic and nuclear degrees of freedom of the transient anion. Guided by anion fragment momentum measurements and predictions of the electron scattering attachment probability in the molecular frame, we demonstrate that accurate predictions of the dissociation dynamics can be achieved without a detailed investigationmore » of the surface topology of the relevant electronic states or the fragment trajectories on those surfaces.« less

Ion-momentum imaging of dissociative attachment of electrons to molecules

DOE PAGES

Slaughter, D. S.; Belkacem, A.; McCurdy, C. W.; ...

2016-10-24

Here, we present an overview of experiments and theory relevant to dissociative electron attachment studied by momentum imaging. We describe several key examples of characteristic transient anion dynamics in the form of small polyatomic electron-molecule systems. In each of these examples the so-called axial recoil approximation is found to break down due to correlation of the electronic and nuclear degrees of freedom of the transient anion. Guided by anion fragment momentum measurements and predictions of the electron scattering attachment probability in the molecular frame, we demonstrate that accurate predictions of the dissociation dynamics can be achieved without a detailed investigationmore » of the surface topology of the relevant electronic states or the fragment trajectories on those surfaces.« less

Effects of continuum breakdown on hypersonic aerothermodynamics for reacting flow

NASA Astrophysics Data System (ADS)

Holman, Timothy D.; Boyd, Iain D.

2011-02-01

This study investigates the effects of continuum breakdown on the surface aerothermodynamic properties (pressure, stress, and heat transfer rate) of a sphere in a Mach 25 flow of reacting air in regimes varying from continuum to a rarefied gas. Results are generated using both continuum [computational fluid dynamics (CFD)] and particle [direct simulation Monte Carlo (DSMC)] approaches. The DSMC method utilizes a chemistry model that calculates the backward rates from an equilibrium constant. A preferential dissociation model is modified in the CFD method to better compare with the vibrationally favored dissociation model that is utilized in the DSMC method. Tests of these models are performed to confirm their validity and to compare the chemistry models in both numerical methods. This study examines the effect of reacting air flow on continuum breakdown and the surface properties of the sphere. As the global Knudsen number increases, the amount of continuum breakdown in the flow and on the surface increases. This increase in continuum breakdown significantly affects the surface properties, causing an increase in the differences between CFD and DSMC. Explanations are provided for the trends observed.

Evaluation of the evidence for the trauma and fantasy models of dissociation.

PubMed

Dalenberg, Constance J; Brand, Bethany L; Gleaves, David H; Dorahy, Martin J; Loewenstein, Richard J; Cardeña, Etzel; Frewen, Paul A; Carlson, Eve B; Spiegel, David

2012-05-01

The relationship between a reported history of trauma and dissociative symptoms has been explained in 2 conflicting ways. Pathological dissociation has been conceptualized as a response to antecedent traumatic stress and/or severe psychological adversity. Others have proposed that dissociation makes individuals prone to fantasy, thereby engendering confabulated memories of trauma. We examine data related to a series of 8 contrasting predictions based on the trauma model and the fantasy model of dissociation. In keeping with the trauma model, the relationship between trauma and dissociation was consistent and moderate in strength, and remained significant when objective measures of trauma were used. Dissociation was temporally related to trauma and trauma treatment, and was predictive of trauma history when fantasy proneness was controlled. Dissociation was not reliably associated with suggestibility, nor was there evidence for the fantasy model prediction of greater inaccuracy of recovered memory. Instead, dissociation was positively related to a history of trauma memory recovery and negatively related to the more general measures of narrative cohesion. Research also supports the trauma theory of dissociation as a regulatory response to fear or other extreme emotion with measurable biological correlates. We conclude, on the basis of evidence related to these 8 predictions, that there is strong empirical support for the hypothesis that trauma causes dissociation, and that dissociation remains related to trauma history when fantasy proneness is controlled. We find little support for the hypothesis that the dissociation-trauma relationship is due to fantasy proneness or confabulated memories of trauma. 2012 APA, all rights reserved

Photodissociation dynamics of allyl chloride at 200 and 266 nm studied by time-resolved mass spectrometry and photoelectron imaging.

PubMed

Shen, Huan; Chen, Jianjun; Hua, Linqiang; Zhang, Bing

2014-06-26

The photodissociation dynamics of allyl chloride at 200 and 266 nm has been studied by femtosecond time-resolved mass spectrometry coupled with photoelectron imaging. The molecule was prepared to different excited states by selectively pumping with 400 or 266 nm pulse. The dissociated products were then probed by multiphoton ionization with 800 nm pulse. After absorbing two photons at 400 nm, several dissociation channels were directly observed from the mass spectrum. The two important channels, C-Cl fission and HCl elimination, were found to decay with multiexponential functions. For C-Cl fission, two time constants, 48 ± 1 fs and 85 ± 40 ps, were observed. The first one was due to the fast predissociation process on the repulsive nσ*/πσ* state. The second one could be ascribed to dissociation on the vibrationally excited ground state which is generated after internal conversion from the initially prepared ππ* state. HCl elimination, which is a typical example of a molecular elimination reaction, was found to proceed with two time constants, 600 ± 135 fs and 14 ± 2 ps. We assigned the first one to dissociation on the excited state and the second one to the internal conversion from the ππ* state to the ground state and then dissociation on the ground state. As we excited the molecule with 266 nm light, the transient signals decayed exponentially with a time constant of ∼48 fs, which is coincident with the time scale of C-halogen direct dissociation. Photoelectron images, which provided translational and angular distributions of the generated electron, were also recorded. Detailed analysis of the kinetic energy distribution strongly suggested that C3H4(+) and C3H5(+) were generated from ionization of the neutral radical. The present study reveals the dissociation dynamics of allyl chloride in a time-resolved way.

X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule

DOE PAGES

Fang, Li; Xiong, Hui; Kukk, Edwin; ...

2017-05-19

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Energetics and dynamics of the fragmentation reactions of protonated peptides containing methionine sulfoxide or aspartic acid via energy- and time-resolved surface induced dissociation.

PubMed

Lioe, Hadi; Laskin, Julia; Reid, Gavin E; O'Hair, Richard A J

2007-10-25

The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64 Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility in these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (nonmobile proton conditions) to lysine (partially mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFECs) reveal that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1-2 orders of magnitude lower than nonselective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to nonselective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes are much slower compared to amide bond cleavage, explaining why these selective bond cleavages are not observed if fragmentation is performed under mobile proton conditions. This study further affirms that fragmentation of peptide ions in the gas phase are predominantly governed by entropic effects.

Phosphorylation of the centrosomal protein, Cep169, by Cdk1 promotes its dissociation from centrosomes in mitosis.

PubMed

Mori, Yusuke; Inoue, Yoko; Taniyama, Yuki; Tanaka, Sayori; Terada, Yasuhiko

2015-12-25

Cep169 is a centrosomal protein conserved among vertebrates. In our previous reports, we showed that mammalian Cep169 interacts and collaborates with CDK5RAP2 to regulate microtubule (MT) dynamics and stabilization. Although Cep169 is required for MT regulation, its precise cellular function remains largely elusive. Here we show that Cep169 associates with centrosomes during interphase, but dissociates from these structures from the onset of mitosis, although CDK5RAP2 (Cep215) is continuously located at the centrosomes throughout cell cycle. Interestingly, treatment with purvalanol A, a Cdk1 inhibitor, nearly completely blocked the dissociation of Cep169 from centrosomes during mitosis. In addition, mass spectrometry analyses identified 7 phosphorylated residues of Cep169 corresponding to consensus phosphorylation sequence for Cdk1. These data suggest that the dissociation of Cep169 from centrosomes is controlled by Cdk1/Cyclin B during mitosis, and that Cep169 might regulate MT dynamics of mitotic spindle. Copyright © 2015 Elsevier Inc. All rights reserved.

An exploration of the influence of diagonal dissociation and moderate changes in speed on locomotor parameters in trotting horses.

PubMed

Hobbs, Sarah Jane; Bertram, John E A; Clayton, Hilary M

2016-01-01

Background. Although the trot is described as a diagonal gait, contacts of the diagonal pairs of hooves are not usually perfectly synchronized. Although subtle, the timing dissociation between contacts of each diagonal pair could have consequences on gait dynamics and provide insight into the functional strategies employed. This study explores the mechanical effects of different diagonal dissociation patterns when speed was matched between individuals and how these effects link to moderate, natural changes in trotting speed. We anticipate that hind-first diagonal dissociation at contact increases with speed, diagonal dissociation at contact can reduce collision-based energy losses and predominant dissociation patterns will be evident within individuals. Methods. The study was performed in two parts: in the first 17 horses performed speed-matched trotting trials and in the second, five horses each performed 10 trotting trials that represented a range of individually preferred speeds. Standard motion capture provided kinematic data that were synchronized with ground reaction force (GRF) data from a series of force plates. The data were analyzed further to determine temporal, speed, GRF, postural, mass distribution, moment, and collision dynamics parameters. Results. Fore-first, synchronous, and hind-first dissociations were found in horses trotting at (3.3 m/s ± 10%). In these speed-matched trials, mean centre of pressure (COP) cranio-caudal location differed significantly between the three dissociation categories. The COP moved systematically and significantly (P = .001) from being more caudally located in hind-first dissociation (mean location = 0.41 ± 0.04) through synchronous (0.36 ± 0.02) to a more cranial location in fore-first dissociation (0.32 ± 0.02). Dissociation patterns were found to influence function, posture, and balance parameters. Over a moderate speed range, peak vertical forelimb GRF had a strong relationship with dissociation time (R = .594; P < .01) and speed (R = .789; P < .01), but peak vertical hindlimb GRF did not have a significant relationship with dissociation time (R = .085; P > 0.05) or speed (R = .223; P = .023). Discussion. The results indicate that at moderate speeds individual horses use dissociation patterns that allow them to maintain trunk pitch stability through management of the cranio-caudal location of the COP. During the hoof-ground collisions, reduced mechanical energy losses were found in hind-first dissociations compared to fully synchronous contacts. As speed increased, only forelimb vertical peak force increased so dissociations tended towards hind-first, which shifted the net COP caudally and balanced trunk pitching moments.

Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane

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

Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V., E-mail: aneimark@rutgers.edu

2016-01-07

Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. Themore » DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.« less

Facilitated dissociation of transcription factors from single DNA binding sites

PubMed Central

Kamar, Ramsey I.; Banigan, Edward J.; Erbas, Aykut; Giuntoli, Rebecca D.; Olvera de la Cruz, Monica; Johnson, Reid C.; Marko, John F.

2017-01-01

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate ∼1×104 M−1s−1, establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap. PMID:28364020

A simplified model for dynamics of cell rolling and cell-surface adhesion

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

Cimrák, Ivan, E-mail: ivan.cimrak@fri.uniza.sk

2015-03-10

We propose a three dimensional model for the adhesion and rolling of biological cells on surfaces. We study cells moving in shear flow above a wall to which they can adhere via specific receptor-ligand bonds based on receptors from selectin as well as integrin family. The computational fluid dynamics are governed by the lattice-Boltzmann method. The movement and the deformation of the cells is described by the immersed boundary method. Both methods are fully coupled by implementing a two-way fluid-structure interaction. The adhesion mechanism is modelled by adhesive bonds including stochastic rules for their creation and rupture. We explore amore » simplified model with dissociation rate independent of the length of the bonds. We demonstrate that this model is able to resemble the mesoscopic properties, such as velocity of rolling cells.« less

Phoretic self-propulsion: a mesoscopic description of reaction dynamics that powers motion.

PubMed

de Buyl, Pierre; Kapral, Raymond

2013-02-21

The fabrication of synthetic self-propelled particles and the experimental investigations of their dynamics have stimulated interest in self-generated phoretic effects that propel nano- and micron-scale objects. Theoretical modeling of these phenomena is often based on a continuum description of the solvent for different phoretic propulsion mechanisms, including, self-electrophoresis, self-diffusiophoresis and self-thermophoresis. The work in this paper considers various types of catalytic chemical reaction at the motor surface and in the bulk fluid that come into play in mesoscopic descriptions of the dynamics. The formulation is illustrated by developing the mesoscopic reaction dynamics for exothermic and dissociation reactions that are used to power motor motion. The results of simulations of the self-propelled dynamics of composite Janus particles by these mechanisms are presented.

Optimal control of multiphoton ionization dynamics of small alkali aggregates

NASA Astrophysics Data System (ADS)

Lindinger, A.; Bartelt, A.; Lupulescu, C.; Vajda, S.; Woste, Ludger

2003-11-01

We have performed transient multi-photon ionization experiments on small alkali clusters of different size in order to probe their wave packet dynamics, structural reorientations, charge transfers and dissociative events in different vibrationally excited electronic states including their ground state. The observed processes were highly dependent on the irradiated pulse parameters like wavelength range or its phase and amplitude; an emphasis to employ a feedback control system for generating the optimum pulse shapes. Their spectral and temporal behavior reflects interesting properties about the investigated system and the irradiated photo-chemical process. First, we present the vibrational dynamics of bound electronically excited states of alkali dimers and trimers. The scheme for observing the wave packet dynamics in the electronic ground state using stimulated Raman-pumping is shown. Since the employed pulse parameters significantly influence the efficiency of the irradiated dynamic pathways photo-induced ioniziation experiments were carried out. The controllability of 3-photon ionization pathways is investigated on the model-like systems NaK and K2. A closed learning loop for adaptive feedback control is used to find the optimal fs pulse shape. Sinusoidal parameterizations of the spectral phase modulation are investigated in regard to the obtained optimal field. By reducing the number of parameters and thereby the complexity of the phase moduation, optimal pulse shapes can be generated that carry fingerprints of the molecule's dynamical properties. This enables to find "understandable" optimal pulse forms and offers the possiblity to gain insight into the photo-induced control process. Characteristic motions of the involved wave packets are proposed to explain the optimized dynamic dissociation pathways.

Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding.

PubMed

Goldman, Nir; Aradi, Bálint; Lindsey, Rebecca K; Fried, Laurence E

2018-05-08

We detail the creation of a multicenter density functional tight binding (DFTB) model for hydrogen on δ-plutonium, using a framework of new Slater-Koster interaction parameters and a repulsive energy based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES), where two- and three-center atomic interactions are represented by linear combinations of Chebyshev polynomials. We find that our DFTB/ChIMES model yields a total electron density of states for bulk δ-Pu that compares well to that from Density Functional Theory, as well as to a grid of energy calculations representing approximate H 2 dissociation paths on the δ-Pu (100) surface. We then perform molecular dynamics simulations and minimum energy pathway calculations to determine the energetics of surface dissociation and subsurface diffusion on the (100) and (111) surfaces. Our approach allows for the efficient creation of multicenter repulsive energies with a relatively small investment in initial DFT calculations. Our efforts are particularly pertinent to studies that rely on quantum calculations for interpretation and validation, such as experimental determination of chemical reactivity both on surfaces and in condensed phases.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly.

PubMed

Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

2017-09-01

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U(x,z) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ, revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly

NASA Astrophysics Data System (ADS)

Chen, Yen-Fu; Chen, Hsuan-Yi; Sheng, Yu-Jane; Tsao, Heng-Kwong

2017-09-01

The unbinding dynamics of a nanosized sphere-and-cavity assembly under the pulling of constant force and constant loading rate is explored by dissipative particle dynamics simulations. The formation of this matched lock-and-key pair in a polymer solution is driven by the depletion attraction. The two-dimensional free energy landscape U (x ,z ) associated with this assembly is constructed. Our results indicate that the unbinding pathway along the orientation of the assembly is unfavorable due to the relatively high energy barrier compared to that along the tortuous minimum path whose energy barrier is not high. It is also found that the dissociation rate depends on the direction of the external force (θ ) with respect to the assembly orientation. The presence of the force component perpendicular to the assembly orientation can reduce the bond lifetime significantly by driving the key particle to approach the minimum path. Moreover, the dissociation dynamics can be facilitated even by a pushing force compared to the spontaneous dissociation (without forces). To elucidate the effective pathway under pulling, the escaping position is analyzed and its mean direction with respect to the assembly orientation rises generally with increasing θ , revealing that the presence of the force component along the minimum pathway is helpful. The importance of the direction of the external pulling has been demonstrated in our simple system. Therefore, this effect should be considered in more complicated unbinding experiments.

Combustion of Methane Hydrate

NASA Astrophysics Data System (ADS)

Roshandell, Melika

A significant methane storehouse is in the form of methane hydrates on the sea floor and in the arctic permafrost. Methane hydrates are ice-like structures composed of water cages housing a guest methane molecule. This caged methane represents a resource of energy and a potential source of strong greenhouse gas. Most research related to methane hydrates has been focused on their formation and dissociation because they can form solid plugs that complicate transport of oil and gas in pipelines. This dissertation explores the direct burning of these methane hydrates where heat from the combustion process dissociates the hydrate into water and methane, and the released methane fuels the methane/air diffusion flame heat source. In contrast to the pipeline applications, very little research has been done on the combustion and burning characteristics of methane hydrates. This is the first dissertation on this subject. In this study, energy release and combustion characteristics of methane hydrates were investigated both theoretically and experimentally. The experimental study involved collaboration with another research group, particularly in the creation of methane hydrate samples. The experiments were difficult because hydrates form at high pressure within a narrow temperature range. The process can be slow and the resulting hydrate can have somewhat variable properties (e.g., extent of clathration, shape, compactness). The experimental study examined broad characteristics of hydrate combustion, including flame appearance, burning time, conditions leading to flame extinguishment, the amount of hydrate water melted versus evaporated, and flame temperature. These properties were observed for samples of different physical size. Hydrate formation is a very slow process with pure water and methane. The addition of small amounts of surfactant increased substantially the hydrate formation rate. The effects of surfactant on burning characteristics were also studied. One finding from the experimental component of the research was that hydrates can burn completely, and that they burn most rapidly just after ignition and then burn steadily when some of the water in the dissociated zone is allowed to drain away. Excessive surfactant in the water creates a foam layer around the hydrate that acts as an insulator. The layer prevents sufficient heat flux from reaching the hydrate surface below the foam to release additional methane and the hydrate flame extinguishes. No self-healing or ice-freezing processes were observed in any of the combustion experiments. There is some variability, but a typical hydrate flame is receiving between one and two moles of water vapor from the liquid dissociated zone of the hydrate for each mole of methane it receives from the dissociating solid region. This limits the flame temperature to approximately 1800 K. In the theoretical portion of the study, a physical model using an energy balance from methane combustion was developed to understand the energy transfer between the three phases of gas, liquid and solid during the hydrate burn. Also this study provides an understanding of the different factors impacting the hydrate's continuous burn, such as the amount of water vapor in the flame. The theoretical study revealed how the water layer thickness on the hydrate surface, and its effect on the temperature gradient through the dissociated zone, plays a significant role in the hydrate dissociation rate and methane release rate. Motivated by the above mentioned observation from the theoretical analysis, a 1-D two-phase numerical simulation based on a moving front model for hydrate dissociation from a thermal source was developed. This model was focused on the dynamic growth of the dissociated zone and its effect on the dissociation rate. The model indicated that the rate of hydrate dissociation with a thermal source is a function of the dissociated zone thickness. It shows that in order for a continuous dissociation and methane release, some of the water from the dissociated zone needs to be drained. The results are consistent with the experimental observations. The understanding derived from the experiments and the numerical model permitted a brief exploration into the potential effects of pressure on the combustion of methane hydrates. The prediction is that combustion should improve under high pressure conditions because the evaporation of water is suppressed allowing more energy into the dissociation. Future experiments are needed to validate these initial findings.

Thermochemical Modeling of Nonequilibrium Oxygen Flows

NASA Astrophysics Data System (ADS)

Neitzel, Kevin Joseph

The development of hypersonic vehicles leans heavily on computational simulation due to the high enthalpy flow conditions that are expensive and technically challenging to replicate experimentally. The accuracy of the nonequilibrium modeling in the computer simulations dictates the design margin that is required for the thermal protection system and flight dynamics. Previous hypersonic vehicles, such as Apollo and the Space Shuttle, were primarily concerned with re-entry TPS design. The strong flow conditions of re-entry, involving Mach numbers of 25, quickly dissociate the oxygen molecules in air. Sustained flight, hypersonic vehicles will be designed to operate in Mach number ranges of 5 to 10. The oxygen molecules will not quickly dissociate and will play an important role in the flow field behavior. The development of nonequilibrium models of oxygen is crucial for limiting modeling uncertainty. Thermochemical nonequilibrium modeling is investigated for oxygen flows. Specifically, the vibrational relaxation and dissociation behavior that dominate the nonequilibrium physics in this flight regime are studied in detail. The widely used two-temperature (2T) approach is compared to the higher fidelity and more computationally expensive state-to-state (STS) approach. This dissertation utilizes a wide range of rate sources, including newly available STS rates, to conduct a comprehensive study of modeling approaches for hypersonic nonequilibrium thermochemical modeling. Additionally, the physical accuracy of the computational methods are assessed by comparing the numerical results with available experimental data. The numerical results and experimental measurements present strong nonequilibrium, and even non-Boltzmann behavior in the vibrational energy mode for the sustained hypersonic flight regime. The STS approach is able to better capture the behavior observed in the experimental data, especially for stronger nonequilibrium conditions. Additionally, a reduced order model (ROM) modification to the 2T model is developed to improve the capability of the 2T approach framework.

CH4 dissociation on Ru(0001): A view from both sides of the barrier

NASA Astrophysics Data System (ADS)

Mortensen, H.; Diekhöner, L.; Baurichter, A.; Luntz, A. C.

2002-04-01

This paper reports measurements of both dissociative adsorption on and associative desorption from CH4 on Ru(0001). We consider the former a view of dissociation from the front side of the barrier, while the latter is considered as a view of dissociation from the back side of the barrier. A combination of both previous and new molecular beam measurements of dissociative adsorption shows that S0 depends on all experimental variables (E, Tn, Ts and isotope) in a manner similar to other close-packed transition metals. The interpretation of this behavior in terms of a theoretical description of the dissociation is discussed critically, with special emphasis on insights from new theoretical studies. The energy-resolved desorption flux Df(E,Ts) is obtained in associative desorption experiments using the technique of laser assisted associative desorption (LAAD). Measurements at several Ts allow both a direct determination of the adiabatic barrier V*(0) and considerable insight into the dynamics of dissociation. The V*(0) obtained from Df(E,Ts) is in excellent agreement with density functional theory (DFT) calculations and with the value indirectly inferred from molecular beam experiments. The chief dynamic conclusion from an analysis of Df(E,Ts) is that both bending and stretching coordinates must be produced in associative desorption, although they are not populated statistically. The absence of an isotope effect in the shape of Df(E,Ts) argues against the importance of tunneling in the desorption/adsorption. When reactive fluxes are compared via detailed balance, both the molecular beam experiment and the LAAD experiment are in good agreement.

Pulsed IR Heating Studies of Single-Molecule DNA Duplex Dissociation Kinetics and Thermodynamics

PubMed Central

Holmstrom, Erik D.; Dupuis, Nicholas F.; Nesbitt, David J.

2014-01-01

Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10−11 liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20–100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation. PMID:24411254

Interfacial disorder drives charge separation in molecular semiconductors

NASA Astrophysics Data System (ADS)

Willard, Adam

One of the fundamental microscopic processes in photocurrent generation is the dissociation of neutral photo-excitations (i.e., Frenkel excitons) into free charge carriers (i.e., electrons and holes). This process requires the physical separation of oppositely charged electrons and holes, which are held to together by an attractive electrostatic binding energy. In traditional inorganic-based photovoltaic (PV) materials, this binding energy is generally small and easily overcome, however, in organic-based PVs (OPVs) the exciton binding energy can significantly exceed thermal energies. The inability of bound charges to overcome this large binding energy has been implicated as a primary source of efficiency loss in OPVs. Here I present results from our recent efforts to explore the role of static molecular disorder in mediating this process. Using a simple lattice model of exciton dynamics we demonstrate that random spatial variations in the energetic landscape can mitigate the attractive Coulomb interaction between electrons and holes. We show that this effect manifests as a reduction in the free energy barrier for exciton dissociation that grows more pronounced with increasing disorder. By considering the competition between this thermodynamic effect and the disorder-induced slowing of dissociation kinetics we demonstrate that exciton dissociation yields are expected to depend non-monotonically on the degree of static disorder.

Time-resolved spectroscopy at surfaces and adsorbate dynamics: Insights from a model-system approach

NASA Astrophysics Data System (ADS)

Boström, Emil; Mikkelsen, Anders; Verdozzi, Claudio

2016-05-01

We introduce a model description of femtosecond laser induced desorption at surfaces. The substrate part of the system is taken into account as a (possibly semi-infinite) linear chain. Here, being especially interested in the early stages of dissociation, we consider a finite-size implementation of the model (i.e., a finite substrate), for which an exact numerical solution is possible. By time-evolving the many-body wave function, and also using results from a time-dependent density functional theory description for electron-nuclear systems, we analyze the competition between several surface-response mechanisms and electronic correlations in the transient and longer time dynamics under the influence of dipole-coupled fields. Our model allows us to explore how coherent multiple-pulse protocols can impact desorption in a variety of prototypical experiments.

Martian Dust Devil Electron Avalanche Process and Associated Electrochemistry

NASA Technical Reports Server (NTRS)

Jackson, Telana L.; Farrell, William M.; Delory, Gregory T.; Nithianandam, Jeyasingh

2010-01-01

Mars' dynamic atmosphere displays localized dust devils and larger, global dust storms. Based on terrestrial analog studies, electrostatic modeling, and laboratory work these features will contain large electrostatic fields formed via triboelectric processes. In the low-pressure Martian atmosphere, these fields may create an electron avalanche and collisional plasma due to an increase in electron density driven by the internal electrical forces. To test the hypothesis that an electron avalanche is sustained under these conditions, a self-consistent atmospheric process model is created including electron impact ionization sources and electron losses via dust absorption, electron dissociation attachment, and electron/ion recombination. This new model is called the Dust Devil Electron Avalanche Model (DDEAM). This model solves simultaneously nine continuity equations describing the evolution of the primary gaseous chemical species involved in the electrochemistry. DDEAM monitors the evolution of the electrons and primary gas constituents, including electron/water interactions. We especially focus on electron dynamics and follow the electrons as they evolve in the E field driven collisional gas. When sources and losses are self-consistently included in the electron continuity equation, the electron density grows exponentially with increasing electric field, reaching an equilibrium that forms a sustained time-stable collisional plasma. However, the character of this plasma differs depending upon the assumed growth rate saturation process (chemical saturation versus space charge). DDEAM also shows the possibility of the loss of atmospheric methane as a function of electric field due to electron dissociative attachment of the hydrocarbon. The methane destruction rates are presented and can be included in other larger atmospheric models.

Theory of the reaction dynamics of small molecules on metal surfaces

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

Jackson, Bret

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 H 2, H 2O and CH 4 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 experimentalmore » 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).« less

Dissociation of sarin on a cement analogue surface: Effects of humidity and confined geometry

DOE PAGES

O’Brien, Christopher J.; Greathouse, Jeffery A.; Tenney, Craig M.

2016-11-22

Here, first-principles molecular dynamics simulations were used to investigate the dissociation of sarin (GB) on the calcium silicate hydrate (CSH) mineral tobermorite (TBM), a surrogate for cement. CSH minerals (including TBM) and amorphous materials of similar composition are the major components of Portland cement, the binding agent of concrete. Metadynamics simulations were used to investigate the effect of the TBM surface and confinement in a microscale pore on the mechanism and free energy of dissociation of GB. Our results indicate that both the adsorption site and the humidity of the local environment significantly affect the sarin dissociation energy. In particular,more » sarin dissociation in a low-water environment occurs via a dealkylation mechanism, which is consistent with previous experimental studies.« less

The dissociative chemisorption of CO2 on Ni(100): A quantum dynamics study

NASA Astrophysics Data System (ADS)

Farjamnia, Azar; Jackson, Bret

2017-02-01

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of CO2 on Ni(100). The largest barrier to reaction corresponds to the formation of a bent anionic molecular precursor, bound to the surface by about 0.24 eV. The barrier to dissociation from this state is small. Our computed dissociative sticking probabilities on Ni(100) for molecules in the ground state are in very good agreement with available experimental data, reasonably reproducing the variation in reactivity with collision energy. Vibrational excitation of the incident CO2 can enhance reactivity, particularly for incident energies at or below threshold, and there is clear mode specific behavior. Both the vibrational enhancement and the increase in dissociative sticking with surface temperature are much weaker than that found in recent studies of methane and water dissociative chemisorption. The energetics for CO2 adsorption and dissociation on the stepped Ni(711) surface are found to be similar to that on Ni(100), except that the barrier to dissociation from the anionic precursor is even smaller on Ni(711). We predict that the dissociative sticking behavior is similar on the two surfaces.

The dissociative chemisorption of CO 2 on Ni(100): A quantum dynamics study

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

Farjamnia, Azar; Jackson, Bret

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of CO 2 on Ni(100). The largest barrier to reaction corresponds to the formation of a bent anionic molecular precursor, bound to the surface by about 0.24 eV. The barrier to dissociation from this state is small. In our computed dissociative sticking probabilities on Ni(100) for molecules, the ground states are in very good agreement with available experimental data, reasonably reproducing the variation in reactivity with collision energy. Vibrational excitation of the incident CO 2 can enhance reactivity, particularly for incident energiesmore » at or below threshold, and there is clear mode specific behavior. Both the vibrational enhancement and the increase in dissociative sticking with surface temperature are much weaker than that found in recent studies of methane and water dissociative chemisorption. The energetics for CO 2 adsorption and dissociation on the stepped Ni(711) surface are found to be similar to that on Ni(100), except that the barrier to dissociation from the anionic precursor is even smaller on Ni(711). Here, we predict that the dissociative sticking behavior is similar on the two surfaces.« less

The dissociative chemisorption of CO 2 on Ni(100): A quantum dynamics study

DOE PAGES

Farjamnia, Azar; Jackson, Bret

2017-02-21

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of CO 2 on Ni(100). The largest barrier to reaction corresponds to the formation of a bent anionic molecular precursor, bound to the surface by about 0.24 eV. The barrier to dissociation from this state is small. In our computed dissociative sticking probabilities on Ni(100) for molecules, the ground states are in very good agreement with available experimental data, reasonably reproducing the variation in reactivity with collision energy. Vibrational excitation of the incident CO 2 can enhance reactivity, particularly for incident energiesmore » at or below threshold, and there is clear mode specific behavior. Both the vibrational enhancement and the increase in dissociative sticking with surface temperature are much weaker than that found in recent studies of methane and water dissociative chemisorption. The energetics for CO 2 adsorption and dissociation on the stepped Ni(711) surface are found to be similar to that on Ni(100), except that the barrier to dissociation from the anionic precursor is even smaller on Ni(711). Here, we predict that the dissociative sticking behavior is similar on the two surfaces.« less

A study of internal energy relaxation in shocks using molecular dynamics based models

NASA Astrophysics Data System (ADS)

Li, Zheng; Parsons, Neal; Levin, Deborah A.

2015-10-01

Recent potential energy surfaces (PESs) for the N2 + N and N2 + N2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N2 + N2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available.

Ab initio molecular dynamics of H2O adsorbed on solid MgO

NASA Astrophysics Data System (ADS)

Langel, Walter; Parrinello, Michele

1995-08-01

The Car-Parrinello method has been applied to study the adsorption of water on solid magnesium oxide with surface defects. A step consisting of an (100) and an (010) surface on an (011) base plane allows us to model the experimentally observed microfaceting. In and on this step dissociation of water into a hydroxyl group and a H-atom took place following a complicated pathway only accessible by the simulation of thermal motion. Under comparable conditions physisorption only was observed on a regular (001) plane. This solves an experimental controversy and it is in agreement with the observation, that disordered surfaces are more active in initiating the dissociation of the water molecules. Our work allows us to identify an important active center. We can also account for the experimentally observed broadening and shifting to the red of the stretching mode of hydrogen bonded hydroxyl groups, and we provide a detailed explanation of the origin of this effect. This allows us to verify earlier theories of hydrogen bonding such as that of the adiabatic separation of the proton dynamics.

Molecular beam studies of stratospheric photochemistry

NASA Astrophysics Data System (ADS)

Moore, Teresa Anne

1998-12-01

Photochemistry of chlorine oxide containing species plays a major role in stratospheric ozone depletion. This thesis discusses two photodissociation studies of the key molecules ClONO2 and ClOOCl which were previously thought to only produce Cl-atom (ozone depleting) products at wavelengths relevant to the stratosphere. The development of a molecular beam source of ClOOCl and the photodissociation dynamics of the model system Cl2O are also discussed. In the first chapter, the photochemistry of ClONO2 is examined at 308 nm using the technique of photofragment translational spectroscopy. Two primary decomposition pathways, leading to Cl + NO3 and ClO + NO2, were observed, with a lower limit of 0.33 for the relative yield of ClO. The angular distributions for both channels were anisotropic, indicating that the dissociation occurs within a rotational period. Chapter two revisits the photodissociation dynamics of Cl2O at 248 and 308 nm, on which we had previously reported preliminary findings. At 248 nm, three distinct dissociation pathways leading to Cl + ClO products were resolved. At 308 nm, the angular distribution was slightly more isotropic that previously reported, leaving open the possibility that Cl2O excited at 308 nm lives longer than a rotational period. Chapter three describes the development and optimization of a molecular beam source of ClOOCl. We utilized pulsed laser photolysis of ClA2O to generate ClO radicals, and cooled the cell to promote three body recombination to form ClOOCl. The principal components in the beam were Cl2, Cl2O, and ClOOCl. In the fourth chapter, the photodissociation dynamics of ClOOCl are investigated at 248 and 308 nm. We observed multiple dissociation pathways which produced ClO + ClO and 2Cl + O2 products. The relative Cl:ClO product yields are 1.0:0.13 and 1.0:0.20 for ClOOCl photolysis at 248 and 308 nm, respectively. The upper limit for the relative yield of the ClO + ClO channel was 0.19 at 248 nm and 0.31 at 308 nm. These results substantially confirm the current assumption but decrease somewhat the efficiency of the ClOOCl ozone-depleting catalytic cycle. At 248 nm, ClOOCl photolysis exhibited novel dissociation dynamics which appeared to depend on the symmetry of the excited state.

A nonequilibrium model for a moderate pressure hydrogen microwave discharge plasma

NASA Technical Reports Server (NTRS)

Scott, Carl D.

1993-01-01

This document describes a simple nonequilibrium energy exchange and chemical reaction model to be used in a computational fluid dynamics calculation for a hydrogen plasma excited by microwaves. The model takes into account the exchange between the electrons and excited states of molecular and atomic hydrogen. Specifically, electron-translation, electron-vibration, translation-vibration, ionization, and dissociation are included. The model assumes three temperatures, translational/rotational, vibrational, and electron, each describing a Boltzmann distribution for its respective energy mode. The energy from the microwave source is coupled to the energy equation via a source term that depends on an effective electric field which must be calculated outside the present model. This electric field must be found by coupling the results of the fluid dynamics and kinetics solution with a solution to Maxwell's equations that includes the effects of the plasma permittivity. The solution to Maxwell's equations is not within the scope of this present paper.

Ultrafast photodissociation dynamics of 1,4-diiodobenzene

NASA Astrophysics Data System (ADS)

Stankus, Brian; Zotev, Nikola; Rogers, David M.; Gao, Yan; Odate, Asami; Kirrander, Adam; Weber, Peter M.

2018-05-01

The photodissociation dynamics of 1,4-diiodobenzene is investigated using ultrafast time-resolved photoelectron spectroscopy. Following excitation by laser pulses at 271 nm, the excited-state dynamics is probed by resonance-enhanced multiphoton ionization with 405 nm probe pulses. A progression of Rydberg states, which come into resonance sequentially, provide a fingerprint of the dissociation dynamics of the molecule. The initial excitation decays with a lifetime of 33 ± 4 fs, in good agreement with a previous study. The spectrum is interpreted by reference to ab initio calculations at the CASPT2(18,14) level, including spin-orbit coupling. We propose that both the 5B1 and 6B1 states are excited initially, and based on the calculations, we identify diabatic spin-orbit coupled states corresponding to the main dissociation pathways.

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses

PubMed Central

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-01-01

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation. PMID:28223697

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

PubMed

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

Li + solvation and kinetics of Li +–BF 4 -/PF 6 - ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

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

Chang, Tsun-Mei; Dang, Liem X.

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine in this paper the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li + and the dissociation kinetics of ion pairs Li +–[BF 4] and Li +–[PF 6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found that the residence times of EC around Li + ions varied from 60 to 450 ps, depending on themore » correction method used. We found that the relaxation times changed significantly from Li +–[BF 4] to Li +–[PF 6] ion pairs in EC. Finally, our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influences the dissociation kinetics of ion pairing.« less

Li + solvation and kinetics of Li +–BF 4 -/PF 6 - ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

DOE PAGES

Chang, Tsun-Mei; Dang, Liem X.

2017-07-19

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine in this paper the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li + and the dissociation kinetics of ion pairs Li +–[BF 4] and Li +–[PF 6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found that the residence times of EC around Li + ions varied from 60 to 450 ps, depending on themore » correction method used. We found that the relaxation times changed significantly from Li +–[BF 4] to Li +–[PF 6] ion pairs in EC. Finally, our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influences the dissociation kinetics of ion pairing.« less

Dynamics of Singlet Fission and Electron Injection in Self-Assembled Acene Monolayers on Titanium Dioxide

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

Johnson, Justin C; Pace, Natalie A; Arias, Dylan H

We employ a combination of linear spectroscopy, electrochemistry, and transient absorption spectroscopy to characterize the interplay between electron transfer and singlet fission dynamics in polyacene-based dyes attached to nanostructured TiO2. For triisopropyl silylethynyl (TIPS)-pentacene, we find that the singlet fission time constant increases to 6.5 ps on a nanostructured TiO2 surface relative to a thin film time constant of 150 fs, and that triplets do not dissociate after they are formed. In contrast, TIPS-tetracene singlets quickly dissociate in 2 ps at the molecule/TiO2 interface, and this dissociation outcompetes the relatively slow singlet fission process. The addition of an alumina layermore » slows down electron injection, allowing the formation of triplets from singlet fission in 40 ps. However, the triplets do not inject electrons, which is likely due to a lack of sufficient driving force for triplet dissociation. These results point to the critical balance required between efficient singlet fission and appropriate energetics for interfacial charge transfer.« less

Contributions of 3'-overhang to the dissociation of small interfering RNAs from the PAZ domain: molecular dynamics simulation study.

PubMed

Lee, Hui Sun; Lee, Soo Nam; Joo, Chul Hyun; Lee, Heuiran; Lee, Han Saem; Yoon, Seung Yong; Kim, Yoo Kyum; Choe, Han

2007-03-01

RNA interference (RNAi) is a 'knock-down' reaction to reduce expression of a specific gene through highly regulated, enzyme-mediated processes. Small interfering RNAs (siRNAs) are RNA molecules that play an effector role in RNAi and can bind the PAZ domains present in Dicer and RISC. We investigated the interaction between the PAZ domain and the siRNA-like duplexes through dissociation molecular dynamics (DMD) simulations. Specifically, we focused on the response of the PAZ domain to various 3'-overhang structures of the siRNA-like duplexes. We found that the siRNA-like duplex with the 3' UU-overhang made relatively more stable complex with the PAZ domain compared to those with 3' CC-, AA-, and GG-overhangs. The siRNA-like duplex with UU-overhang was easily dissociated from the PAZ domain once the structural stability of the complex is impaired. Interestingly, the 3' UU-overhang spent the least time at the periphery region of the binding pocket during the dissociation process, which can be mainly attributable to UU-overhang's smallest number of hydrogen bonds.

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

Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto

The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-chargedmore » bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)« less

Modeling the Extended Neutral Atmosphere and Plasma Environment near Saturn

NASA Technical Reports Server (NTRS)

Richardson, John D.

2003-01-01

In the three years of this study we have published five papers in refereed journals. We have first examined satellite sources and their contribution to the observed neutral cloud. Based on the total calculated satellite sources and the spatial distribution of sputtered H20, we concluded that they cannot produce observed OH cloud. The E-ring contribution has been also studied in detail.In order to produce observed OH cloud we suggested that the E-ring might be the dominant source in inner Saturnian magnetosphere. We proposed a possible resupply mechanism which is needed to keep both E-ring and OH cloud in the present state: collisions between E-ring grains and remains of a disrupted satellite near Enceladus Lagrangian points. In this scenario a large amount of material, ranging from a few micrometers to hundred of meters, which is optically invisible at present, is likely to exist there. The fourth paper compares the magnetosheaths of the outer planets. A surprising result is that the hot proton component comprises about 40% of the total density, much larger than predicted by shock theory. Gas dynamic models of the boundaries show that the magnetospheres of Jupiter and Saturn are flattened at the poles. The last paper was published in GRL and is the first based of the model of neutrals developed as a main goal of this grant and which is now operational.This Monte Carlo collision code self- consistently determines the neutral distribution. from the rings and satellites until they are lost by ionization, by collisions with rings, moons, or Saturn, or by escape from Saturn. Our model is unique in that it includes the effects of plasma chemistry and both plasma-neutral and neutral neutral collisions to determine the dynamical evolution of the water group neutrals in Saturn's magnetosphere. The lifetimes of the neutrals against loss to photoionization, charge exchange, electron dissociation and electron impact dissociation are based on the model given by (Richardson et al. 1998) and vary with position in the magnetosphere. The dominant neutral dissociation channels H20->OH+H, H20-> O+H2, and OH->O+H2 are considered.

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Dibak, Manuel; del Razo, Mauricio J.; De Sancho, David; Schütte, Christof; Noé, Frank

2018-06-01

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature.

PubMed

Litman, Yair; Donadio, Davide; Ceriotti, Michele; Rossi, Mariana

2018-03-14

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We thus perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account the conformational entropy and anharmonicities at finite temperatures. We propose that when adsorption is weak and NQEs on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We then calculate the full contribution of NQEs to the free energies, including also anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared with the harmonic estimates. We also find that the dissociation process has a negligible contribution from tunneling but is dominated by zero point energies, which can enhance the rate of dissociation by three orders of magnitude. Finally we highlight how both temperature and NQEs indirectly impact dipoles and the redistribution of electron density, causing work function changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in the work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces.

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature

NASA Astrophysics Data System (ADS)

Litman, Yair; Donadio, Davide; Ceriotti, Michele; Rossi, Mariana

2018-03-01

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We thus perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account the conformational entropy and anharmonicities at finite temperatures. We propose that when adsorption is weak and NQEs on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We then calculate the full contribution of NQEs to the free energies, including also anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared with the harmonic estimates. We also find that the dissociation process has a negligible contribution from tunneling but is dominated by zero point energies, which can enhance the rate of dissociation by three orders of magnitude. Finally we highlight how both temperature and NQEs indirectly impact dipoles and the redistribution of electron density, causing work function changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in the work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces.

Beyond the Impasse - Reflections on Dissociative Identity Disorder from a Freudian-Lacanian Perspective.

PubMed

Meganck, Reitske

2017-01-01

Dissociative identity disorder (DID) is a widely contested diagnosis. The dominant posttraumatic model (PTM) considers early life trauma to be the direct cause of the creation of alter identities and assumes that working directly with alter identities should be at the core of the therapeutic work. The socio-cognitive model, on the other hand, questions the validity of the DID diagnosis and proposes an iatrogenic origin of the disorder claiming that reigning therapeutic and socio-cultural discourses create and reify the problem. The author argues that looking at the underlying psychical dynamics can provide a way out of the debate on the veracity of the diagnosis. A structural conception of hysteria is presented to understand clinical and empirical observations on the prevalence, appearance and treatment of DID. On a more fundamental level, the concept of identification and the fundamental division of human psychic functioning are proposed as crucial for understanding the development and treatment of DID.

Beyond the Impasse – Reflections on Dissociative Identity Disorder from a Freudian–Lacanian Perspective

PubMed Central

Meganck, Reitske

2017-01-01

Dissociative identity disorder (DID) is a widely contested diagnosis. The dominant posttraumatic model (PTM) considers early life trauma to be the direct cause of the creation of alter identities and assumes that working directly with alter identities should be at the core of the therapeutic work. The socio-cognitive model, on the other hand, questions the validity of the DID diagnosis and proposes an iatrogenic origin of the disorder claiming that reigning therapeutic and socio-cultural discourses create and reify the problem. The author argues that looking at the underlying psychical dynamics can provide a way out of the debate on the veracity of the diagnosis. A structural conception of hysteria is presented to understand clinical and empirical observations on the prevalence, appearance and treatment of DID. On a more fundamental level, the concept of identification and the fundamental division of human psychic functioning are proposed as crucial for understanding the development and treatment of DID. PMID:28559875

Tracking dissociation dynamics of strong-field ionized 1,2-dibromoethane with femtosecond XUV transient absorption spectroscopy.

PubMed

Chatterley, Adam S; Lackner, Florian; Neumark, Daniel M; Leone, Stephen R; Gessner, Oliver

2016-06-07

Using femtosecond time-resolved extreme ultraviolet absorption spectroscopy, the dissociation dynamics of the haloalkane 1,2-dibromoethane (DBE) have been explored following strong field ionization by femtosecond near infrared pulses at intensities between 7.5 × 10(13) and 2.2 × 10(14) W cm(-2). The major elimination products are bromine atoms in charge states of 0, +1, and +2. The charge state distribution is strongly dependent on the incident NIR intensity. While the yield of neutral fragments is essentially constant for all measurements, charged fragment yields grow rapidly with increasing NIR intensities with the most pronounced effect observed for Br(++). However, the appearance times of all bromine fragments are independent of the incident field strength; these are found to be 320 fs, 70 fs, and 30 fs for Br˙, Br(+), and Br(++), respectively. Transient molecular ion features assigned to DBE(+) and DBE(++) are observed, with dynamics linked to the production of Br(+) products. Neutral Br˙ atoms are produced on a timescale consistent with dissociation of DBE(+) ions on a shallow potential energy surface. The appearance of Br(+) ions by dissociative ionization is also seen, as evidenced by the simultaneous decay of a DBE(+) ionic species. Dicationic Br(++) products emerge within the instrument response time, presumably from Coulomb explosion of triply charged DBE.

Tracking dissociation dynamics of strong-field ionized 1,2-dibromoethane with femtosecond XUV transient absorption spectroscopy

DOE PAGES

Chatterley, Adam S.; Lackner, Florian; Neumark, Daniel M.; ...

2016-05-11

Using femtosecond time-resolved extreme ultraviolet absorption spectroscopy, the dissociation dynamics of the haloalkane 1,2-dibromoethane (DBE) have been explored following strong field ionization by femtosecond near infrared pulses at intensities between 7.5 × 10 13 and 2.2 × 10 14 W cm -2. The major elimination products are bromine atoms in charge states of 0, +1, and +2. The charge state distribution is strongly dependent on the incident NIR intensity. While the yield of neutral fragments is essentially constant for all measurements, charged fragment yields grow rapidly with increasing NIR intensities with the most pronounced effect observed for Br ++. However,more » the appearance times of all bromine fragments are independent of the incident field strength; these are found to be 320 fs, 70 fs, and 30 fs for Br˙, Br +, and Br ++, respectively. Transient molecular ion features assigned to DBE + and DBE ++ are observed, with dynamics linked to the production of Br + products. Neutral Br˙ atoms are produced on a timescale consistent with dissociation of DBE + ions on a shallow potential energy surface. The appearance of Br + ions by dissociative ionization is also seen, as evidenced by the simultaneous decay of a DBE + ionic species. Dicationic Br ++ products emerge within the instrument response time, presumably from Coulomb explosion of triply charged DBE.« less

Coherent control of alkali cluster fragmentation dynamics

NASA Astrophysics Data System (ADS)

Lindinger, Albrecht; Lupulescu, Cosmin; Bartelt, Andreas; Vajda, Štefan; Wöste, Ludger

2003-06-01

Metal clusters exhibit extraordinary chemical and catalytic properties, which sensitively depend upon their size. This behavior makes them interesting candidates for the real-time analysis of ultrafast photo-induced processes—ultimately leading to coherent control scenarii. We have performed transient multi-photon ionization experiments on small alkali clusters of different size in order to probe their wave packet dynamics, structural reorientations, charge transfers and dissociative events in different vibrationally excited electronic states including their ground state. The observed processes were highly dependent on the irradiated pulse parameters, like its phase, amplitude and duration; an emphasis to employ a feedback control system for generating the optimum pulse shapes. Their spectral and temporal behavior reflects interesting properties about the investigated system and the irradiated photochemical process. We present first the vibrational dynamics of bound, dissociated, and pre-dissociated electronically excited states of alkali dimers and trimers. The scheme for observing the wave packet dynamics in the electronic ground state using stimulated Raman-pumping is shown. Since the employed pulse parameters significantly influence the efficiency of the irradiated dynamic pathways photo-induced fragmentation experiments on bifurcating reaction channels were carried out. In these experiments different branching ionization and fragmentation pathways of electronically excited Na 2K were investigated. By employing an evolutionary algorithm for optimizing the phase and amplitude of the applied laser field, the yield of the resulting parent or fragment ions could significantly be influenced and interesting features could be concluded from the obtained optimum pulse shapes revealing the characteristic molecular oscillation period. Moreover, the influence on the optimal pulse shape due to fragmentation from larger clusters into NaK is obtained. The substructure of the optimal pulse shape thereby offers new insight into the fragmentation channel during the control process. Characteristic motions of the involved wave packets are proposed, in order to explain the optimized dynamic dissociation pathways.

The cAMP-induced G protein subunits dissociation monitored in live Dictyostelium cells by BRET reveals two activation rates, a positive effect of caffeine and potential role of microtubules.

PubMed

Tariqul Islam, A F M; Yue, Haicen; Scavello, Margarethakay; Haldeman, Pearce; Rappel, Wouter-Jan; Charest, Pascale G

2018-08-01

To study the dynamics and mechanisms controlling activation of the heterotrimeric G protein Gα2βγ in Dictyostelium in response to stimulation by the chemoattractant cyclic AMP (cAMP), we monitored the G protein subunit interaction in live cells using bioluminescence resonance energy transfer (BRET). We found that cAMP induces the cAR1-mediated dissociation of the G protein subunits to a similar extent in both undifferentiated and differentiated cells, suggesting that only a small number of cAR1 (as expressed in undifferentiated cells) is necessary to induce the full activation of Gα2βγ. In addition, we found that treating cells with caffeine increases the potency of cAMP-induced Gα2βγ activation; and that disrupting the microtubule network but not F-actin inhibits the cAMP-induced dissociation of Gα2βγ. Thus, microtubules are necessary for efficient cAR1-mediated activation of the heterotrimeric G protein. Finally, kinetics analyses of Gα2βγ subunit dissociation induced by different cAMP concentrations indicate that there are two distinct rates at which the heterotrimeric G protein subunits dissociate when cells are stimulated with cAMP concentrations above 500 nM versus only one rate at lower cAMP concentrations. Quantitative modeling suggests that the kinetics profile of Gα2βγ subunit dissociation results from the presence of both uncoupled and G protein pre-coupled cAR1 that have differential affinities for cAMP and, consequently, induce G protein subunit dissociation through different rates. We suggest that these different signaling kinetic profiles may play an important role in initial chemoattractant gradient sensing. Copyright © 2018 Elsevier Inc. All rights reserved.

Dissociation dynamics of simple chlorine containing molecules upon resonant Cl K-σ{sup *} excitation

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

Bohinc, R., E-mail: rok.bohinc@ijs.si; Bučar, K.; Kavčič, M.

2014-04-28

A theoretical analysis of dissociation dynamics of chlorine K-σ{sup *} core-excited molecules is performed. The potential energy surfaces of HCl, Cl{sub 2}, CH{sub 3}Cl, CH{sub 2}Cl{sub 2}, CHCl{sub 3}, CCl{sub 4}, CFCl{sub 3}, CF{sub 2}Cl{sub 2}, and CF{sub 3}Cl are calculated along the normal vibrational modes of the ground electronic state yielding the widths of the corresponding Franck-Condon distributions. An insight into the potential energy surface of 1st σ{sup *} resonances shows that the initial dissociation dynamics of chloro(fluoro)methanes mainly involves the distancing of the carbon and the core-excited chlorine atom and is practically independent of other atoms in themore » molecule, which is in agreement with the recent experimental findings. The carbon atom pulls out the remaining three atoms shortly after piercing the three-atom plane resulting in a high vibrationally excited state of the fragment if the reconnection time is smaller than the lifetime of the L shell.« less

Dynamic crystallography reveals early signalling events in ultraviolet photoreceptor UVR8

DOE PAGES

Zeng, Xiaoli; Ren, Zhong; Wu, Qi; ...

2015-01-08

Arabidopsis thaliana UVR8 (AtUVR8) is a long-sought-after photoreceptor that undergoes dimer dissociation in response to UV-B light. Crystallographic and mutational studies have identified two crucial tryptophan residues for UV-B responses in AtUVR8. However, the mechanism of UV-B perception and structural events leading up to dimer dissociation remain elusive at the molecular level. We applied dynamic crystallography to capture light-induced structural events in photoactive AtUVR8 crystals. Here we report two intermediate structures at 1.67Å resolution. At the epicenter of UV-B signaling, concerted motions associated with Trp285/Trp233 lead to ejection of a water molecule, which weakens an intricate network of hydrogen bondsmore » and salt bridges at the dimer interface. Partial opening of the β-propeller structure due to thermal relaxation of conformational strains originating in the epicenter further disrupts the dimer interface and leads to dimer dissociation. Ultimately, these dynamic crystallographic observations provide structural insights into the photo-perception and signaling mechanism of UVR8.« less

Capturing the temporal evolution of choice across prefrontal cortex

PubMed Central

Hunt, Laurence T; Behrens, Timothy EJ; Hosokawa, Takayuki; Wallis, Jonathan D; Kennerley, Steven W

2015-01-01

Activity in prefrontal cortex (PFC) has been richly described using economic models of choice. Yet such descriptions fail to capture the dynamics of decision formation. Describing dynamic neural processes has proven challenging due to the problem of indexing the internal state of PFC and its trial-by-trial variation. Using primate neurophysiology and human magnetoencephalography, we here recover a single-trial index of PFC internal states from multiple simultaneously recorded PFC subregions. This index can explain the origins of neural representations of economic variables in PFC. It describes the relationship between neural dynamics and behaviour in both human and monkey PFC, directly bridging between human neuroimaging data and underlying neuronal activity. Moreover, it reveals a functionally dissociable interaction between orbitofrontal cortex, anterior cingulate cortex and dorsolateral PFC in guiding cost-benefit decisions. We cast our observations in terms of a recurrent neural network model of choice, providing formal links to mechanistic dynamical accounts of decision-making. DOI: http://dx.doi.org/10.7554/eLife.11945.001 PMID:26653139

A thermodynamic study of Abeta(16-21) dissociation from a fibril using computer simulations

NASA Astrophysics Data System (ADS)

Dias, Cristiano; Mahmoudinobar, Farbod; Su, Zhaoqian

Here, I will discuss recent all-atom molecular dynamics simulations with explicit water in which we studied the thermodynamic properties of Abeta(16-21) dissociation from an amyloid fibril. Changes in thermodynamics quantities, e.g., entropy, enthalpy, and volume, are computed from the temperature dependence of the free-energy computed using the umbrella sampling method. We find similarities and differences between the thermodynamics of peptide dissociation and protein unfolding. Similarly to protein unfolding, Abeta(16-21) dissociation is characterized by an unfavorable change in enthalpy, a favorable change in the entropic energy, and an increase in the heat capacity. A main difference is that peptide dissociation is characterized by a weak enthalpy-entropy compensation. We characterize dock and lock states of the peptide based on the solvent accessible surface area. The Lennard-Jones energy of the system is observed to increase continuously in lock and dock states as the peptide dissociates. The electrostatic energy increases in the lock state and it decreases in the dock state as the peptide dissociates. These results will be discussed as well as their implication for fibril growth.

Buffers and Oscillations in Intracellular Ca2+ Dynamics

PubMed Central

Falcke, Martin

2003-01-01

I model the behavior of intracellular Ca2+ release with high buffer concentrations. The model uses a spatially discrete array of channel clusters. The channel subunit dynamics is a stochastic representation of the DeYoung-Keizer model. The calculations show that the concentration profile of fast buffer around an open channel is more localized than that of slow buffers. Slow buffers allow for release of larger amounts of Ca2+ from the endoplasmic reticulum and hence bind more Ca2+ than fast buffers with the same dissociation constant and concentration. I find oscillation-like behavior for high slow buffer concentration and low Ca2+ content of the endoplasmic reticulum. High concentration of slow buffer leads to oscillation-like behavior by repetitive wave nucleation for high Ca2+ content of the endoplasmic reticulum. Localization of Ca2+ release by slow buffer, as used in experiments, can be reproduced by the modeling approach. PMID:12524263

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

PubMed

Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

2015-12-08

Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.

Mesoscopic Modeling of Blood Clotting: Coagulation Cascade and Platelets Adhesion

NASA Astrophysics Data System (ADS)

Yazdani, Alireza; Li, Zhen; Karniadakis, George

2015-11-01

The process of clot formation and growth at a site on a blood vessel wall involve a number of multi-scale simultaneous processes including: multiple chemical reactions in the coagulation cascade, species transport and flow. To model these processes we have incorporated advection-diffusion-reaction (ADR) of multiple species into an extended version of Dissipative Particle Dynamics (DPD) method which is considered as a coarse-grained Molecular Dynamics method. At the continuum level this is equivalent to the Navier-Stokes equation plus one advection-diffusion equation for each specie. The chemistry of clot formation is now understood to be determined by mechanisms involving reactions among many species in dilute solution, where reaction rate constants and species diffusion coefficients in plasma are known. The role of blood particulates, i.e. red cells and platelets, in the clotting process is studied by including them separately and together in the simulations. An agonist-induced platelet activation mechanism is presented, while platelets adhesive dynamics based on a stochastic bond formation/dissociation process is included in the model.

Reality versus fantasy: reply to Lynn et al. (2014).

PubMed

Dalenberg, Constance J; Brand, Bethany L; Loewenstein, Richard J; Gleaves, David H; Dorahy, Martin J; Cardeña, Etzel; Frewen, Paul A; Carlson, Eve B; Spiegel, David

2014-05-01

We respond to Lynn et al.'s (2014) comments on our review (Dalenberg et al., 2012) demonstrating the superiority of the trauma model (TM) over the fantasy model (FM) in explaining the trauma-dissociation relationship. Lynn et al. conceded that our meta-analytic results support the TM hypothesis that trauma exposure is a causal risk factor for the development of dissociation. Although Lynn et al. suggested that our meta-analyses were selective, we respond that each omitted study failed to meet inclusion criteria; our meta-analyses thus reflect a balanced view of the predominant trauma-dissociation findings. In contrast, Lynn et al. were hypercritical of studies that supported the TM while ignoring methodological problems in studies presented as supportive of the FM. We clarify Lynn et al.'s misunderstandings of the TM and demonstrate consistent superiority in prediction of time course of dissociative symptoms, response to psychotherapy of dissociative patients, and pattern of relationships of trauma to dissociation. We defend our decision not to include studies using the Dissociative Experiences Scale-Comparison, a rarely used revision of the Dissociative Experiences Scale that shares less than 10% of the variance with the original scale. We highlight several areas of agreement: (a) Trauma plays a complex role in dissociation, involving indirect and direct paths; (b) dissociation-suggestibility relationships are small; and (c) controls and measurement issues should be addressed in future suggestibility and dissociation research. Considering the lack of evidence that dissociative individuals simply fantasize trauma, future researchers should examine more complex models of trauma and valid measures of dissociation.

A nontoxic pain killer designed by modeling of pathological receptor conformations.

PubMed

Spahn, V; Del Vecchio, G; Labuz, D; Rodriguez-Gaztelumendi, A; Massaly, N; Temp, J; Durmaz, V; Sabri, P; Reidelbach, M; Machelska, H; Weber, M; Stein, C

2017-03-03

Indiscriminate activation of opioid receptors provides pain relief but also severe central and intestinal side effects. We hypothesized that exploiting pathological (rather than physiological) conformation dynamics of opioid receptor-ligand interactions might yield ligands without adverse actions. By computer simulations at low pH, a hallmark of injured tissue, we designed an agonist that, because of its low acid dissociation constant, selectively activates peripheral μ-opioid receptors at the source of pain generation. Unlike the conventional opioid fentanyl, this agonist showed pH-sensitive binding, heterotrimeric guanine nucleotide-binding protein (G protein) subunit dissociation by fluorescence resonance energy transfer, and adenosine 3',5'-monophosphate inhibition in vitro . It produced injury-restricted analgesia in rats with different types of inflammatory pain without exhibiting respiratory depression, sedation, constipation, or addiction potential. Copyright © 2017, American Association for the Advancement of Science.

Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

NASA Astrophysics Data System (ADS)

Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

2017-06-01

We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

Reconsidering the autohypnotic model of the dissociative disorders.

PubMed

Dell, Paul F

2018-03-22

The dissociative disorders field and the hypnosis field currently reject the autohypnotic model of the dissociative disorders, largely because many correlational studies have shown hypnotizability and dissociation to be minimally related (r = .12). Curiously, it is also widely accepted that dissociative patients are highly hypnotizable. If dissociative patients are highly hypnotizable because only highly hypnotizable individuals can develop a dissociative disorder - as the author proposes - then the methodology of correlational studies of hypnotizability and dissociation in random clinical and community samples would necessarily be constitutively unable to detect, and statistically unable to reflect, that fact. That is, the autohypnotic, dissociative distancing of that small subset of highly hypnotizable individuals who repeatedly encountered intolerable circumstances is statistically lost among the data of (1) the highly hypnotizable subjects who do not dissociate and (2) subjects (of all levels of hypnotizability) who manifest other kinds of dissociation. The author proposes that, when highly hypnotizable individuals repeatedly engage in autohypnotic distancing from intolerable circumstances, they develop an overlearned, highly-motivated, automatized pattern of dissociative self-protection (i.e., a dissociative disorder). The author urges that theorists of hypnosis and the dissociative disorders explicitly include in their theories (a) the trait of high hypnotizability, (b) the phenomena of autohypnosis, and (c) the manifestations of systematized, autohypnotic pathology. Said differently, the author is suggesting that autohypnosis and autohypnotic pathology are unacknowledged nodes in the nomothetic networks of both hypnosis and dissociation.

A context-based theory of recency and contiguity in free recall

PubMed Central

Sederberg, Per B.; Howard, Marc W.; Kahana, Michael J.

2008-01-01

We present a new model of free recall based on Howard and Kahana’s (2002) temporal context model and Usher and McClelland’s (2001) leaky-accumulator decision model. In this model, contextual drift gives rise to both short-term and long-term recency effects, and contextual retrieval gives rise to short-term and long-term contiguity effects, Recall decisions are controlled by a race between competitive leaky-accumulators. The model captures the dynamics of immediate, delayed, and continual distractor free recall, demonstrating that dissociations between short- and long-term recency can naturally arise from a model that uses an internal contextual state as the sole cue for retrieval across time scales. PMID:18954208

Dynamic structural disorder in supported nanoscale catalysts

NASA Astrophysics Data System (ADS)

Rehr, J. J.; Vila, F. D.

2014-04-01

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Effects of electrostatic interactions on ligand dissociation kinetics

NASA Astrophysics Data System (ADS)

Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

2018-02-01

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Excited-state dissociation dynamics of phenol studied by a new time-resolved technique

NASA Astrophysics Data System (ADS)

Lin, Yen-Cheng; Lee, Chin; Lee, Shih-Huang; Lee, Yin-Yu; Lee, Yuan T.; Tseng, Chien-Ming; Ni, Chi-Kung

2018-02-01

Phenol is an important model molecule for the theoretical and experimental investigation of dissociation in the multistate potential energy surfaces. Recent theoretical calculations [X. Xu et al., J. Am. Chem. Soc. 136, 16378 (2014)] suggest that the phenoxyl radical produced in both the X and A states from the O-H bond fission in phenol can contribute substantially to the slow component of photofragment translational energy distribution. However, current experimental techniques struggle to separate the contributions from different dissociation pathways. A new type of time-resolved pump-probe experiment is described that enables the selection of the products generated from a specific time window after molecules are excited by a pump laser pulse and can quantitatively characterize the translational energy distribution and branching ratio of each dissociation pathway. This method modifies conventional photofragment translational spectroscopy by reducing the acceptance angles of the detection region and changing the interaction region of the pump laser beam and the molecular beam along the molecular beam axis. The translational energy distributions and branching ratios of the phenoxyl radicals produced in the X, A, and B states from the photodissociation of phenol at 213 and 193 nm are reported. Unlike other techniques, this method has no interference from the undissociated hot molecules. It can ultimately become a standard pump-probe technique for the study of large molecule photodissociation in multistates.

Modelling fragmentations of aminoacids after resonant electron attachment: quantum evidence of possible direct -OH detachment

NASA Astrophysics Data System (ADS)

Panosetti, C.; Baccarelli, I.; Sebastianelli, F.; Gianturco, F. A.

2010-10-01

We investigate some aspects of the radiation damage mechanisms in biomolecules, focusing on the modelling of resonant fragmentation caused by the attachment of low-energy electrons (LEEs) initially ejected by biological tissues when exposed to ionizing radiation. Scattering equations are formulated within a symmetry-adapted, single-center expansion of both continuum and bound electrons, and the interaction forces are obtained from a combination of ab initio calculations and a nonempirical model of exchange and correlation effects developped in our group. We present total elastic scattering cross-sections and resonance features obtained for the equilibrium geometries of glycine, alanine, proline and valine. Our results at those geometries of the target molecules are briefly shown to qualitatively explain some of the fragmentation patterns obtained in experiments. We further carry out a one-dimensional (1D) modeling for the dynamics of intramolecular energy transfers mediated by the vibrational activation of selected bonds: our calculations indicate that resonant electron attachment to glycine can trigger direct, dissociative evolution of the complex into (Gly-OH)- and -OH losses, while they also find that the same process does not occur via a direct, 1D dissociative path in the larger aminoacids of the present study.

Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

NASA Astrophysics Data System (ADS)

Schachel, Tilo D.; Metwally, Haidy; Popa, Vlad; Konermann, Lars

2016-11-01

Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na( n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase.

Multiple exciton dissociation in CdSe quantum dots by ultrafast electron transfer to adsorbed methylene blue.

PubMed

Huang, Jier; Huang, Zhuangqun; Yang, Ye; Zhu, Haiming; Lian, Tianquan

2010-04-07

Multiexciton generation in quantum dots (QDs) may provide a new approach for improving the solar-to-electric power conversion efficiency in QD-based solar cells. However, it remains unclear how to extract these excitons before the ultrafast exciton-exciton annihilation process. In this study we investigate multiexciton dissociation dynamics in CdSe QDs adsorbed with methylene blue (MB(+)) molecules by transient absorption spectroscopy. We show that excitons in QDs dissociate by ultrafast electron transfer to MB(+) with an average time constant of approximately 2 ps. The charge separated state is long-lived (>1 ns), and the charge recombination rate increases with the number of dissociated excitons. Up to three MB(+) molecules per QD can be reduced by exciton dissociation. Our result demonstrates that ultrafast interfacial charge separation can effectively compete with exciton-exciton annihilation, providing a viable approach for utilizing short-lived multiple excitons in QDs.

High pressure stability of protein complexes studied by static and dynamic light scattering

NASA Astrophysics Data System (ADS)

Gebhardt, Ronald; Kulozik, Ulrich

2011-03-01

The high pressure dissociation of hemocyanin prepared from the lobster Homarus americanus and casein micelles from cow milk were observed by in situ light scattering. The hemocyanin dodecamer dissociated via a hexamer into monomers in a two-step three-species reaction. The influence of ligands and the effector l-lactate on the dissociation behavior was investigated. While no effect by carbon monoxide after exchanging the ligand oxygen was observed, the addition of the effector l-lactate led to a decrease in the pressure stability. Due to a trimer intermediate which was found to be stabilized by l-lactate, the dissociation reaction in the presence of the effector was analyzed by a three-step four-species reaction. In the case of casein micelles, a two-step dissociation mechanism was found. The stabilizing interactions of casein micelles were identified and separated.

Recognition and stabilization of geranylgeranylated human Rab5 by the GDP Dissociation Inhibitor (GDI).

PubMed

Edler, Eileen; Stein, Matthias

2017-10-25

The small GTPase Rab5 is the key regulator of early endosomal fusion. It is post-translationally modified by covalent attachment of two geranylgeranyl (GG) chains to adjacent cysteine residues of the C-terminal hypervariable region (HVR). The GDP dissociation inhibitor (GDI) recognizes membrane-associated Rab5(GDP) and serves to release it into the cytoplasm where it is kept in a soluble state. A detailed new structural and dynamic model for human Rab5(GDP) recognition and binding with human GDI at the early endosome membrane and in its dissociated state is presented. In the cytoplasm, the GDI protein accommodates the GG chains in a transient hydrophobic binding pocket. In solution, two different binding modes of the isoprenoid chains inserted into the hydrophobic pocket of the Rab5(GDP):GDI complex can be identified. This equilibrium between the two states helps to stabilize the protein-protein complex in solution. Interprotein contacts between the Rab5 switch regions and characteristic patches of GDI residues from the Rab binding platform (RBP) and the C-terminus coordinating region (CCR) reveal insight on the formation of such a stable complex. GDI binding to membrane-anchored Rab5(GDP) is initially mediated by the solvent accessible switch regions of the Rab-specific RBP. Formation of the membrane-associated Rab5(GDP):GDI complex induces a GDI reorientation to establish additional interactions with the Rab5 HVR. These results allow to devise a detailed structural model for the process of extraction of GG-Rab5(GDP) by GDI from the membrane and the dissociation from targeting factors and effector proteins prior to GDI binding.

Quantum dynamics of the intramolecular vibrational energy redistribution in OCS: From localization to quasi-thermalization

NASA Astrophysics Data System (ADS)

Pérez, J. B.; Arce, J. C.

2018-06-01

We report a fully quantum-dynamical study of the intramolecular vibrational energy redistribution (IVR) in the electronic ground state of carbonyl sulfide, which is a prototype of an isolated many-body quantum system with strong internal couplings and non-Rice-Ramsperger-Kassel-Marcus (RRKM) behavior. We pay particular attention to the role of many-body localization and the approach to thermalization, which currently are topics of considerable interest, as they pertain to the very foundations of statistical mechanics and thermodynamics. We employ local-mode (valence) coordinates and consider initial excitations localized in one local mode, with energies ranging from low to near the dissociation threshold, where the classical dynamics have been shown to be chaotic. We propagate the nuclear wavepacket on the potential energy surface by means of the numerically exact multiconfiguration time-dependent Hartree method and employ mean local energies, time-dependent and time-averaged populations in quantum number space, energy distributions, entanglement entropies, local population distributions, microcanonical averages, and dissociation probabilities, as diagnostic tools. This allows us to identify a continuous localization → delocalization transition in the energy flow, associated with the onset of quantum chaos, as the excitation energy increases up to near the dissociation threshold. Moreover, we find that at this energy and ˜1 ps the molecule nearly thermalizes. Furthermore, we observe that IVR is so slow that the molecule begins to dissociate well before such quasi-thermalization is complete, in accordance with earlier classical-mechanical predictions of non-RRKM behavior.

Quantum dynamics of the intramolecular vibrational energy redistribution in OCS: From localization to quasi-thermalization.

PubMed

Pérez, J B; Arce, J C

2018-06-07

We report a fully quantum-dynamical study of the intramolecular vibrational energy redistribution (IVR) in the electronic ground state of carbonyl sulfide, which is a prototype of an isolated many-body quantum system with strong internal couplings and non-Rice-Ramsperger-Kassel-Marcus (RRKM) behavior. We pay particular attention to the role of many-body localization and the approach to thermalization, which currently are topics of considerable interest, as they pertain to the very foundations of statistical mechanics and thermodynamics. We employ local-mode (valence) coordinates and consider initial excitations localized in one local mode, with energies ranging from low to near the dissociation threshold, where the classical dynamics have been shown to be chaotic. We propagate the nuclear wavepacket on the potential energy surface by means of the numerically exact multiconfiguration time-dependent Hartree method and employ mean local energies, time-dependent and time-averaged populations in quantum number space, energy distributions, entanglement entropies, local population distributions, microcanonical averages, and dissociation probabilities, as diagnostic tools. This allows us to identify a continuous localization → delocalization transition in the energy flow, associated with the onset of quantum chaos, as the excitation energy increases up to near the dissociation threshold. Moreover, we find that at this energy and ∼1 ps the molecule nearly thermalizes. Furthermore, we observe that IVR is so slow that the molecule begins to dissociate well before such quasi-thermalization is complete, in accordance with earlier classical-mechanical predictions of non-RRKM behavior.

Direct simulation with vibration-dissociation coupling

NASA Technical Reports Server (NTRS)

Hash, David B.; Hassan, H. A.

1992-01-01

The majority of implementations of the Direct Simulation Monte Carlo (DSMC) method of Bird do not account for vibration-dissociation coupling. Haas and Boyd have proposed the vibrationally-favored dissociation model to accomplish this task. This model requires measurements of induction distance to determine model constants. A more general expression has been derived that does not require any experimental input. The model is used to calculate one-dimensional shock waves in nitrogen and the flow past a lunar transfer vehicle (LTV). For the conditions considered in the simulation, the influence of vibration-dissociation coupling on heat transfer in the stagnation region of the LTV can be significant.

Theoretical study of dissociative recombination of Cl{sub 2}{sup +}

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

Zhang Mingwu; Graduate School of Chinese Academy of Sciences, Beijing 100039; Department of Physics, Stockholm University, S-106 91 Stockholm

Theoretical studies of low-energy electron collisions with Cl{sub 2}{sup +} leading to direct dissociative recombination are presented. The relevant potential energy curves and autoionization widths are calculated by combining electron scattering calculations using the complex Kohn variational method with multireference configuration interaction structure calculations. The dynamics on the four lowest resonant states of all symmetries is studied by the solution of a driven Schroedinger equation. The thermal rate coefficient for dissociative recombination of Cl{sub 2}{sup +} is calculated and the influence on the thermal rate coefficient from vibrational excited target ions is investigated.

O(1S) from dissociative recombination of O2(+) - Nonthermal line profile measurements from Dynamics Explorer

NASA Technical Reports Server (NTRS)

Killeen, T. L.; Hays, P. B.

1983-01-01

The measurements reported were made of the O(1S) emission line profile at 5577 A at high spectral resolution with the Fabry-Perot interferometer on the Dynamics Explorer spacecraft. It is found that the line profile has marked nonthermal characteristics in the nightglow. A simple collisional relaxation model is used to analyze the nighttime emission line profiles, measured in the equatorial region. The branching ratio is inferred for the dissociative recombination of O2(+) leading to O(1S). The result reveals that the O(1S) + O(1D) channel is favored over the O(1S). The result reveals that the O(1S) + O(1D) channel is favored over the O(1S) + O(3P) channel by a factor of 4; this does not agree with the ratio reported by Hernandez (1971). It is noted, however, that the result is consistent with the active channel for O(1S) production being via the 1Sigma u + repulsive state of O2, as suggested by the theoretical calculations of Guberman (1983). In addition, a value is obtained for the excitation exchange cross section for O(1S).

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

Lehmann, C. S.; Picón, A.; Bostedt, C.

The availability at x-ray free electron lasers of generating two intense, femtosecond x-ray pulses with controlled time delay opens the possibility of performing time-resolved experiments for x-ray induced phenomena. We have applied this capability to molecular dynamics. In diatomic molecules composed of low-Z elements, K-shell ionization creates a core-hole state in which the main decay is an Auger process involving two electrons in the valence shell. After Auger decay, the nuclear wavepackets of the transient two-valence-hole states continue evolving on the femtosecond timescale, leading either to separated atomic ions or long-lived quasi-bound states. By using an x-ray pump and anmore » x-ray probe pulse tuned above the K-shell ionization threshold of the nitrogen molecule, we are able to observe ion dissociation in progress by measuring the time-dependent kinetic energy releases of different breakup channels. We simulated the measurements on N2 with a molecular dynamics model that accounts for K-shell ionization, Auger decay, and time evolution of the nuclear wavepackets. In addition to explaining the time-dependent feature in the measured kinetic energy release distributions from the dissociative states, the simulation also reveals the contributions of quasi-bound states.« less

Knowledge-based probabilistic representations of branching ratios in chemical networks: The case of dissociative recombinations

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

Plessis, Sylvain; Carrasco, Nathalie; Pernot, Pascal

Experimental data about branching ratios for the products of dissociative recombination of polyatomic ions are presently the unique information source available to modelers of natural or laboratory chemical plasmas. Yet, because of limitations in the measurement techniques, data for many ions are incomplete. In particular, the repartition of hydrogen atoms among the fragments of hydrocarbons ions is often not available. A consequence is that proper implementation of dissociative recombination processes in chemical models is difficult, and many models ignore invaluable data. We propose a novel probabilistic approach based on Dirichlet-type distributions, enabling modelers to fully account for the available information.more » As an application, we consider the production rate of radicals through dissociative recombination in an ionospheric chemistry model of Titan, the largest moon of Saturn. We show how the complete scheme of dissociative recombination products derived with our method dramatically affects these rates in comparison with the simplistic H-loss mechanism implemented by default in all recent models.« less

Knowledge-based probabilistic representations of branching ratios in chemical networks: the case of dissociative recombinations.

PubMed

Plessis, Sylvain; Carrasco, Nathalie; Pernot, Pascal

2010-10-07

Experimental data about branching ratios for the products of dissociative recombination of polyatomic ions are presently the unique information source available to modelers of natural or laboratory chemical plasmas. Yet, because of limitations in the measurement techniques, data for many ions are incomplete. In particular, the repartition of hydrogen atoms among the fragments of hydrocarbons ions is often not available. A consequence is that proper implementation of dissociative recombination processes in chemical models is difficult, and many models ignore invaluable data. We propose a novel probabilistic approach based on Dirichlet-type distributions, enabling modelers to fully account for the available information. As an application, we consider the production rate of radicals through dissociative recombination in an ionospheric chemistry model of Titan, the largest moon of Saturn. We show how the complete scheme of dissociative recombination products derived with our method dramatically affects these rates in comparison with the simplistic H-loss mechanism implemented by default in all recent models.

Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

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

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp; Ho, Tak-San, E-mail: tsho@Princeton.EDU; Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU

We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O{sub 2} + O asymptote on the ground-state {sup 1}A{sup ′} potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excitedmore » electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.« less

The capacity fading mechanism and improvement of cycling stability in MoS2-based anode materials for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Shu, Haibo; Li, Feng; Hu, Chenli; Liang, Pei; Cao, Dan; Chen, Xiaoshuang

2016-01-01

Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance.Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance. Electronic supplementary information (ESI) available: Models and energetics of Li adsorption/intercalation onto MoS2 sheets, details of the phase diagram calculations, schematic illustration for the structural evolution of lithiated MoS2 nanosheets, AIMD trajectories for lithiated silicene/MoS2/silicene composites, and movies for recording the AIMD simulation results. See DOI: 10.1039/c5nr07909h

Theoretical Studies of Dissociative Recombination of Electrons with SH+ Ions

NASA Astrophysics Data System (ADS)

Kashinski, D. O.; di Nallo, O. E.; Hickman, A. P.; Mezei, J. Zs.; Colboc, F.; Schneider, I. F.; Chakrabarti, K.; Talbi, D.

2017-04-01

We are investigating the dissociative recombination (DR) of electrons with the molecular ion SH+, i.e. e- +SH+ -> S + H . SH+ is found in the interstellar medium (ISM), and little is known concerning its chemistry. Understanding the role of DR of electrons with SH+ will lead to more accurate astrophysical models. Large active-space multi-reference configuration interaction (MRCI) electronic structure calculations were performed using the GAMESS code to obtain ground and excited 2 Π state potential energy curves (PECs) for several values of SH separation. Core-excited Rydberg states have proven to be of huge importance. The block diagonalization method was used to disentangle interacting states and form a diabatic representation of the PECs. Currently we are performing dynamics calculations using Multichannel Quantum Defect Theory (MQDT) to obtain DR rates. The status of the work will be presented at the conference. Work supported by the French CNRS, the NSF, the XSEDE, and USMA.

Dynamics of associating networks

NASA Astrophysics Data System (ADS)

Tang, Shengchang; Habicht, Axel; Wang, Muzhou; Li, Shuaili; Seiffert, Sebastian; Olsen, Bradley

Associating polymers offer important technological solutions to renewable and self-healing materials, conducting electrolytes for energy storage and transport, and vehicles for cell and protein deliveries. The interplay between polymer topologies and association chemistries warrants new interesting physics from associating networks, yet poses significant challenges to study these systems over a wide range of time and length scales. In a series of studies, we explored self-diffusion mechanisms of associating polymers above the percolation threshold, by combining experimental measurements using forced Rayleigh scattering and analytical insights from a two-state model. Despite the differences in molecular structures, a universal super-diffusion phenomenon is observed when diffusion of molecular species is hindered by dissociation kinetics. The molecular dissociation rate can be used to renormalize shear rheology data, which yields an unprecedented time-temperature-concentration superposition. The obtained shear rheology master curves provide experimental evidence of the relaxation hierarchy in associating networks.

Theoretical Studies of Dissociative Recombination of Electrons with SH+ Ions

NASA Astrophysics Data System (ADS)

Kashinski, D. O.; di Nallo, O. E.; Hickman, A. P.; Mezei, J. Zs.; Colboc, F.; Schneider, I. F.; Chakrabarti, K.; Talbi, D.

2016-05-01

We are investigating the dissociative recombination (DR) of electrons with the molecular ion SH+, i.e. e- +SH+ --> S + H . SH+ is found in the interstellar medium (ISM), and little is known concerning its chemistry. Understanding the role of DR of electrons with SH+ will lead to more accurate astrophysical models. Large active-space multi-reference configuration interaction (MRCI) electronic structure calculations were performed using the GAMESS code to obtain ground and excited 2 Π state potential energy curves (PECs) for several values of SH separation. Core-excited Rydberg states have proven to be of huge importance. The block diagonalization method was used to disentangle interacting states and form a diabatic representation of the PECs. Currently we are performing dynamics calculations using Multichannel Quantum Defect Theory (MQDT) to obtain DR rates. The status of the work will be presented at the conference. work supported by the French CNRS, the NSF, the XSEDE, and USMA.

Dissociative Functions in the Normal Mourning Process.

ERIC Educational Resources Information Center

Kauffman, Jeffrey

1994-01-01

Sees dissociative functions in mourning process as occurring in conjunction with integrative trends. Considers initial shock reaction in mourning as model of normal dissociation in mourning process. Dissociation is understood to be related to traumatic significance of death in human consciousness. Discerns four psychological categories of…

Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis.

PubMed

Yonetani, Yoshiteru

2015-07-28

Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

EEG and chaos: Description of underlying dynamics and its relation to dissociative states

NASA Technical Reports Server (NTRS)

Ray, William J.

1994-01-01

The goal of this work is the identification of states especially as related to the process of error production and lapses of awareness as might be experienced during aviation. Given the need for further articulation of the characteristics of 'error prone state' or 'hazardous state of awareness,' this NASA grant focused on basic ground work for the study of the psychophysiology of these states. In specific, the purpose of this grant was to establish the necessary methodology for addressing three broad questions. The first is how the error prone state should be conceptualized, and whether it is similar to a dissociative state, a hypnotic state, or absent mindedness. Over 1200 subjects completed a variety of psychometric measures reflecting internal states and proneness to mental lapses and absent mindedness; the study suggests that there exists a consistency of patterns displayed by individuals who self-report dissociative experiences such that those individuals who score high on measures of dissociation also score high on measures of absent mindedness, errors, and absorption, but not on scales of hypnotizability. The second broad question is whether some individuals are more prone to enter these states than others. A study of 14 young adults who scored either high or low on the dissociation experiences scale performed a series of six tasks. This study suggests that high and low dissociative individuals arrive at the experiment in similar electrocortical states and perform cognitive tasks (e.g., mental math) in a similar manner; it is in the processing of internal emotional states that differences begin to emerge. The third question to be answered is whether recent research in nonlinear dynamics, i.e., chaos, offer an addition and/or alternative to traditional signal processing methods, i.e., fast Fourier transforms, and whether chaos procedures can be modified to offer additional information useful in identifying brain states. A preliminary review suggests that current nonlinear dynamical techniques such as dimensional analysis can be successfully applied to electrocortical activity. Using the data set developed in the study of the young adults, chaos analyses using the Farmer algorithm were performed; it is concluded that dimensionality measures reflect information not contained in traditional EEG Fourier analysis.

Development of a kinetic model of hydrogen absorption and desorption in magnesium and analysis of the rate-determining step

NASA Astrophysics Data System (ADS)

Kitagawa, Yuta; Tanabe, Katsuaki

2018-05-01

Mg is promising as a new light-weight and low-cost hydrogen-storage material. We construct a numerical model to represent the hydrogen dynamics on Mg, comprising dissociative adsorption, desorption, bulk diffusion, and chemical reaction. Our calculation shows a good agreement with experimental data for hydrogen absorption and desorption on Mg. Our model clarifies the evolution of the rate-determining processes as absorption and desorption proceed. Furthermore, we investigate the optimal condition and materials design for efficient hydrogen storage in Mg. By properly understanding the rate-determining processes using our model, one can determine the design principle for high-performance hydrogen-storage systems.

Trauma-related dissociation and altered states of consciousness: a call for clinical, treatment, and neuroscience research

PubMed Central

Lanius, Ruth A.

2015-01-01

The primary aim of this commentary is to describe trauma-related dissociation and altered states of consciousness in the context of a four-dimensional model that has recently been proposed (Frewen & Lanius, 2015). This model categorizes symptoms of trauma-related psychopathology into (1) those that occur within normal waking consciousness and (2) those that are dissociative and are associated with trauma-related altered states of consciousness (TRASC) along four dimensions: (1) time; (2) thought; (3) body; and (4) emotion. Clinical applications and future research directions relevant to each dimension are discussed. Conceptualizing TRASC across the dimensions of time, thought, body, and emotion has transdiagnostic implications for trauma-related disorders described in both the Diagnostic Statistical Manual and the International Classifications of Diseases. The four-dimensional model provides a framework, guided by existing models of dissociation, for future research examining the phenomenological, neurobiological, and physiological underpinnings of trauma-related dissociation. PMID:25994026

Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

NASA Technical Reports Server (NTRS)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

Collisional Dissociation of CO: ab initio Potential Energy Surfaces and Quasiclassical Trajectory Rate Coefficients

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Jaffe, Richard L.; Chaban, Galina M.

2016-01-01

We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.

Fractional Brownian motion and the critical dynamics of zipping polymers.

PubMed

Walter, J-C; Ferrantini, A; Carlon, E; Vanderzande, C

2012-03-01

We consider two complementary polymer strands of length L attached by a common-end monomer. The two strands bind through complementary monomers and at low temperatures form a double-stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature T=T(c) using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as τ∼L(2.26(2)), exceeding the Rouse time ∼L(2.18). We investigate the probability distribution function, velocity autocorrelation function, survival probability, and boundary behavior of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent H=0.44(1). We discuss similarities to and differences from unbiased polymer translocation.

A cumulant functional for static and dynamic correlation

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

Hollett, Joshua W., E-mail: j.hollett@uwinnipeg.ca; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2; Hosseini, Hessam

A functional for the cumulant energy is introduced. The functional is composed of a pair-correction and static and dynamic correlation energy components. The pair-correction and static correlation energies are functionals of the natural orbitals and the occupancy transferred between near-degenerate orbital pairs, rather than the orbital occupancies themselves. The dynamic correlation energy is a functional of the statically correlated on-top two-electron density. The on-top density functional used in this study is the well-known Colle-Salvetti functional. Using the cc-pVTZ basis set, the functional effectively models the bond dissociation of H{sub 2}, LiH, and N{sub 2} with equilibrium bond lengths and dissociationmore » energies comparable to those provided by multireference second-order perturbation theory. The performance of the cumulant functional is less impressive for HF and F{sub 2}, mainly due to an underestimation of the dynamic correlation energy by the Colle-Salvetti functional.« less

New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

PubMed

Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

2013-10-07

An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

Dynamics of vortices in polariton quantum fluids : From full vortices, to half vortices and vortex pairs

NASA Astrophysics Data System (ADS)

Deveaud-Plédran, Benoit

2012-02-01

Polariton quantum fluids may be created both spontaneously through a standard phase transition towards a Bose Einstein condensate, or may be resonantly driven with a well-defined speed. Thanks to the photonic component of polaritons, the properties of the quantum fluid may be accessed rather directly with in particular the possibility of detained interferometric studies. Here, I will detail the dynamics of vortices, obtained with a picosecond time resolution, in different configurations, with in particular their phase dynamics. I will show in particular the dynamics the dynamics of spontaneous creation of a vortex, the dissociation of a full vortex into two half vortices as well as the dynamics of the dissociation of a dark soliton line into a street of pairs of vortices. Work done at EPFL by a dream team of Postdocs PhD students and collaborators: K. Lagoudakis, G. Nardin, T. Paraiso, G. Grosso, F. Manni, Y L'eger, M. Portella Oberli, F. Morier-Genoud and the help of our friend theorists V, Savona, M. Vouters and T. Liew.

Reactive molecular dynamics simulation of solid nitromethane impact on (010) surfaces induced and nonimpact thermal decomposition.

PubMed

Guo, Feng; Cheng, Xin-lu; Zhang, Hong

2012-04-12

Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures.

Evaluation of the Evidence for the Trauma and Fantasy Models of Dissociation

ERIC Educational Resources Information Center

Dalenberg, Constance J.; Brand, Bethany L.; Gleaves, David H.; Dorahy, Martin J.; Loewenstein, Richard J.; Cardena, Etzel; Frewen, Paul A.; Carlson, Eve B.; Spiegel, David

2012-01-01

The relationship between a reported history of trauma and dissociative symptoms has been explained in 2 conflicting ways. Pathological dissociation has been conceptualized as a response to antecedent traumatic stress and/or severe psychological adversity. Others have proposed that dissociation makes individuals prone to fantasy, thereby…

Molecular and Cellular Mechanisms of Apoptosis during Dissociated Spermatogenesis

PubMed Central

Liu, Tengfei; Wang, Lingling; Chen, Hong; Huang, Yufei; Yang, Ping; Ahmed, Nisar; Wang, Taozhi; Liu, Yi; Chen, Qiusheng

2017-01-01

Apoptosis is a tightly controlled process by which tissues eliminate unwanted cells. Spontaneous germ cell apoptosis in testis has been broadly investigated in mammals that have an associated spermatogenesis pattern. However, the mechanism of germ cell apoptosis in seasonally breeding reptiles following a dissociated spermatogenesis has remained enigmatic. In the present study, morphological evidence has clearly confirmed the dissociated spermatogenesis pattern in Pelodiscus sinensis. TUNEL and TEM analyses presented dynamic changes and ultrastructural characteristics of apoptotic germ cells during seasonal spermatogenesis, implying that apoptosis might be one of the key mechanisms to clear degraded germ cells. Furthermore, using RNA-Seq and digital gene expression (DGE) profiling, a large number of apoptosis-related differentially expressed genes (DEGs) at different phases of spermatogenesis were identified and characterized in the testis. DGE and RT-qPCR analysis revealed that the critical anti-apoptosis genes, such as Bcl-2, BAG1, and BAG5, showed up-regulated patterns during intermediate and late spermatogenesis. Moreover, the increases in mitochondrial transmembrane potential in July and October were detected by JC-1 staining. Notably, the low protein levels of pro-apoptotic cleaved caspase-3 and CytC in cytoplasm were detected by immunohistochemistry and western blot analyses, indicating that the CytC-Caspase model might be responsible for the effects of germ cell apoptosis on seasonal spermatogenesis. These results facilitate understanding the regulatory mechanisms of apoptosis during spermatogenesis and uncovering the biological process of the dissociated spermatogenesis system in reptiles. PMID:28424629

Are major dissociative disorders characterized by a qualitatively different kind of dissociation?

PubMed

Rodewald, Frauke; Dell, Paul F; Wilhelm-Gossling, Claudia; Gast, Ursula

2011-01-01

A total of 66 patients with a major dissociative disorder, 54 patients with nondissociative disorders, and 30 nonclinical controls were administered the Structured Clinical Interview for DSM-IV Dissociative Disorders-Revised, the Dissociative Experiences Scale, the Multidimensional Inventory of Dissociation, and the Symptom Checklist 90-Revised. Dissociative patients reported significantly more dissociative and nondissociative symptoms than did nondissociative patients and nonclinical controls. When general psychopathology was controlled, the dissociation scores of dissociative patients were still significantly higher than those of both other groups, whereas the dissociation scores of nondissociative patients and nonclinical controls no longer differed. These findings appear to be congruent with a typological model of dissociation that distinguishes between 2 qualitatively different kinds of dissociation. Specifically, the results of this study suggest that the dissociation that occurs in major dissociative disorders (i.e., dissociative identity disorder [DID] and dissociative disorder not otherwise specified, Type 1 [DDNOS-1]) is qualitatively different from the dissociation that occurs in persons who do not have a dissociative disorder. In contrast to previous research, the dissociation of persons who do not have a dissociative disorder is not limited to absorption; it covers a much wider range of phenomena. The authors hypothesize that different mechanisms produce the dissociation of persons with DID and DDNOS-1 as opposed to the dissociation of persons who do not have a dissociative disorder.

Atomistic simulation of orientation dependence in shock-induced initiation of pentaerythritol tetranitrate.

PubMed

Shan, Tzu-Ray; Wixom, Ryan R; Mattsson, Ann E; Thompson, Aidan P

2013-01-24

The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.

Laser Photochemistry.

DTIC Science & Technology

1981-07-01

continuum and is the important parameter for determining the dissociation yield (Grant et al., 1978). The phenomenon of infrared MPE and MPD seems well under...incoherent absorption processes in MPE and MPD? What is the magnitude of the absorption cross section and how does it change with molecular parameters ...iv) What is the dynamics of the dissociation event and what are the parameters that determine the rate of unimolecular decom- position? (v) How can

Dynamics of singlet fission and electron injection in self-assembled acene monolayers on titanium dioxide† †Electronic supplementary information (ESI) available: Steady-state UV-VIS and PL, solution transient absorption, X-ray diffraction, decay associated spectra, and TIPS Tc COOH/Al2O3/TiO2 film kinetics. See DOI: 10.1039/c7sc04688j

PubMed Central

Pace, Natalie A.; Arias, Dylan H.; Granger, Devin B.; Christensen, Steven; Anthony, John E.

2018-01-01

We employ a combination of linear spectroscopy, electrochemistry, and transient absorption spectroscopy to characterize the interplay between electron transfer and singlet fission dynamics in polyacene-based dyes attached to nanostructured TiO2. For triisopropyl silylethynyl (TIPS)-pentacene, we find that the singlet fission time constant increases to 6.5 ps on a nanostructured TiO2 surface relative to a thin film time constant of 150 fs, and that triplets do not dissociate after they are formed. In contrast, TIPS-tetracene singlets quickly dissociate in 2 ps at the molecule/TiO2 interface, and this dissociation outcompetes the relatively slow singlet fission process. The addition of an alumina layer slows down electron injection, allowing the formation of triplets from singlet fission in 40 ps. However, the triplets do not inject electrons, which is likely due to a lack of sufficient driving force for triplet dissociation. These results point to the critical balance required between efficient singlet fission and appropriate energetics for interfacial charge transfer. PMID:29732084

A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination.

PubMed

Yu, Hua-Gen

2008-05-21

A spherical electron cloud hopping (SECH) model is proposed to study the product branching ratios of dissociative recombination (DR) of polyatomic systems. In this model, the fast electron-captured process is treated as an instantaneous hopping of a cloud of uniform spherical fractional point charges onto a target M+q ion (or molecule). The sum of point charges (-1) simulates the incident electron. The sphere radius is determined by a critical distance (Rc eM) between the incoming electron (e-) and the target, at which the potential energy of the e(-)-M+q system is equal to that of the electron-captured molecule M+q(-1) in a symmetry-allowed electronic state with the same structure as M(+q). During the hopping procedure, the excess energies of electron association reaction are dispersed in the kinetic energies of M+q(-1) atoms to conserve total energy. The kinetic energies are adjusted by linearly adding atomic momenta in the direction of driving forces induced by the scattering electron. The nuclear dynamics of the resultant M+q(-1) molecule are studied by using a direct ab initio dynamics method on the adiabatic potential energy surface of M+q(-1), or together with extra adiabatic surface(s) of M+q(-1). For the latter case, the "fewest switches" surface hopping algorithm of Tully was adapted to deal with the nonadiabaticity in trajectory propagations. The SECH model has been applied to study the DR of both CH+ and H3O+(H2O)2. The theoretical results are consistent with the experiment. It was found that water molecules play an important role in determining the product branching ratios of the molecular cluster ion.

Multiscale modeling and general theory of non-equilibrium plasma-assisted ignition and combustion

NASA Astrophysics Data System (ADS)

Yang, Suo; Nagaraja, Sharath; Sun, Wenting; Yang, Vigor

2017-11-01

A self-consistent framework for modeling and simulations of plasma-assisted ignition and combustion is established. In this framework, a ‘frozen electric field’ modeling approach is applied to take advantage of the quasi-periodic behaviors of the electrical characteristics to avoid the re-calculation of electric field for each pulse. The correlated dynamic adaptive chemistry (CO-DAC) method is employed to accelerate the calculation of large and stiff chemical mechanisms. The time-step is dynamically updated during the simulation through a three-stage multi-time scale modeling strategy, which utilizes the large separation of time scales in nanosecond pulsed plasma discharges. A general theory of plasma-assisted ignition and combustion is then proposed. Nanosecond pulsed plasma discharges for ignition and combustion can be divided into four stages. Stage I is the discharge pulse, with time scales of O (1-10 ns). In this stage, input energy is coupled into electron impact excitation and dissociation reactions to generate charged/excited species and radicals. Stage II is the afterglow during the gap between two adjacent pulses, with time scales of O (1 0 0 ns). In this stage, quenching of excited species dissociates O2 and fuel molecules, and provides fast gas heating. Stage III is the remaining gap between pulses, with time scales of O (1-100 µs). The radicals generated during Stages I and II significantly enhance exothermic reactions in this stage. The cumulative effects of multiple pulses is seen in Stage IV, with time scales of O (1-1000 ms), which include preheated gas temperatures and a large pool of radicals and fuel fragments to trigger ignition. For flames, plasma could significantly enhance the radical generation and gas heating in the pre-heat zone, thereby enhancing the flame establishment.

Observing electron localization in a dissociating H2+ molecule in real time

PubMed Central

Xu, H.; Li, Zhichao; He, Feng; Wang, X.; Atia-Tul-Noor, A.; Kielpinski, D.; Sang, R. T.; Litvinyuk, I. V.

2017-01-01

Dissociation of diatomic molecules with odd number of electrons always causes the unpaired electron to localize on one of the two resulting atomic fragments. In the simplest diatomic molecule H2+ dissociation yields a hydrogen atom and a proton with the sole electron ending up on one of the two nuclei. That is equivalent to breaking of a chemical bond—the most fundamental chemical process. Here we observe such electron localization in real time by performing a pump–probe experiment. We demonstrate that in H2+ electron localization is complete in just 15 fs when the molecule’s internuclear distance reaches 8 atomic units. The measurement is supported by a theoretical simulation based on numerical solution of the time-dependent Schrödinger equation. This observation advances our understanding of detailed dynamics of molecular dissociation. PMID:28621332

Process dissociation and mixture signal detection theory.

PubMed

DeCarlo, Lawrence T

2008-11-01

The process dissociation procedure was developed in an attempt to separate different processes involved in memory tasks. The procedure naturally lends itself to a formulation within a class of mixture signal detection models. The dual process model is shown to be a special case. The mixture signal detection model is applied to data from a widely analyzed study. The results suggest that a process other than recollection may be involved in the process dissociation procedure.

On the interplay of gas dynamics and the electromagnetic field in an atmospheric Ar/H2 microwave plasma torch

NASA Astrophysics Data System (ADS)

Synek, Petr; Obrusník, Adam; Hübner, Simon; Nijdam, Sander; Zajíčková, Lenka

2015-04-01

A complementary simulation and experimental study of an atmospheric pressure microwave torch operating in pure argon or argon/hydrogen mixtures is presented. The modelling part describes a numerical model coupling the gas dynamics and mixing to the electromagnetic field simulations. Since the numerical model is not fully self-consistent and requires the electron density as an input, quite extensive spatially resolved Stark broadening measurements were performed for various gas compositions and input powers. In addition, the experimental part includes Rayleigh scattering measurements, which are used for the validation of the model. The paper comments on the changes in the gas temperature and hydrogen dissociation with the gas composition and input power, showing in particular that the dependence on the gas composition is relatively strong and non-monotonic. In addition, the work provides interesting insight into the plasma sustainment mechanism by showing that the power absorption profile in the plasma has two distinct maxima: one at the nozzle tip and one further upstream.

Does phasic trauma treatment make patients with dissociative identity disorder treatment more dissociative?

PubMed

Brand, Bethany; Loewenstein, Richard J

2014-01-01

Proponents of the iatrogenic model of the etiology of dissociative identity disorder (DID) have expressed concern that treatment focused on direct engagement and interaction with dissociated self-states harms DID patients. However, empirical data have shown that this type of DID treatment is beneficial. Analyzing data from the prospective Treatment of Patients With Dissociative Disorders (TOP DD) Study, we test empirically whether DID treatment is associated with clinically adverse manifestations of dissociated self-states: acting so differently that one feels like different people, hearing voices, and dissociative amnesia. We show that, over the course of the study, there were significant decreases in feeling like different people and hearing voices. These results indicate that this form of DID treatment does not lead to symptomatic worsening in these dimensions, as predicted by the iatrogenic model. Indeed, treatment provided by TOP DD therapists reduced, rather than increased, the extent to which patients experienced manifestations of pathological dissociation. Because severe symptomatology and impairment are associated with DID, iatrogenic harm may come from depriving DID patients of treatment that targets DID symptomatology.

Dissociative recombination in aeronomy

NASA Technical Reports Server (NTRS)

Fox, J. L.

1989-01-01

The importance of dissociative recombination in planetary aeronomy is summarized, and two examples are discussed. The first is the role of dissociative recombination of N2(+) in the escape of nitrogen from Mars. A previous model is updated to reflect new experimental data on the electronic states of N produced in this process. Second, the intensity of the atomic oxygen green line on the nightside of Venus is modeled. Use is made of theoretical rate coefficients for production of O (1S) in dissociative recombination from different vibrational levels of O2(+).

ATP Hydrolysis Mechanism in a Maltose Transporter Explored by QM/MM Metadynamics Simulation.

PubMed

Hsu, Wei-Lin; Furuta, Tadaomi; Sakurai, Minoru

2016-11-03

Translocation of substrates across the cell membrane by adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporters depends on the energy provided by ATP hydrolysis within the nucleotide-binding domains (NBDs). However, the detailed mechanism remains unclear. In this study, we focused on maltose transporter NBDs (MalK 2 ) and performed a quantum mechanical/molecular mechanical (QM/MM) well-tempered metadynamics simulation to address this issue. We explored the free-energy profile along an assigned collective variable. As a result, it was determined that the activation free energy is approximately 10.5 kcal/mol, and the reaction released approximately 3.8 kcal/mol of free energy, indicating that the reaction of interest is a one-step exothermic reaction. The dissociation of the ATP γ-phosphate seems to be the rate-limiting step, which supports the so-called dissociative model. Moreover, Glu159, located in the Walker B motif, acts as a base to abstract the proton from the lytic water, but is not the catalytic base, which corresponds to an atypical general base catalysis model. We also observed two interesting proton transfers: transfer from the His192 ε-position nitrogen to the dissociated inorganic phosphate, Pi, and transfer from the Lys42 side chain to adenosine 5'-diphosphate β-phosphate. These proton transfers would stabilize the posthydrolysis state. Our study provides significant insight into the ATP hydrolysis mechanism in MalK 2 from a dynamical viewpoint, and this insight would be applicable to other ABC transporters.

Accounting for dissociation and photolysis: a review of the algal toxicity of triclosan.

PubMed

Roberts, Jayne; Price, Oliver R; Bettles, Nicola; Rendal, Cecilie; van Egmond, Roger

2014-11-01

Triclosan, an antimicrobial agent commonly used in down-the-drain consumer products, is toxic to freshwater microalgae. However, the rapid photolysis and pH-dependent dissociation of this compound may give rise to uncertainty in growth inhibition tests with freshwater microalgae, if these are not well characterized. Methods are presented to minimize these uncertainties by stabilizing pH with an organic buffering agent (Bis-Tris) and by the application of ultraviolet (UV) covers to remove UV wavelengths. Toxicity tests with these methods were in compliance with the validity criteria of the Organisation for Economic Co-operation and Development test 201, and no negative effects were seen in controls relative to the unmodified method. The methods were used for toxicity tests with triclosan at pH levels of 7.0, 8.0, and 8.5, yielding effective concentration, 10% values of 0.5 µg/L, 0.6 µg/L, and 12.1 µg/L, respectively. The observed change in toxicity with pH was proportional to the change in bioconcentration factor (BCF) as calculated using the cell model (a dynamic flux model based on the Fick-Nernst-Planck equations, in this case parameterized for an algal cell). Effect concentrations produced with the methods presented in the present study offer robust data on which to base risk assessment, and it is suggested that similar approaches be used to minimize uncertainty when other compounds that dissociate and photolyse are tested. © 2014 SETAC.

Binding Energies of the Proton-Bound Amino Acid Dimers Gly·Gly, Ala·Ala, Gly·Ala, and Lys·Lys Measured by Blackbody Infrared Radiative Dissociation

PubMed Central

Price, William D.; Schnier, Paul D.

2005-01-01

Arrhenius activation energies in the zero-pressure limit for dissociation of gas-phase proton-bound homodimers of N,N-dimethylacetamide (N,N-DMA), glycine, alanine, and lysine and the heterodimer alanine·glycine were measured using blackbody infrared radiative dissociation (BIRD). In combination with master equation modeling of the kinetic data, binding energies of these dimers were determined. A value of 1.25 ± 0.05 eV is obtained for N,N-DMA and is in excellent agreement with that reported in the literature. The value obtained from the truncated Boltzmann model is significantly higher, indicating that the assumptions of this model do not apply to these ions. This is due to the competitive rates of photon emission and dissociation for these relatively large ions. The binding energies of the amino acid dimers are ~1.15 ± 0.05 eV and are indistinguishable despite the difference in their gas-phase basicity and structure. The threshold dissociation energies can be accurately modeled using a range of dissociation parameters and absorption/emission rates. However, the absolute values of the dissociation rates depend more strongly on the absorption/emission rates. For N,N-DMA and glycine, an accurate fit was obtained using frequencies and transition dipole moments calculated at the ab initio RHF/2-31G* and MP2/2-31G* level, respectively. In order to obtain a similar accuracy using values obtained from AM1 semiempirical calculations, it was necessary to multiply the transition dipole moments by a factor of 3. These results demonstrate that in combination with master equation modeling, BIRD can be used to obtain accurate threshold dissociation energies of relatively small ions of biological interest. PMID:17235378

Reconstructing dynamic mental models of facial expressions in prosopagnosia reveals distinct representations for identity and expression.

PubMed

Richoz, Anne-Raphaëlle; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Caldara, Roberto

2015-04-01

The human face transmits a wealth of signals that readily provide crucial information for social interactions, such as facial identity and emotional expression. Yet, a fundamental question remains unresolved: does the face information for identity and emotional expression categorization tap into common or distinct representational systems? To address this question we tested PS, a pure case of acquired prosopagnosia with bilateral occipitotemporal lesions anatomically sparing the regions that are assumed to contribute to facial expression (de)coding (i.e., the amygdala, the insula and the posterior superior temporal sulcus--pSTS). We previously demonstrated that PS does not use information from the eye region to identify faces, but relies on the suboptimal mouth region. PS's abnormal information use for identity, coupled with her neural dissociation, provides a unique opportunity to probe the existence of a dichotomy in the face representational system. To reconstruct the mental models of the six basic facial expressions of emotion in PS and age-matched healthy observers, we used a novel reverse correlation technique tracking information use on dynamic faces. PS was comparable to controls, using all facial features to (de)code facial expressions with the exception of fear. PS's normal (de)coding of dynamic facial expressions suggests that the face system relies either on distinct representational systems for identity and expression, or dissociable cortical pathways to access them. Interestingly, PS showed a selective impairment for categorizing many static facial expressions, which could be accounted for by her lesion in the right inferior occipital gyrus. PS's advantage for dynamic facial expressions might instead relate to a functionally distinct and sufficient cortical pathway directly connecting the early visual cortex to the spared pSTS. Altogether, our data provide critical insights on the healthy and impaired face systems, question evidence of deficits obtained from patients by using static images of facial expressions, and offer novel routes for patient rehabilitation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Strong field control of predissociation dynamics.

PubMed

Corrales, María E; Balerdi, Garikoitz; Loriot, Vincent; de Nalda, Rebeca; Bañares, Luis

2013-01-01

Strong field control scenarios are investigated in the CH3I predissociation dynamics at the origin of the second absorption B-band, in which state-selective electronic predissociation occurs through the crossing with a valence dissociative state. Dynamic Stark control (DSC) and pump-dump strategies are shown capable of altering both the predissociation lifetime and the product branching ratio.

Modeling heat dissipation at the nanoscale: an embedding approach for chemical reaction dynamics on metal surfaces.

PubMed

Meyer, Jörg; Reuter, Karsten

2014-04-25

We present an embedding technique for metallic systems that makes it possible to model energy dissipation into substrate phonons during surface chemical reactions from first principles. The separation of chemical and elastic contributions to the interaction potential provides a quantitative description of both electronic and phononic band structure. Application to the dissociation of O2 at Pd(100) predicts translationally "hot" oxygen adsorbates as a consequence of the released adsorption energy (ca. 2.6 eV). This finding questions the instant thermalization of reaction enthalpies generally assumed in models of heterogeneous catalysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

X-ray scattering measurements of dissociation-induced metallization of dynamically compressed deuterium

DOE PAGES

Davis, P.; Döppner, T.; Rygg, J. R.; ...

2016-04-18

Hydrogen, the simplest element in the universe, has a surprisingly complex phase diagram. Because of applications to planetary science, inertial confinement fusion and fundamental physics, its high-pressure properties have been the subject of intense study over the past two decades. While sophisticated static experiments have probed hydrogen’s structure at ever higher pressures, studies examining the higher-temperature regime using dynamic compression have mostly been limited to optical measurement techniques. Here we present spectrally resolved x-ray scattering measurements from plasmons in dynamically compressed deuterium. Combined with Compton scattering, and velocity interferometry to determine shock pressure and mass density, this allows us tomore » extract ionization state as a function of compression. Furthermore, the onset of ionization occurs close in pressure to where density functional theory-molecular dynamics (DFT-MD) simulations show molecular dissociation, suggesting hydrogen transitions from a molecular and insulating fluid to a conducting state without passing through an intermediate atomic phase.« less

Ultrafast dynamics of ligand and substrate interaction in endothelial nitric oxide synthase under Soret excitation.

PubMed

Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S

2016-01-01

Ultrafast transient absorption spectroscopy of endothelial NOS oxygenase domain (eNOS-oxy) was performed to study dynamics of ligand or substrate interaction under Soret band excitation. Photo-excitation dissociates imidazole ligand in <300fs, then followed by vibrational cooling and recombination within 2ps. Such impulsive bond breaking and late rebinding generate proteinquakes, which relaxes in several tens of picoseconds. The photo excited dynamics of eNOS-oxy with L-arginine substrate mainly occurs at the local site of heme, including ultrafast internal conversion within 400fs, vibrational cooling, charge transfer, and complete ground-state recovery within 1.4ps. The eNOS-oxy without additive is partially bound with water molecule, thus its photoexcited dynamics also shows ligand dissociation in <800fs. Then it followed by vibrational cooling coupled with charge transfer in 4.8ps, and recombination of ligand to distal side of heme in 12ps. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamics of nanoparticle-protein corona complex formation: analytical results from population balance equations.

PubMed

Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

2013-01-01

Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid.

Molecular dynamics simulation of low dielectric constant polymer electrolytes

NASA Astrophysics Data System (ADS)

Wheatle, Bill; Lynd, Nathaniel; Ganesan, Venkat

Recent experimental studies measured the ionic conductivities of a series of poly(glycidyl ether)s with varying neat dielectric constants (ɛ), viscosities (η), and glass transition temperatures (Tg), as hosts for lithium bistrifluoromethanesulfonimide (LiTFSI) salt. In such a context, it was demonstrated that the ionic conductivity of these polymer electrolytes was a function of ɛ rather than Tg or η, suggesting that there may exist regimes in which ionic conductivity is not limited by slow segmental dynamics but rather by low ionic dissociation. Motivated by such results, we used atomistic molecular dynamics to study the structure and transport characteristics of the same set of host polymers. We found that the coordination number of TFSI- about Li+ in the first solvation shell and the total fraction of free ions increased as a function of ɛ, implying the polymer hosts enhanced ion dissociation. In addition, we found that increasing the dielectric constant of the host polymer enhanced self-correlated ion transport, as evidenced by an increase in the diffusion coefficients of each ion species. Overall, we confirmed that limited ion dissociation in low- ɛ polymer electrolyte hosts hampers ionic conductivity. We would like to thank the National Science Foundation Graduate Research Fellowship Program for funding this research endeavor.

Mapping and controlling ultrafast dynamics of highly excited H 2 molecules by VUV-IR pump-probe schemes

DOE PAGES

Sturm, F. P.; Tong, X. M.; Palacios, A.; ...

2017-01-09

Here, we used ultrashort femtosecond vacuum ultraviolet (VUV) and infrared (IR) pulses in a pump-probe scheme to map the dynamics and nonequilibrium dissociation channels of excited neutral H 2 molecules. A nuclear wave packet is created in the B 1Σmore » $$+\\atop{u}$$ state of the neutral H 2 molecule by absorption of the ninth harmonic of the driving infrared laser field. Due to the large stretching amplitude of the molecule excited in the B 1Σ$$+\\atop{u}$$ electronic state, the effective H 2 + ionization potential changes significantly as the nuclear wave packet vibrates in the bound, highly electronically and vibrationally excited B potential-energy curve. We probed such dynamics by ionizing the excited neutral molecule using time-delayed VUV-or-IR radiation. We identified the nonequilibrium dissociation channels by utilizing three-dimensional momentum imaging of the ion fragments. We also found that different dissociation channels can be controlled, to some extent, by changing the IR laser intensity and by choosing the wavelength of the probe laser light. Furthermore, we concluded that even in a benchmark molecular system such as H 2*, the interpretation of the nonequilibrium multiphoton and multicolor ionization processes is still a challenging task, requiring intricate theoretical analysis.« less

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

The photodissociation dynamics of the ethyl radical, C2H5, investigated by velocity map imaging.

PubMed

Steinbauer, Michael; Giegerich, Jens; Fischer, Kathrin H; Fischer, Ingo

2012-07-07

The photodissociation dynamics of the ethyl radical C(2)H(5) has been investigated by velocity map imaging. Ethyl was produced by flash pyrolysis from n-propyl nitrite and excited to the à (2)A(') (3s) Rydberg state around 250 nm. The energetically most favorable reaction channel in this wavelength region is dissociation to C(2)H(4) (ethene) + H. The H-atom dissociation products were ionized in a [1+1(')] process via the 1s-2p transition. The observed translational energy distribution is bimodal: A contribution of slow H-atoms with an isotropic angular distribution peaks at low translational energies. An expectation value for the fraction of excess energy released into translation of = 0.19 is derived from the data, typical for statistical dissociation reactions. In addition, a fast H-atom channel is observed, peaking around 1.8 eV. The latter shows an anisotropic distribution with β = 0.45. It originates from a direct dissociation process within less than a rotational period. Time-delay scans with varying extraction voltages indicate the presence of two rates for the formation of H-atoms. One rate with a sub-nanosecond time constant is associated with H-atoms with large translational energy; a second one with a time constant on the order of 100 ns is associated with H-atoms formed with low translational energy. The data confirm and extend those from previous experiments and remove some inconsistencies. Possible mechanisms for the dissociation are discussed in light of the new results as well as previous ones.

Dissociative Recombination Chemistry and Plasma Dynamics

DTIC Science & Technology

2008-06-16

the fractional square of product momentum with product momentum vectors . Qx and Qy denote the degenerate bend two-body dissociation limits...with product momentum vectors . Qx and Qy denote the degenerate bend normal modes for C2v symmetry H2D and HD2 isomers of H3. symmetry for the Qx...heavy (D atom) products in general receive a greater partitioning of energy than the light product. This may have important implications for

Resonant inelastic collisions of electrons with diatomic molecules

NASA Astrophysics Data System (ADS)

Houfek, Karel

2012-05-01

In this contribution we give a review of applications of the nonlocal resonance theory which has been successfully used for treating the nuclear dynamics of low-energy electron collisions with diatomic molecules over several decades. We give examples and brief explanations of various structures observed in the cross sections of vibrational excitation and dissociative electron attachment to diatomic molecules such as threshold peaks, boomerang oscillations below the dissociative attachment threshold, or outer-well resonances.

Initial state-specific photodissociation dynamics of pyrrole via 1 π σ ∗/ S 0 conical intersection initiated with optimally controlled UV-laser pulses

NASA Astrophysics Data System (ADS)

Nandipati, K. R.; Kanakati, Arun Kumar; Singh, H.; Lan, Z.; Mahapatra, S.

2017-09-01

Optimal initiation of quantum dynamics of N-H photodissociation of pyrrole on the S0-1πσ∗(1A2) coupled electronic states by UV-laser pulses in an effort to guide the subsequent dynamics to dissociation limits is studied theoretically. Specifically, the task of designing optimal laser pulses that act on initial vibrational states of the system for an effective UV-photodissociation is considered by employing optimal control theory. The associated control mechanism(s) for the initial state dependent photodissociation dynamics of pyrrole in the presence of control pulses is examined and discussed in detail. The initial conditions determine implicitly the variation in the dissociation probabilities for the two channels, upon interaction with the field. The optimal pulse corresponds to the objective fixed as maximization of overall reactive flux subject to constraints of reasonable fluence and quantum dynamics. The simple optimal pulses obtained by the use of genetic algorithm based optimization are worth an experimental implementation given the experimental relevance of πσ∗-photochemistry in recent times.

Trauma-induced dissociative amnesia in World War I combat soldiers. II. Treatment dimensions.

PubMed

Brown, P; van der Hart, O; Graafland, M

1999-06-01

This is the second part of a study of posttraumatic amnesia in World War I (WW I) soldiers. It moves beyond diagnostic validation of posttraumatic amnesia (PTA), to examine treatment findings, and relates these to contemporary treatment of dissociative amnesia, including treatment of victims of civilian trauma (e.g. childhood sexual abuse). Key WW I studies are surveyed which focus on the treatment of PTA and traumatic memories. The dissociation-integration and repression-abreaction models are contrasted. Descriptive evidence is cited in support of preferring Myers' and McDougalls' dissociation-integration treatment approach over Brown's repression-abreaction model. Therapeutic findings in this paper complement diagnostic data from the first report. Although effective treatment includes elements of both the dissociative-integrative and abreactive treatment approaches, cognitive integration of dissociated traumatic memories and personality functions is primary, while emotional release is secondary.

Comfortably Numb: The Role of Momentary Dissociation in the Experience of Negative Affect Around Binge Eating.

PubMed

Mason, Tyler B; Lavender, Jason M; Wonderlich, Stephen A; Steiger, Howard; Cao, Li; Engel, Scott G; Mitchell, James E; Crosby, Ross D

2017-05-01

Evidence suggests that both dissociation and negative affect (NA) may precipitate binge eating. The extent to which dissociation may impact the experience of NA around binge eating is unclear. Women with bulimia nervosa completed a 2-week ecological momentary assessment protocol of dissociation, NA, and binge eating. Multilevel modeling was used to examine dissociation as a moderator of NA before and after binge eating. NA was greater at the time of binge eating for participants higher in average dissociation (between subjects) and when momentary dissociation was greater than one's average (within subjects). The trajectory of NA was characterized by a sharper increase before binge eating for participants higher in average dissociation; the NA trajectories were characterized by sharper increases before and decreases after binge eating when momentary dissociation was greater than one's average. Results support the salience of both dissociation and NA in relation to the occurrence of binge eating.

State resolved vibrational relaxation modeling for strongly nonequilibrium flows

NASA Astrophysics Data System (ADS)

Boyd, Iain D.; Josyula, Eswar

2011-05-01

Vibrational relaxation is an important physical process in hypersonic flows. Activation of the vibrational mode affects the fundamental thermodynamic properties and finite rate relaxation can reduce the degree of dissociation of a gas. Low fidelity models of vibrational activation employ a relaxation time to capture the process at a macroscopic level. High fidelity, state-resolved models have been developed for use in continuum gas dynamics simulations based on computational fluid dynamics (CFD). By comparison, such models are not as common for use with the direct simulation Monte Carlo (DSMC) method. In this study, a high fidelity, state-resolved vibrational relaxation model is developed for the DSMC technique. The model is based on the forced harmonic oscillator approach in which multi-quantum transitions may become dominant at high temperature. Results obtained for integrated rate coefficients from the DSMC model are consistent with the corresponding CFD model. Comparison of relaxation results obtained with the high-fidelity DSMC model shows significantly less excitation of upper vibrational levels in comparison to the standard, lower fidelity DSMC vibrational relaxation model. Application of the new DSMC model to a Mach 7 normal shock wave in carbon monoxide provides better agreement with experimental measurements than the standard DSMC relaxation model.

Dissociative electron attachment and vibrational excitation of CF{sub 3}Cl: Effect of two vibrational modes revisited

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

Tarana, Michal; JILA, University of Colorado and NIST, Boulder, Colorado 80309-0440; Houfek, Karel

We present a study of dissociative electron attachment and vibrational excitation processes in electron collisions with the CF{sub 3}Cl molecule. The calculations are based on the two-dimensional nuclear dynamics including the C-Cl symmetric stretch coordinate and the CF{sub 3} symmetric deformation (umbrella) coordinate. The complex potential energy surfaces are calculated using the ab initio R-matrix method. The results for dissociative attachment and vibrational excitation of the umbrella mode agree quite well with experiment whereas the cross section for excitation of the C-Cl symmetric stretch vibrations is about a factor-of-three too low in comparison with experimental data.

Li + solvation and kinetics of Li +–BF 4 -/PF 6 - ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

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

Chang, Tsun-Mei; Dang, Liem X.

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux; Impey, Madden, and McDonald approaches; and Grote-Hynes theory. We found the residence times of EC around Li+ ions varied from 70 to 450 ps, depending on the correction method used. We found the relaxation times changed significantlymore » from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influence the dissociation kinetics of ion pairing. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Electrostatics Control Actin Filament Nucleation and Elongation Kinetics*

PubMed Central

Crevenna, Alvaro H.; Naredi-Rainer, Nikolaus; Schönichen, André; Dzubiella, Joachim; Barber, Diane L.; Lamb, Don C.; Wedlich-Söldner, Roland

2013-01-01

The actin cytoskeleton is a central mediator of cellular morphogenesis, and rapid actin reorganization drives essential processes such as cell migration and cell division. Whereas several actin-binding proteins are known to be regulated by changes in intracellular pH, detailed information regarding the effect of pH on the actin dynamics itself is still lacking. Here, we combine bulk assays, total internal reflection fluorescence microscopy, fluorescence fluctuation spectroscopy techniques, and theory to comprehensively characterize the effect of pH on actin polymerization. We show that both nucleation and elongation are strongly enhanced at acidic pH, with a maximum close to the pI of actin. Monomer association rates are similarly affected by pH at both ends, although dissociation rates are differentially affected. This indicates that electrostatics control the diffusional encounter but not the dissociation rate, which is critical for the establishment of actin filament asymmetry. A generic model of protein-protein interaction, including electrostatics, explains the observed pH sensitivity as a consequence of charge repulsion. The observed pH effect on actin in vitro agrees with measurements of Listeria propulsion in pH-controlled cells. pH regulation should therefore be considered as a modulator of actin dynamics in a cellular environment. PMID:23486468

Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo.

PubMed

Parsons, Neal; Levin, Deborah A; van Duin, Adri C T; Zhu, Tong

2014-12-21

The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(Σg+1)-N2(Σg+1) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

Fragmentation dynamics of ionized neon clusters (Ne(n), n=3-14) embedded in helium nanodroplets.

PubMed

Bonhommeau, David; Halberstadt, Nadine; Viel, Alexandra

2006-01-14

We report a theoretical study of the nonadiabatic fragmentation dynamics of ionized neon clusters embedded in helium nanodroplets for cluster sizes up to n=14 atoms. The dynamics of the neon atoms is modeled using the molecular dynamics with quantum transitions method of Tully [J. Chem. Phys. 93, 1061 (1990)] with the nuclei treated classically and transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model to which induced dipole-induced dipole interactions are added. The effect of the spin-orbit interaction is also discussed. The helium environment is modeled by a friction force acting on charged atoms whose speed exceeds the critical Landau velocity. The dependence of the fragment size distribution on the friction strength and on the initial nanodroplet size is investigated. By comparing with the available experimental data obtained for Ne3+ and Ne4+, a reasonable value for the friction coefficient, the only parameter of the model, is deduced. This value is then used to predict the effect of the helium environment on the dissociation dynamics of larger neon clusters, n=5-14. The results show stabilization of larger fragments than in the gas phase, but fragmentation is not completely caged. In addition, two types of dynamics are characterized for Ne4+: fast and explosive, therefore leaving no time for friction to cool down the process when dynamics starts on one of the highest electronic states, and slower, therefore leading to some stabilization by helium when it starts on one of the lowest electronic states.

Investigating the thermal dissociation of viral capsid by lattice model

NASA Astrophysics Data System (ADS)

Chen, Jingzhi; Chevreuil, Maelenn; Combet, Sophie; Lansac, Yves; Tresset, Guillaume

2017-11-01

The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.

Dissociative recombination by frame transformation to Siegert pseudostates: A comparison with a numerically solvable model

NASA Astrophysics Data System (ADS)

Hvizdoš, Dávid; Váňa, Martin; Houfek, Karel; Greene, Chris H.; Rescigno, Thomas N.; McCurdy, C. William; Čurík, Roman

2018-02-01

We present a simple two-dimensional model of the indirect dissociative recombination process. The model has one electronic and one nuclear degree of freedom and it can be solved to high precision, without making any physically motivated approximations, by employing the exterior complex scaling method together with the finite-elements method and discrete variable representation. The approach is applied to solve a model for dissociative recombination of H2 + in the singlet ungerade channels, and the results serve as a benchmark to test validity of several physical approximations commonly used in the computational modeling of dissociative recombination for real molecular targets. The second, approximate, set of calculations employs a combination of multichannel quantum defect theory and frame transformation into a basis of Siegert pseudostates. The cross sections computed with the two methods are compared in detail for collision energies from 0 to 2 eV.

Aurora-B/AIM-1 Regulates the Dynamic Behavior of HP1α at the G2–M Transition

PubMed Central

2006-01-01

Heterochromatin protein 1 (HP1) plays an important role in heterochromatin formation and undergoes large-scale, progressive dissociation from heterochromatin in prophase cells. However, the mechanisms regulating the dynamic behavior of HP1 are poorly understood. In this study, the role of Aurora-B was investigated with respect to the dynamic behavior of HP1α. Mammalian Aurora-B, AIM-1, colocalizes with HP1α to the heterochromatin in G2. Depletion of Aurora-B/AIM-1 inhibited dissociation of HP1α from the chromosome arms at the G2–M transition. In addition, depletion of INCENP led to aberrant cellular localization of Aurora-B/AIM-1, but it did not affect heterochromatin targeting of HP1α. It was proposed in the binary switch hypothesis that phosphorylation of histone H3 at Ser-10 negatively regulates the binding of HP1α to the adjacent methylated Lys-9. However, Aurora-B/AIM-1-mediated phosphorylation of H3 induced dissociation of the HP1α chromodomain but not of the intact protein in vitro, indicating that the center and/or C-terminal domain of HP1α interferes with the effect of H3 phosphorylation on HP1α dissociation. Interestingly, Lys-9 methyltransferase SUV39H1 is abnormally localized together along the metaphase chromosome arms in Aurora-B/AIM-1–depleted cells. In conclusion, these results showed that Aurora-B/AIM-1 is necessary for regulated histone modifications involved in binding of HP1α by the N terminus of histone H3 during mitosis. PMID:16687578

Rabi oscillations in the dissociative continuum: Rotation and alignment effects

NASA Astrophysics Data System (ADS)

Granucci, Giovanni; Magnier, Sylvie; Persico, Maurizio

2002-01-01

We have simulated a set of experiments in which Rabi oscillations are induced in bound-free and free-free transitions of a diatomic molecule. Dissociative vibrational states belonging to different electronic terms are involved. We show analytically and confirm computationally that a simple relationship exists between the one-dimensional dynamics of a molecule with fixed orientation with respect to the polarization of the radiation field and the three-dimensional dynamics of a rotating system. It is demonstrated that sufficiently short laser pulses can induce oscillations in the probabilities of two coupled electronic states, and in the yields of the respective dissociation products, as functions of the radiation intensity. As a result of molecular rotation the oscillations are damped but not washed out. The initial thermal distribution on several rotational levels has a negligible effect on the photodissociation yields and other experimentally relevant quantities. Since the molecule undergoes a strong alignment along the polarization axis of the laser field, the ejection of atoms and ions is anisotropic. We have chosen the well known diatomic ion Na2+ as a convenient example.

Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

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

Makarov, G N; Petin, A N

2016-03-31

We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF{sub 6} and CF{sub 3}I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF{sub 6} molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with amore » surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation. (laser separation of isotopes)« less

Probing the Structure of the Escherichia coli Periplasmic Proteins HdeA and YmgD by Molecular Dynamics Simulations.

PubMed

Socher, Eileen; Sticht, Heinrich

2016-11-23

HdeA and YmgD are structurally homologous proteins in the periplasm of Escherichia coli. HdeA has been shown to represent an acid-activated chaperone, whereas the function of YmgD has not yet been characterized. We performed pH-titrating molecular dynamics simulations (pHtMD) to investigate the structural changes of both proteins and to assess whether YmgD may also exhibit an unfolding behavior similar to that of HdeA. The unfolding pathway of HdeA includes partially unfolded dimer structures, which represent a prerequisite for subsequent dissociation. In contrast to the coupled unfolding and dissociation of HdeA, YmgD displays dissociation of the folded subunits, and the subunits do not undergo significant unfolding even at low pH values. The differences in subunit stability between HdeA and YmgD may be explained by the structural features of helix D, which represents the starting point of unfolding in HdeA. In summary, the present study suggests that YmgD either is not an acid-activated chaperone or, at least, does not require unfolding for activation.

A molecular dynamic study on the dissociation mechanism of SI methane hydrate in inorganic salt aqueous solutions.

PubMed

Xu, Jiafang; Chen, Zhe; Liu, Jinxiang; Sun, Zening; Wang, Xiaopu; Zhang, Jun

2017-08-01

Gas hydrate is not only a potential energy resource, but also almost the biggest challenge in oil/gas flow assurance. Inorganic salts such as NaCl, KCl and CaCl 2 are widely used as the thermodynamic inhibitor to reduce the risk caused by hydrate formation. However, the inhibition mechanism is still unclear. Therefore, molecular dynamic (MD) simulation was performed to study the dissociation of structure I (SI) methane hydrate in existence of inorganic salt aqueous solution on a micro-scale. The simulation results showed that, the dissociation became stagnant due to the presence of liquid film formed by the decomposed water molecules, and more inorganic ions could shorten the stagnation-time. The diffusion coefficients of ions and water molecules were the largest in KCl system. The structures of ion/H 2 O and H 2 O/H 2 O were the most compact in hydrate/NaCl system. The ionic ability to decompose hydrate cells followed the sequence of: Ca 2+ >2K + >2Cl - >2Na + . Copyright © 2017 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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.

Free energy landscape of dissociative adsorption of methane on ideal and defected graphene from ab initio simulations

NASA Astrophysics Data System (ADS)

Wlazło, M.; Majewski, J. A.

2018-03-01

We study the dissociative adsorption of methane at the surface of graphene. Free energy profiles, which include activation energies for different steps of the reaction, are computed from constrained ab initio molecular dynamics. At 300 K, the reaction barriers are much lower than experimental bond dissociation energies of gaseous methane, strongly indicating that the graphene surface acts as a catalyst of methane decomposition. On the other hand, the barriers are still much higher than on the nickel surface. Methane dissociation therefore occurs at a higher rate on nickel than on graphene. This reaction is a prerequisite for graphene growth from a precursor gas. Thus, the growth of the first monolayer should be a fast and efficient process while subsequent layers grow at a diminished rate and in a more controllable manner. Defects may also influence reaction energetics. This is evident from our results, in which simple defects (Stone-Wales defect and nitrogen substitution) lead to different free energy landscapes at both dissociation and adsorption steps of the process.

Breakdown electric fields in dissociated hot gas mixtures of sulfur hexafluoride including teflon: Calculations with experimental validations and utilization in fluid dynamics arc simulations

NASA Astrophysics Data System (ADS)

Yousfi, M.; Merbahi, N.; Reichert, F.; Petchanka, A.

2017-03-01

Measurements of breakdown voltage Vb, gas temperature Tg, and density N and the associated critical electric field Ecr/N are performed in hot dissociated SF6 highly diluted in argon and in hot dissociated SF6 mixed with PTFE (Polytetrafluoroethylene or C2F4) also highly diluted in argon. Gases are heated using a microwave source and optical emission spectroscopy is used for measurements of Tg and N while Vb is measured from a specific inter-electrode arrangement placed inside of the cell of the hot gas conditioning. The experimental Ecr/N data in the numerous considered cases of gas temperatures and compositions have been used to evaluate and validate the sets of the collision cross sections of the 11 species involved in hot dissociated SF6 (i.e., SF6, SF5, SF4, S2F2, SF3, SF2, SF, S2, F2, F, and S), the 13 additional species involved either in hot C2F4 or CF4 (C2F6, C2F4, C2F2, CF4, CF3, CF2, CF, F2, F and carbon species as C, C2, C3, C4) and also the 2 further species (CS and CS2) present only in the considered mixtures SF6 + C2F4. The fitted sets of collision cross sections of all these 26 species are then used without argon dilution in hot SF6 and hot SF6 + C2F4 mixtures to calculate and to analyze the Ecr/N data obtained for a wide range of gas temperature (up to 4000 K) and gas pressure (8 bar and more) using a rigorous multi-term solution of the Boltzmann equation for electron energy distribution function and standard calculations of hot gas composition for the species proportions. Such Ecr/N data have been then successfully used to evaluate from a Computational Fluid Dynamics model the switching capacity at terminal fault from a coupled simulation of the electrostatic field and the hot gas flow after current zero.

Electron beam induced deposition of silacyclohexane and dichlorosilacyclohexane: the role of dissociative ionization and dissociative electron attachment in the deposition process.

PubMed

P, Ragesh Kumar T; Hari, Sangeetha; Damodaran, Krishna K; Ingólfsson, Oddur; Hagen, Cornelis W

2017-01-01

We present first experiments on electron beam induced deposition of silacyclohexane (SCH) and dichlorosilacyclohexane (DCSCH) under a focused high-energy electron beam (FEBID). We compare the deposition dynamics observed when growing pillars of high aspect ratio from these compounds and we compare the proximity effect observed for these compounds. The two precursors show similar behaviour with regards to fragmentation through dissociative ionization in the gas phase under single-collision conditions. However, while DCSCH shows appreciable cross sections with regards to dissociative electron attachment, SCH is inert with respect to this process. We discuss our deposition experiments in context of the efficiency of these different electron-induced fragmentation processes. With regards to the deposition dynamics, we observe a substantially faster growth from DCSCH and a higher saturation diameter when growing pillars with high aspect ratio. However, both compounds show similar behaviour with regards to the proximity effect. With regards to the composition of the deposits, we observe that the C/Si ratio is similar for both compounds and in both cases close to the initial molecular stoichiometry. The oxygen content in the DCSCH deposits is about double that of the SCH deposits. Only marginal chlorine is observed in the deposits of from DCSCH. We discuss these observations in context of potential approaches for Si deposition.

The Conference on the Dynamics of Molecular Collisions Held at Snowbird, Utah on 14-19 July 1985.

DTIC Science & Technology

1985-07-01

prototype- ’o:’ the i-nfrar&ec mu-t iphoto- dissociation meon1-anasms of more general =-PO compounds , w-here X, Y, aId 7 -ave i-oaln icrds. exa;zple, thp...34 - * . . . - . .-. . .--. 2- -. . r y’.. 1.0 Ws [1. 1. 1125- 11111 224 F. MICROCOP RESOLUTION TEST CHART NA’ ONAL BUQFA. Of STAO)ARDS- 96 5 F...maffect this energy flow, such as the presence of a heavy atom blocker in model organometallic compounds , are also studied. In addition to processes

At the Interface: Dynamic Interactions of Explicit and Implicit Language Knowledge

ERIC Educational Resources Information Center

Ellis, Nick C.

2005-01-01

This paper considers how implicit and explicit knowledge are dissociable but cooperative. It reviews various psychological and neurobiological processes by which explicit knowledge of form-meaning associations impacts upon implicit language learning. The interface is dynamic: It happens transiently during conscious processing, but the influence…

Binding Energies of Proton-Bound Dimers of Imidazole and n-Acetylalanine Methyl Ester Obtained by Blackbody Infrared Radiative Dissociation

PubMed Central

Jockusch, Rebecca A.; Williams*, Evan R.

2005-01-01

The dissociation kinetics of protonated n-acetyl-L-alanine methyl ester dimer (AcAlaMEd), imidazole dimer, and their cross dimer were measured using blackbody infrared radiative dissociation (BIRD). Master equation modeling of these data was used to extract threshold dissociation energies (Eo) for the dimers. Values of 1.18 ± 0.06, 1.11 ± 0.04, and 1.12 ± 0.08 eV were obtained for AcAlaMEd, imidazole dimer, and the cross dimer, respectively. Assuming that the reverse activation barrier for dissociation of the ion–molecule complex is negligible, the value of Eo can be compared to the dissociation enthalpy (ΔHd°) from HPMS data. The Eo values obtained for the imidazole dimer and the cross dimer are in agreement with HPMS values; the value for AcAlaMEd is somewhat lower. Radiative rate constants used in the master equation modeling were determined using transition dipole moments calculated at the semiempirical (AM1) level for all dimers and compared to ab initio (RHF/3-21G*) calculations where possible. To reproduce the experimentally measured dissociation rates using master equation modeling, it was necessary to multiply semiempirical transition dipole moments by a factor between 2 and 3. Values for transition dipole moments from the ab initio calculations could be used for two of the dimers but appear to be too low for AcAlaMEd. These results demonstrate that BIRD, in combination with master equation modeling, can be used to determine threshold dissociation energies for intermediate size ions that are in neither the truncated Boltzmann nor the rapid energy exchange limit. PMID:16604163

Ionic screening and dissociation are crucial for understanding chemical self-propulsion in polar solvents.

PubMed

Brown, Aidan T; Poon, Wilson C K; Holm, Christian; de Graaf, Joost

2017-02-08

Polar solvents like water support the bulk dissociation of themselves and their solutes into ions, and the re-association of these ions into neutral molecules in a dynamic equilibrium, e.g., H 2 O 2 ⇌ H + + HO 2 - . Using continuum theory, we study the influence of these association-dissociation reactions on the self-propulsion of colloids driven by surface chemical reactions (chemical swimmers). We find that association-dissociation reactions should have a strong influence on swimmers' behaviour, and therefore should be included in future modelling. In particular, such bulk reactions should permit charged swimmers to propel electrophoretically even if all species involved in the surface reactions are neutral. The bulk reactions also significantly modify the predicted speed of chemical swimmers propelled by ionic currents, by up to an order of magnitude. For swimmers whose surface reactions produce both anions and cations (ionic self-diffusiophoresis), the bulk reactions produce an additional reactive screening length, analogous to the Debye length in electrostatics. This in turn leads to an inverse relationship between swimmer radius and swimming speed, which could provide an alternative explanation for recent experimental observations on Pt-polystyrene Janus swimmers [S. Ebbens et al., Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2012, 85, 020401]. We also use our continuum theory to investigate the effect of the Debye screening length itself, going beyond the infinitely-thin-screening-length approximation used by previous analytical theories. We identify significant departures from this limiting behaviour for micron-sized swimmers under typical experimental conditions and find that the approximation fails entirely for nanoscale swimmers.

Isotherm-Based Thermodynamic Model for Solute Activities of Asymmetric Electrolyte Aqueous Solutions.

PubMed

Nandy, Lucy; Dutcher, Cari S

2017-09-21

Adsorption isotherm-based statistical thermodynamic models can be used to determine solute concentration and solute and solvent activities in aqueous solutions. Recently, the number of adjustable parameters in the isotherm model of Dutcher et al. J. Phys. Chem. A/C 2011, 2012, 2013 were reduced for neutral solutes as well as symmetric 1:1 electrolytes by using a Coulombic model to describe the solute-solvent energy interactions (Ohm et al. J. Phys. Chem. A 2015, Nandy et al. J. Phys. Chem. A 2016). Here, the Coulombic treatment for symmetric electrolytes is extended to establish improved isotherm model equations for asymmetric 1-2 and 1-3 electrolyte systems. The Coulombic model developed here results in prediction of activities and other thermodynamic properties in multicomponent systems containing ions of arbitrary charge. The model is found to accurately calculate the osmotic coefficient over the entire solute concentration range with two model parameters, related to intermolecular solute-solute and solute-solvent spacing. The inorganic salts and acids treated here are generally considered to be fully dissociated. However, there are certain weak acids that do not dissociate completely, such as the bisulfate ion. In this work, partial dissociation of the bisulfate ion from sulfuric acid is treated as a mixture, with an additional model parameter that accounts for the dissociation ratio of the dissociated ions to nondissociated ions.

Influence of Brownian motion on blood platelet flow behavior and adhesive dynamics near a planar wall.

PubMed

Mody, Nipa A; King, Michael R

2007-05-22

We used the platelet adhesive dynamics computational method to study the influence of Brownian motion of a platelet on its flow characteristics near a surface in the creeping flow regime. Two important characterizations were done in this regard: (1) quantification of the platelet's ability to contact the surface by virtue of the Brownian forces and torques acting on it, and (2) determination of the relative importance of Brownian motion in promoting surface encounters in the presence of shear flow. We determined the Peclet number for a platelet undergoing Brownian motion in shear flow, which could be expressed as a simple linear function of height of the platelet centroid, H from the surface Pe (platelet) = . (1.56H + 0.66) for H > 0.3 microm. Our results demonstrate that at timescales relevant to shear flow in blood Brownian motion plays an insignificant role in influencing platelet motion or creating further opportunities for platelet-surface contact. The platelet Peclet number at shear rates >100 s-1 is large enough (>200) to neglect platelet Brownian motion in computational modeling of flow in arteries and arterioles for most practical purposes even at very close distances from the surface. We also conducted adhesive dynamics simulations to determine the effects of platelet Brownian motion on GPIbalpha-vWF-A1 single-bond dissociation dynamics. Brownian motion was found to have little effect on bond lifetime and caused minimal bond stressing as bond rupture forces were calculated to be less than 0.005 pN. We conclude from our results that, for the case of platelet-shaped cells, Brownian motion is not expected to play an important role in influencing flow characteristics, platelet-surface contact frequency, and dissociative binding phenomena under flow at physiological shear rates (>50 s(-1)).

Peas, please: a case report and neuroscientific review of dissociative amnesia and fugue.

PubMed

MacDonald, Kai; MacDonald, Tina

2009-01-01

Dissociative amnesia that encompasses one's entire life and identity is a rare disorder, as is dissociative fugue. In evaluating such cases, a dichotomy is often invoked between functional and organic etiologies. However, this dichotomy suffers from both conceptual and ethical flaws. Conceptually, putative brain-based, organic etiologies for many dissociative disorders-including dissociative amnesia-exist. Ethically, such dichotomies may result in dismissive care for patients with distress-based disorders like dissociative amnesia. In support of humane, neurobiologically informed treatment of patients with dissociative amnesia, we present excerpts from 2 post-event interviews with a patient who suffered and recovered from an episode of dissociative amnesia and fugue. Following this, we review current neurobiological models of dissociative amnesia that undermine the dichotomy of functional versus organic, and suggest that the crucial distinction in such cases is between a patient's willful, conscious deceit and processes that occur without conscious intent.

A theoretical study of the dissociation of the sI methane hydrate induced by an external electric field

NASA Astrophysics Data System (ADS)

Luis, D. P.; Herrera-Hernández, E. C.; Saint-Martin, H.

2015-11-01

Molecular dynamics simulations in the equilibrium isobaric—isothermal (NPT) ensemble were used to examine the strength of an external electric field required to dissociate the methane hydrate sI structure. The water molecules were modeled using the four-site TIP4P/Ice analytical potential and methane was described as a simple Lennard-Jones interaction site. A series of simulations were performed at T = 260 K with P = 80 bars and at T = 285 K with P = 400 bars with an applied electric field ranging from 1.0 V nm-1 to 5.0 V nm-1. For both (T,P) conditions, applying a field greater than 1.5 V nm-1 resulted in the orientation of the water molecules such that an ice Ih-type structure was formed, from which the methane was segregated. When the simulations were continued without the external field, the ice-like structures became disordered, resulting in two separate phases: gas methane and liquid water.

Theoretical Studies of Dissociative Recombination of Electrons with SH+ Ions

NASA Astrophysics Data System (ADS)

Kashinski, D. O.; di Nallo, O. E.; Hickman, A. P.; Mezei, J. Zs.; Schneider, I. F.; Talbi, D.

2015-05-01

We are investigating the dissociative recombination (DR) of electrons with the molecular ion SH+. (The process is e- +SH+ --> S + H .) SH+ is found in the interstellar medium (ISM), and little is known concerning its interstellar chemistry. The abundance of SH+ in the ISM suggests that destruction processes, like DR, are inefficient. Understanding the role of DR as a destruction pathway for SH+ will lead to more accurate astrophysical models. Large active-space multi-reference configuration interaction (MRCI) electronic structure calculations were performed to obtain excited-state potential energy curves (PECs) for several values of SH separation. Excited Rydberg states have proven to be of importance. The block diagonalization method was used to disentangle interacting states, forming a diabatic representation of the PECs. Currently we are performing Multichannel Quantum Defect Theory (MQDT) dynamics calculations to obtain DR rates. The status of the work will be presented at the conference. Work supported by the French CNRS, the NSF, the XSEDE, and USMA.

A modeling study of methane hydrate decomposition in contact with the external surface of zeolites.

PubMed

Smirnov, Konstantin S

2017-08-30

The behavior of methane hydrate (MH) enclosed between the (010) surfaces of the silicalite-1 zeolite was studied by means of molecular dynamics simulations at temperatures of 150 and 250 K. Calculations reveal that the interaction with the hydrophilic surface OH groups destabilizes the clathrate structure of hydrate. While MH mostly conserves the structure in the simulation at the low temperature, thermal motion at the high temperature breaks the fragilized cages of H-bonded water molecules, thus leading to the release of methane. The dissociation proceeds in a layer-by-layer manner starting from the outer parts of the MH slab until complete hydrate decomposition. The released CH 4 molecules are absorbed by the microporous solid, whereas water is retained at the surfaces of hydrophobic silicalite and forms a meniscus in the interlayer space. Methane uptake reaches 70% of the silicalite sorption capacity. The energy necessary for the endothermic MH dissociation is supplied by the exothermic methane absorption by the zeolite.

Sensitivity of the global submarine hydrate inventory to scenarios of future climate change

NASA Astrophysics Data System (ADS)

Hunter, S. J.; Goldobin, D. S.; Haywood, A. M.; Ridgwell, A.; Rees, J. G.

2013-04-01

The global submarine inventory of methane hydrate is thought to be considerable. The stability of marine hydrates is sensitive to changes in temperature and pressure and once destabilised, hydrates release methane into sediments and ocean and potentially into the atmosphere, creating a positive feedback with climate change. Here we present results from a multi-model study investigating how the methane hydrate inventory dynamically responds to different scenarios of future climate and sea level change. The results indicate that a warming-induced reduction is dominant even when assuming rather extreme rates of sea level rise (up to 20 mm yr-1) under moderate warming scenarios (RCP 4.5). Over the next century modelled hydrate dissociation is focussed in the top ˜100m of Arctic and Subarctic sediments beneath <500m water depth. Predicted dissociation rates are particularly sensitive to the modelled vertical hydrate distribution within sediments. Under the worst case business-as-usual scenario (RCP 8.5), upper estimates of resulting global sea-floor methane fluxes could exceed estimates of natural global fluxes by 2100 (>30-50TgCH4yr-1), although subsequent oxidation in the water column could reduce peak atmospheric release rates to 0.75-1.4 Tg CH4 yr-1.

Fluid modeling of radical species generation mechanism in dense methane-air mixture streamer discharge

NASA Astrophysics Data System (ADS)

Qian, Muyang; Li, Gui; Kang, Jinsong; Liu, Sanqiu; Ren, Chunsheng; Zhang, Jialiang; Wang, Dezhen

2018-01-01

Atmospheric dielectric barrier discharge (DBD) was found to be promising in the context of plasma chemistry, plasma medicine, and plasma-assisted combustion. In this paper, we present a detailed fluid modeling study of abundant radical species produced by a positive streamer in atmospheric dense methane-air DBD. A two-dimensional axisymmetric fluid model is constructed, in which 82 plasma chemical reactions and 30 different species are considered. Spatial and temporal density distributions of dominant radicals and ions are presented. We lay our emphasis on the effect of varying relative permittivity (ɛr = 2, 4.5, and 9) on the streamer dynamics in the plasma column, such as electric field behavior, production, and destruction pathways of dominant radical species. We find that higher relative permittivity promotes propagation of electric field and formation of conduction channel in the plasma column. The streamer discharge is sustained by the direct electron-impact ionization of methane molecule. Furthermore, the electron-impact dissociation of methane (e + CH4 = >e + H+CH3) is found to be the dominant reaction pathway to produce CH3 and H radicals. Similarly, the electron-impact dissociations of oxygen (e + O2 = >e + O+O(1D), e + O2 = >e + O+O) are the major routes for O production.

Can xenon in water inhibit ice growth? Molecular dynamics of phase transitions in water-Xe system.

PubMed

Artyukhov, Vasilii I; Pulver, Alexander Yu; Peregudov, Alex; Artyuhov, Igor

2014-07-21

Motivated by recent experiments showing the promise of noble gases as cryoprotectants, we perform molecular dynamics modeling of phase transitions in water with xenon under cooling. We follow the structure and dynamics of xenon water solution as a function of temperature. Homogeneous nucleation of clathrate hydrate phase is observed and characterized. As the temperature is further reduced we observe hints of dissociation of clathrate due to stronger hydrophobic hydration, pointing towards a possible instability of clathrate at cryogenic temperatures and conversion to an amorphous phase comprised of "xenon + hydration shell" Xe·(H2O)21.5 clusters. Simulations of ice-xenon solution interface in equilibrium and during ice growth reveal the effects of xenon on the ice-liquid interface, where adsorbed xenon causes roughening of ice surface but does not preferentially form clathrate. These results provide evidence against the ice-blocker mechanism of xenon cryoprotection.

Photodissociation dynamics of nitromethane at 226 and 271 nm at both nanosecond and femtosecond time scales.

PubMed

Guo, Y Q; Bhattacharya, A; Bernstein, E R

2009-01-08

Photodissociation of nitromethane has been investigated for decades both theoretically and experimentally; however, as a whole picture, the dissociation dynamics for nitromethane are still not clear, although many different mechanisms have been proposed. To make a complete interpretation of these different mechanisms, photolysis of nitromethane at 226 and 271 nm under both collisional and collisionless conditions is investigated at nanosecond and femtosecond time scales. These two laser wavelengths correspond to the pi* <-- pi and pi* <-- n excitations of nitromethane, respectively. In nanosecond 226 nm (pi* <-- pi) photolysis experiments, CH(3) and NO radicals are observed as major products employing resonance enhanced multiphoton ionization techniques and time-of-flight mass spectrometry. Additionally, OH and CH(3)O radicals are weakly observed as dissociation products employing laser induced fluorescence spectroscopy; the CH(3)O product is only observed under collisional conditions. In femtosecond 226 nm experiments, CH(3), NO(2), and NO products are observed. These results confirm that rupture of C-N bond should be the main primary process for the photolysis of nitromethane after the pi* <-- pi excitation at 226 nm, and the NO(2) molecule should be the precursor of the observed NO product. Formation of the CH(3)O radical after the recombination of CH(3) and NO(2) species under collisional conditions rules out a nitro-nitrite isomerization mechanism for the generation of CH(3)O and NO from pi pi* CH(3)NO(2). The OH radical formation for pi pi* CH(3)NO(2) should be a minor dissociation channel because of the weak OH signal in both nanosecond and femtosecond (nonobservable) experiments. Single color femtosecond pump-probe experiments at 226 nm are also employed to monitor the dynamics of the dissociation of nitromethane after the pi* <-- pi excitation. Because of the ultrafast dynamics of product formation at 226 nm, the pump-probe transients for the three dissociation products are measured as an autocorrelation of the laser pulse, indicating the dissociation of nitromethane in the pi pi* excited state is faster than the laser pulse duration (180 fs). In nanosecond 271 nm (pi* <-- n) photolysis experiments, pump-probe experiments are performed to detect potential dissociation products, such as CH(3), NO(2), CH(3)O, and OH; however, none of them is observed. In femtosecond 271 nm laser experiments, the nitromethane parent ion is observed with major intensity, together with CH(3), NO(2), and NO fragment ions with only minor intensities. Pump-probe transients for both nitromethane parent and fragment ions at 271 nm excitation and 406.5 nm ionization display a fast exponential decay with a constant time of 36 fs, which we suggest to be the lifetime of the excited n pi* state of nitromethane. Combined with the 271 nm nanosecond pump-probe experiments, in which none of the CH(3), NO(2), CH(3)O, or OH fragment is observed, we suggest that all the fragment ions generated in 271 nm femtosecond laser experiments are derived from the parent ion, and dissociation of nitromethane from the n pi* excited electronic state does not occur in a supersonic molecular beam under collisionless conditions.

Direct Dynamics Simulation of Dissociation of the [CH3--I--OH]- Ion-Molecule Complex

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

Xie, Jing; McClellan, Miranda; Sun, Rui

Direct dynamics simulations were used to study dissociation of the [CH3--I--OH]- complex ion, which was observed in a previous study of the OH- + CH3I gas phase reaction (J. Phys. Chem. A 2013, 117, 7162). Restricted B97-1 simulations were performed to study dissociation at 65, 75 and 100 kcal/mol and the [CH3--I--OH]- ion dissociated exponentially, in accord with RRKM theory. For these energies the major dissociation products are CH3I + OH-, CH2I- + H2O, and CH3OH + I-. Unrestricted B97-1 and restricted and unrestricted CAM-B3LYP simulations were also performed at 100 kcal/mol to compare with the restricted B97-1 results. Themore » {CH3I + OH-}:{CH2I- + H2O}:{CH3OH + I-} product ratio is 0.72 : 0.15 : 0.13, 0.81 : 0.05 : 0.14, 0.71 : 0.19 : 0.10 , and 0.83 : 0.13 : 0.04 for the restricted B97-1, unrestricted B97-1, restricted CAM-B3LYP, and unrestricted CAM-B3LYP simulations, respectively. Other product channels found are CH2 + I- + H2O, CH2 + I-(H2O), CH4 + IO-, CH3 - + IOH, and CH3 + IOH-. The CH3 - + IOH singlet products are only given by the restricted B97-1 simulation and the lower energy CH3 + IOH- doublet products are only formed by the unrestricted B97-1 simulation. Also studied were the direct and indirect atomic-level mechanisms for forming CH3I + OH-, CH2I- + H2O, and CH3OH + I-. The majority of CH3I + OH- were formed through a direct mechanism. For both CH2I- + H2O and CH3OH + I-, the direct mechanism is overall more important than the indirect mechanisms, with the round-about like mechanism the most important indirect mechanism at high excitation energies. Mechanism comparisons between the B97-1 and CAM-B3LYP simulations showed that formation of the CH3OH---I- complex is favored for the B97-1 simulations, while formation of the HO----HCH2I complex is favored for the CAM-B3LYP simulations. The unrestricted simulations give a higher percentage of indirect mechanisms than the restricted simulations. The possible role of the self-interaction error in the simulations is also discussed. The work presented here gives a detailed picture of the [CH3--I--OH]- dissociation dynamics, and is very important for unraveling the role of [CH3--I--OH]- in the dynamics of the OH-(H2O)n=1,2 + CH3I reactions.« less

Dissociation and Alterations in Brain Function and Structure: Implications for Borderline Personality Disorder.

PubMed

Krause-Utz, Annegret; Frost, Rachel; Winter, Dorina; Elzinga, Bernet M

2017-01-01

Dissociation involves disruptions of usually integrated functions of consciousness, perception, memory, identity, and affect (e.g., depersonalization, derealization, numbing, amnesia, and analgesia). While the precise neurobiological underpinnings of dissociation remain elusive, neuroimaging studies in disorders, characterized by high dissociation (e.g., depersonalization/derealization disorder (DDD), dissociative identity disorder (DID), dissociative subtype of posttraumatic stress disorder (D-PTSD)), have provided valuable insight into brain alterations possibly underlying dissociation. Neuroimaging studies in borderline personality disorder (BPD), investigating links between altered brain function/structure and dissociation, are still relatively rare. In this article, we provide an overview of neurobiological models of dissociation, primarily based on research in DDD, DID, and D-PTSD. Based on this background, we review recent neuroimaging studies on associations between dissociation and altered brain function and structure in BPD. These studies are discussed in the context of earlier findings regarding methodological differences and limitations and concerning possible implications for future research and the clinical setting.

Dissociation of doubly charged clusters of lithium acetate: Asymmetric fission and breakdown of the liquid drop model: Dissociation of doubly charged clusters of lithium acetate

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

Shukla, Anil

2016-06-08

Unimolecular and collision-induced dissociation of doubly charged lithium acetate clusters, (CH3COOLi)nLi22+, demonstrated that Coulomb fission via charge separation is the dominant dissociation process with no contribution from the neutral evaporation processes for all such ions from the critical limit to larger cluster ions, although latter process have normally been observed in all earlier studies. These results are clearly in disagreement with the Rayleigh’s liquid drop model that has been used successfully to predict the critical size and explain the fragmentation behavior of multiply charged clusters.

Rate equations for nitrogen molecules in ultrashort and intense x-ray pulses

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

Liu, Ji -Cai; Berrah, Nora; Cederbaum, Lorenz S.

Here, we study theoretically the quantum dynamics of nitrogen molecules (N2) exposed to intense and ultrafast x-rays at a wavelength ofmore » $$1.1\\;{\\rm{nm}}$$ ($$1100\\;{\\rm{eV}}$$ photon energy) from the Linac Coherent Light Source (LCLS) free electron laser. Molecular rate equations are derived to describe the intertwined photoionization, decay, and dissociation processes occurring for N2. This model complements our earlier phenomenological approaches, the single-atom, symmetric-sharing, and fragmentation-matrix models of 2012 (J. Chem. Phys. 136 214310). Our rate-equations are used to obtain the effective pulse energy at the sample and the time scale for the dissociation of the metastable dication $${{\\rm{N}}}_{2}^{2+}$$. This leads to a very good agreement between the theoretically and experimentally determined ion yields and, consequently, the average charge states. The effective pulse energy is found to decrease with shortening pulse duration. This variation together with a change in the molecular fragmentation pattern and frustrated absorption—an effect that reduces absorption of x-rays due to (double) core hole formation—are the causes for the drop of the average charge state with shortening LCLS pulse duration discovered previously.« less

Rate equations for nitrogen molecules in ultrashort and intense x-ray pulses

DOE PAGES

Liu, Ji -Cai; Berrah, Nora; Cederbaum, Lorenz S.; ...

2016-03-16

Here, we study theoretically the quantum dynamics of nitrogen molecules (N2) exposed to intense and ultrafast x-rays at a wavelength ofmore » $$1.1\\;{\\rm{nm}}$$ ($$1100\\;{\\rm{eV}}$$ photon energy) from the Linac Coherent Light Source (LCLS) free electron laser. Molecular rate equations are derived to describe the intertwined photoionization, decay, and dissociation processes occurring for N2. This model complements our earlier phenomenological approaches, the single-atom, symmetric-sharing, and fragmentation-matrix models of 2012 (J. Chem. Phys. 136 214310). Our rate-equations are used to obtain the effective pulse energy at the sample and the time scale for the dissociation of the metastable dication $${{\\rm{N}}}_{2}^{2+}$$. This leads to a very good agreement between the theoretically and experimentally determined ion yields and, consequently, the average charge states. The effective pulse energy is found to decrease with shortening pulse duration. This variation together with a change in the molecular fragmentation pattern and frustrated absorption—an effect that reduces absorption of x-rays due to (double) core hole formation—are the causes for the drop of the average charge state with shortening LCLS pulse duration discovered previously.« less

Analysis of Memory Formation during General Anesthesia (Propofol/Remifentanil) for Elective Surgery Using the Process-dissociation Procedure.

PubMed

Hadzidiakos, Daniel; Horn, Nadja; Degener, Roland; Buchner, Axel; Rehberg, Benno

2009-08-01

There have been reports of memory formation during general anesthesia. The process-dissociation procedure has been used to determine if these are controlled (explicit/conscious) or automatic (implicit/unconscious) memories. This study used the process-dissociation procedure with the original measurement model and one which corrected for guessing to determine if more accurate results were obtained in this setting. A total of 160 patients scheduled for elective surgery were enrolled. Memory for words presented during propofol and remifentanil general anesthesia was tested postoperatively by using a word-stem completion task in a process-dissociation procedure. To assign possible memory effects to different levels of anesthetic depth, the authors measured depth of anesthesia using the BIS XP monitor (Aspect Medical Systems, Norwood, MA). Word-stem completion performance showed no evidence of memory for intraoperatively presented words. Nevertheless, an evaluation of these data using the original measurement model for process-dissociation data suggested an evidence of controlled (C = 0.05; 95% confidence interval [CI] 0.02-0.08) and automatic (A = 0.11; 95% CI 0.09-0.12) memory processes (P < 0.01). However, when the data were evaluated with an extended measurement model taking base rates into account adequately, no evidence for controlled (C = 0.00; 95% CI -0.04 to 0.04) or automatic (A = 0.00; 95% CI -0.02 to 0.02) memory processes was obtained. The authors report and discuss parallel findings for published data sets that were generated by using the process-dissociation procedure. Patients had no memories for auditory information presented during propofol/remifentanil anesthesia after midazolam premedication. The use of the process-dissociation procedure with the original measurement model erroneously detected memories, whereas the extended model, corrected for guessing, correctly revealed no memory.

The Association among Childhood Trauma, Pathological Dissociation and Gambling Severity in Casino Gamblers.

PubMed

Imperatori, Claudio; Innamorati, Marco; Bersani, Francesco Saverio; Imbimbo, Francesca; Pompili, Maurizio; Contardi, Anna; Farina, Benedetto

2017-01-01

The aim of the present study was to explore the role of pathological dissociation in mediating the association between childhood trauma (CT) and gambling severity. One hundred seventy-one (134 men and 37 women) gamblers recruited in gambling environments (i.e., two Italian casinos) have been enrolled in the study. Psychopathological assessments included the Childhood Trauma Questionnaire (CTQ), the Dissociative Experiences Scale-Taxon (DES-T), the South Oaks Gambling Screen (SOGS), the CAGE and the Hospital Anxiety and Depression Scale. A mediational model, analyzing the direct and indirect effects of CTQ on SOGS through the mediating role of DES-T, showed that the relation between CTQ and SOGS was fully mediated by DES-T scores (b = 0.07; se = 0.15; p < 0.001). This finding raises the possibility that CT explains gambling severity through the presence of pathological dissociative symptoms and dissociative pathogenetic processes. Copyright © 2015 John Wiley & Sons, Ltd. Gambling severity is associated with both childhood trauma and pathological dissociation in casino gamblers. A mediational model shows that the effect of childhood trauma on gambling severity is entirely mediated by pathological dissociation. From a clinical point of view, our results highlight the importance of assessing, and possibly treating, dissociative symptoms in individuals with gambling disorder. Copyright © 2015 John Wiley & Sons, Ltd.

Formaldehyde roaming dynamics: Comparison of quasi-classical trajectory calculations and experiments.

PubMed

Houston, Paul L; Wang, Xiaohong; Ghosh, Aryya; Bowman, Joel M; Quinn, Mitchell S; Kable, Scott H

2017-07-07

The photodissociation dynamics of roaming in formaldehyde are studied by comparing quasi-classical trajectory calculations performed on a new potential energy surface (PES) to new and detailed experimental results detailing the CO + H 2 product state distributions and their correlations. The new PES proves to be a significant improvement over the past one, now more than a decade old. The new experiments probe both the CO and H 2 products of the formaldehyde dissociation. The experimental and trajectory data offer unprecedented detail about the correlations between internal states of the CO and H 2 dissociation products as well as information on how these distributions are different for the roaming and transition-state pathways. The data investigated include, for dissociation on the formaldehyde 2 1 4 3 band, (a) the speed distributions for individual vibrational/rotational states of the CO products, providing information about the correlated internal energy distributions of the H 2 product, and (b) the rotational and vibrational distributions for the CO and H 2 products as well as the contributions to each from both the transition state and roaming channels. The agreement between the trajectory and experimental data is quite satisfactory, although minor differences are noted. The general agreement provides support for future use of the experimental techniques and the new PES in understanding the dynamics of photodissociative processes.

Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association-diffusion models

NASA Astrophysics Data System (ADS)

Deshpande, Sneha A.; Pawar, Aiswarya B.; Dighe, Anish; Athale, Chaitanya A.; Sengupta, Durba

2017-06-01

G protein-coupled receptor (GPCR) association is an emerging paradigm with far reaching implications in the regulation of signalling pathways and therapeutic interventions. Recent super resolution microscopy studies have revealed that receptor dimer steady state exhibits sub-second dynamics. In particular the GPCRs, muscarinic acetylcholine receptor M1 (M1MR) and formyl peptide receptor (FPR), have been demonstrated to exhibit a fast association/dissociation kinetics, independent of ligand binding. In this work, we have developed a spatial kinetic Monte Carlo model to investigate receptor homo-dimerisation at a single receptor resolution. Experimentally measured association/dissociation kinetic parameters and diffusion coefficients were used as inputs to the model. To test the effect of membrane spatial heterogeneity on the simulated steady state, simulations were compared to experimental statistics of dimerisation. In the simplest case the receptors are assumed to be diffusing in a spatially homogeneous environment, while spatial heterogeneity is modelled to result from crowding, membrane micro-domains and cytoskeletal compartmentalisation or ‘corrals’. We show that a simple association-diffusion model is sufficient to reproduce M1MR association statistics, but fails to reproduce FPR statistics despite comparable kinetic constants. A parameter sensitivity analysis is required to reproduce the association statistics of FPR. The model reveals the complex interplay between cytoskeletal components and their influence on receptor association kinetics within the features of the membrane landscape. These results constitute an important step towards understanding the factors modulating GPCR organisation.

Global functioning and disability in dissociative disorders.

PubMed

Mueller-Pfeiffer, Christoph; Rufibach, Kaspar; Perron, Noelle; Wyss, Daniela; Kuenzler, Cornelia; Prezewowsky, Cornelia; Pitman, Roger K; Rufer, Michael

2012-12-30

Dissociative disorders are frequent comorbid conditions of other mental disorders. Yet, there is controversy about their clinical relevance, and little systematic research has been done on how they influence global functioning. Outpatients and day care patients (N=160) of several psychiatric units in Switzerland were assessed with the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV Axis I Disorders, Structured Clinical Interview for DSM-IV Dissociative Disorders, Global Assessment of Functioning Scale, and World Health Organization Disability Assessment Schedule-II. The association between subjects with a dissociative disorder (N=30) and functional impairment after accounting for non-dissociative axis I disorders was evaluated by linear regression models. We found a proportion of 18.8% dissociative disorders (dissociative amnesia=0%, dissociative fugue=0.6%, depersonalization disorder=4.4%, dissociative identity disorder=7.5%, dissociative disorder-not-otherwise-specified=6.3%) across treatment settings. Adjusted for other axis I disorders, subjects with a comorbid dissociative identity disorder or dissociative disorder-not-otherwise-specified had a median global assessment of functioning score that was 0.86 and 0.88 times, respectively, the score of subjects without a comorbid dissociative disorder. These findings support the hypothesis that complex dissociative disorders, i.e., dissociative identity disorder and dissociative disorder-not-otherwise-specified, contribute to functional impairment above and beyond the impact of co-existing non-dissociative axis I disorders, and that they qualify as "serious mental illness". Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Dynamics of Nanoparticle-Protein Corona Complex Formation: Analytical Results from Population Balance Equations

PubMed Central

Darabi Sahneh, Faryad; Scoglio, Caterina; Riviere, Jim

2013-01-01

Background Nanoparticle-protein corona complex formation involves absorption of protein molecules onto nanoparticle surfaces in a physiological environment. Understanding the corona formation process is crucial in predicting nanoparticle behavior in biological systems, including applications of nanotoxicology and development of nano drug delivery platforms. Method This paper extends the modeling work in to derive a mathematical model describing the dynamics of nanoparticle corona complex formation from population balance equations. We apply nonlinear dynamics techniques to derive analytical results for the composition of nanoparticle-protein corona complex, and validate our results through numerical simulations. Results The model presented in this paper exhibits two phases of corona complex dynamics. In the first phase, proteins rapidly bind to the free surface of nanoparticles, leading to a metastable composition. During the second phase, continuous association and dissociation of protein molecules with nanoparticles slowly changes the composition of the corona complex. Given sufficient time, composition of the corona complex reaches an equilibrium state of stable composition. We find analytical approximate formulae for metastable and stable compositions of corona complex. Our formulae are very well-structured to clearly identify important parameters determining corona composition. Conclusion The dynamics of biocorona formation constitute vital aspect of interactions between nanoparticles and living organisms. Our results further understanding of these dynamics through quantitation of experimental conditions, modeling results for in vitro systems to better predict behavior for in vivo systems. One potential application would involve a single cell culture medium related to a complex protein medium, such as blood or tissue fluid. PMID:23741371

Ab initio-informed maximum entropy modeling of rovibrational relaxation and state-specific dissociation with application to the O2 + O system

NASA Astrophysics Data System (ADS)

Kulakhmetov, Marat; Gallis, Michael; Alexeenko, Alina

2016-05-01

Quasi-classical trajectory (QCT) calculations are used to study state-specific ro-vibrational energy exchange and dissociation in the O2 + O system. Atom-diatom collisions with energy between 0.1 and 20 eV are calculated with a double many body expansion potential energy surface by Varandas and Pais [Mol. Phys. 65, 843 (1988)]. Inelastic collisions favor mono-quantum vibrational transitions at translational energies above 1.3 eV although multi-quantum transitions are also important. Post-collision vibrational favoring decreases first exponentially and then linearly as Δv increases. Vibrationally elastic collisions (Δv = 0) favor small ΔJ transitions while vibrationally inelastic collisions have equilibrium post-collision rotational distributions. Dissociation exhibits both vibrational and rotational favoring. New vibrational-translational (VT), vibrational-rotational-translational (VRT) energy exchange, and dissociation models are developed based on QCT observations and maximum entropy considerations. Full set of parameters for state-to-state modeling of oxygen is presented. The VT energy exchange model describes 22 000 state-to-state vibrational cross sections using 11 parameters and reproduces vibrational relaxation rates within 30% in the 2500-20 000 K temperature range. The VRT model captures 80 × 106 state-to-state ro-vibrational cross sections using 19 parameters and reproduces vibrational relaxation rates within 60% in the 5000-15 000 K temperature range. The developed dissociation model reproduces state-specific and equilibrium dissociation rates within 25% using just 48 parameters. The maximum entropy framework makes it feasible to upscale ab initio simulation to full nonequilibrium flow calculations.

The Shutdown Dissociation Scale (Shut-D)

PubMed Central

Schalinski, Inga; Schauer, Maggie; Elbert, Thomas

2015-01-01

The evolutionary model of the defense cascade by Schauer and Elbert (2010) provides a theoretical frame for a short interview to assess problems underlying and leading to the dissociative subtype of posttraumatic stress disorder. Based on known characteristics of the defense stages “fright,” “flag,” and “faint,” we designed a structured interview to assess the vulnerability for the respective types of dissociation. Most of the scales that assess dissociative phenomena are designed as self-report questionnaires. Their items are usually selected based on more heuristic considerations rather than a theoretical model and thus include anything from minor dissociative experiences to major pathological dissociation. The shutdown dissociation scale (Shut-D) was applied in several studies in patients with a history of multiple traumatic events and different disorders that have been shown previously to be prone to symptoms of dissociation. The goal of the present investigation was to obtain psychometric characteristics of the Shut-D (including factor structure, internal consistency, retest reliability, predictive, convergent and criterion-related concurrent validity). A total population of 225 patients and 68 healthy controls were accessed. Shut-D appears to have sufficient internal reliability, excellent retest reliability, high convergent validity, and satisfactory predictive validity, while the summed score of the scale reliably separates patients with exposure to trauma (in different diagnostic groups) from healthy controls. The Shut-D is a brief structured interview for assessing the vulnerability to dissociate as a consequence of exposure to traumatic stressors. The scale demonstrates high-quality psychometric properties and may be useful for researchers and clinicians in assessing shutdown dissociation as well as in predicting the risk of dissociative responding. PMID:25976478

Imaging a multidimensional multichannel potential energy surface: Photodetachment of H(-)(NH3) and NH4 (.).

PubMed

Hu, Qichi; Song, Hongwei; Johnson, Christopher J; Li, Jun; Guo, Hua; Continetti, Robert E

2016-06-28

Probes of the Born-Oppenheimer potential energy surfaces governing polyatomic molecules often rely on spectroscopy for the bound regions or collision experiments in the continuum. A combined spectroscopic and half-collision approach to image nuclear dynamics in a multidimensional and multichannel system is reported here. The Rydberg radical NH4 and the double Rydberg anion NH4 (-) represent a polyatomic system for benchmarking electronic structure and nine-dimensional quantum dynamics calculations. Photodetachment of the H(-)(NH3) ion-dipole complex and the NH4 (-) DRA probes different regions on the neutral NH4 PES. Photoelectron energy and angular distributions at photon energies of 1.17, 1.60, and 2.33 eV compare well with quantum dynamics. Photoelectron-photofragment coincidence experiments indicate dissociation of the nascent NH4 Rydberg radical occurs to H + NH3 with a peak kinetic energy of 0.13 eV, showing the ground state of NH4 to be unstable, decaying by tunneling-induced dissociation on a time scale beyond the present scope of multidimensional quantum dynamics.

Regulating energy transfer of excited carriers and the case for excitation-induced hydrogen dissociation on hydrogenated graphene

PubMed Central

Bang, Junhyeok; Meng, Sheng; Sun, Yi-Yang; West, Damien; Wang, Zhiguo; Gao, Fei; Zhang, S. B.

2013-01-01

Understanding and controlling of excited carrier dynamics is of fundamental and practical importance, particularly in photochemistry and solar energy applications. However, theory of energy relaxation of excited carriers is still in its early stage. Here, using ab initio molecular dynamics (MD) coupled with time-dependent density functional theory, we show a coverage-dependent energy transfer of photoexcited carriers in hydrogenated graphene, giving rise to distinctively different ion dynamics. Graphene with sparsely populated H is difficult to dissociate due to inefficient transfer of the excitation energy into kinetic energy of the H. In contrast, H can easily desorb from fully hydrogenated graphane. The key is to bring down the H antibonding state to the conduction band minimum as the band gap increases. These results can be contrasted to those of standard ground-state MD that predict H in the sparse case should be much less stable than that in fully hydrogenated graphane. Our findings thus signify the importance of carrying out explicit electronic dynamics in excited-state simulations. PMID:23277576

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

Fang, Li; Xiong, Hui; Kukk, Edwin

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. Here, we present our investigation of photoionization and nuclear dynamics in methyl iodine (CH 3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and delay apparatus. Time-of-flight mass spectra at various pump–probe delay times were recorded to obtain the time profile for the creation of high charge states via sequential ionization and for molecular dissociation. We observed high charge states of atomic iodine up tomore » 29+, and visualized the evolution of creating these high atomic ion charge states, including their population suppression and enhancement as the arrival time of the second X-ray pulse was varied. We also show the evolution of the kinetics of the high charge states upon the timing of their creation during the ionization-dissociation coupled dynamics. We demonstrate the implementation of X-ray pump–probe methodology for investigating X-ray induced molecular dynamics with femtosecond temporal resolution. The results indicate the footprints of ionization that lead to high charge states, probing the long-range potential curves of the high charge states.« less

Quantitative analysis of protein-ligand interactions by NMR.

PubMed

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Parvalbumin, Sarcoplasmatic Reticulum Calcium Pump Rate, Rates of Cross-Bridge Dynamics, and Ryanodine Receptor Calcium Current on Peripheral Muscle Fatigue: A Simulation Study

PubMed Central

Neumann, Verena

2016-01-01

A biophysical model of the excitation-contraction pathway, which has previously been validated for slow-twitch and fast-twitch skeletal muscles, is employed to investigate key biophysical processes leading to peripheral muscle fatigue. Special emphasis hereby is on investigating how the model's original parameter sets can be interpolated such that realistic behaviour with respect to contraction time and fatigue progression can be obtained for a continuous distribution of the model's parameters across the muscle units, as found for the functional properties of muscles. The parameters are divided into 5 groups describing (i) the sarcoplasmatic reticulum calcium pump rate, (ii) the cross-bridge dynamics rates, (iii) the ryanodine receptor calcium current, (iv) the rates of binding of magnesium and calcium ions to parvalbumin and corresponding dissociations, and (v) the remaining processes. The simulations reveal that the first two parameter groups are sensitive to contraction time but not fatigue, the third parameter group affects both considered properties, and the fourth parameter group is only sensitive to fatigue progression. Hence, within the scope of the underlying model, further experimental studies should investigate parvalbumin dynamics and the ryanodine receptor calcium current to enhance the understanding of peripheral muscle fatigue. PMID:27980606

Shame, Dissociation, and Complex PTSD Symptoms in Traumatized Psychiatric and Control Groups: Direct and Indirect Associations With Relationship Distress.

PubMed

Dorahy, Martin J; Corry, Mary; Black, Rebecca; Matheson, Laura; Coles, Holly; Curran, David; Seager, Lenaire; Middleton, Warwick; Dyer, Kevin F W

2017-04-01

Elevated shame and dissociation are common in dissociative identity disorder (DID) and chronic posttraumatic stress disorder (PTSD) and are part of the constellation of symptoms defined as complex PTSD. Previous work examined the relationship between shame, dissociation, and complex PTSD and whether they are associated with intimate relationship anxiety, relationship depression, and fear of relationships. This study investigated these variables in traumatized clinical samples and a nonclinical community group. Participants were drawn from the DID (n = 20), conflict-related chronic PTSD (n = 65), and nonclinical (n = 125) populations and completed questionnaires assessing the variables of interest. A model examining the direct impact of shame and dissociation on relationship functioning, and their indirect effect via complex PTSD symptoms, was tested through path analysis. The DID sample reported significantly higher dissociation, shame, complex PTSD symptom severity, relationship anxiety, relationship depression, and fear of relationships than the other two samples. Support was found for the proposed model, with shame directly affecting relationship anxiety and fear of relationships, and pathological dissociation directly affecting relationship anxiety and relationship depression. The indirect effect of shame and dissociation via complex PTSD symptom severity was evident on all relationship variables. Shame and pathological dissociation are important for not only the effect they have on the development of other complex PTSD symptoms, but also their direct and indirect effects on distress associated with relationships. © 2016 Wiley Periodicals, Inc.

Absolute total and partial dissociative cross sections of pyrimidine at electron and proton intermediate impact velocities

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

Wolff, Wania, E-mail: wania@if.ufrj.br; Luna, Hugo; Sigaud, Lucas

Absolute total non-dissociative and partial dissociative cross sections of pyrimidine were measured for electron impact energies ranging from 70 to 400 eV and for proton impact energies from 125 up to 2500 keV. MOs ionization induced by coulomb interaction were studied by measuring both ionization and partial dissociative cross sections through time of flight mass spectrometry and by obtaining the branching ratios for fragment formation via a model calculation based on the Born approximation. The partial yields and the absolute cross sections measured as a function of the energy combined with the model calculation proved to be a useful toolmore » to determine the vacancy population of the valence MOs from which several sets of fragment ions are produced. It was also a key point to distinguish the dissociation regimes induced by both particles. A comparison with previous experimental results is also presented.« less

Calculation of rates of exciton dissociation into hot charge-transfer states in model organic photovoltaic interfaces

NASA Astrophysics Data System (ADS)

Vázquez, Héctor; Troisi, Alessandro

2013-11-01

We investigate the process of exciton dissociation in ordered and disordered model donor/acceptor systems and describe a method to calculate exciton dissociation rates. We consider a one-dimensional system with Frenkel states in the donor material and states where charge transfer has taken place between donor and acceptor. We introduce a Green's function approach to calculate the generation rates of charge-transfer states. For disorder in the Frenkel states we find a clear exponential dependence of charge dissociation rates with exciton-interface distance, with a distance decay constant β that increases linearly with the amount of disorder. Disorder in the parameters that describe (final) charge-transfer states has little effect on the rates. Exciton dissociation invariably leads to partially separated charges. In all cases final states are “hot” charge-transfer states, with electron and hole located far from the interface.

Quantum vs Classical Mechanics for a 'Simple' Dissociation Reaction. Should They Give the Same Results?

NASA Astrophysics Data System (ADS)

Holloway, Stephen

1997-03-01

When performing molecular dynamical simulations on light systems at low energies, there is always the risk of producing data that bear no similarity to experiment. Indeed, John Barker himself was particularly anxious about treating Ar scattering from surfaces using classical mechanics where it had been shown experimentally in his own lab that diffraction occurs. In such cases, the correct procedure is probably to play the trump card "... well of course, quantum effects will modify this so that....." and retire gracefully. For our particular interests, the tables are turned in that we are interested in gas-surface dynamical studies for highly quantized systems, but would be interested to know when it is possible to use classical mechanics in order that a greater dimensionality might be treated. For molecular dissociation and scattering, it has been oft quoted that the greater the number of degrees of freedom, the more appropriate is classical mechanics, primarily because of the mass averaging over the quantized dimensions. Is this true? We have been investigating the dissociation of hydrogen molecules at surfaces and in this talk I will present quantum results for dissociation and scattering, along with a novel method for their interpretation based upon adiabatic potential energy surfaces. Comparison with classical calculations will be made and conclusions drawn. a novel method for their interpretation based upon adiabatic potential energy surfaces

Vibrational wave packet dynamics in NaK: The A 1Σ+ state

NASA Astrophysics Data System (ADS)

Andersson, L. Mauritz; Karlsson, Hans O.; Goscinski, Osvaldo; Berg, Lars-Erik; Beutter, Matthias; Hansson, Tony

1999-02-01

A combined experimental and theoretical study of the vibrational wave packet dynamics for the NaK molecule in the A 1Σ+ state is presented. The experiment utilises a 790 nm one-colour femtosecond pump-probe scheme with detection of a previously not reported dissociation pathway of the 3 1Π+ state, leading to the Na(3p)+K(4s) product channel. The dissociation is suggested to proceed via either collisionally mediated processes or a molecular cascading process via the 4 1Σ+ state, which crosses several states correlating to the Na(3p)+K(4s) limit. Time-dependent quantum mechanical calculations are used for studying the dynamics in detail. Simulations are performed both for 790 nm and for 766 nm, to relate also to earlier studies. The previous interpretations of the probe processes are revised. Inclusion of vibrational and rotational temperature effects are shown to be crucial for explaining the shape of the signal and the vibrational period, and leads to excellent agreement with the experiments.

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

An ab initio molecular dynamics study of S0 ketene fragmentation

NASA Astrophysics Data System (ADS)

Forsythe, Kelsey M.; Gray, Stephen K.; Klippenstein, Stephen J.; Hall, Gregory E.

2001-08-01

The dynamical origins of product state distributions in the unimolecular dissociation of S0 ketene, CH2CO (X˜ 1A1)→CH2(ã1A1)+CO, are studied with ab initio molecular dynamics. We focus on rotational distributions associated with ground vibrational state fragments. Trajectories are integrated between an inner, variational transition state (TS) and separated fragments in both the dissociative and associative directions. The average rotational energy in both CO and CH2 fragments decreases during the motion from the TS to separated fragments. However, the CO distribution remains slightly hotter than phase space theory (PST) predictions, whereas that for CH2 ends up significantly colder than PST, in good agreement with experiment. Our calculations do not, however, reproduce the experimentally observed correlations between CH2 and CO rotational states, in which the simultaneous formation of low rotational levels of each fragment is suppressed relative to PST. A limited search for nonstatistical behavior in the strong interaction region also fails to explain this discrepancy.

Molecular modeling of the dissociation of methane hydrate in contact with a silica surface.

PubMed

Bagherzadeh, S Alireza; Englezos, Peter; Alavi, Saman; Ripmeester, John A

2012-03-15

We use constant energy, constant volume (NVE) molecular dynamics simulations to study the dissociation of the fully occupied structure I methane hydrate in a confined geometry between two hydroxylated silica surfaces between 36 and 41 Å apart, at initial temperatures of 283, 293, and 303 K. Simulations of the two-phase hydrate/water system are performed in the presence of silica, with and without a 3 Å thick buffering water layer between the hydrate phase and silica surfaces. Faster decomposition is observed in the presence of silica, where the hydrate phase is prone to decomposition from four surfaces, as compared to only two sides in the case of the hydrate/water simulations. The existence of the water layer between the hydrate phase and the silica surface stabilizes the hydrate phase relative to the case where the hydrate is in direct contact with silica. Hydrates bound between the silica surfaces dissociate layer-by-layer in a shrinking core manner with a curved decomposition front which extends over a 5-8 Å thickness. Labeling water molecules shows that there is exchange of water molecules between the surrounding liquid and intact cages in the methane hydrate phase. In all cases, decomposition of the methane hydrate phase led to the formation of methane nanobubbles in the liquid water phase. © 2012 American Chemical Society

Process Dissociation and Mixture Signal Detection Theory

ERIC Educational Resources Information Center

DeCarlo, Lawrence T.

2008-01-01

The process dissociation procedure was developed in an attempt to separate different processes involved in memory tasks. The procedure naturally lends itself to a formulation within a class of mixture signal detection models. The dual process model is shown to be a special case. The mixture signal detection model is applied to data from a widely…

High Throughput pharmacokinetic modeling using computationally predicted parameter values: dissociation constants (TDS)

EPA Science Inventory

Estimates of the ionization association and dissociation constant (pKa) are vital to modeling the pharmacokinetic behavior of chemicals in vivo. Methodologies for the prediction of compound sequestration in specific tissues using partition coefficients require a parameter that ch...

Binding interaction of SGLT with sugar and thiosugar by the molecular dynamics simulation.

PubMed

Tamura, Yunoshin; Miyagawa, Hiroh; Yoshida, Tatsusada; Chuman, Hiroshi

2015-11-01

The human sodium-glucose co-transporter 2 (hSGLT2) is a transporter responsible for reabsorption of glucose in the proximal convoluted tubule of the kidney. hSGLT2 inhibitors, including luseogliflozin, have been developed as drugs for type 2 diabetes mellitus. Only luseogliflozin contains a thiosugar ring in its chemical structure, while other hSGLT2 inhibitors contain glucose rings. Consequently, we focused on the binding interactions of hSGLT2 with sugars and thiosugars. We first revealed that the binding affinities of thiosugars are stronger than those of sugars through molecular dynamics simulations of Vibrio parahaemolyticus, sodium-galactose co-transporter, and human hSGLT2. We then demonstrated that Na(+) dissociates from the protein to the cytoplasmic solution more slowly in the thiosugar system than in the sugar system. These differences between sugars and thiosugars are discussed on the basis of the different binding modes due to the atom at the 5-position of the sugar and thiosugar rings. Finally, as a result of Na(+) dissociation, we suggest that the dissociation of thiosugars is slower than that of sugars. Copyright © 2015 Elsevier B.V. All rights reserved.

Furfural reduction mechanism of a zinc-dependent alcohol dehydrogenase from Cupriavidus necator JMP134

PubMed Central

Kang, ChulHee; Hayes, Robert; Sanchez, Emiliano J.; Webb, Brian N.; Li, Qunrui; Hooper, Travis; Nissen, Mark S.; Xun, Luying

2012-01-01

Summary FurX is a tetrameric Zn-dependent alcohol dehydrogenase (ADH) from Cupriavidus necator JMP134. The enzyme rapidly reduces furfural with NADH as the reducing power. For the first time among characterized ADHs, the high-resolution structures of all reaction steps were obtained in a time-resolved manner, thereby illustrating the complete catalytic events of NADH-dependent reduction of furfural and the dynamic Zn2+ coordination among Glu66, water, substrate and product. In the fully closed conformation of the NADH complex, the catalytic turnover proved faster than observed for the partially closed conformation due to an effective proton transfer network. The domain motion triggered by NAD(H) association/dissociation appeared to facilitate dynamic interchanges in Zn2+ coordination with substrate and product molecules, ultimately increasing the enzymatic turnover rate. NAD+ dissociation appeared to be a slow process, involving multiple steps in concert with a domain opening and reconfiguration of Glu66. This agrees with the report that the cofactor is not dissociated from FurX during ethanol-dependent reduction of furfural, in which ethanol reduces NAD+ to NADH that is subsequently used for furfural reduction. PMID:22081946

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

Sturm, F. P.; Tong, X. M.; Palacios, A.

Here, we used ultrashort femtosecond vacuum ultraviolet (VUV) and infrared (IR) pulses in a pump-probe scheme to map the dynamics and nonequilibrium dissociation channels of excited neutral H 2 molecules. A nuclear wave packet is created in the B 1Σmore » $$+\\atop{u}$$ state of the neutral H 2 molecule by absorption of the ninth harmonic of the driving infrared laser field. Due to the large stretching amplitude of the molecule excited in the B 1Σ$$+\\atop{u}$$ electronic state, the effective H 2 + ionization potential changes significantly as the nuclear wave packet vibrates in the bound, highly electronically and vibrationally excited B potential-energy curve. We probed such dynamics by ionizing the excited neutral molecule using time-delayed VUV-or-IR radiation. We identified the nonequilibrium dissociation channels by utilizing three-dimensional momentum imaging of the ion fragments. We also found that different dissociation channels can be controlled, to some extent, by changing the IR laser intensity and by choosing the wavelength of the probe laser light. Furthermore, we concluded that even in a benchmark molecular system such as H 2*, the interpretation of the nonequilibrium multiphoton and multicolor ionization processes is still a challenging task, requiring intricate theoretical analysis.« less

Trauma-related dissociative (conversion) disorders in children and adolescents--an overview of assessment tools and treatment principles.

PubMed

Diseth, Trond H; Christie, Helen J

2005-01-01

A high proportion of patients in child and adolescent psychiatry with significant dissociative symptomatology after early childhood traumatization may go undiagnosed, be wrongly diagnosed and/or inappropriately treated. The diagnostics and treatment of dissociative disorders have been limited by lack of comprehensive, reliable and valid instruments and the ongoing polarization and fierce controversy regarding treatment. However, recent neurobiological findings of neurochemical, functional and structural cerebral consequences of early stressful childhood experiences point out a need for active, early and effective identification and treatment interventions. We present an update on assessment tools available in the Nordic countries, and an overview of different appropriate therapeutic intervention models for children and adolescents. A systematic overview of studies of dissociation in children and adolescent published over the last decade disclosed a total of 1019 references. The 465 papers describing aspects of assessment tools and/or treatment were studied in detail. Reliable and valid screening questionnaires and diagnostic interviews for children and adolescents now allow for effective early identification of dissociative disorders. A combination of individual psychotherapy, pharmacotherapy and family therapy are often required to handle dissociative disorders in children and adolescents. Cognitive-behavioural therapy, hypnotherapy, Eye-Movement Desensitization-Reprocessing (EMDR), psychodynamic therapy and an integrated approach are the main described psychotherapeutic approaches, but treatment of dissociation in children and adolescent does not require allegiance to any one particular treatment model. However, achievement of physical safety by providing a safe environment is a primary goal that supersedes any other therapeutic work. Assessments tools are now available, and appropriate therapeutic intervention models may hopefully contribute to reduce the risk of wrong diagnoses and inappropriate treatment of dissociative symptomatology in children and adolescents. However, controlled clinical trials of the various interventions and longitudinal outcome studies are needed.

Déjà vu experiences are rarely associated with pathological dissociation.

PubMed

Adachi, Naoto; Akanuma, Nozomi; Akanu, Nozomi; Adachi, Takuya; Takekawa, Yoshikazu; Adachi, Yasushi; Ito, Masumi; Ikeda, Hiroshi

2008-05-01

We investigated the relation between déjà vu and dissociative experiences in nonclinical subjects. In 227 adult volunteers, déjà vu and dissociative experiences were evaluated by means of the inventory of déjà vu experiences assessment and dissociative experiences scale (DES). Déjà vu experiences occurred in 162 (71.4%) individuals. In univariate correlation analysis, the frequency of déjà vu experiences, as well as 5 other inventory of déjà vu experiences assessment symptoms and age at the time of evaluation, correlated significantly with the DES score. After exclusion of intercorrelative effects using multiple regression analysis, déjà vu experiences did not remain in the model. The DES score was best correlated with a model that included age, jamais vu, depersonalization, and precognitive dreams. Two indices for pathological dissociation (DES-taxon and DES > or = 30) were not associated with déjà vu experiences. Our findings suggest that déjà vu experiences are unlikely to be core pathological dissociative experiences.

Toward understanding the dissociation of I2 in chemical oxygen-iodine lasers: Combined experimental and theoretical studies

NASA Astrophysics Data System (ADS)

Waichman, K.; Rybalkin, V.; Katz, A.; Dahan, Z.; Barmashenko, B. D.; Rosenwaks, S.

2007-07-01

The dissociation of I2 molecules at the optical axis of a supersonic chemical oxygen-iodine laser (COIL) was studied via detailed measurements and three-dimensional computational fluid dynamics calculations. The measurements, briefly reported in a recent paper [Rybalkin et al., Appl. Phys. Lett. 89, 021115 (2006)] and reanalyzed in detail here, revealed that the number N of consumed O2(aΔg1) molecules per dissociated I2 molecule depends on the experimental conditions: it is 4.5±0.4 for typical conditions and I2 densities applied for optimal operation of the COIL but increases at lower I2 densities. Comparing the measurements and the calculations enabled critical examination of previously proposed dissociation mechanisms and suggestion of a mechanism consistent with the experimental and theoretical results obtained in a supersonic COIL for the gain, temperature, I2 dissociation fraction, and N at the optical axis. The suggested mechanism combines the recent scheme of Azyazov and Heaven [AIAA J. 44, 1593 (2006)], where I2(A'Π2u3), I2(AΠ1u3), and O2(aΔg1,v) are significant dissociation intermediates, with the "standard" chain branching mechanism of Heidner III et al. [J. Phys. Chem. 87, 2348 (1983)], involving I(P1/22) and I2(XΣg +1,v).

Blackbody Infrared Radiative Dissociation of Bradykinin and Its Analogues: Energetics, Dynamics, and Evidence for Salt-Bridge Structures in the Gas Phase

PubMed Central

Schnier, Paul D.; Price, William D.; Jockusch, Rebecca A.

2005-01-01

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (Ea) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 105 to 1012 s−1, respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 108 and 1012 s−1, respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 104. This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an Ea of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 ± 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the Ea of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s−1. This modification also dramatically changes the dissociation products. Similar results are observed for [Ala6]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure. PMID:16525512

Stochastic Approaches to Understanding Dissociations in Inflectional Morphology

ERIC Educational Resources Information Center

Plunkett, Kim; Bandelow, Stephan

2006-01-01

Computer modelling research has undermined the view that double dissociations in behaviour are sufficient to infer separability in the cognitive mechanisms underlying those behaviours. However, all these models employ "multi-modal" representational schemes, where functional specialisation of processing emerges from the training process.…

[Verification of the double dissociation model of shyness using the implicit association test].

PubMed

Fujii, Tsutomu; Aikawa, Atsushi

2013-12-01

The "double dissociation model" of shyness proposed by Asendorpf, Banse, and Mtücke (2002) was demonstrated in Japan by Aikawa and Fujii (2011). However, the generalizability of the double dissociation model of shyness was uncertain. The present study examined whether the results reported in Aikawa and Fujii (2011) would be replicated. In Study 1, college students (n = 91) completed explicit self-ratings of shyness and other personality scales. In Study 2, forty-eight participants completed IAT (Implicit Association Test) for shyness, and their friends (n = 141) rated those participants on various personality scales. The results revealed that only the explicit self-concept ratings predicted other-rated low praise-seeking behavior, sociable behavior and high rejection-avoidance behavior (controlled shy behavior). Only the implicit self-concept measured by the shyness IAT predicted other-rated high interpersonal tension (spontaneous shy behavior). The results of this study are similar to the findings of the previous research, which supports generalizability of the double dissociation model of shyness.

Molecular and Kinetic Models for High-rate Thermal Degradation of Polyethylene

DOE PAGES

Lane, J. Matthew; Moore, Nathan W.

2018-02-01

Thermal degradation of polyethylene is studied under the extremely high rate temperature ramps expected in laser-driven and X-ray ablation experiments—from 10 10 to 10 14 K/s in isochoric, condensed phases. The molecular evolution and macroscopic state variables are extracted as a function of density from reactive molecular dynamics simulations using the ReaxFF potential. The enthalpy, dissociation onset temperature, bond evolution, and observed cross-linking are shown to be rate dependent. These results are used to parametrize a kinetic rate model for the decomposition and coalescence of hydrocarbons as a function of temperature, temperature ramp rate, and density. In conclusion, the resultsmore » are contrasted to first-order random-scission macrokinetic models often assumed for pyrolysis of linear polyethylene under ambient conditions.« less

Molecular and Kinetic Models for High-rate Thermal Degradation of Polyethylene

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

Lane, J. Matthew; Moore, Nathan W.

Thermal degradation of polyethylene is studied under the extremely high rate temperature ramps expected in laser-driven and X-ray ablation experiments—from 10 10 to 10 14 K/s in isochoric, condensed phases. The molecular evolution and macroscopic state variables are extracted as a function of density from reactive molecular dynamics simulations using the ReaxFF potential. The enthalpy, dissociation onset temperature, bond evolution, and observed cross-linking are shown to be rate dependent. These results are used to parametrize a kinetic rate model for the decomposition and coalescence of hydrocarbons as a function of temperature, temperature ramp rate, and density. In conclusion, the resultsmore » are contrasted to first-order random-scission macrokinetic models often assumed for pyrolysis of linear polyethylene under ambient conditions.« less

Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution.

PubMed

Eibinger, Manuel; Zahel, Thomas; Ganner, Thomas; Plank, Harald; Nidetzky, Bernd

2016-01-01

Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field. We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate. Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.

Brain functional integration: an epidemiologic study on stress-producing dissociative phenomena.

PubMed

Sperandeo, Raffaele; Monda, Vincenzo; Messina, Giovanni; Carotenuto, Marco; Maldonato, Nelson Mauro; Moretto, Enrico; Leone, Elena; De Luca, Vincenzo; Monda, Marcellino; Messina, Antonietta

2018-01-01

Dissociative phenomena are common among psychiatric patients; the presence of these symptoms can worsen the prognosis, increasing the severity of their clinical conditions and exposing them to increased risk of suicidal behavior. Personality disorders as long duration stressful experiences may support the development of dissociative phenomena. In 933 psychiatric outpatients consecutively recruited, presence of dissociative phenomena was identified with the Dissociative Experience Scale (DES). Dissociative phenomena were significantly more severe in the group of people with mental disorders and/or personality disorders. All psychopathologic traits detected with the symptom checklist-90-revised had a significant correlation with the total score on the DES. Using total DES score as the dependent variable, a linear regression model was constructed. Mental and personality disorders which were associated with greater severity of dissociative phenomena on analysis of variance were included as predictors; scores from the nine scales of symptom checklist-90-revised, significantly correlated to total DES score, were used as covariates. The model consisted of seven explanatory variables (four factors and three covariates) explaining 82% of variance. The four significant factors were the presence of borderline and narcissistic personality disorder, substance abuse disorders and psychotic disorders. Significant covariates were psychopathologic traits of anger, psychoticism and obsessiveness. This study, confirming Janet's theory, explains that, mental disorders and psychopathologic experiences of patients can configure the chronic stress condition that produces functional damage to the adaptive executive system. The symptoms of dissociative depersonalization/derealization and dissociative amnesia can be explained, in large part, through their current and previous psychopathologic experiences.

Brain functional integration: an epidemiologic study on stress-producing dissociative phenomena

PubMed Central

Messina, Giovanni; Carotenuto, Marco; Maldonato, Nelson Mauro; Moretto, Enrico; Leone, Elena; De Luca, Vincenzo; Monda, Marcellino; Messina, Antonietta

2018-01-01

Dissociative phenomena are common among psychiatric patients; the presence of these symptoms can worsen the prognosis, increasing the severity of their clinical conditions and exposing them to increased risk of suicidal behavior. Personality disorders as long duration stressful experiences may support the development of dissociative phenomena. In 933 psychiatric outpatients consecutively recruited, presence of dissociative phenomena was identified with the Dissociative Experience Scale (DES). Dissociative phenomena were significantly more severe in the group of people with mental disorders and/or personality disorders. All psychopathologic traits detected with the symptom checklist-90-revised had a significant correlation with the total score on the DES. Using total DES score as the dependent variable, a linear regression model was constructed. Mental and personality disorders which were associated with greater severity of dissociative phenomena on analysis of variance were included as predictors; scores from the nine scales of symptom checklist-90-revised, significantly correlated to total DES score, were used as covariates. The model consisted of seven explanatory variables (four factors and three covariates) explaining 82% of variance. The four significant factors were the presence of borderline and narcissistic personality disorder, substance abuse disorders and psychotic disorders. Significant covariates were psychopathologic traits of anger, psychoticism and obsessiveness. This study, confirming Janet’s theory, explains that, mental disorders and psychopathologic experiences of patients can configure the chronic stress condition that produces functional damage to the adaptive executive system. The symptoms of dissociative depersonalization/derealization and dissociative amnesia can be explained, in large part, through their current and previous psychopathologic experiences. PMID:29296086

[Dissociative disorders: from Janet to DSM-IV].

PubMed

Nakatani, Y

2000-01-01

I reviewed the literature on dissociation and dissociative disorders from Pierre Janet to DSM-IV, and examined the current trends in research. Janet's theory on hysteria is multifaceted, and is based on three psychological models. Based on a hierarchical model, Janet related hysteric symptoms to the activities within the lower strata of mental hierarchy (automatisms psychologiques), which were demonstrably shown in somnambulism. A second model was based on the concept of a psychological system, which was hypothetically composed of ideas, images, feelings, sensations, and movements. According to this model, dissociation of psychological functions was fundamental to the mechanism of hysteria: loss of integration was thought to engender fixed ideas (ideas fixes) and to lead to the development of a system totally isolated from the whole personality system. Janet also attempted to explain various mental disorders using an economic model. He referred to a loss of equilibration between psychological force and psychological tension. Thus, an unexpected emotional experience was conceived to cause a consumption of reserved psychological force, which was in turn followed by exhaustion associated with hysteric symptoms. Whereas most current researchers regard Janet as the first to study psychological trauma as a principal cause of dissociation, I feel it is important to note that he also emphasized the role of stigmata, i.e., permanent traits of hysteric patients, which were represented as a suggestibility and a tendency toward a narrowing of the consciousness field. Discussion about dissociation and its relation to trauma all but disappeared after Janet. However, during the Second World War and post-war period, some psychiatrists began to pay attention to two emerging phenomena: a high incidence of dissociative symptoms such as fugue and amnesia among combatants, and traumatic neurosis frequently observed among ex-inmates of concentration camps. In the 1970s, interest in dissociation and trauma was revived in different areas: the feminism movement was linked with concerns about child sexual abuse, public curiosity about multiple personalities was heightened by novels and movies, and recognition of posttraumatic stress disorder (PTSD) among Vietnam War veterans. In 1980, dissociative disorders were finally adopted as a diagnostic category in the official nomenclature of DSM-III. Although current research on dissociation is being carried out in various fields, two basic assumptions, reflected in the definition of DSM-IV, can be made. One is the "trauma-genic hypothesis," and the other is the great importance attached to multiple personality disorder (MPD). According to the predominantly held view, dissociation represents a reaction to early traumatic experience, especially sexual and physical abuse in childhood. In contrast, some authors argue that the causality of childhood traumatic experience has not been empirically confirmed, and other factors such as the influence of the environment and the predisposition of patients should be taken into consideration. MPD, which was originally described as an unusual phenomenon in classical literature, is currently thought to be a common type of dissociation. However, the reported rapid increase in the number of MPD patients in North America may be partially due to over-diagnosis and inclusion of iatrogenic cases. Significance is also given to MPD in respect to classification of dissociative phenomena. According to the widely held scheme of a "dissociative continuum," which ranges from normal experiences such as daydreams to pathological states, MPD is placed at the extreme end of the continuum. Furthermore, most researchers tend to classify MPD as the severest dissociative disorder due to chronic trauma. On this point, there seems to be confusion about "extremity" and "severity" of MPD. I conclude that the trauma-genic hypothesis of dissociation and the overemphasis placed on MPD should be reexamin

A Molecular Dynamics Simulation of the Human Lysozyme – Camelid VHH HL6 Antibody System

PubMed Central

Su, Zhi-Yuan; Wang, Yeng-Tseng

2009-01-01

Amyloid diseases such as Alzheimer’s and thrombosis are characterized by an aberrant assembly of specific proteins or protein fragments into fibrils and plaques that are deposited in various tissues and organs. The single-domain fragment of a camelid antibody was reported to be able to combat against wild-type human lysozyme for inhibiting in-vitro aggregations of the amyloidogenic variant (D67H). The present study is aimed at elucidating the unbinding mechanics between the D67H lysozyme and VHH HL6 antibody fragment by using steered molecular dynamics (SMD) simulations on a nanosecond scale with different pulling velocities. The results of the simulation indicated that stretching forces of more than two nano Newton (nN) were required to dissociate the proteinantibody system, and the hydrogen bond dissociation pathways were computed. PMID:19468335

Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops.

PubMed

Lang, Walter H; Coats, Julie E; Majka, Jerzy; Hura, Greg L; Lin, Yuyen; Rasnik, Ivan; McMurray, Cynthia T

2011-10-18

Insertion and deletion of small heteroduplex loops are common mutations in DNA, but why some loops are prone to mutation and others are efficiently repaired is unknown. Here we report that the mismatch recognition complex, MSH2/MSH3, discriminates between a repair-competent and a repair-resistant loop by sensing the conformational dynamics of their junctions. MSH2/MSH3 binds, bends, and dissociates from repair-competent loops to signal downstream repair. Repair-resistant Cytosine-Adenine-Guanine (CAG) loops adopt a unique DNA junction that traps nucleotide-bound MSH2/MSH3, and inhibits its dissociation from the DNA. We envision that junction dynamics is an active participant and a conformational regulator of repair signaling, and governs whether a loop is removed by MSH2/MSH3 or escapes to become a precursor for mutation.

Linking photochemistry in the gas and solution phase: S-H bond fission in p-methylthiophenol following UV photoexcitation.

PubMed

Oliver, Thomas A A; Zhang, Yuyuan; Ashfold, Michael N R; Bradforth, Stephen E

2011-01-01

Gas-phase H (Rydberg) atom photofragment translational spectroscopy and solution-phase femtosecond-pump dispersed-probe transient absorption techniques are applied to explore the excited state dynamics of p-methylthiophenol connecting the short time reactive dynamics in the two phases. The molecule is excited at a range of UV wavelengths from 286 to 193 nm. The experiments clearly demonstrate that photoexcitation results in S-H bond fission--both in the gas phase and in ethanol solution-and that the resulting p-methythiophenoxyl radical fragments are formed with significant vibrational excitation. In the gas phase, the recoil anisotropy of the H atom and the vibrational energy disposal in the p-MePhS radical products formed at the longer excitation wavelengths reveal the operation of two excited state dissociation mechanisms. The prompt excited state dissociation motif appears to map into the condensed phase also. In both phases, radicals are produced in both their ground and first excited electronic states; characteristic signatures for both sets of radical products are already apparent in the condensed phase studies after 50 fs. No evidence is seen for either solute ionisation or proton coupled electron transfer--two alternate mechanisms that have been proposed for similar heteroaromatics in solution. Therefore, at least for prompt S-H bond fissions, the direct observation of the dissociation process in solution confirms that the gas phase photofragmentation studies indeed provide important insights into the early time dynamics that transfer to the condensed phase.

Full-dimensional quantum dynamics study on the mode-specific unimolecular dissociation reaction of HFCO

NASA Astrophysics Data System (ADS)

Yamamoto, Takeshi; Kato, Shigeki

2000-05-01

The mode specificity of the unimolecular reaction of HFCO is studied by six-dimensional quantum dynamics calculations. The energy and mode dependency of the dissociation rate is examined by propagating a number of wave packets with a small energy dispersion representing highly excited states with respect to a specific vibrational mode. The wave packets are generated by applying a set of filter operators onto a source vibrational state. All the information necessary for propagating the wave packets is obtained from a single propagation of the source state, thus allowing a significant decrease of computational effort. The relevant spectral peaks are assigned using the three-dimensional CH chromophore Hamiltonian. The resulting dissociation rate of the CH stretching excited state is in agreement with that obtained from a statistical theory, while the rates of the out-of-plane bending excited states are about one order of magnitude smaller than the statistical rates. A local-mode analysis also shows that the relaxation of the out-of-plane excitation proceeds very slowly within 3 ps. These results clearly indicate weak couplings of the out-of-plane bending excited states with other in-plane vibrational states, which is in qualitative agreement with experimental findings. From a computational point of view, a parallel supercomputer is utilized efficiently to handle an ultra large basis set of an order of 108, and 200 Gflops rate on average is achieved in the dynamics calculations.

Effects of defects on thermal decomposition of HMX via ReaxFF molecular dynamics simulations.

PubMed

Zhou, Ting-Ting; Huang, Feng-Lei

2011-01-20

Effects of molecular vacancies on the decomposition mechanisms and reaction dynamics of condensed-phase β-HMX at various temperatures were studied using ReaxFF molecular dynamics simulations. Results show that three primary initial decomposition mechanisms, namely, N-NO(2) bond dissociation, HONO elimination, and concerted ring fission, exist at both high and lower temperatures. The contribution of the three mechanisms to the initial decomposition of HMX is influenced by molecular vacancies, and the effects vary with temperature. At high temperature (2500 K), molecular vacancies remarkably promote N-N bond cleavage and concerted ring breaking but hinder HONO formation. N-N bond dissociation and HONO elimination are two primary competing reaction mechanisms, and the former is dominant in the initial decomposition. Concerted ring breaking of condensed-phase HMX is not favored at high temperature. At lower temperature (1500 K), the most preferential initial decomposition pathway is N-N bond dissociation followed by the formation of NO(3) (O migration), although all three mechanisms are promoted by molecular vacancies. The promotion effect on concerted ring breaking is considerable at lower temperature. Products resulting from concerted ring breaking appear in the defective system but not in the perfect crystal. The mechanism of HONO elimination is less important at lower temperature. We also estimated the reaction rate constant and activation barriers of initial decomposition with different vacancy concentrations. Molecular vacancies accelerate the decomposition of condensed-phase HMX by increasing the reaction rate constant and reducing activation barriers.

Dissociative absorption: An empirically unique, clinically relevant, dissociative factor.

PubMed

Soffer-Dudek, Nirit; Lassri, Dana; Soffer-Dudek, Nir; Shahar, Golan

2015-11-01

Research of dissociative absorption has raised two questions: (a) Is absorption a unique dissociative factor within a three-factor structure, or a part of one general dissociative factor? Even when three factors are found, the specificity of the absorption factor is questionable. (b) Is absorption implicated in psychopathology? Although commonly viewed as "non-clinical" dissociation, absorption was recently hypothesized to be specifically associated with obsessive-compulsive symptoms. To address these questions, we conducted exploratory and confirmatory factor analyses on 679 undergraduates. Analyses supported the three-factor model, and a "purified" absorption scale was extracted from the original inclusive absorption factor. The purified scale predicted several psychopathology scales. As hypothesized, absorption was a stronger predictor of obsessive-compulsive symptoms than of general psychopathology. In addition, absorption was the only dissociative scale that longitudinally predicted obsessive-compulsive symptoms. We conclude that absorption is a unique and clinically relevant dissociative tendency that is particularly meaningful to obsessive-compulsive symptoms. Copyright © 2015 Elsevier Inc. All rights reserved.

Data Base for CFD Validation

NASA Technical Reports Server (NTRS)

Deiwert, George S.

1997-01-01

The flow behind the shock wave formed around objects which fly at hypervelocity behaves differently from that of a perfect gas. Molecules become vibrationally excited, dissociated, and ionized. The hot gas may emit or absorb radiation. When the atoms produced by dissociation reach the wall surface, chemical reactions, including recombination, may occur. The thermochemical phenomena of vibration, dissociation, ionization, surface chemical reaction, and radiation are referred to commonly as high-temperature real-gas phenomena. The phenomena cause changes in the dynamic behavior of the flow and the surface pressure and heat transfer distribution around the object. The character of a real gas is described by the internal degrees of freedom and state of constituent molecules; nitrogen and oxygen for air. The internal energy states, rotation, vibration and electronic, of the molecules are excited and, in the limit, the molecular bonds are exceeded and the gas dissociated into atomic and, possibly, ionic constituents. The process of energy transfer causing excitation, dissociation and recombination is a rate process controlled by particle collisions. Binary, two-body, collisions are sufficient to cause internal excitation, dissociation and ionization while three-body collisions are required to recombine the particles into molecular constituents. If the rates of energy transfer are fast with respect to the local fluid dynamic time scale the gas is in, or nearly in, equilibrium. If the energy transfer rates are very slow the gas can be described as frozen. In all other instances, wherein any of the energy exchange rates are comparable to the local fluid time scale, the gas will be thermally or chemically reacting and out of equilibrium. Real gas thermochemical nonequilibrium processes are important in the determination of aerodynamic heating; both convective (including wall catalytic effects) and radiative heating. To illustrate this we consider the hypervelocity flow over a bluff body typical of an atmospheric entry vehicle or an aerospace transfer vehicle (ASTV). The qualitative aspects of a hypersonic flow field over a bluff body are discussed in two parts, forebody and afterbody, with attention to which particular physical effects must be included in an analysis. This will indicate what type of numerical modeling will be adequate in each region of the flow. A bluff forebody flow field is dominated by the presence of the strong bow shock wave and the consequent heating, and chemical reaction of the gas. At high altitude hypersonic flight conditions the thermal excitation and chemical reaction of the gas occur slowly enough that a significant portion of the flow field is in a state of thermochemical nonequilibrium. A second important effect is the presence of the thick boundary layer along the forebody surface. In this region there are large thermal and chemical species gradients due to the interaction of the gas with the wall. Also at high altitudes the shock wave and the boundary layer may become so thick that they merge; in this case the entire shock layer is dominated by viscous effects.

A re-examination of neural basis of language processing: proposal of a dynamic hodotopical model from data provided by brain stimulation mapping during picture naming.

PubMed

Duffau, Hugues; Moritz-Gasser, Sylvie; Mandonnet, Emmanuel

2014-04-01

From recent findings provided by brain stimulation mapping during picture naming, we re-examine the neural basis of language. We studied structural-functional relationships by correlating the types of language disturbances generated by stimulation in awake patients, mimicking a transient virtual lesion both at cortical and subcortical levels (white matter and deep grey nuclei), with the anatomical location of the stimulation probe. We propose a hodotopical (delocalized) and dynamic model of language processing, which challenges the traditional modular and serial view. According to this model, following the visual input, the language network is organized in parallel, segregated (even if interconnected) large-scale cortico-subcortical sub-networks underlying semantic, phonological and syntactic processing. Our model offers several advantages (i) it explains double dissociations during stimulation (comprehension versus naming disorders, semantic versus phonemic paraphasias, syntactic versus naming disturbances, plurimodal judgment versus naming disorders); (ii) it takes into account the cortical and subcortical anatomic constraints; (iii) it explains the possible recovery of aphasia following a lesion within the "classical" language areas; (iv) it establishes links with a model executive functions. Copyright © 2013 Elsevier Inc. All rights reserved.

Dissociative amnesia.

PubMed

Staniloiu, Angelica; Markowitsch, Hans J

2014-08-01

Dissociative amnesia is one of the most enigmatic and controversial psychiatric disorders. In the past two decades, interest in the understanding of its pathophysiology has surged. In this report, we review new data about the epidemiology, neurobiology, and neuroimaging of dissociative amnesia and show how advances in memory research and neurobiology of dissociation inform proposed pathogenetic models of the disorder. Dissociative amnesia is characterised by functional impairment. Additionally, preliminary data suggest that affected people have an increased and possibly underestimated suicide risk. The prevalence of dissociative amnesia differs substantially across countries and populations. Symptoms and disease course also vary, indicating a possibly heterogeneous disorder. The accompanying clinical features differ across cultural groups. Most dissociative amnesias are retrograde, with memory impairments mainly involving the episodic-autobiographical memory domain. Anterograde dissociative amnesia occurring without significant retrograde memory impairments is rare. Functional neuroimaging studies of dissociative amnesia with prevailing retrograde memory impairments show changes in the network that subserves autobiographical memory. At present, no evidence-based treatments are available for dissociative amnesia and no broad framework exists for its rehabilitation. Further research is needed into its neurobiology, course, treatment options, and strategies to improve differential diagnoses. Copyright © 2014 Elsevier Ltd. All rights reserved.

Invasion of drilling mud into gas-hydrate-bearing sediments. Part I: effect of drilling mud properties

NASA Astrophysics Data System (ADS)

Ning, Fulong; Zhang, Keni; Wu, Nengyou; Zhang, Ling; Li, Gang; Jiang, Guosheng; Yu, Yibing; Liu, Li; Qin, Yinghong

2013-06-01

To our knowledge, this study is the first to perform a numerical simulation and analysis of the dynamic behaviour of drilling mud invasion into oceanic gas-hydrate-bearing sediment (GHBS) and to consider the effects of such an invasion on borehole stability and the reliability of well logging. As a case study, the simulation background sets up the conditions of mud temperature over hydrate equilibrium temperature and overbalanced drilling, considering the first Chinese expedition to drill gas hydrate (GMGS-1). The results show that dissociating gas may form secondary hydrates in the sediment around borehole by the combined effects of increased pore pressure (caused by mud invasion and flow resistance), endothermic cooling that accompanies hydrate dissociation compounded by the Joule-Thompson effect and the lagged effect of heat transfer in sediments. The secondary hydrate ring around the borehole may be more highly saturated than the in situ sediment. Mud invasion in GHBS is a dynamic process of thermal, fluid (mud invasion), chemical (hydrate dissociation and reformation) and mechanical couplings. All of these factors interact and influence the pore pressure, flow ability, saturation of fluid and hydrates, mechanical parameters and electrical properties of sediments around the borehole, thereby having a strong effect on borehole stability and the results of well logging. The effect is particularly clear in the borehole SH7 of GMGS-1 project. The borehole collapse and resistivity distortion were observed during practical drilling and wireline logging operations in borehole SH7 of the GMGS-1.mud density (i.e. the corresponding borehole pressure), temperature and salinity have a marked influence on the dynamics of mud invasion and on hydrate stability. Therefore, perhaps well-logging distortion caused by mud invasion, hydrate dissociation and reformation should be considered for identifying and evaluating gas hydrate reservoirs. And some suitable drilling measurements need to be adopted to reduce the risk of well-logging distortion and borehole instability.

The role of peripartum dissociation as a predictor of posttraumatic stress symptoms following childbirth in Israeli Jewish women.

PubMed

Lev-Wiesel, Rachel; Daphna-Tekoah, Shir

2010-01-01

This study aimed to assess the role of peripartum dissociation in the development of childbirth-related posttraumatic stress (PTS) symptoms. Furthermore, it examined the relation between life-traumatizing events, in particular childhood sexual abuse (CSA), dissociation tendencies, prenatal PTS, prenatal depression, peripartum dissociation, and postnatal PTS symptoms. A self-report questionnaire was administered to 1,003 Israeli Jewish women (sample after attrition) at mid-pregnancy (18-28 weeks) and at 2 months postnatally. Women with a history of CSA scored higher on all variables during pregnancy and postpartum. Prenatal PTS symptoms, depression, and dissociation tendencies coincided with higher levels of peripartum dissociation. Screening pregnant women, especially CSA victims, and implementing models of prevention and intervention can assist these women in acquiring better coping strategies during childbirth. Such practices are likely to decrease peripartum dissociation, which may in turn lessen postpartum PTS symptoms.

Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling.

PubMed

Grøntved, Lars; Waterfall, Joshua J; Kim, Dong Wook; Baek, Songjoon; Sung, Myong-Hee; Zhao, Li; Park, Jeong Won; Nielsen, Ronni; Walker, Robert L; Zhu, Yuelin J; Meltzer, Paul S; Hager, Gordon L; Cheng, Sheue-yann

2015-04-28

A bimodal switch model is widely used to describe transcriptional regulation by the thyroid hormone receptor (TR). In this model, the unliganded TR forms stable, chromatin-bound complexes with transcriptional co-repressors to repress transcription. Binding of hormone dissociates co-repressors and facilitates recruitment of co-activators to activate transcription. Here we show that in addition to hormone-independent TR occupancy, ChIP-seq against endogenous TR in mouse liver tissue demonstrates considerable hormone-induced TR recruitment to chromatin associated with chromatin remodelling and activated gene transcription. Genome-wide footprinting analysis using DNase-seq provides little evidence for TR footprints both in the absence and presence of hormone, suggesting that unliganded TR engagement with repressive complexes on chromatin is, similar to activating receptor complexes, a highly dynamic process. This dynamic and ligand-dependent interaction with chromatin is likely shared by all steroid hormone receptors regardless of their capacity to repress transcription in the absence of ligand.

Mechanisms and energetics of hydride dissociation reactions on surfaces of plasma-deposited silicon thin films

NASA Astrophysics Data System (ADS)

Singh, Tejinder; Valipa, Mayur S.; Mountziaris, T. J.; Maroudas, Dimitrios

2007-11-01

We report results from a detailed analysis of the fundamental silicon hydride dissociation processes on silicon surfaces and discuss their implications for the surface chemical composition of plasma-deposited hydrogenated amorphous silicon (a-Si:H) thin films. The analysis is based on a synergistic combination of first-principles density functional theory (DFT) calculations of hydride dissociation on the hydrogen-terminated Si(001)-(2×1) surface and molecular-dynamics (MD) simulations of adsorbed SiH3 radical precursor dissociation on surfaces of MD-grown a-Si :H films. Our DFT calculations reveal that, in the presence of fivefold coordinated surface Si atoms, surface trihydride species dissociate sequentially to form surface dihydrides and surface monohydrides via thermally activated pathways with reaction barriers of 0.40-0.55eV. The presence of dangling bonds (DBs) results in lowering the activation barrier for hydride dissociation to 0.15-0.20eV, but such DB-mediated reactions are infrequent. Our MD simulations on a-Si :H film growth surfaces indicate that surface hydride dissociation reactions are predominantly mediated by fivefold coordinated surface Si atoms, with resulting activation barriers of 0.35-0.50eV. The results are consistent with experimental measurements of a-Si :H film surface composition using in situ attenuated total reflection Fourier transform infrared spectroscopy, which indicate that the a-Si :H surface is predominantly covered with the higher hydrides at low temperatures, while the surface monohydride, SiH(s ), becomes increasingly more dominant as the temperature is increased.

The dissociation of vibrationally excited CH3OSO radicals and their photolytic precursor, methoxysulfinyl chloride.

PubMed

Alligood, Bridget W; Womack, Caroline C; Straus, Daniel B; Blase, Frances R; Butler, Laurie J

2011-05-21

The dissociation dynamics of methoxysulfinyl radicals generated from the photodissociation of CH(3)OS(O)Cl at 248 nm is investigated using both a crossed laser-molecular beam scattering apparatus and a velocity map imaging apparatus. There is evidence of only a single photodissociation channel of the precursor: S-Cl fission to produce Cl atoms and CH(3)OSO radicals. Some of the vibrationally excited CH(3)OSO radicals undergo subsequent dissociation to CH(3) + SO(2). The velocities of the detected CH(3) and SO(2) products show that the dissociation occurs via a transition state having a substantial barrier beyond the endoergicity; appropriately, the distribution of velocities imparted to these momentum-matched products is fit by a broad recoil kinetic energy distribution extending out to 24 kcal/mol in translational energy. Using 200 eV electron bombardment detection, we also detect the CH(3)OSO radicals that have too little internal energy to dissociate. These radicals are observed both at the parent CH(3)OSO(+) ion as well as at the CH(3)(+) and SO(2)(+) daughter ions; they are distinguished by virtue of the velocity imparted in the original photolytic step. The detected velocities of the stable radicals are roughly consistent with the calculated barriers (both at the CCSD(T) and G3B3 levels of theory) for the dissociation of CH(3)OSO to CH(3) + SO(2) when we account for the partitioning of internal energy between rotation and vibration as the CH(3)OSOCl precursor dissociates. © 2011 American Institute of Physics.

The dissociation and recombination rates of CH4 through the Ni(111) surface: The effect of lattice motion

NASA Astrophysics Data System (ADS)

Wang, Wenji; Zhao, Yi

2017-07-01

Methane dissociation is a prototypical system for the study of surface reaction dynamics. The dissociation and recombination rates of CH4 through the Ni(111) surface are calculated by using the quantum instanton method with an analytical potential energy surface. The Ni(111) lattice is treated rigidly, classically, and quantum mechanically so as to reveal the effect of lattice motion. The results demonstrate that it is the lateral displacements rather than the upward and downward movements of the surface nickel atoms that affect the rates a lot. Compared with the rigid lattice, the classical relaxation of the lattice can increase the rates by lowering the free energy barriers. For instance, at 300 K, the dissociation and recombination rates with the classical lattice exceed the ones with the rigid lattice by 6 and 10 orders of magnitude, respectively. Compared with the classical lattice, the quantum delocalization rather than the zero-point energy of the Ni atoms further enhances the rates by widening the reaction path. For instance, the dissociation rate with the quantum lattice is about 10 times larger than that with the classical lattice at 300 K. On the rigid lattice, due to the zero-point energy difference between CH4 and CD4, the kinetic isotope effects are larger than 1 for the dissociation process, while they are smaller than 1 for the recombination process. The increasing kinetic isotope effect with decreasing temperature demonstrates that the quantum tunneling effect is remarkable for the dissociation process.

Analytical model for the photocurrent-voltage characteristics of bilayer MEH-PPV/TiO2 photovoltaic devices

PubMed Central

2011-01-01

The photocurrent in bilayer polymer photovoltaic cells is dominated by the exciton dissociation efficiency at donor/acceptor interface. An analytical model is developed for the photocurrent-voltage characteristics of the bilayer polymer/TiO2 photovoltaic cells. The model gives an analytical expression for the exciton dissociation efficiency at the interface, and explains the dependence of the photocurrent of the devices on the internal electric field, the polymer and TiO2 layer thicknesses. Bilayer polymer/TiO2 cells consisting of poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) and TiO2, with different thicknesses of the polymer and TiO2 films, were prepared for experimental purposes. The experimental results for the prepared bilayer MEH-PPV/TiO2 cells under different conditions are satisfactorily fitted to the model. Results show that increasing TiO2 or the polymer layer in thickness will reduce the exciton dissociation efficiency in the device and further the photocurrent. It is found that the photocurrent is determined by the competition between the exciton dissociation and charge recombination at the donor/acceptor interface, and the increase in photocurrent under a higher incident light intensity is due to the increased exciton density rather than the increase in the exciton dissociation efficiency. PMID:21711905

Model for a transformer-coupled toroidal plasma source

NASA Astrophysics Data System (ADS)

Rauf, Shahid; Balakrishna, Ajit; Chen, Zhigang; Collins, Ken

2012-01-01

A two-dimensional fluid plasma model for a transformer-coupled toroidal plasma source is described. Ferrites are used in this device to improve the electromagnetic coupling between the primary coils carrying radio frequency (rf) current and a secondary plasma loop. Appropriate components of the Maxwell equations are solved to determine the electromagnetic fields and electron power deposition in the model. The effect of gas flow on species transport is also considered. The model is applied to 1 Torr Ar/NH3 plasma in this article. Rf electric field lines form a loop in the vacuum chamber and generate a plasma ring. Due to rapid dissociation of NH3, NHx+ ions are more prevalent near the gas inlet and Ar+ ions are the dominant ions farther downstream. NH3 and its by-products rapidly dissociate into small fragments as the gas flows through the plasma. With increasing source power, NH3 dissociates more readily and NHx+ ions are more tightly confined near the gas inlet. Gas flow rate significantly influences the plasma characteristics. With increasing gas flow rate, NH3 dissociation occurs farther from the gas inlet in regions with higher electron density. Consequently, more NH4+ ions are produced and dissociation by-products have higher concentrations near the outlet.

Effects of Charge State on Fragmentation Pathways, Dynamics, and Activation Energies of Ubiquitin Ions Measured by Blackbody Infrared Radiative Dissociation

PubMed Central

Jockusch, Rebecca A.; Schnier, Paul D.; Price, William D.; Strittmatter, Eric. F.; Demirev, Plamen A.; Williams*, Evan R.

2005-01-01

Blackbody infrared radiative dissociation spectra of the (M + 5H)5+ through (M + 11H)11+ ions of the protein ubiquitin (8.6 kDa) formed by electrospray ionization were measured in a Fourier-transform mass spectrometer. The 5+ ion dissociates exclusively by loss of water and/or ammonia, whereas the 11+ charge state dissociates only by formation of complementary y and b ions. These two processes are competitive for intermediate charge state ions, with the formation of y and b ions increasingly favored for the higher charge states. The y and b ions are formed by cleavage of the backbone amide bond on the C-terminal side of acidic residues exclusively, with cleavage adjacent to aspartic acid favored. Thermal unimolecular dissociation rate constants for the dissociation of each of these charge states were measured. From the temperature dependence of these rates, Arrhenius activation parameters in the rapid energy exchange limit are obtained. The activation energies (Ea) and preexponential factors (A) for the 5+, 8+, and 9+ ions are 1.2 eV and 1012 s−1, respectively. These values for the 6+ and 7+ ions are 0.9–1.0 eV and 109 s−1, and those for the 10+ and 11+ ions are 1.6 eV and 1016–1017 s−1. Thus, with the exception of the 5+ ion, the higher charge states of ubiquitin have larger dissociation activation energies than the lower charge states. The different A factors observed for production of y and b ions from different precursor charge states indicate that they are formed by different mechanisms, ranging from relatively complex rearrangements to direct bond cleavages. These results clearly demonstrate that the relative dissociation rates of large biomolecule ions by themselves are not necessarily a reliable indicator of their relative dissociation energies, even when similar fragment ions are formed. PMID:9075403

Effects of charge state on fragmentation pathways, dynamics, and activation energies of ubiquitin ions measured by blackbody infrared radiative dissociation.

PubMed

Jockusch, R A; Schnier, P D; Price, W D; Strittmatter, E F; Demirev, P A; Williams, E R

1997-03-15

Blackbody infrared radiative dissociation spectra of the (M + 5H)5+ through (M + 11H)11+ ions of the protein ubiquitin (8.6 kDa) formed by electrospray ionization were measured in a Fourier-transform mass spectrometer. The 5+ ion dissociates exclusively by loss of water and/or ammonia, whereas the 11+ charge state dissociates only by formation of complementary y and b ions. These two processes are competitive for intermediate charge state ions, with the formation of y and b ions increasingly favored for the higher charge states. The y and b ions are formed by cleavage of the backbone amide bond on the C-terminal side of acidic residues exclusively, with cleavage adjacent to aspartic acid favored. Thermal unimolecular dissociation rate constants for the dissociation of each of these charge states were measured. From the temperature dependence of these rates, Arrhenius activation parameters in the rapid energy exchange limit are obtained. The activation energies (Ea) and preexponential factors (A) for the 5+, 8+, and 9+ ions are 1.2 eV and 10(12) s-1, respectively. These values for the 6+ and 7+ ions are 0.9-1.0 eV and 10(9) s-1, and those for the 10+ and 11+ ions are 1.6 eV and 10(16)-10(17) s-1. Thus, with the exception of the 5+ ion, the higher charge states of ubiquitin have larger dissociation activation energies than the lower charge states. The different A factors observed for production of y and b ions from different precursor charge states indicate that they are formed by different mechanisms, ranging from relatively complex rearrangements to direct bond cleavages. These results clearly demonstrate that the relative dissociation rates of large biomolecule ions by themselves are not necessarily a reliable indicator of their relative dissociation energies, even when similar fragment ions are formed.

Isotherm-Based Thermodynamic Models for Solute Activities of Organic Acids with Consideration of Partial Dissociation.

PubMed

Nandy, Lucy; Ohm, Peter B; Dutcher, Cari S

2016-06-23

Organic acids make up a significant fraction of the organic mass in atmospheric aerosol particles. The calculation of gas-liquid-solid equilibrium partitioning of the organic acid is therefore critical for accurate determination of atmospheric aerosol physicochemical properties and processes such as new particle formation and activation to cloud condensation nuclei. Previously, an adsorption isotherm-based statistical thermodynamic model was developed for capturing solute concentration-activity relationships for multicomponent aqueous solutions over the entire concentration range (Dutcher et al. J. Phys. Chem. C/A 2011, 2012, 2013), with model parameters for energies of adsorption successfully related to dipole-dipole electrostatic forces in solute-solvent and solvent-solvent interactions for both electrolytes and organics (Ohm et al. J. Phys. Chem. A 2015). However, careful attention is needed for weakly dissociating semivolatile organic acids. Dicarboxylic acids, such as malonic acid and glutaric acid are treated here as a mixture of nondissociated organic solute (HA) and dissociated solute (H(+) + A(-)). It was found that the apparent dissociation was greater than that predicted by known dissociation constants alone, emphasizing the effect of dissociation on osmotic and activity coefficient predictions. To avoid additional parametrization from the mixture approach, an expression was used to relate the Debye-Hückel hard-core collision diameter to the adjustable solute-solvent intermolecular distance. An improved reference state treatment for electrolyte-organic aqueous mixtures, such as that observed here with partial dissociation, has also been proposed. This work results in predictive correlations for estimation of organic acid and water activities for which there is little or no activity data.

Vibrational dynamics of aniline(Ar)1 and aniline(CH4)1 clusters

NASA Astrophysics Data System (ADS)

Nimlos, M. R.; Young, M. A.; Bernstein, E. R.; Kelley, D. F.

1989-11-01

The first excited electronic state (S1) vibrational dynamics of aniline(Ar)1 and aniline(CH4)1 van der Waals (vdW) clusters have been studied using molecular jet and time resolved emission spectroscopic techniques. The rates of intramolecular vibrational energy redistribution (IVR) and vibrational predissociation (VP) as functions of vibrational energy are reported for both clusters. For vibrational energy in excess of the cluster binding energy, both clusters are observed to dissociate. The dispersed emission spectra of these clusters demonstrate that aniline(Ar)1 dissociates to all energetically accessible bare molecule states and that aniline(CH4)1 dissociates selectively to only the bare molecule vibrationless state. The emission kinetics show that in the aniline(Ar)1 case, the initially excited states have nanosecond lifetimes, and intermediate cluster states have very short lifetimes. In contrast, the initially excited aniline(CH4)1 states and other intermediate vibrationally excited cluster states are very short lived (<100 ps), and the intermediate cluster 00 state is observed. These results can be understood semiquantitatively in terms of an overall serial IVR/VP mechanism which consists of the following: (1) the rates of chromophore to vdW mode IVR are given by Fermi's golden rule, and the density of vdW vibrational states is the most important factor in determining the relative [aniline(Ar)1 vs aniline(CH4)1] rates of IVR; (2) IVR among the vdW modes is rapid; and (3) VP rates can be calculated by a restricted vdW mode phase space Rice-Ramsberger-Kassel-Marcus theory. Since the density of vdW states is three orders of magnitude greater for aniline(CH4)1 than aniline(Ar)1 at 700 cm-1, the model predicts that IVR is slow and rate limiting in aniline(Ar)1, whereas VP is slow and rate limiting in aniline(CH4)1. The agreement of these predictions with the experimental results is very good and is discussed in detail.

Computational and empirical simulations of selective memory impairments: Converging evidence for a single-system account of memory dissociations.

PubMed

Curtis, Evan T; Jamieson, Randall K

2018-04-01

Current theory has divided memory into multiple systems, resulting in a fractionated account of human behaviour. By an alternative perspective, memory is a single system. However, debate over the details of different single-system theories has overshadowed the converging agreement among them, slowing the reunification of memory. Evidence in favour of dividing memory often takes the form of dissociations observed in amnesia, where amnesic patients are impaired on some memory tasks but not others. The dissociations are taken as evidence for separate explicit and implicit memory systems. We argue against this perspective. We simulate two key dissociations between classification and recognition in a computational model of memory, A Theory of Nonanalytic Association. We assume that amnesia reflects a quantitative difference in the quality of encoding. We also present empirical evidence that replicates the dissociations in healthy participants, simulating amnesic behaviour by reducing study time. In both analyses, we successfully reproduce the dissociations. We integrate our computational and empirical successes with the success of alternative models and manipulations and argue that our demonstrations, taken in concert with similar demonstrations with similar models, provide converging evidence for a more general set of single-system analyses that support the conclusion that a wide variety of memory phenomena can be explained by a unified and coherent set of principles.

Dissociation mediates the relationship between peer victimization and hallucinatory experiences among early adolescents.

PubMed

Yamasaki, Syudo; Ando, Shuntaro; Koike, Shinsuke; Usami, Satoshi; Endo, Kaori; French, Paul; Sasaki, Tsukasa; Furukawa, Toshi A; Hasegawa-Hiraiwa, Mariko; Kasai, Kiyoto; Nishida, Atsushi

2016-06-01

Peer victimization increases the risk of experiencing psychotic symptoms among clinical and general populations, but the mechanism underlying this association remains unclear. Dissociation, which is related to peer victimization and hallucinatory experiences, has been demonstrated as a significant mediator in the relation between childhood victimization and hallucinatory experience among adult patients with psychosis. However, no studies have examined the mediating effect of dissociation in a general early adolescent population. We examined whether dissociation mediates the relationship between peer victimization and hallucinatory experiences among 10-year-old adolescents using a population-based cross-sectional survey of early adolescents and their main parent (Tokyo Early Adolescence Survey; N  = 4478). We examined the mediating effect of dissociation, as well as external locus of control and depressive symptoms, on the relationship between peer victimization and hallucinatory experiences using path analysis. The model assuming mediation effects indicated good model fit (comparative fit index = .999; root mean square error of approximation = .015). The mediation effect between peer victimization and hallucination via dissociation (standardized indirect effect = .038, p  < .001) was statistically significant, whereas the mediation effects of depressive symptoms (standardized indirect effect = -.0066, p  = 0.318) and external locus of control (standardized indirect effect = .0024, p  = 0.321) were not significant. These results suggest that dissociation is a mediator in the relation between peer victimization and hallucinatory experiences in early adolescence. For appropriate intervention strategies, assessing dissociation and peer victimization as they affect hallucinatory experiences is necessary.

Ultrafast Multi-Level Logic Gates with Spin-Valley Coupled Polarization Anisotropy in Monolayer MoS2

PubMed Central

Wang, Yu-Ting; Luo, Chih-Wei; Yabushita, Atsushi; Wu, Kaung-Hsiung; Kobayashi, Takayoshi; Chen, Chang-Hsiao; Li, Lain-Jong

2015-01-01

The inherent valley-contrasting optical selection rules for interband transitions at the K and K′ valleys in monolayer MoS2 have attracted extensive interest. Carriers in these two valleys can be selectively excited by circularly polarized optical fields. The comprehensive dynamics of spin valley coupled polarization and polarized exciton are completely resolved in this work. Here, we present a systematic study of the ultrafast dynamics of monolayer MoS2 including spin randomization, exciton dissociation, free carrier relaxation, and electron-hole recombination by helicity- and photon energy-resolved transient spectroscopy. The time constants for these processes are 60 fs, 1 ps, 25 ps, and ~300 ps, respectively. The ultrafast dynamics of spin polarization, valley population, and exciton dissociation provides the desired information about the mechanism of radiationless transitions in various applications of 2D transition metal dichalcogenides. For example, spin valley coupled polarization provides a promising way to build optically selective-driven ultrafast valleytronics at room temperature. Therefore, a full understanding of the ultrafast dynamics in MoS2 is expected to provide important fundamental and technological perspectives. PMID:25656222

Imaging a multidimensional multichannel potential energy surface: Photodetachment of H{sup −}(NH{sub 3}) and NH{sub 4}{sup −}

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

Hu, Qichi; Johnson, Christopher J.; Continetti, Robert E., E-mail: hguo@umn.edu, E-mail: rcontinetti@ucsd.edu

2016-06-28

Probes of the Born-Oppenheimer potential energy surfaces governing polyatomic molecules often rely on spectroscopy for the bound regions or collision experiments in the continuum. A combined spectroscopic and half-collision approach to image nuclear dynamics in a multidimensional and multichannel system is reported here. The Rydberg radical NH{sub 4} and the double Rydberg anion NH{sub 4}{sup −} represent a polyatomic system for benchmarking electronic structure and nine-dimensional quantum dynamics calculations. Photodetachment of the H{sup −}(NH{sub 3}) ion-dipole complex and the NH{sub 4}{sup −} DRA probes different regions on the neutral NH{sub 4} PES. Photoelectron energy and angular distributions at photon energiesmore » of 1.17, 1.60, and 2.33 eV compare well with quantum dynamics. Photoelectron-photofragment coincidence experiments indicate dissociation of the nascent NH{sub 4} Rydberg radical occurs to H + NH{sub 3} with a peak kinetic energy of 0.13 eV, showing the ground state of NH{sub 4} to be unstable, decaying by tunneling-induced dissociation on a time scale beyond the present scope of multidimensional quantum dynamics.« less

Microscale Mechanics of Actin Networks During Dynamic Assembly and Dissociation

NASA Astrophysics Data System (ADS)

Gurmessa, Bekele; Robertson-Anderson, Rae; Ross, Jennifer; Nguyen, Dan; Saleh, Omar

Actin is one of the key components of the cytoskeleton, enabling cells to move and divide while maintaining shape by dynamic polymerization, dissociation and crosslinking. Actin polymerization and network formation is driven by ATP hydrolysis and varies depending on the concentrations of actin monomers and crosslinking proteins. The viscoelastic properties of steady-state actin networks have been well-characterized, yet the mechanical properties of these non-equilibrium systems during dynamic assembly and disassembly remain to be understood. We use semipermeable microfluidic devices to induce in situ dissolution and re-polymerization of entangled and crosslinked actin networks, by varying ATP concentrations in real-time, while measuring the mechanical properties during disassembly and re-assembly. We use optical tweezers to sinusoidally oscillate embedded microspheres and measure the resulting force at set time-intervals and in different regions of the network during cyclic assembly/disassembly. We determine the time-dependent viscoelastic properties of non-equilibrium network intermediates and the reproducibility and homogeneity of network formation and dissolution. Results inform the role that cytoskeleton reorganization plays in the dynamic multifunctional mechanics of cells. NSF CAREER Award (DMR-1255446) and a Scialog Collaborative Innovation Award funded by Research Corporation for Scientific Advancement (Grant No. 24192).

Vortex dynamics in superconducting transition edge sensors

NASA Astrophysics Data System (ADS)

Ezaki, S.; Maehata, K.; Iyomoto, N.; Asano, T.; Shinozaki, B.

2018-02-01

The temperature dependence of the electrical resistance (R-T) and the current-voltage (I-V) characteristics has been measured and analyzed in a 40 nm thick Ti thin film, which is used as a transition edge sensor (TES). The analyses of the I-V characteristics with the vortex-antivortex pair dissociation model indicate the possible existence of the Berezinskii-Kosterlitz-Thouless (BKT) transition in two-dimensional superconducting Ti thin films. We investigated the noise due to the vortices' flow in TESs. The values of the current noise spectral density in the TESs were estimated by employing the vortex dynamics caused by the BKT transition in the Ti thin films. The estimated values of the current noise spectral density induced by the vortices' flow were in respectable agreement with the values of excess noise experimentally observed in the TESs with Ti/Au bilayer.

Peritraumatic dissociation mediates the relationship between acute panic and chronic posttraumatic stress disorder.

PubMed

Bryant, Richard A; Brooks, Robert; Silove, Derrick; Creamer, Mark; O'Donnell, Meaghan; McFarlane, Alexander C

2011-05-01

Although peritraumatic dissociation predicts subsequent posttraumatic stress disorder (PTSD), little is understood about the mechanism of this relationship. This study examines the role of panic during trauma in the relationship between peritraumatic dissociation and subsequent PTSD. Randomized eligible admissions to 4 major trauma hospitals across Australia (n=244) were assessed during hospital admission and within one month of trauma exposure for panic, peritraumatic dissociation and PTSD symptoms, and subsequently re-assessed for PTSD three months after the initial assessment (n=208). Twenty (9.6%) patients met criteria for PTSD at 3-months post injury. Structural equation modeling supported the proposition that peritraumatic derealization (a subset of dissociation) mediated the effect of panic reactions during trauma and subsequent PTSD symptoms. The mediation model indicated that panic reactions are linked to severity of subsequent PTSD via derealization, indicating a significant indirect relationship. Whereas peritraumatic derealization is associated with chronic PTSD symptoms, this relationship is influenced by initial acute panic responses. Copyright © 2011 Elsevier Ltd. All rights reserved.

Dissociation of 1P states in hot QCD Medium Using Quasi-Particle Model

NASA Astrophysics Data System (ADS)

Nilima, Indrani; Agotiya, Vineet Kumar

2018-03-01

We extend the analysis of a very recent work [1] to study the dissociation phenomenon of 1P states of the charmonium and bottomonium spectra (χc and χb) in a hot QCD medium using Quasi-Particle Model. This study employed a medium modified heavy quark potential which has quite different form in the sense that it has a lomg range Coulombic tail in addition to the Yukawa term even above the deconfinement temperature. Then we study the flavor dependence of their binding energies and explore the nature of dissociation temperatures by employing the Quasi-Particle debye mass for pure gluonic and full QCD case. Interestingly, the dissociation temperatures obtained by employing EoS1 and EoS2 with the Γ criterion, is closer to the upper bound of the dissociation temperatures which are obtained by the dissolution of a given quarkonia state by the mean thermal energy of the quasi-partons in the hot QCD/QGP medium.

The Biotin/Avidin complex adhesion force

NASA Astrophysics Data System (ADS)

Balsera, Manel A.; Izrailev, Sergei; Stepaniants, Sergey; Oono, Yoshitsugu; Schulten, Klaus

1997-03-01

The vitamin Biotin and the protein avidin form one of the strongest non-covalent bonds between biological molecules. We have performed molecular and stochastic dynamic modeling of the unbinding of this complex(Izrailev et al., Biophysical Journal, In press). These simulations provide insight into the effect of particular residues and water on the tight binding of the system. With the aid of simple phenomenological models we have related qualitatively our results to Atomic Force Microscopy adhesion force measurements (E.-L. Florin, V. T. Moy and H. E. Gaub Science) 264:415-417 and kinetic dissociation experiments( A. Chilcotti and P. S. Stayton, J. Am. Chem. Soc.) 117:10622-10628. We will discuss the difficulties preventing a more quantitative understanding of the unbinding force and kinetics.

Prestimulus alpha-band power biases visual discrimination confidence, but not accuracy.

PubMed

Samaha, Jason; Iemi, Luca; Postle, Bradley R

2017-09-01

The magnitude of power in the alpha-band (8-13Hz) of the electroencephalogram (EEG) prior to the onset of a near threshold visual stimulus predicts performance. Together with other findings, this has been interpreted as evidence that alpha-band dynamics reflect cortical excitability. We reasoned, however, that non-specific changes in excitability would be expected to influence signal and noise in the same way, leaving actual discriminability unchanged. Indeed, using a two-choice orientation discrimination task, we found that discrimination accuracy was unaffected by fluctuations in prestimulus alpha power. Decision confidence, on the other hand, was strongly negatively correlated with prestimulus alpha power. This finding constitutes a clear dissociation between objective and subjective measures of visual perception as a function of prestimulus cortical excitability. This dissociation is predicted by a model where the balance of evidence supporting each choice drives objective performance but only the magnitude of evidence supporting the selected choice drives subjective reports, suggesting that human perceptual confidence can be suboptimal with respect to tracking objective accuracy. Copyright © 2017 Elsevier Inc. All rights reserved.

Quintet multiexciton dynamics in singlet fission

DOE PAGES

Tayebjee, Murad J. Y.; Sanders, Samuel N.; Kumarasamy, Elango; ...

2016-10-17

Singlet fission, in which two triplet excitons are generated from a single absorbed photon, is a key third-generation solar cell concept. Conservation of angular momentum requires that singlet fission populates correlated multiexciton states, which can subsequently dissociate to generate free triplets. However, little is known about electronic and spin correlations in these systems since, due to its typically short lifetime, the multiexciton state is challenging to isolate and study. Here, we use bridged pentacene dimers, which undergo intramolecular singlet fission while isolated in solution and in solid matrices, as a unimolecular model system that can trap long-lived multiexciton states. Wemore » also combine transient absorption and time-resolved electron spin resonance spectroscopies to show that spin correlations in the multiexciton state persist for hundreds of nanoseconds. Furthermore, we confirm long-standing predictions that singlet fission produces triplet pair states of quintet character. Finally, we compare two different pentacene–bridge–pentacene chromophores, systematically tuning the coupling between the pentacenes to understand how differences in molecular structure affect the population and dissociation of multiexciton quintet states.« less

Simplified model to describe the dissociative recombination of linear polyatomic ions of astrophysical interest

NASA Astrophysics Data System (ADS)

Douguet, N.; Fonseca dos Santos, S.; Kokoouline, V.; Orel, A. E.

2015-01-01

We present results of a theoretical study on dissociative recombination of the HCNH+, HCO+ and N2H+ linear polyatomic ions at low energies using a simple theoretical model. In the present study, the indirect mechanism for recombination proceeds through the capture of the incoming electron in excited vibrational Rydberg states attached to the degenerate transverse modes of the linear ions. The strength of the non-adiabatic coupling responsible for dissociative recombination is determined directly from the near-threshold scattering matrix obtained numerically using the complex Kohn variational method. The final cross sections for the process are compared with available experimental data. It is demonstrated that at low collision energies, the major contribution to the dissociative recombination cross section is due to the indirect mechanism.

Measurement of the velocity of neutral fragments by the "correlated ion and neutral time of flight" method combined with "velocity-map imaging"

NASA Astrophysics Data System (ADS)

Berthias, F.; Feketeová, L.; Della Negra, R.; Dupasquier, T.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Märk, T. D.

2017-08-01

In the challenging field of imaging molecular dynamics, a novel method has been developed and implemented that allows the measurement of the velocity of neutral fragments produced in collision induced dissociation experiments on an event-by-event basis. This has been made possible by combining a correlated ion and neutral time of flight method with a velocity map imaging technique. This new method relies on a multiparametric correlated detection of the neutral and charged fragments from collision induced dissociation on one single detector. Its implementation on the DIAM device (Device for irradiation of biomolecular clusters) (Dispositif d'Irradiation d'Agrégats bioMoléculaires) allowed us to measure the velocity distribution of water molecules evaporated from collision induced dissociation of mass- and energy-selected protonated water clusters.

ArF laser photodissociation dynamics of hydroxyacetone: LIF observation of OH and its reaction rate with the parent

NASA Astrophysics Data System (ADS)

Chowdhury, Pradyot K.; Upadhyaya, Hari P.; Naik, Prakash D.; Mittal, Jai P.

2002-01-01

Upon photoexcitation at 193 nm, hydroxyacetone dissociation appears to give CH 3 and COCH 2OH radicals as primary products, and the latter undergoes further dissociation to OH and ketene. Real time LIF observation of OH formation shows a dissociation rate of COCH 2OH as (4.6±0.5)×10 6 s-1. There is no significant population (<1%) in excited vibrational levels of OH ( X2Π) observed. The rotational state distribution has a Boltzmann temperature of the OH photofragment 380±40 K. Doppler spectroscopy shows an average translational energy with the OH photofragment as 3.6±1.3 kcal mol-1. The bimolecular rate constant for OH + hydroxyacetone is (2.8±0.2)×10 -12 cm3 molecule-1 s-1.

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

Li, Chunhua; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108; Lv, Dashuai

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regionsmore » between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.« less

Seniority number description of potential energy surfaces: Symmetric dissociation of water, N{sub 2}, C{sub 2}, and Be{sub 2}

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

Bytautas, Laimutis; Scuseria, Gustavo E.; Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589

2015-09-07

The present study further explores the concept of the seniority number (Ω) by examining different configuration interaction (CI) truncation strategies in generating compact wave functions in a systematic way. While the role of Ω in addressing static (strong) correlation problem has been addressed in numerous previous studies, the usefulness of seniority number in describing weak (dynamic) correlation has not been investigated in a systematic way. Thus, the overall objective in the present work is to investigate the role of Ω in addressing also dynamic electron correlation in addition to the static correlation. Two systematic CI truncation strategies are compared beyondmore » minimal basis sets and full valence active spaces. One approach is based on the seniority number (defined as the total number of singly occupied orbitals in a determinant) and another is based on an excitation-level limitation. In addition, molecular orbitals are energy-optimized using multiconfigurational-self-consistent-field procedure for all these wave functions. The test cases include the symmetric dissociation of water (6-31G), N{sub 2} (6-31G), C{sub 2} (6-31G), and Be{sub 2} (cc-pVTZ). We find that the potential energy profile for H{sub 2}O dissociation can be reasonably well described using only the Ω = 0 sector of the CI wave function. For the Be{sub 2} case, we show that the full CI potential energy curve (cc-pVTZ) is almost exactly reproduced using either Ω-based (including configurations having up to Ω = 2 in the virtual-orbital-space) or excitation-based (up to single-plus-double-substitutions) selection methods, both out of a full-valence-reference function. Finally, in dissociation cases of N{sub 2} and C{sub 2}, we shall also consider novel hybrid wave functions obtained by a union of a set of CI configurations representing the full valence space and a set of CI configurations where seniority-number restriction is imposed for a complete set (full-valence-space and virtual) of correlated molecular orbitals, simultaneously. We discuss the usefulness of the seniority number concept in addressing both static and dynamic electron correlation problems along dissociation paths.« less

Dissociation as a mediator of the relationship between childhood trauma and nonsuicidal self-injury in females: a path analytic approach.

PubMed

Franzke, Iris; Wabnitz, Pascal; Catani, Claudia

2015-01-01

New theoretical models of nonsuicidal self-injury (NSSI) postulate that symptoms subsequent to childhood maltreatment rather than childhood maltreatment itself may lead to engagement in NSSI. However, little is known concerning which specific syndromes serve as underlying mechanisms. In this study we sought to examine the mediating effects of dissociative, posttraumatic, and depressive symptoms, 3 often comorbid syndromes following childhood trauma. In addition, we aimed to assess differences between women with and without NSSI. A sample of 87 female inpatients with a history of childhood abuse and neglect was divided into 2 subgroups (NSSI: n = 42, no NSSI: n = 45). The assessment included measures of NSSI characteristics; adverse childhood experiences; and posttraumatic, dissociative, and depressive symptoms. The NSSI group reported significantly more cases of childhood maltreatment and higher levels of current dissociative, posttraumatic, and depressive symptoms than patients without NSSI. The results of a path analysis showed that only dissociation mediated the relationship between a history of child maltreatment and NSSI when all 3 psychopathological variables were included in the model. The findings point toward a strong and rather specific association between dissociative experiences and NSSI and therefore have important implications for clinical practice.

Activation of Peptide ions by blackbody radiation: factors that lead to dissociation kinetics in the rapid energy exchange limit.

PubMed

Price, W D; Williams, E R

1997-11-20

Unimolecular rate constants for blackbody infrared radiative dissociation (BIRD) were calculated for the model protonated peptide (AlaGly)(n) (n = 2-32) using a variety of dissociation parameters. Combinations of dissociation threshold energies ranging from 0.8 to 1.7 eV and transition entropies corresponding to Arrhenius preexponential factors ranging from very "tight" (A(infinity) = 10(9.9) s(-1)) to "loose" (A(infinity) = 10(16.8) s(-1)) were selected to represent dissociation parameters within the experimental temperature range (300-520 K) and kinetic window (k(uni) = 0.001-0.20 s(-1)) typically used in the BIRD experiment. Arrhenius parameters were determined from the temperature dependence of these values and compared to those in the rapid energy exchange (REX) limit. In this limit, the internal energy of a population of ions is given by a Boltzmann distribution, and kinetics are the same as those in the traditional high-pressure limit. For a dissociation process to be in this limit, the rate of photon exchange between an ion and the vacuum chamber walls must be significantly greater than the dissociation rate. Kinetics rapidly approach the REX limit either as the molecular size or threshold dissociation energy increases or as the transition-state entropy or experimental temperature decreases. Under typical experimental conditions, peptide ions larger than 1.6 kDa should be in the REX limit. Smaller ions may also be in the REX limit depending on the value of the threshold dissociation energy and transition-state entropy. Either modeling or information about the dissociation mechanism must be known in order to confirm REX limit kinetics for these smaller ions. Three principal factors that lead to the size dependence of REX limit kinetics are identified. With increasing molecular size, rates of radiative absorption and emission increase, internal energy distributions become relatively narrower, and the microcanonical dissociation rate constants increase more slowly over the energy distribution of ions. Guidelines established here should make BIRD an even more reliable method to obtain information about dissociation energetics and mechanisms for intermediate size molecules.

Activation of Peptide Ions by Blackbody Radiation: Factors That Lead to Dissociation Kinetics in the Rapid Energy Exchange Limit

PubMed Central

Price, William D.

2005-01-01

Unimolecular rate constants for blackbody infrared radiative dissociation (BIRD) were calculated for the model protonated peptide (AlaGly)n (n = 2–32) using a variety of dissociation parameters. Combinations of dissociation threshold energies ranging from 0.8 to 1.7 eV and transition entropies corresponding to Arrhenius preexponential factors ranging from very “tight” (A∞ = 109.9 s−1) to “loose” (A∞ = 1016.8 s−1) were selected to represent dissociation parameters within the experimental temperature range (300–520 K) and kinetic window (kuni = 0.001–0.20 s−1) typically used in the BIRD experiment. Arrhenius parameters were determined from the temperature dependence of these values and compared to those in the rapid energy exchange (REX) limit. In this limit, the internal energy of a population of ions is given by a Boltzmann distribution, and kinetics are the same as those in the traditional high-pressure limit. For a dissociation process to be in this limit, the rate of photon exchange between an ion and the vacuum chamber walls must be significantly greater than the dissociation rate. Kinetics rapidly approach the REX limit either as the molecular size or threshold dissociation energy increases or as the transition-state entropy or experimental temperature decreases. Under typical experimental conditions, peptide ions larger than 1.6 kDa should be in the REX limit. Smaller ions may also be in the REX limit depending on the value of the threshold dissociation energy and transition-state entropy. Either modeling or information about the dissociation mechanism must be known in order to confirm REX limit kinetics for these smaller ions. Three principal factors that lead to the size dependence of REX limit kinetics are identified. With increasing molecular size, rates of radiative absorption and emission increase, internal energy distributions become relatively narrower, and the microcanonical dissociation rate constants increase more slowly over the energy distribution of ions. Guidelines established here should make BIRD an even more reliable method to obtain information about dissociation energetics and mechanisms for intermediate size molecules. PMID:16604162

Dynamic Interaction of cBid with Detergents, Liposomes and Mitochondria

PubMed Central

Bleicken, Stephanie; García-Sáez, Ana J.; Conte, Elena; Bordignon, Enrica

2012-01-01

The BH3-only protein Bid plays a key role in the induction of mitochondrial apoptosis, but its mechanism of action is still not completely understood. Here we studied the two main activation events of Bid: Caspase-8 cleavage and interaction with the membrane bilayer. We found a striking reversible behaviour of the dissociation-association events between the Bid fragments p15 and p7. Caspase-8 cleavage does not induce per se separation of the two Bid fragments, which remain in a stable complex resembling the full length Bid. Detergents trigger a complete dissociation, which can be fully reversed by detergent removal in a range of protein concentrations from 100 µM down to 500 nM. Incubation of cBid with cardiolipin-containing liposomes leads to partial dissociation of the complex. Only p15 (tBid) fragments are found at the membrane, while p7 shows no tendency to interact with the bilayer, but complete removal of p7 strongly increases the propensity of tBid to become membrane-associated. Despite the striking structural similarities of inactive Bid and Bax, Bid does not form oligomers and reacts differently in the presence of detergents and membranes, highlighting clear differences in the modes of action of the two proteins. The partial dissociation of cBid triggered by the membrane is suggested to depend on the strong and specific interaction between p15 and p7. The reversible disassembly and re-assembly of the cBid molecules at the membrane was as well proven by EPR using spin labeled cBid in the presence of isolated mitochondria. The observed dynamic dissociation of the two Bid fragments could allow the assistance to the pore-forming Bax to occur repeatedly and may explain the proposed “hit-and-run" mode of action of Bid at the bilayer. PMID:22540011

Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

NASA Astrophysics Data System (ADS)

Lyons, John L.

Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S. Hybertsen. It made use of resources at the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Lab.

HCl dissociating on a rigid Au(111) surface: A six-dimensional quantum mechanical study on a new potential energy surface based on the RPBE functional.

PubMed

Liu, Tianhui; Fu, Bina; Zhang, Dong H

2017-04-28

The dissociative chemisorption of HCl on the Au(111) surface has recently been an interesting and important subject, regarding the discrepancy between the theoretical dissociation probabilities and the experimental sticking probabilities. We here constructed an accurate full-dimensional (six-dimensional (6D)) potential energy surface (PES) based on the density functional theory (DFT) with the revised Perdew-Burke-Ernzerhof (RPBE) functional, and performed 6D quantum mechanical (QM) calculations for HCl dissociating on a rigid Au(111) surface. The effects of vibrational excitations, rotational orientations, and site-averaging approximation on the present RPBE PES are investigated. Due to the much higher barrier height obtained on the RPBE PES than on the PW91 PES, the agreement between the present theoretical and experimental results is greatly improved. In particular, at the very low kinetic energy, the QM-RPBE dissociation probability agrees well with the experimental data. However, the computed QM-RPBE reaction probabilities are still markedly different from the experimental values at most of the energy regions. In addition, the QM-RPBE results achieve good agreement with the recent ab initio molecular dynamics calculations based on the RPBE functional at high kinetic energies.

Reservoir Models for Gas Hydrate Numerical Simulation

NASA Astrophysics Data System (ADS)

Boswell, R.

2016-12-01

Scientific and industrial drilling programs have now providing detailed information on gas hydrate systems that will increasingly be the subject of field experiments. The need to carefully plan these programs requires reliable prediction of reservoir response to hydrate dissociation. Currently, a major emphasis in gas hydrate modeling is the integration of thermodynamic/hydrologic phenomena with geomechanical response for both reservoir and bounding strata. However, also critical to the ultimate success of these efforts is the appropriate development of input geologic models, including several emerging issues, including (1) reservoir heterogeneity, (2) understanding of the initial petrophysical characteristics of the system (reservoirs and seals), the dynamic evolution of those characteristics during active dissociation, and the interdependency of petrophysical parameters and (3) the nature of reservoir boundaries. Heterogeneity is ubiquitous aspect of every natural reservoir, and appropriate characterization is vital. However, heterogeneity is not random. Vertical variation can be evaluated with core and well log data; however, core data often are challenged by incomplete recovery. Well logs also provide interpretation challenges, particularly where reservoirs are thinly-bedded due to limitation in vertical resolution. This imprecision will extend to any petrophysical measurements that are derived from evaluation of log data. Extrapolation of log data laterally is also complex, and should be supported by geologic mapping. Key petrophysical parameters include porosity, permeability and it many aspects, and water saturation. Field data collected to date suggest that the degree of hydrate saturation is strongly controlled by/dependant upon reservoir quality and that the ratio of free to bound water in the remaining pore space is likely also controlled by reservoir quality. Further, those parameters will also evolve during dissociation, and not necessary in a simple/linear way. Significant progress has also occurred in recent years with regard to the geologic characterization of reservoir boundaries. Vertical boundaries with overlying clay-rich "seals" are now widely-appreciated to have non-zero permeability, and lateral boundaries are sources of potential lateral fluid flow.

Assessing the existence of dissociative PTSD in sub-acute patients of whiplash.

PubMed

Hansen, Maj; Hyland, Philip; Armour, Cherie; Andersen, Tonny E

2018-03-16

Numerous studies investigating dissociative posttraumatic stress disorder (D-PTSD) have emerged. However, there is a lack of studies investigating D-PTSD following a wider range of traumatic exposure. Thus, the present study investigates D-PTSD using latent class analysis (LCA) in sub-acute patients of whiplash and associated risk factors. The results of LCA showed a three-class solution primarily distributed according to posttraumatic stress disorder (PTSD) symptom severity and thus no indication of D-PTSD. Dissociative symptoms, psychological distress (i.e. anxiety/depression), and pain severity significantly predicted PTSD severity. Combined, the results support the component model of dissociation and PTSD, while still stressing the importance of dissociative symptoms when planning treatment for PTSD.

Perspectives on the conceptualization of the dissociative subtype of PTSD and implications for treatment.

PubMed

Dutra, Sunny J; Wolf, Erika J

2017-04-01

A dissociative subtype of PTSD was added to the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) to denote a distinct presentation of PTSD marked by symptoms of derealization and depersonalization. The subtype has brought renewed interest in the conceptualization of dissociation in PTSD, and raised questions about its treatment. We review the evidence for two models of PTSD-related dissociative symptoms and the treatment approaches that align with each. We find support for the contributions of biologically-based trait-level factors to dissociation, and suggest that empirically supported treatments for PTSD demonstrate efficacy for patients with the subtype. Published by Elsevier Ltd.

On the origin of ultrafast nonradiative transitions in nitro-polycyclic aromatic hydrocarbons: Excited-state dynamics in 1-nitronaphthalene.

PubMed

Reichardt, Christian; Vogt, R Aaron; Crespo-Hernández, Carlos E

2009-12-14

The electronic energy relaxation of 1-nitronaphthalene was studied in nonpolar, aprotic, and protic solvents in the time window from femtoseconds to microseconds. Excitation at 340 or 360 nm populates the Franck-Condon S(1)(pipi( *)) state, which is proposed to bifurcate into two essentially barrierless nonradiative decay channels with sub-200 fs lifetimes. The first main decay channel connects the S(1) state with a receiver T(n) state that has considerable npi( *) character. The receiver T(n) state undergoes internal conversion to populate the vibrationally excited T(1)(pipi( *)) state in 2-4 ps. It is shown that vibrational cooling dynamics in the T(1) state depends on the solvent used, with average lifetimes in the range from 6 to 12 ps. Furthermore, solvation dynamics competes effectively with vibrational cooling in the triplet manifold in primary alcohols. The relaxed T(1) state undergoes intersystem crossing back to the ground state within a few microseconds in N(2)-saturated solutions in all the solvents studied. The second minor channel involves conformational relaxation of the bright S(1) state (primarily rotation of the NO(2)-group) to populate a dissociative singlet state with significant charge-transfer character and negligible oscillator strength. This dissociative channel is proposed to be responsible for the observed photochemistry in 1-nitronaphthalene. Ground- and excited-state calculations at the density functional level of theory that include bulk and explicit solvent effects lend support to the proposed mechanism where the fluorescent S(1) state decays rapidly and irreversibly to dark excited states. A four-state kinetic model is proposed that satisfactorily explains the origin of the nonradiative electronic relaxation pathways in 1-nitronaphthalene.

Synaptic activity induces input-specific rearrangements in a targeted synaptic protein interaction network.

PubMed

Lautz, Jonathan D; Brown, Emily A; VanSchoiack, Alison A Williams; Smith, Stephen E P

2018-05-27

Cells utilize dynamic, network level rearrangements in highly interconnected protein interaction networks to transmit and integrate information from distinct signaling inputs. Despite the importance of protein interaction network dynamics, the organizational logic underlying information flow through these networks is not well understood. Previously, we developed the quantitative multiplex co-immunoprecipitation platform, which allows for the simultaneous and quantitative measurement of the amount of co-association between large numbers of proteins in shared complexes. Here, we adapt quantitative multiplex co-immunoprecipitation to define the activity dependent dynamics of an 18-member protein interaction network in order to better understand the underlying principles governing glutamatergic signal transduction. We first establish that immunoprecipitation detected by flow cytometry can detect activity dependent changes in two known protein-protein interactions (Homer1-mGluR5 and PSD-95-SynGAP). We next demonstrate that neuronal stimulation elicits a coordinated change in our targeted protein interaction network, characterized by the initial dissociation of Homer1 and SynGAP-containing complexes followed by increased associations among glutamate receptors and PSD-95. Finally, we show that stimulation of distinct glutamate receptor types results in different modular sets of protein interaction network rearrangements, and that cells activate both modules in order to integrate complex inputs. This analysis demonstrates that cells respond to distinct types of glutamatergic input by modulating different combinations of protein co-associations among a targeted network of proteins. Our data support a model of synaptic plasticity in which synaptic stimulation elicits dissociation of preexisting multiprotein complexes, opening binding slots in scaffold proteins and allowing for the recruitment of additional glutamatergic receptors. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Using open hole and cased-hole resistivity logs to monitor gas hydrate dissociation during a thermal test in the mallik 5L-38 research well, Mackenzie Delta, Canada

USGS Publications Warehouse

Anderson, B.I.; Collett, T.S.; Lewis, R.E.; Dubourg, I.

2008-01-01

Gas hydrates, which are naturally occurring ice-like combinations of gas and water, have the potential to provide vast amounts of natural gas from the world's oceans and polar regions. However, producing gas economically from hydrates entails major technical challenges. Proposed recovery methods such as dissociating or melting gas hydrates by heating or depressurization are currently being tested. One such test was conducted in northern Canada by the partners in the Mallik 2002 Gas Hydrate Production Research Well Program. This paper describes how resistivity logs were used to determine the size of the annular region of gas hydrate dissociation that occurred around the wellbore during the thermal test in the Mallik 5L-38 well. An open-hole logging suite, run prior to the thermal test, included array induction, array laterolog, nuclear magnetic resonance and 1.1-GHz electromagnetic propagation logs. The reservoir saturation tool was run both before and after the thermal test to monitor formation changes. A cased-hole formation resistivity log was run after the test.Baseline resistivity values in each formation layer (Rt) were established from the deep laterolog data. The resistivity in the region of gas hydrate dissociation near the wellbore (Rxo) was determined from electromagnetic propagation and reservoir saturation tool measurements. The radius of hydrate dissociation as a function of depth was then determined by means of iterative forward modeling of cased-hole formation resistivity tool response. The solution was obtained by varying the modeled dissociation radius until the modeled log overlaid the field log. Pretest gas hydrate production computer simulations had predicted that dissociation would take place at a uniform radius over the 13-ft test interval. However, the post-test resistivity modeling showed that this was not the case. The resistivity-derived dissociation radius was greatest near the outlet of the pipe that circulated hot water in the wellbore, where the highest temperatures were recorded. The radius was smallest near the center of the test interval, where a conglomerate section with low values of porosity and permeability inhibited dissociation. The free gas volume calculated from the resistivity-derived dissociation radii yielded a value within 20 per cent of surface gauge measurements. These results show that the inversion of resistivity measurements holds promise for use in future gas hydrate monitoring. ?? 2008 Society of Petrophysicists and Well Log Analysts. All rights reserved.

Communication: Direct evidence for sequential dissociation of gas-phase Fe(CO)5 via a singlet pathway upon excitation at 266 nm

PubMed Central

Leitner, T.; Mazza, T.; Schröder, H.; Kunnus, K.; Schreck, S.; Radcliffe, P.; Düsterer, S.; Meyer, M.; Föhlisch, A.

2017-01-01

We prove the hitherto hypothesized sequential dissociation of Fe(CO)5 in the gas phase upon photoexcitation at 266 nm via a singlet pathway with time-resolved valence and core-level photoelectron spectroscopy with an x-ray free-electron laser. Valence photoelectron spectra are used to identify free CO molecules and to determine the time constants of stepwise dissociation to Fe(CO)4 within the temporal resolution of the experiment and further to Fe(CO)3 within 3 ps. Fe 3p core-level photoelectron spectra directly reflect the singlet spin state of the Fe center in Fe(CO)5, Fe(CO)4, and Fe(CO)3 showing that the dissociation exclusively occurs along a singlet pathway without triplet-state contribution. Our results are important for assessing intra- and intermolecular relaxation processes in the photodissociation dynamics of the prototypical Fe(CO)5 complex in the gas phase and in solution, and they establish time-resolved core-level photoelectron spectroscopy as a powerful tool for determining the multiplicity of transition metals in photochemical reactions of coordination complexes. PMID:28595420

Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation.

PubMed

Saba, Julian; Dutta, Sucharita; Hemenway, Eric; Viner, Rosa

2012-01-01

Currently, glycans are attracting attention from the scientific community as potential biomarkers or as posttranslational modifications (PTMs) of therapeutic proteins. However, structural characterization of glycoproteins and glycopeptides remains analytically challenging. Here, we report on the implementation of a novel acquisition strategy termed higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation (HCD-PD-ETD) on a hybrid linear ion trap-orbitrap mass spectrometer. This acquisition strategy uses the complementary fragmentations of ETD and HCD for glycopeptides analysis in an intelligent fashion. Furthermore, the approach minimizes user input for optimizing instrumental parameters and enables straightforward detection of glycopeptides. ETD spectra are only acquired when glycan oxonium ions from MS/MS HCD are detected. The advantage of this approach is that it streamlines data analysis and improves dynamic range and duty cycle. Here, we present the benefits of HCD-PD-ETD relative to the traditional alternating HCD/ETD for a trainer set containing twelve-protein mixture with two glycoproteins: human serotransferrin, ovalbumin and contaminations of two other: bovine alpha 1 acid glycoprotein (bAGP) and bovine fetuin.

Parallel-Distinct Structures of Internal World and External Reality: Disavowing and Re-Claiming the Self-Identity in the Aftermath of Trauma-Generated Dissociation

PubMed Central

Şar, Vedat

2017-01-01

The nature of consciousness and the autonomy of the individual's mind have been a focus of interest throughout the past century and inspired many theories and models. Revival of studies on psychological trauma and dissociation, which remained outside mainstream psychiatry, psychology, and psychoanalysis for the most part of the past century, has provided a new opportunity to revisit this intellectual and scientific endeavor. This paper attempts to integrate a series of empirical and theoretical studies on psychological consequences of developmental traumatization, which may yield further insight into factors which threaten the integrity of human consciousness. The paper proposes that an individual's experience of distorted reality and betrayal precipitates a cyclical dynamic between the individual and the external world by disrupting the developmental function of mutuality which is essential for maintenance of the integrity of the internal world while this inner world is in turn regulated vis-à-vis external reality. Dissociation -the common factor in all types of post-traumatic syndromes- is facilitated by violation of boundaries by relational omission and intrusion as represented by distinct effects and consequences of childhood neglect and abuse. Recent research conducted on clinical and non-clinical populations shows both bimodal (undermodulation and overmodulation) and bipolar (intrusion and avoidance) neurobiological and phenomenological characteristics of post-traumatic response. These seem to reflect “parallel-distinct structures” that control separate networks covering sensori-motor and cognitive-emotional systems. This understanding provides a conceptual framework to assist explanation of diverse post-traumatic mental trajectories which culminate in a common final pathway comprised of partly overlapping clinical syndromes such as complex PTSD, dissociative depression, dissociative identity disorder (DID), or “borderline” phenomena. Of crucial theoretical and clinical importance is that these maladaptive post-traumatic psychological formations are regarded as processes in their own right rather than as a personality disorder innate to the individual. Such mental division may perform in that internal detachment can serve to preserve the genuine aspects of the subject until such time as they can be reclaimed via psychotherapy. The paper attempts to integrate these ideas with reference to the previously proposed theory of the “Functional Dissociation of Self” (Şar and Öztürk, 2007). PMID:28261144

Parallel-Distinct Structures of Internal World and External Reality: Disavowing and Re-Claiming the Self-Identity in the Aftermath of Trauma-Generated Dissociation.

PubMed

Şar, Vedat

2017-01-01

The nature of consciousness and the autonomy of the individual's mind have been a focus of interest throughout the past century and inspired many theories and models. Revival of studies on psychological trauma and dissociation, which remained outside mainstream psychiatry, psychology, and psychoanalysis for the most part of the past century, has provided a new opportunity to revisit this intellectual and scientific endeavor. This paper attempts to integrate a series of empirical and theoretical studies on psychological consequences of developmental traumatization, which may yield further insight into factors which threaten the integrity of human consciousness. The paper proposes that an individual's experience of distorted reality and betrayal precipitates a cyclical dynamic between the individual and the external world by disrupting the developmental function of mutuality which is essential for maintenance of the integrity of the internal world while this inner world is in turn regulated vis-à-vis external reality. Dissociation -the common factor in all types of post-traumatic syndromes- is facilitated by violation of boundaries by relational omission and intrusion as represented by distinct effects and consequences of childhood neglect and abuse. Recent research conducted on clinical and non-clinical populations shows both bimodal (undermodulation and overmodulation) and bipolar (intrusion and avoidance) neurobiological and phenomenological characteristics of post-traumatic response. These seem to reflect "parallel-distinct structures" that control separate networks covering sensori-motor and cognitive-emotional systems. This understanding provides a conceptual framework to assist explanation of diverse post-traumatic mental trajectories which culminate in a common final pathway comprised of partly overlapping clinical syndromes such as complex PTSD, dissociative depression, dissociative identity disorder (DID), or "borderline" phenomena. Of crucial theoretical and clinical importance is that these maladaptive post-traumatic psychological formations are regarded as processes in their own right rather than as a personality disorder innate to the individual. Such mental division may perform in that internal detachment can serve to preserve the genuine aspects of the subject until such time as they can be reclaimed via psychotherapy. The paper attempts to integrate these ideas with reference to the previously proposed theory of the "Functional Dissociation of Self" (Şar and Öztürk, 2007).

Investigation of the external flow analysis for density measurements at high altitude

NASA Technical Reports Server (NTRS)

Bienkowski, G. K.

1984-01-01

The results of analysis performed on the external flow around the shuttle orbiter nose regions at the Shuttle Upper Atmosphere Mass Spectrometer (SUMS) inlet orifice are presented. The purpose of the analysis is to quantitatively characterize the flow conditions to facilitate SUMS flight data reduction and subsequent determination of orbiter aerodynamic force coefficients in the hypersonic rarefied flow regime. Experimental determination of aerodynamic force coefficients requires accurate simultaneous measurement of forces (or acceleration) and dynamic pressure along with independent knowledge of density and velocity. The SUMS provides independent measurement of dynamic pressure; however, it does so indirectly and requires knowledge of the relationship between measured orifice conditions and the dynamic pressure which can only be determined on the basis of molecule or theory for a winged configuration. Monte Carlo direct simulation computer codes were developed for both the flow field solution at the orifice and for the internal orifice flow. These codes were used to study issues associated with geometric modeling of the orbiter nose geometry and the modeling of intermolecular collisions including rotational energy exchange and a preliminary analysis of vibrational excitation and dissociation effects. Data obtained from preliminary simulation runs are presented.

In Situ Graphene Growth Dynamics on Polycrystalline Catalyst Foils

PubMed Central

2016-01-01

The dynamics of graphene growth on polycrystalline Pt foils during chemical vapor deposition (CVD) are investigated using in situ scanning electron microscopy and complementary structural characterization of the catalyst with electron backscatter diffraction. A general growth model is outlined that considers precursor dissociation, mass transport, and attachment to the edge of a growing domain. We thereby analyze graphene growth dynamics at different length scales and reveal that the rate-limiting step varies throughout the process and across different regions of the catalyst surface, including different facets of an individual graphene domain. The facets that define the domain shapes lie normal to slow growth directions, which are determined by the interfacial mobility when attachment to domain edges is rate-limiting, as well as anisotropy in surface diffusion as diffusion becomes rate-limiting. Our observations and analysis thus reveal that the structure of CVD graphene films is intimately linked to that of the underlying polycrystalline catalyst, with both interfacial mobility and diffusional anisotropy depending on the presence of step edges and grain boundaries. The growth model developed serves as a general framework for understanding and optimizing the growth of 2D materials on polycrystalline catalysts. PMID:27576749

Chemistry at molecular junctions: Rotation and dissociation of O2 on the Ag(110) surface induced by a scanning tunneling microscope.

PubMed

Roy, Sharani; Mujica, Vladimiro; Ratner, Mark A

2013-08-21

The scanning tunneling microscope (STM) is a fascinating tool used to perform chemical processes at the single-molecule level, including bond formation, bond breaking, and even chemical reactions. Hahn and Ho [J. Chem. Phys. 123, 214702 (2005)] performed controlled rotations and dissociations of single O2 molecules chemisorbed on the Ag(110) surface at precise bias voltages using STM. These threshold voltages were dependent on the direction of the bias voltage and the initial orientation of the chemisorbed molecule. They also observed an interesting voltage-direction-dependent and orientation-dependent pathway selectivity suggestive of mode-selective chemistry at molecular junctions, such that in one case the molecule underwent direct dissociation, whereas in the other case it underwent rotation-mediated dissociation. We present a detailed, first-principles-based theoretical study to investigate the mechanism of the tunneling-induced O2 dynamics, including the origin of the observed threshold voltages, the pathway dependence, and the rate of O2 dissociation. Results show a direct correspondence between the observed threshold voltage for a process and the activation energy for that process. The pathway selectivity arises from a competition between the voltage-modified barrier heights for rotation and dissociation, and the coupling strength of the tunneling electrons to the rotational and vibrational modes of the adsorbed molecule. Finally, we explore the "dipole" and "resonance" mechanisms of inelastic electron tunneling to elucidate the energy transfer between the tunneling electrons and chemisorbed O2.

Pressure-Accelerated Dissociation of Amyloid Fibrils in Wild-Type Hen Lysozyme

PubMed Central

Shah, Buddha R.; Maeno, Akihiro; Matsuo, Hiroshi; Tachibana, Hideki; Akasaka, Kazuyuki

2012-01-01

The dynamics of amyloid fibrils, including their formation and dissociation, could be of vital importance in life. We studied the kinetics of dissociation of the amyloid fibrils from wild-type hen lysozyme at 25°C in vitro as a function of pressure using Trp fluorescence as a probe. Upon 100-fold dilution of 8 mg ml−1 fibril solution in 80 mM NaCl, pH 2.2, no immediate change occurred in Trp fluorescence, but at pressures of 50–450 MPa the fluorescence intensity decreased rapidly with time (kobs = 0.00193 min−1 at 0.1 MPa, 0.0348 min−1 at 400 MPa). This phenomenon is attributable to the pressure-accelerated dissociation of amyloid fibrils into monomeric hen lysozyme. From the pressure dependence of the rates, which reaches a plateau at ∼450 MPa, we determined the activation volume ΔV0‡ = −32.9 ± 1.7 ml mol(monomer)−1 and the activation compressibility Δκ‡ = −0.0075 ± 0.0006 ml mol(monomer)−1 bar−1 for the dissociation reaction. The negative ΔV0‡ and Δκ‡ values are consistent with the notion that the amyloid fibril from wild-type hen lysozyme is in a high-volume and high-compressibility state, and the transition state for dissociation is coupled with a partial hydration of the fibril. PMID:22225805

EEG source reconstruction evidence for the noun-verb neural dissociation along semantic dimensions.

PubMed

Zhao, Bin; Dang, Jianwu; Zhang, Gaoyan

2017-09-17

One of the long-standing issues in neurolinguistic research is about the neural basis of word representation, concerning whether grammatical classification or semantic difference causes the neural dissociation of brain activity patterns when processing different word categories, especially nouns and verbs. To disentangle this puzzle, four orthogonalized word categories in Chinese: unambiguous nouns (UN), unambiguous verbs (UV), ambiguous words with noun-biased semantics (AN), and ambiguous words with verb-biased semantics (AV) were adopted in an auditory task for recording electroencephalographic (EEG) signals from 128 electrodes on the scalps of twenty-two subjects. With the advanced current density reconstruction (CDR) algorithm and the constraint of standardized low-resolution electromagnetic tomography, the spatiotemporal brain dynamics of word processing were explored with the results that in multiple time periods including P1 (60-90ms), N1 (100-140ms), P200 (150-250ms) and N400 (350-450ms), noun-verb dissociation over the parietal-occipital and frontal-central cortices appeared not only between the UN-UV grammatical classes but also between the grammatically identical but semantically different AN-AV pairs. The apparent semantic dissociation within one grammatical class strongly suggests that the semantic difference rather than grammatical classification could be interpreted as the origin of the noun-verb neural dissociation. Our results also revealed that semantic dissociation occurs from an early stage and repeats in multiple phases, thus supporting a functionally hierarchical word processing mechanism. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

The effects of individual biological rhythm differences on sleep quality, daytime sleepiness, and dissociative experiences.

PubMed

Selvi, Yavuz; Kandeger, Ali; Boysan, Murat; Akbaba, Nursel; Sayin, Ayca A; Tekinarslan, Emine; Koc, Basak O; Uygur, Omer F; Sar, Vedat

2017-10-01

Individuals who differ markedly by sleep chronotype, i.e., morning-type or evening-type also differ on a number of psychological, behavioral, and biological variables. Among several other psychological functions, dissociation may also lead to disruption and alteration of consciousness, which may facilitate dream-like experiences. Our study was aimed at an inquiry into the effects of individual biological rhythm differences on sleep quality and daytime sleepiness in conjunction with dissociative experiences. Participants were 372 undergraduate college students, completed a package of psychological instruments, including the Morningness-Eveningness Questionnaire, Dissociative Experiences Scale, Insomnia Severity Index, and Epworth Sleepiness Scale. Using logistic regression models, direct relations of pathological dissociation with sleepiness, sleep quality and circadian preferences were investigated. Poor sleep quality and sleepiness significantly contributed to the variance of dissociative symptomatology. Although there was no substantial linear association between circadian preferences and pathological dissociation, having evening-type preferences of sleep was indirectly associated with higher dissociation mediated by poor sleep quality. Poor sleep quality and daytime sleepiness seems to be significant antecedents of pathological dissociation. Sleep chronotype preferences underlie this relational pattern that chronobiological characteristics seem to influence indirectly on dissociative tendency via sleep quality. Copyright © 2017 Elsevier B.V. All rights reserved.

Frontal and occipital perfusion changes in dissociative identity disorder.

PubMed

Sar, Vedat; Unal, Seher N; Ozturk, Erdinc

2007-12-15

The aim of the study was to investigate if there were any characteristics of regional cerebral blood flow (rCBF) in dissociative identity disorder. Twenty-one drug-free patients with dissociative identity disorder and nine healthy volunteers participated in the study. In addition to a clinical evaluation, dissociative psychopathology was assessed using the Structured Clinical Interview for DSM-IV Dissociative Disorders, the Dissociative Experiences Scale and the Clinician-Administered Dissociative States Scale. A semi-structured interview for borderline personality disorder, the Hamilton Depression Rating Scale, and the Childhood Trauma Questionnaire were also administered to all patients. Normal controls had to be without a history of childhood trauma and without any depressive or dissociative disorder. Regional cerebral blood flow (rCBF) was studied with single photon emission computed tomography (SPECT) with Tc99m-hexamethylpropylenamine (HMPAO) as a tracer. Compared with findings in the control group, the rCBF ratio was decreased among patients with dissociative identity disorder in the orbitofrontal region bilaterally. It was increased in median and superior frontal regions and occipital regions bilaterally. There was no significant correlation between rCBF ratios of the regions of interest and any of the psychopathology scale scores. An explanation for the neurophysiology of dissociative psychopathology has to invoke a comprehensive model of interaction between anterior and posterior brain regions.

The influence of family environment on dissociation in pediatric injury patients.

PubMed

Nugent, Nicole R; Sledjeski, Eve M; Christopher, Norman C; Delahanty, Douglas L

2011-10-01

Emerging support for the roles of both early trauma and family environment in the development of dissociative symptomatology is complicated by the frequent co-occurrence of dysfunctional family environments and childhood maltreatment. The present investigation prospectively examined the influence of family environment on dissociative symptom course in 82 youths (8-18 years) who experienced accidental injury. The primary caretaker reported on six-week family environment (including family cohesion and adaptability) and on youth symptoms of dissociation prior to injury at six weeks and at six months; dissociation prior to injury was assessed via retrospective parent account at the six-week timepoint. Adolescents (aged 11-18) also reported on their own dissociative symptoms at six weeks. Latent growth modeling indicated that youth in more cohesive family environments evidenced decreased symptoms of dissociation at the six-week intercept (z = -2.80). Furthermore, parent income was negatively related to symptoms of dissociation at intercept (z = -1.96) and parent education was associated with a decrease in youth dissociation symptoms over time (z = -2.57). The present findings provide support for the importance of acute family environment in pediatric post-injury adjustment and further highlight the importance of parent resources, including income and education, in post-injury adjustment.

Attachment insecurity as a mediator of the relationship between childhood trauma and adult dissociation.

PubMed

Kong, Seong Sook; Kang, Dae Ryong; Oh, Min Jung; Kim, Nam Hee

2018-01-01

This study aimed to investigate whether attachment insecurity mediates the relationship between childhood trauma and adult dissociation, specifically with regard to individual forms of childhood maltreatment. Psychiatric outpatients who visited a specialized trauma clinic (n = 115) participated in the study. Data were collected via the Childhood Trauma Questionnaire, Revised Adult Attachment Scale, and Dissociative Experience Scale. Structural equation modeling and path analysis were performed to analyze the mediating effects of attachment insecurity on the relationship between childhood trauma and adult dissociation. Greater childhood trauma was associated with higher dissociation, and the relationship between them was fully mediated by attachment anxiety. In path analysis of trauma subtypes, the effects of emotional abuse, physical abuse, and physical neglect as a child on adult dissociation were found to be fully mediated by attachment anxiety. The effect of sexual abuse on dissociation was mediated by a synergistic effect from both attachment anxiety and attachment avoidance. Regarding emotional neglect, a countervailing interaction was discovered between the direct and indirect effects thereof on dissociation; the indirect effect of emotional neglect on dissociation was partially mediated by attachment insecurity. Specific aspects of attachment insecurity may help explain the relationships between individual forms of childhood trauma and adult dissociative symptoms. Tailored treatments based on affected areas of attachment insecurity may improve outcomes among patients with dissociative symptoms and a history of childhood trauma.

Calculation of laser induced impulse based on the laser supported detonation wave model with dissociation, ionization and radiation

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

Gan, Li, E-mail: ligan0001@gmail.com; Mousen, Cheng; Xiaokang, Li

In the laser intensity range that the laser supported detonation (LSD) wave can be maintained, dissociation, ionization and radiation take a substantial part of the incidence laser energy. There is little treatment on the phenomenon in the existing models, which brings obvious discrepancies between their predictions and the experiment results. Taking into account the impact of dissociation, ionization and radiation in the conservations of mass, momentum and energy, a modified LSD wave model is developed which fits the experimental data more effectively rather than the existing models. Taking into consideration the pressure decay of the normal and the radial rarefaction,more » the laser induced impulse that is delivered to the target surface is calculated in the air; and the dependencies of impulse performance on laser intensity, pulse width, ambient pressure and spot size are indicated. The results confirm that the dissociation is the pivotal factor of the appearance of the momentum coupling coefficient extremum. This study focuses on a more thorough understanding of LSD and the interaction between laser and matter.« less

Tracking slow modulations in synaptic gain using dynamic causal modelling: validation in epilepsy.

PubMed

Papadopoulou, Margarita; Leite, Marco; van Mierlo, Pieter; Vonck, Kristl; Lemieux, Louis; Friston, Karl; Marinazzo, Daniele

2015-02-15

In this work we propose a proof of principle that dynamic causal modelling can identify plausible mechanisms at the synaptic level underlying brain state changes over a timescale of seconds. As a benchmark example for validation we used intracranial electroencephalographic signals in a human subject. These data were used to infer the (effective connectivity) architecture of synaptic connections among neural populations assumed to generate seizure activity. Dynamic causal modelling allowed us to quantify empirical changes in spectral activity in terms of a trajectory in parameter space - identifying key synaptic parameters or connections that cause observed signals. Using recordings from three seizures in one patient, we considered a network of two sources (within and just outside the putative ictal zone). Bayesian model selection was used to identify the intrinsic (within-source) and extrinsic (between-source) connectivity. Having established the underlying architecture, we were able to track the evolution of key connectivity parameters (e.g., inhibitory connections to superficial pyramidal cells) and test specific hypotheses about the synaptic mechanisms involved in ictogenesis. Our key finding was that intrinsic synaptic changes were sufficient to explain seizure onset, where these changes showed dissociable time courses over several seconds. Crucially, these changes spoke to an increase in the sensitivity of principal cells to intrinsic inhibitory afferents and a transient loss of excitatory-inhibitory balance. Copyright © 2014. Published by Elsevier Inc.

The influence of porosity and structural parameters on different kinds of gas hydrate dissociation

PubMed Central

Misyura, S. Y.

2016-01-01

Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores. PMID:27445113

Reciprocity theory of homogeneous reactions

NASA Astrophysics Data System (ADS)

Agbormbai, Adolf A.

1990-03-01

The reciprocity formalism is applied to the homogeneous gaseous reactions in which the structure of the participating molecules changes upon collision with one another, resulting in a change in the composition of the gas. The approach is applied to various classes of dissociation, recombination, rearrangement, ionizing, and photochemical reactions. It is shown that for the principle of reciprocity to be satisfied it is necessary that all chemical reactions exist in complementary pairs which consist of the forward and backward reactions. The backward reaction may be described by either the reverse or inverse process. The forward and backward processes must satisfy the same reciprocity equation. Because the number of dynamical variables is usually unbalanced on both sides of a chemical equation, it is necessary that this balance be established by including as many of the dynamical variables as needed before the reciprocity equation can be formulated. Statistical transformation models of the reactions are formulated. The models are classified under the titles free exchange, restricted exchange and simplified restricted exchange. The special equations for the forward and backward processes are obtained. The models are consistent with the H theorem and Le Chatelier's principle. The models are also formulated in the context of the direct simulation Monte Carlo method.

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

NASA Astrophysics Data System (ADS)

Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

2018-05-01

The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system

PubMed Central

Raimondo, Joseph V.; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E.; Srinivas, Shankar; Akerman, Colin J.

2013-01-01

Within the nervous system, intracellular Cl− and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl− and pH are often co-regulated, and network activity results in the movement of both Cl− and H+. Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl− and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN—a new genetically-encoded ratiometric Cl− and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl− and H+ concentrations under a variety of conditions. In addition, we establish the sensor's utility by characterizing activity-dependent ion dynamics in hippocampal neurons. PMID:24312004

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system.

PubMed

Raimondo, Joseph V; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E; Srinivas, Shankar; Akerman, Colin J

2013-01-01

Within the nervous system, intracellular Cl(-) and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl(-) and pH are often co-regulated, and network activity results in the movement of both Cl(-) and H(+). Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl(-) and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN-a new genetically-encoded ratiometric Cl(-) and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl(-) and H(+) concentrations under a variety of conditions. In addition, we establish the sensor's utility by characterizing activity-dependent ion dynamics in hippocampal neurons.

Hydrolyzable Polyureas Bearing Hindered Urea Bonds

PubMed Central

2015-01-01

Hydrolyzable polymers are widely used materials that have found numerous applications in biomedical, agricultural, plastic, and packaging industrials. They usually contain ester and other hydrolyzable bonds, such as anhydride, acetal, ketal, or imine, in their backbone structures. Here, we report the first design of hydrolyzable polyureas bearing dynamic hindered urea bonds (HUBs) that can reversibly dissociate to bulky amines and isocyanates, the latter of which can be further hydrolyzed by water, driving the equilibrium to facilitate the degradation of polyureas. Polyureas bearing 1-tert-butyl-1-ethylurea bonds that show high dynamicity (high bond dissociation rate), in the form of either linear polymers or cross-linked gels, can be completely degraded by water under mild conditions. Given the simplicity and low cost for the production of polyureas by simply mixing multifunctional bulky amines and isocyanates, the versatility of the structures, and the tunability of the degradation profiles of HUB-bearing polyureas, these materials are potentially of very broad applications. PMID:25406025

Kinesin regulation dynamics through cargo delivery, a single molecule investigation

NASA Astrophysics Data System (ADS)

Kovacs, Anthony; Kessler, Jonathan; Lin, Huawen; Dutcher, Susan; Wang, Yan Mei

2015-03-01

Kinesins are microtubule-based motors that deliver cargo to their destinations in a highly regulated manner. Although in recent years numerous regulators of cargo delivery have been identified, the regulation mechanism of kinesin through the cargo delivery and recycling process is not known. By performing single molecule fluorescence imaging measurements in Chlamydomonas flagella, which are 200 nm in diameter, 10 microns in length, and contain 9 sets of microtubule doublets, we tracked the intraflagellar transport (IFT) trains, BBSome cargo, and kinesin-2 motors through the cargo delivery process and determined the aforementioned dynamics. Upon arrival at the microtubule plus end at the flagellar tip, (1) IFT trains and BBSome cargo remain intact, dissociate together from kinesins and microtubules, and diffuse along flagellar membrane for a mean of 2.3 sec before commencing retrograde travel. (2) Kinesin motors remain bound to and diffuse along microtubules for 1.3 sec before dissociating into the flagellar lumen for recycling.

Influence of Coulombic repulsion on the dissociation pathways and energetics of multiprotein complexes in the gas phase.

PubMed

Sinelnikov, Igor; Kitova, Elena N; Klassen, John S

2007-04-01

Thermal dissociation experiments, implemented with blackbody infrared radiative dissociation and Fourier-transform ion cyclotron resonance mass spectrometry, are performed on gaseous protonated and deprotonated ions of the homopentameric B subunits of Shiga toxin 1 (Stx1 B5) and Shiga toxin 2 (Stx2 B5) and the homotetramer streptavidin (S4). Dissociation of the gaseous, multisubunit complexes proceeds predominantly by the loss of a single subunit. Notably, the fractional partitioning of charge between the product ions, i.e., the leaving subunit and the resulting multimer, for a given complex is, within error, constant over the range of charge states investigated. The Arrhenius activation parameters (E(a), A) measured for the loss of subunit decrease with increasing charge state of the complex. However, the parameters for the protonated and deprotonated ions, with the same number of charges, are indistinguishable. The influence of the complex charge state on the dissociation pathways and the magnitude of the dissociation E(a) are modeled theoretically with the discrete charge droplet model (DCDM) and the protein structure model (PSM), wherein the structure of the subunits is considered. Importantly, the major subunit charge states observed experimentally for the Stx1 B5(n+/-) ions correspond to the minimum energy charge distribution predicted by DCDM and PSM assuming a late dissociative transition-state (TS); while for structurally-related Stx2 B5(n+) ions, the experimental charge distribution corresponds to an early TS. It is proposed that the lateness of the TS is related, in part, to the degree of unfolding of the leaving subunit, with Stx1 B being more unfolded than Stx2 B. PSM, incorporating significant subunit unfolding is necessary to account for the product ions observed for the S4(n+) ions. The contribution of Coulombic repulsion to the dissociation E(a) is quantified and the intrinsic activation energy is estimated for the first time.

Dissociation of hydrophobic and charged nano particles in aqueous guanidinium chloride and urea solutions: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Li, Weifeng; Mu, Yuguang

2012-02-01

It has been a long history that urea and guanidinium chloride (GdmCl) are used as agents for denaturing proteins. The underlying mechanism has been extensively studied in the past several decades. However, the question regarding why GdmCl is much stronger than urea has seldom been touched. Here, through molecular dynamics simulations, we show that a 4 M GdmCl solution is more able than 7 M urea solution to dissociate both hydrophobic and charged nano-particles (NP). Both urea and GdmCl affect the NPs' aggregation through direct binding to the NP surface. The advantages of GdmCl originate from the net charge of bound guanidinium ions which can generate a local positively charged environment around hydrophobic and negatively charged NPs. This effective coating can introduce Coulombic repulsion between all the NPs. Urea shows certain ability to dissociate hydrophobic NPs. However, in the case of charged NPs, urea molecules located between two opposite-charged NPs will form ordered hydrogen bonds, acting like ``glue'' which prevents separation of the NPs. Although urea can form hydrogen bonds with either hydrophilic amino acids or the protein backbone, which are believed to contribute to protein denaturation, our findings strongly suggest that this property does not always contribute positively to urea's denaturation power.

Attempting to model dissociations of memory.

PubMed

Reber, Paul J.

2002-05-01

Kinder and Shanks report simulations aimed at describing a single-system model of the dissociation between declarative and non-declarative memory. This model attempts to capture both Artificial Grammar Learning (AGL) and recognition memory with a single underlying representation. However, the model fails to reflect an essential feature of recognition memory - that it occurs after a single exposure - and the simulations may instead describe a potentially interesting property of over-training non-declarative memory.

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model.

PubMed

Maurer, Patrick; Thomas, Vibin; Rivard, Ugo; Iftimie, Radu

2010-07-28

Ultrafast, time-resolved investigations of acid-base neutralization reactions have recently been performed using systems containing the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and various Bronsted bases. Two conflicting neutralization mechanisms have been formulated by Mohammed et al. [Science 310, 83 (2005)] and Siwick et al. [J. Am. Chem. Soc. 129, 13412 (2007)] for the same acid-base system. Herein an ab initio molecular dynamics based computational model is formulated, which is able to investigate the validity of the proposed mechanisms in the general context of ground-state acid-base neutralization reactions. Our approach consists of using 2,4,6-tricyanophenol (exp. pKa congruent with 1) as a model for excited-state HPTS( *) (pKa congruent with 1.4) and carboxylate ions for the accepting base. We employ our recently proposed dipole-field/quantum mechanics (QM) treatment [P. Maurer and R. Iftimie, J. Chem. Phys. 132, 074112 (2010)] of the proton donor and acceptor molecules. This approach allows one to tune the free energy of neutralization to any desired value as well as model initial nonequilibrium hydration effects caused by a sudden increase in acidity, making it possible to achieve a more realistic comparison with experimental data than could be obtained via a full-QM treatment of the entire system. It is demonstrated that the dipole-field/QM model reproduces correctly key properties of the 2,4,6-tricyanophenol acid molecule including gas-phase proton dissociation energies and dipole moments, and condensed-phase hydration structure and pKa values.

The effects of different substrates on the electron stimulated desorption dynamics of O - from physisorbed O2

NASA Astrophysics Data System (ADS)

Hedhili, M. N.; Parenteau, L.; Huels, M. A.; Azria, R.; Tronc, M.; Sanche, L.

1997-11-01

We report condensed phase measurements of kinetic energy (Ek) distributions of O-, produced by dissociative electron attachment (DEA) at 6 eV incident electron energy; they are obtained under identical experimental conditions from submonolayer quantities of 16O2 deposited on disordered multilayer substrates of 18O2, Ar, Kr, Xe, CH4, and C2H6, all condensed at 20 K on polycrystalline platinum (Pt). The results suggest that the desorption dynamics of O- DEA fragments is, in part, determined by large angle elastic scattering of O- prior to desorption, as well as the net image charge potential (Ep) induced in the condensed dielectric solid and the Pt metal. The measurements also indicate that, particularly at small Kr substrate thicknesses, the Ep may not necessarily be uniform across the surface, but may fluctuate due to surface roughness. Thus, in addition to energy losses in the substrate prior to, and during, DEA, these effects may influence the dissociation dynamics of the O2- resonance itself, as well as the desorption of the DEA O- fragment.

The co-occurrence of PTSD and dissociation: differentiating severe PTSD from dissociative-PTSD.

PubMed

Armour, Cherie; Karstoft, Karen-Inge; Richardson, J Don

2014-08-01

A dissociative-posttraumatic stress disorder (PTSD) subtype has been included in the DSM-5. However, it is not yet clear whether certain socio-demographic characteristics or psychological/clinical constructs such as comorbid psychopathology differentiate between severe PTSD and dissociative-PTSD. The current study investigated the existence of a dissociative-PTSD subtype and explored whether a number of trauma and clinical covariates could differentiate between severe PTSD alone and dissociative-PTSD. The current study utilized a sample of 432 treatment seeking Canadian military veterans. Participants were assessed with the Clinician Administered PTSD Scale (CAPS) and self-report measures of traumatic life events, depression, and anxiety. CAPS severity scores were created reflecting the sum of the frequency and intensity items from each of the 17 PTSD and 3 dissociation items. The CAPS severity scores were used as indicators in a latent profile analysis (LPA) to investigate the existence of a dissociative-PTSD subtype. Subsequently, several covariates were added to the model to explore differences between severe PTSD alone and dissociative-PTSD. The LPA identified five classes: one of which constituted a severe PTSD group (30.5 %), and one of which constituted a dissociative-PTSD group (13.7 %). None of the included, demographic, trauma, or clinical covariates were significantly predictive of membership in the dissociative-PTSD group compared to the severe PTSD group. In conclusion, a significant proportion of individuals report high levels of dissociation alongside their PTSD, which constitutes a dissociative-PTSD subtype. Further investigation is needed to identify which factors may increase or decrease the likelihood of membership in a dissociative-PTSD subtype group compared to a severe PTSD only group.

Model for a transformer-coupled toroidal plasma source

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

Rauf, Shahid; Balakrishna, Ajit; Chen Zhigang

2012-01-15

A two-dimensional fluid plasma model for a transformer-coupled toroidal plasma source is described. Ferrites are used in this device to improve the electromagnetic coupling between the primary coils carrying radio frequency (rf) current and a secondary plasma loop. Appropriate components of the Maxwell equations are solved to determine the electromagnetic fields and electron power deposition in the model. The effect of gas flow on species transport is also considered. The model is applied to 1 Torr Ar/NH{sub 3} plasma in this article. Rf electric field lines form a loop in the vacuum chamber and generate a plasma ring. Due tomore » rapid dissociation of NH{sub 3}, NH{sub x}{sup +} ions are more prevalent near the gas inlet and Ar{sup +} ions are the dominant ions farther downstream. NH{sub 3} and its by-products rapidly dissociate into small fragments as the gas flows through the plasma. With increasing source power, NH{sub 3} dissociates more readily and NH{sub x}{sup +} ions are more tightly confined near the gas inlet. Gas flow rate significantly influences the plasma characteristics. With increasing gas flow rate, NH{sub 3} dissociation occurs farther from the gas inlet in regions with higher electron density. Consequently, more NH{sub 4}{sup +} ions are produced and dissociation by-products have higher concentrations near the outlet.« less

Use of Computed X-ray Tomographic Data for Analyzing the Thermodynamics of a Dissociating Porous Sand/Hydrate Mixture

DOE R&D Accomplishments Database

Freifeld, Barry M.; Kneafsey, Timothy J.; Tomutsa, Liviu; Stern, Laura A.; Kirby, Stephen H.

2002-02-28

X-ray computed tomography (CT) is a method that has been used extensively in laboratory experiments for measuring rock properties and fluid transport behavior. More recently, CT scanning has been applied successfully to detect the presence and study the behavior of naturally occurring hydrates. In this study, we used a modified medical CT scanner to image and analyze the progression of a dissociation front in a synthetic methane hydrate/sand mixture. The sample was initially scanned under conditions at which the hydrate is stable (atmospheric pressure and liquid nitrogen temperature, 77 K). The end of the sample holder was then exposed to the ambient air, and the core was continuously scanned as dissociation occurred in response to the rising temperature. CT imaging captured the advancing dissociation front clearly and accurately. The evolved gas volume was monitored as a function of time. Measured by CT, the advancing hydrate dissociation front was modeled as a thermal conduction problem explicitly incorporating the enthalpy of dissociation, using the Stefan moving-boundary-value approach. The assumptions needed to perform the analysis consisted of temperatures at the model boundaries. The estimated value for thermal conductivity of 2.6 W/m K for the remaining water ice/sand mixture is higher than expected based on conduction alone; this high value may represent a lumped parameter that incorporates the processes of heat conduction, methane gas convection, and any kinetic effects that occur during dissociation. The technique presented here has broad implications for future laboratory and field testing that incorporates geophysical techniques to monitor gas hydrate dissociation.

Influence of Brownian Motion on Blood Platelet Flow Behavior and Adhesive Dynamics near a Planar Wall

PubMed Central

Mody, Nipa A.; King, Michael R.

2008-01-01

We used the Platelet Adhesive Dynamics computational method to study the influence of Brownian motion of a platelet on its flow characteristics near a surface in the creeping flow regime. Two important characterizations were done in this regard: (1) quantification of the platelet’s ability to contact the surface by virtue of the Brownian forces and torques acting on it, and (2) determination of the relative importance of Brownian motion in promoting surface encounters in the presence of shear flow. We determined the Peclet number for a platelet undergoing Brownian motion in shear flow, which could be expressed as a simple linear function of height of the platelet centroid, H from the surface Pe (platelet) = γ. · (1.56H + 0.66) for H > 0.3 μm. Our results demonstrate that at timescales relevant to shear flow in blood, Brownian motion plays an insignificant role in influencing platelet motion or creating further opportunities for platelet-surface contact. The platelet Peclet number at shear rates > 100 s-1 is large enough (> 200) to neglect platelet Brownian motion in computational modeling of flow in arteries and arterioles for most practical purposes even at very close distances from the surface. We also conducted adhesive dynamics simulations to determine the effects of platelet Brownian motion on GPIbα-vWF-A1 single-bond dissociation dynamics. Brownian motion was found to have little effect on bond lifetime and caused minimal bond stressing as bond rupture forces were calculated to be less than 0.005 pN. We conclude from our results that for the case of platelet-shaped cells, Brownian motion is not expected to play an important role in influencing flow characteristics, platelet-surface contact frequency and dissociative binding phenomena under flow at physiological shear rates (> 50 s-1). PMID:17417890

Bond-selective photodissociation of partially deuterated ammonia molecules: Photodissociations of vibrationally excited NHD2 in the 5νNH state and NH2D in the 5νND state

NASA Astrophysics Data System (ADS)

Akagi, Hiroshi; Yokoyama, Keiichi; Yokoyama, Atsushi

2004-03-01

Ultraviolet photodissociation of NHD2 excited to the fourth overtone state of the NH stretching mode (5νNH) and NH2D excited to that of the ND stretching mode (5νND) has been investigated by using a crossed laser and molecular beams method. Branching ratio between the NH and ND bond dissociations has been determined by utilizing a (2+1) resonance enhanced multiphoton ionization scheme of H and D atoms. For the photolysis of NHD2 in the 5νNH state, the NH dissociation cross section is 5.1±1.4 times as large as the ND dissociation cross section per bond. On the other hand, for the photolysis of NH2D in the 5νND state, the ratio of the NH dissociation cross section per bond to the ND dissociation cross section decreases to 0.68±0.16. In comparison with the branching ratios for the photolysis of vibrationally unexcited NH2D and NHD2 [Koda and Back, Can. J. Chem. 55, 1380 (1977)], the present results indicate that the excitation of the NH stretching mode enhances the NH dissociation with ca. two times larger NH/ND branching ratio, whereas the excitation of the ND stretching mode results in the preferential ND dissociation with ca. 3-4 times larger ND/NH branching ratio than that for the vibrational ground states. The mechanism of the bond-selective enhancement has been discussed in terms of the energetics and dynamics of wave packet.

Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides

NASA Astrophysics Data System (ADS)

Moss, Christopher L.; Chung, Thomas W.; Wyer, Jean A.; Nielsen, Steen Brøndsted; Hvelplund, Preben; Tureček, František

2011-04-01

Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H2PO4 radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.

Relations between childhood traumatic experiences, dissociation, and cognitive models in obsessive compulsive disorder.

PubMed

Selvi, Yavuz; Besiroglu, Lutfullah; Aydin, Adem; Gulec, Mustafa; Atli, Abdullah; Boysan, Murat; Celik, Cihat

2012-03-01

Previous studies have indicated that obsessive compulsive disorder (OCD) is associated with childhood traumatic experiences and higher levels of dissociation. Dissociative tendency may arise when individual attempt to incorporate adverse experiences into cognitive schema. We investigated the possible links among childhood trauma, dissociation, and cognitive processes. We evaluated 95 patients with OCD using the Beck Depression Inventory (BDI), Thought-Action Fusion Scale (TAFS), Metacognitions Questionnaire (MCQ-30), White Bear Suppression Inventory (WBSI), Dissociative Experiences Scale (DES), and Childhood Trauma Questionnaire (CTQ-28). The CTQ-28 total scores were not associated with Y-BOCS total, Y-BOCS insight, BDI, TAFS, MCQ-30, and WBSI scores. The TAFS Total, MCQ-30, WBSI, and BDI scores were significantly associated with DES scores. Regression analysis revealed that MCQ-30 and WBSI scores significantly predicted the DES scores. These results suggest that in spite of pathological connotation of dissociative experiences, dissociation may primarily constitute a cognitive trait which is strongly associated with cognitive processes.

Dissociative Ionization of Benzene by Electron Impact

NASA Technical Reports Server (NTRS)

Huo, Winifred; Dateo, Christopher; Kwak, Dochan (Technical Monitor)

2002-01-01

We report a theoretical study of the dissociative ionization (DI) of benzene from the low-lying ionization channels. Our approach makes use of the fact that electron motion is much faster than nuclear motion and DI is treated as a two-step process. The first step is electron-impact ionization resulting in an ion with the same nuclear geometry as the neutral molecule. In the second step the nuclei relax from the initial geometry and undergo unimolecular dissociation. For the ionization process we use the improved binary-encounter dipole (iBED) model. For the unimolecular dissociation step, we study the steepest descent reaction path to the minimum of the ion potential energy surface. The path is used to analyze the probability of unimolecular dissociation and to determine the product distributions. Our analysis of the dissociation products and the thresholds of the productions are compared with the result dissociative photoionization measurements of Feng et al. The partial oscillator strengths from Feng et al. are then used in the iBED cross section calculations.

Facilitated release of substrate protein from prefoldin by chaperonin.

PubMed

Zako, Tamotsu; Iizuka, Ryo; Okochi, Mina; Nomura, Tomoko; Ueno, Taro; Tadakuma, Hisashi; Yohda, Masafumi; Funatsu, Takashi

2005-07-04

Prefoldin is a chaperone that captures a protein-folding intermediate and transfers it to the group II chaperonin for correct folding. However, kinetics of interactions between prefoldin and substrate proteins have not been investigated. In this study, dissociation constants and dissociation rate constants of unfolded proteins with prefoldin were firstly measured using fluorescence microscopy. Our results suggest that binding and release of prefoldin from hyperthermophilic archaea with substrate proteins were in a dynamic equilibrium. Interestingly, the release of substrate proteins from prefoldin was facilitated when chaperonin was present, supporting a handoff mechanism of substrate proteins from prefoldin to the chaperonin.

Dissociation of single-strand DNA: single-walled carbon nanotube hybrids by Watson-Crick base-pairing.

PubMed

Jung, Seungwon; Cha, Misun; Park, Jiyong; Jeong, Namjo; Kim, Gunn; Park, Changwon; Ihm, Jisoon; Lee, Junghoon

2010-08-18

It has been known that single-strand DNA wraps around a single-walled carbon nanotube (SWNT) by pi-stacking. In this paper it is demonstrated that such DNA is dissociated from the SWNT by Watson-Crick base-pairing with a complementary sequence. Measurement of field effect transistor characteristics indicates a shift of the electrical properties as a result of this "unwrapping" event. We further confirm the suggested process through Raman spectroscopy and gel electrophoresis. Experimental results are verified in view of atomistic mechanisms with molecular dynamics simulations and binding energy analyses.

Hard-X-Ray-Induced Multistep Ultrafast Dissociation

NASA Astrophysics Data System (ADS)

Travnikova, Oksana; Marchenko, Tatiana; Goldsztejn, Gildas; Jänkälä, Kari; Sisourat, Nicolas; Carniato, Stéphane; Guillemin, Renaud; Journel, Loïc; Céolin, Denis; Püttner, Ralph; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Simon, Marc

2016-05-01

Creation of deep core holes with very short (τ ≤1 fs ) lifetimes triggers a chain of relaxation events leading to extensive nuclear dynamics on a few-femtosecond time scale. Here we demonstrate a general multistep ultrafast dissociation on an example of HCl following Cl 1 s →σ* excitation. Intermediate states with one or multiple holes in the shallower core electron shells are generated in the course of the decay cascades. The repulsive character and large gradients of the potential energy surfaces of these intermediates enable ultrafast fragmentation after the absorption of a hard x-ray photon.

Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.

PubMed

Purohit, Anirban; England, Jennifer K; Douma, Lauren G; Tondnevis, Farzaneh; Bloom, Linda B; Levitus, Marcia

2017-08-22

Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the β-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Causes of plasma column contraction in surface-wave-driven discharges in argon at atmospheric pressure

NASA Astrophysics Data System (ADS)

Ridenti, Marco Antonio; de Amorim, Jayr; Dal Pino, Arnaldo; Guerra, Vasco; Petrov, George

2018-01-01

In this work we compute the main features of a surface-wave-driven plasma in argon at atmospheric pressure in view of a better understanding of the contraction phenomenon. We include the detailed chemical kinetics dynamics of Ar and solve the mass conservation equations of the relevant neutral excited and charged species. The gas temperature radial profile is calculated by means of the thermal diffusion equation. The electric field radial profile is calculated directly from the numerical solution of the Maxwell equations assuming the surface wave to be propagating in the TM00 mode. The problem is considered to be radially symmetrical, the axial variations are neglected, and the equations are solved in a self-consistent fashion. We probe the model results considering three scenarios: (i) the electron energy distribution function (EEDF) is calculated by means of the Boltzmann equation; (ii) the EEDF is considered to be Maxwellian; (iii) the dissociative recombination is excluded from the chemical kinetics dynamics, but the nonequilibrium EEDF is preserved. From this analysis, the dissociative recombination is shown to be the leading mechanism in the constriction of surface-wave plasmas. The results are compared with mass spectrometry measurements of the radial density profile of the ions Ar+ and Ar2+. An explanation is proposed for the trends seen by Thomson scattering diagnostics that shows a substantial increase of electron temperature towards the plasma borders where the electron density is small.

Hypersonics. Volume 1 - Defining the hypersonic environment; Proceedings of the First Joint Europe/U.S. Short Course on Hypersonics, Paris, France, Dec. 7-11, 1987

NASA Astrophysics Data System (ADS)

Bertin, John J.; Glowinski, Roland; Periaux, Jacques

1989-05-01

The present work discusses the general characterization of hypersonic flows, the hypersonic phenomena to be encountered by the Hermes spacecraft, industrial methodologies for the design of hypersonic vehicles, the definition of aerodynamic methodology, and hypersonic airbreathing-propulsion vehicle design practices applicable to the U.S. National Aerospace Plane. Also discussed are real gas effects in the hypersonic regime, the influence of thermochemistry and of nonequilibrium and surface catalysis on hypersonic vehicle design, the modelling of nonequilibrium effects in high speed flows, air-dissociation thermochemistry, and rarefied gas dynamics effects for spacecraft.

Communication: a density functional with accurate fractional-charge and fractional-spin behaviour for s-electrons.

PubMed

Johnson, Erin R; Contreras-García, Julia

2011-08-28

We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)] and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems. © 2011 American Institute of Physics

Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism

NASA Astrophysics Data System (ADS)

Das, Anusheela; Chaudhury, Srabanti

2015-11-01

Metal nanoparticles are heterogeneous catalysts and have a multitude of non-equivalent, catalytic sites on the nanoparticle surface. The product dissociation step in such reaction schemes can follow multiple pathways. Proposed here for the first time is a completely analytical theoretical framework, based on the first passage time distribution, that incorporates the effect of heterogeneity in nanoparticle catalysis explicitly by considering multiple, non-equivalent catalytic sites on the nanoparticle surface. Our results show that in nanoparticle catalysis, the effect of dynamic disorder is manifested even at limiting substrate concentrations in contrast to an enzyme that has only one well-defined active site.

Prepared stimuli enhance aversive learning without weakening the impact of verbal instructions

PubMed Central

2018-01-01

Fear-relevant stimuli such as snakes and spiders are thought to capture attention due to evolutionary significance. Classical conditioning experiments indicate that these stimuli accelerate learning, while instructed extinction experiments suggest they may be less responsive to instructions. We manipulated stimulus type during instructed aversive reversal learning and used quantitative modeling to simultaneously test both hypotheses. Skin conductance reversed immediately upon instruction in both groups. However, fear-relevant stimuli enhanced dynamic learning, as measured by higher learning rates in participants conditioned with images of snakes and spiders. Results are consistent with findings that dissociable neural pathways underlie feedback-driven and instructed aversive learning. PMID:29339561

A cognitive model for multidigit number reading: Inferences from individuals with selective impairments.

PubMed

Dotan, Dror; Friedmann, Naama

2018-04-01

We propose a detailed cognitive model of multi-digit number reading. The model postulates separate processes for visual analysis of the digit string and for oral production of the verbal number. Within visual analysis, separate sub-processes encode the digit identities and the digit order, and additional sub-processes encode the number's decimal structure: its length, the positions of 0, and the way it is parsed into triplets (e.g., 314987 → 314,987). Verbal production consists of a process that generates the verbal structure of the number, and another process that retrieves the phonological forms of each number word. The verbal number structure is first encoded in a tree-like structure, similarly to syntactic trees of sentences, and then linearized to a sequence of number-word specifiers. This model is based on an investigation of the number processing abilities of seven individuals with different selective deficits in number reading. We report participants with impairment in specific sub-processes of the visual analysis of digit strings - in encoding the digit order, in encoding the number length, or in parsing the digit string to triplets. Other participants were impaired in verbal production, making errors in the number structure (shifts of digits to another decimal position, e.g., 3,040 → 30,004). Their selective deficits yielded several dissociations: first, we found a double dissociation between visual analysis deficits and verbal production deficits. Second, several dissociations were found within visual analysis: a double dissociation between errors in digit order and errors in the number length; a dissociation between order/length errors and errors in parsing the digit string into triplets; and a dissociation between the processing of different digits - impaired order encoding of the digits 2-9, without errors in the 0 position. Third, within verbal production, a dissociation was found between digit shifts and substitutions of number words. A selective deficit in any of the processes described by the model would cause difficulties in number reading, which we propose to term "dysnumeria". Copyright © 2017 Elsevier Ltd. All rights reserved.

Photodissociation dynamics of OClO

NASA Astrophysics Data System (ADS)

Davis, H. Floyd; Lee, Yuan T.

1996-11-01

Photofragment translational energy spectroscopy was used to study the dissociation dynamics of a range of electronically excited OClO(A 2A2) vibrational states. For all levels studied, corresponding to OClO(A 2A2←X 2B1) excitation wavelengths between 350 and 475 nm, the dominant product (≳96%) was ClO(2Π)+O(3P). We also observed production of Cl+O2 with a quantum yield of up to 3.9±0.8% near 404 nm, decreasing at longer and shorter wavelengths. The branching ratios between the two channels were dependent on the OClO(A 2A2) excited state vibrational mode. The Cl+O2 yield was enhanced slightly by exciting A 2A2 levels having symmetric stretching+bending, but diminished by as much as a factor of 10 for neighboring peaks associated with symmetric stretching+asymmetric stretching. Mode specificity was also observed in the vibrationally state resolved translational energy distributions for the dominant ClO(2Π)+O(3P) channel. The photochemical dynamics of OClO possesses two energy regimes with distinctly different dynamics observed for excitation energies above and below ˜3.1 eV (λ˜400 nm). At excitation energies below 3.1 eV (λ≳400 nm), nearly all energetically accessible ClO vibrational energy levels were populated, and the minor Cl+O2 channel was observed. Although at least 20% of the O2 product is formed in the ground (X 3Σ-g) state, most O2 is electronically excited (a 1Δg). At E<3.1 eV, both dissociation channels occur by an indirect mechanism involving two nearby excited states, 2A1 and 2B2. Long dissociation time scales and significant parent bending before dissociation led to nearly isotropic polarization angular distributions (β˜0). At excitation energies above 3.1 eV (λ<400 nm), the Cl+O2 yield began to decrease sharply, with this channel becoming negligible at λ<370 nm. At these higher excitation energies, the ClO product was formed with relatively little vibrational energy and a large fraction of the excess energy was channeled into ClO+O translational energy. The photofragment anisotropy parameter (β) also increased, implying shorter dissociation time scales. The sharp change in the disposal of excess energy into the ClO products, the decrease of Cl+O2 production, and more anisotropic product angular distributions at E≳3.1 eV signify the opening of a new ClO+O channel. From our experimental results and recent ab initio calculations, dissociation at wavelengths shorter than 380 nm to ClO+O proceeds via a direct mechanism on the optically prepared A 2A2 surface over a large potential energy barrier. From the ClO(2Π)+O(3P) translational energy distributions, D0(O-ClO) was found to be less than or equal to 59.0±0.2 kcal/mol.

Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase.

PubMed

Schnier, P D; Price, W D; Jockusch, R A; Williams, E R

1996-07-31

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.

I Working with dissociative dynamics and the longing for excess in binge eating disorders.

PubMed

Austin, Sue

2013-06-01

In this paper the author describes her work with a woman who, in her mid 20s, sought analysis for her non-vomiting binge eating disorder. The paper explores how two aspects of Jung's view of the psyche as healthily dissociable were used to think about the potential for change contained within the explosive, aggressive energies in this patient's bingeing. The resultant approach takes the patient's splitting defences, dissociations and self-destructive behaviour as a point of access to her unconscious. Seen in this way, these behaviours contain the seeds of recovery and are the starting point for analysis rather than defences against it. The paper also brings a number of Jungian and post-Jungian ideas into conversation with aspects of contemporary thinking about subjectivity, identity and the longing for excess developed by Leo Bersani and Judith Butler. © 2013, The Society of Analytical Psychology.

Glacigenic sedimentation pulses triggered post-glacial gas hydrate dissociation.

PubMed

Karstens, Jens; Haflidason, Haflidi; Becker, Lukas W M; Berndt, Christian; Rüpke, Lars; Planke, Sverre; Liebetrau, Volker; Schmidt, Mark; Mienert, Jürgen

2018-02-12

Large amounts of methane are stored in continental margins as gas hydrates. They are stable under high pressure and low, but react sensitively to environmental changes. Bottom water temperature and sea level changes were considered as main contributors to gas hydrate dynamics after the last glaciation. However, here we show with numerical simulations that pulses of increased sedimentation dominantly controlled hydrate stability during the end of the last glaciation offshore mid-Norway. Sedimentation pulses triggered widespread gas hydrate dissociation and explains the formation of ubiquitous blowout pipes in water depths of 600 to 800 m. Maximum gas hydrate dissociation correlates spatially and temporally with the formation or reactivation of pockmarks, which is constrained by radiocarbon dating of Isorropodon nyeggaensis bivalve shells. Our results highlight that rapid changes of sedimentation can have a strong impact on gas hydrate systems affecting fluid flow and gas seepage activity, slope stability and the carbon cycle.

Mechanical instability of monocrystalline and polycrystalline methane hydrates

PubMed Central

Wu, Jianyang; Ning, Fulong; Trinh, Thuat T.; Kjelstrup, Signe; Vlugt, Thijs J. H.; He, Jianying; Skallerud, Bjørn H.; Zhang, Zhiliang

2015-01-01

Despite observations of massive methane release and geohazards associated with gas hydrate instability in nature, as well as ductile flow accompanying hydrate dissociation in artificial polycrystalline methane hydrates in the laboratory, the destabilising mechanisms of gas hydrates under deformation and their grain-boundary structures have not yet been elucidated at the molecular level. Here we report direct molecular dynamics simulations of the material instability of monocrystalline and polycrystalline methane hydrates under mechanical loading. The results show dislocation-free brittle failure in monocrystalline hydrates and an unexpected crossover from strengthening to weakening in polycrystals. Upon uniaxial depressurisation, strain-induced hydrate dissociation accompanied by grain-boundary decohesion and sliding destabilises the polycrystals. In contrast, upon compression, appreciable solid-state structural transformation dominates the response. These findings provide molecular insight not only into the metastable structures of grain boundaries, but also into unusual ductile flow with hydrate dissociation as observed during macroscopic compression experiments. PMID:26522051

Somatoform and dissociative disorders in children and adolescents: A comparative study

PubMed Central

Malhotra, Savita; Singh, Gagandeep; Mohan, Ashwin

2005-01-01

Background: Somatoform and dissociative (conversion) disorders in adults have been reported to have a close relationship because of a diagnostic overlap and comparable aetiological models. The literature on these disorders in children and adolescents is scarce. Aim: The present study attempted to compare these two disorders in children and adolescents since antecedents of these disorders are said to be laid in childhood. Methods: Case files of 118 patients (69 of somatoform disorders and 49 of dissociative disorders) were reviewed and the two groups were compared with respect to sociodemographic profile, clinical profile, neurotic traits, behavioural problems, temperament, intelligence and family dysfunction. Results: Age at presentation and intelligence were significantly higher in those with somatoform disorders than in those with dissociative disorders. Patients with dissociative disorders had a significantly higher number of co-morbid somatoform symptoms. Conclusion: Somatoform and dissociative disorders are closely linked.

Quantitative Kinetic Study of the Actin-Bundling Protein L-Plastin and of Its Impact on Actin Turn-Over

PubMed Central

Al Tanoury, Ziad; Schaffner-Reckinger, Elisabeth; Halavatyi, Aliaksandr; Hoffmann, Céline; Moes, Michèle; Hadzic, Ermin; Catillon, Marie; Yatskou, Mikalai; Friederich, Evelyne

2010-01-01

Background Initially detected in leukocytes and cancer cells derived from solid tissues, L-plastin/fimbrin belongs to a large family of actin crosslinkers and is considered as a marker for many cancers. Phosphorylation of L-plastin on residue Ser5 increases its F-actin binding activity and is required for L-plastin-mediated cell invasion. Methodology/Principal Findings To study the kinetics of L-plastin and the impact of L-plastin Ser5 phosphorylation on L-plastin dynamics and actin turn-over in live cells, simian Vero cells were transfected with GFP-coupled WT-L-plastin, Ser5 substitution variants (S5/A, S5/E) or actin and analyzed by fluorescence recovery after photobleaching (FRAP). FRAP data were explored by mathematical modeling to estimate steady-state reaction parameters. We demonstrate that in Vero cell focal adhesions L-plastin undergoes rapid cycles of association/dissociation following a two-binding-state model. Phosphorylation of L-plastin increased its association rates by two-fold, whereas dissociation rates were unaffected. Importantly, L-plastin affected actin turn-over by decreasing the actin dissociation rate by four-fold, increasing thereby the amount of F-actin in the focal adhesions, all these effects being promoted by Ser5 phosphorylation. In MCF-7 breast carcinoma cells, phorbol 12-myristate 13-acetate (PMA) treatment induced L-plastin translocation to de novo actin polymerization sites in ruffling membranes and spike-like structures and highly increased its Ser5 phosphorylation. Both inhibition studies and siRNA knock-down of PKC isozymes pointed to the involvement of the novel PKC-δ isozyme in the PMA-elicited signaling pathway leading to L-plastin Ser5 phosphorylation. Furthermore, the L-plastin contribution to actin dynamics regulation was substantiated by its association with a protein complex comprising cortactin, which is known to be involved in this process. Conclusions/Significance Altogether these findings quantitatively demonstrate for the first time that L-plastin contributes to the fine-tuning of actin turn-over, an activity which is regulated by Ser5 phosphorylation promoting its high affinity binding to the cytoskeleton. In carcinoma cells, PKC-δ signaling pathways appear to link L-plastin phosphorylation to actin polymerization and invasion. PMID:20169155

Biopsychosocial model in Depression revisited.

PubMed

Garcia-Toro, Mauro; Aguirre, Iratxe

2007-01-01

There are two fundamental etiological perspectives about mental disorders; biomedical and psychosocial. The biopsychosocial model has claimed to integrate these two perspectives in a scientific way, signalling their interconnection and interdependence. To that end, it used a systemic conceptual framework, taking advantage of the possibilities which it offers to establish general principles for diverse systems, independently of their physical, biological or sociological nature. In recent years, drawing on the theory of systems, theories have been developing of the dynamic non-linear systems, applicable to networks of a large quantity of densely interconnected elements (also called complex systems), like the mind or the brain. We believe that this revised systemic conceptual framework can bring integrative ideas to apply to Depression, such as the "binding dysfunction" concept we use in this article. According to this, vulnerability or predisposition to Depression would be associated with the imbalance between activating and inhibiting interactions (between some cognitions and emotions at a mental level, and between certain neuronal groups at a cerebral level). Precipitating factors would imply the increase of the activation level over this pattern of cognitions and emotions, or over those neuronal systems. When stress goes beyond the vulnerability threshold an excessive positive feedback between cognitions and emotions would appear (and between groups of neurons) with insufficient inhibitory control to mitigate it, which would imply a mental/cerebral dissociation in dominions of different level of activation. As a consequence, the generation and dissolution of patterns of cerebral and mental activation will no longer have the dynamism and flexibility that permits an optimal interaction with the environment ("binding dysfunction"). Therefore, our hypothesis is that the person with Depression will suffer at a cerebral level a functional dissociation in neural dominions (some rigidly hyperactive and others rigidly hypoactive) in determined locations, which would be a different combination from those found in other mental disorders. At a mental level, this would correlate with a functional dissociation in several cognitive-emotive dominions; some corresponds to over activated patterns of "depressive" cognitions and emotions that for that reason invade the consciousness frequently, intrusively and repetitively; meanwhile there are other alternative hypoactive emotions and cognitions that do not manage to become powerful enough to avoid the consequent distortion in the communication with the environment.

Unique and Overlapping Symptoms in Schizophrenia Spectrum and Dissociative Disorders in Relation to Models of Psychopathology: A Systematic Review

PubMed Central

Renard, Selwyn B.; Huntjens, Rafaele J. C.; Lysaker, Paul H.; Moskowitz, Andrew; Aleman, André; Pijnenborg, Gerdina H. M.

2017-01-01

Schizophrenia spectrum disorders (SSDs) and dissociative disorders (DDs) are described in the fifth edition of the Diagnostic and Statistical Manual for Mental Disorders (DSM-5) and tenth edition of the International Statistical Classification of Diseases and Related Health Problems (ICD-10) as 2 categorically distinct diagnostic categories. However, several studies indicate high levels of co-occurrence between these diagnostic groups, which might be explained by overlapping symptoms. The aim of this systematic review is to provide a comprehensive overview of the research concerning overlap and differences in symptoms between schizophrenia spectrum and DDs. For this purpose the PubMed, PsycINFO, and Web of Science databases were searched for relevant literature. The literature contained a large body of evidence showing the presence of symptoms of dissociation in SSDs. Although there are quantitative differences between diagnoses, overlapping symptoms are not limited to certain domains of dissociation, nor to nonpathological forms of dissociation. In addition, dissociation seems to be related to a history of trauma in SSDs, as is also seen in DDs. There is also evidence showing that positive and negative symptoms typically associated with schizophrenia may be present in DD. Implications of these results are discussed with regard to different models of psychopathology and clinical practice. PMID:27209638

Single- and Dual-Process Models of Biased Contingency Detection.

PubMed

Vadillo, Miguel A; Blanco, Fernando; Yarritu, Ion; Matute, Helena

2016-01-01

Decades of research in causal and contingency learning show that people's estimations of the degree of contingency between two events are easily biased by the relative probabilities of those two events. If two events co-occur frequently, then people tend to overestimate the strength of the contingency between them. Traditionally, these biases have been explained in terms of relatively simple single-process models of learning and reasoning. However, more recently some authors have found that these biases do not appear in all dependent variables and have proposed dual-process models to explain these dissociations between variables. In the present paper we review the evidence for dissociations supporting dual-process models and we point out important shortcomings of this literature. Some dissociations seem to be difficult to replicate or poorly generalizable and others can be attributed to methodological artifacts. Overall, we conclude that support for dual-process models of biased contingency detection is scarce and inconclusive.

Dynamic Diglyme-Mediated Self-Assembly of Gold Nanoclusters.

PubMed

Compel, W Scott; Wong, O Andrea; Chen, Xi; Yi, Chongyue; Geiss, Roy; Häkkinen, Hannu; Knappenberger, Kenneth L; Ackerson, Christopher J

2015-12-22

We report the assembly of gold nanoclusters by the nonthiolate ligand diglyme into discrete and dynamic assemblies. To understand this surprising phenomenon, the assembly of Au20(SC2H4Ph)15-diglyme into Au20(SC2H4Ph)15-diglyme-Au20(SC2H4Ph)15 is explored in detail. The assembly is examined by high-angle annular dark field scanning transmission electron microscopy, size exclusion chromatography, mass spectrometry, IR spectroscopy, and calorimetry. We establish a dissociation constant for dimer to monomer conversion of 20.4 μM. Theoretical models validated by transient absorption spectroscopy predict a low-spin monomer and a high-spin dimer, with assembly enabled through weak diglyme oxygen-gold interactions. Close spatial coupling allows electron delocalization between the nanoparticle cores. The resulting assemblies thus possess optical and electronic properties that emerge as a result of assembly.

[How our subjective coherence is built? The model of cognitive dissonance].

PubMed

Naccache, Lionel; El Karoui, Imen; Salti, Moti; Chammat, Mariam; Maillet, Mathurin; Allali, Sébastien

2015-01-01

Our conscious, subjective discourse, demonstrates a temporal coherence that distinguishes it from the many unconscious cognitive representations explored by cognitive neuroscience. This subjective coherence, --particularly its dynamics--can be modified in certain psychiatric syndromes including a " dissociative state " (e.g. schizophrenia), or in several neuropsychiatric disorders (e.g. frontal lobe syndrome). The medical and environmental consequences of these changes are significant. However, the psychological and neural mechanisms of this fundamental property remain largely unknown. We explored the dynamics of subjective coherence in an experimental paradigm (the "free choice "paradigm) originating for the field of cognitive dissonance. Using a series of behavioral experiments, conducted in healthy volunteers, we have discovered a key role for the episodic memory in the preference change process when simply making a choice. These results highlight the importance of conscious memory in the construction of subjective consistency, of which the subjects do not yet seem to be the conscious agents.

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study

NASA Astrophysics Data System (ADS)

Kamarchik, E.; Rodrigo, C.; Bowman, J. M.; Reisler, H.; Krylov, A. I.

2012-02-01

The dissociation of the hydroxymethyl radical, CH2OH, and its isotopolog, CD2OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH2OH and CH3O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH2OH equilibrium structure. The energies of key stationary points are refined using high-level electronic structure calculations. Vibrational energies and wavefunctions are computed by coupled anharmonic vibrational calculations. They show that high OH-stretch overtones are mixed with other modes. Consequently, trajectory calculations carried out at energies about ˜3000 cm-1 above the barriers reveal that despite initial excitation of the OH stretch, the direct OH bond fission is relatively slow (10 ps) and a considerable fraction of the radicals undergoes isomerization to the methoxy radical. The computed dissociation energies are: D0(CH2OH → CH2O + H) = 10 188 cm-1, D0(CD2OH → CD2O + H) = 10 167 cm-1, D0(CD2OH → CHDO + D) = 10 787 cm-1. All are in excellent agreement with the experimental results. For CH2OH, the barriers for the direct OH bond fission and isomerization are: 14 205 and 13 839 cm-1, respectively.

Shattering of SiMe3+ during surface-induced dissociation

NASA Astrophysics Data System (ADS)

Schultz, David G.; Hanley, Luke

1998-12-01

We provide experimental evidence that upon hyperthermal impact of Si(CD3)3+ ions with an organic surface, a portion of the ions undergo dissociation while still in contact with the surface. We use a tandem configuration of quadrupole mass spectrometers along with an energy analyzer to measure the kinetic energy distributions of the fragments that form as a result of the surface scattering of 25 eV Si(CD3)3+. These distributions are different for scattering from a clean Au(111) surface versus scattering from an organic surface composed of a self-assembled monolayer of hexanethiolate on Au(111). Parent and fragment ions recoil from the clean Au(111) surface with the same velocity, as is expected for fragmentation away from the surface. However, the same scattering products recoil from the organic surface with different velocities but similar energies, suggesting that the fragmentation dynamics are modified by surface interactions. We perform molecular dynamics simulations which predict residence times of ˜210 fs at the organic surface and ˜20 fs at the Au surface. The simulations also predict that 13% and 31% of the ions fragment within 1.1 ps of surface impact at the organic and Au surfaces, respectively. Thus, the experimental observation of dissociation at only the organic surface results from its longer ion-surface interaction time. The fragmentation time scale predicted by Rice-Ramsperger-Kassel-Marcus calculations is yet longer, suggesting that at least a portion of the surface-induced dissociation of Si(CD3)3+ may occur via a nonstatistical mechanism. Our interpretation draws heavily from an analogous "shattering" mechanism previously proposed for cluster-surface scattering [E. Hendell, U. Even, T. Raz, and R. D. Levine, Phys. Rev. Lett. 75, 2670 (1995)].

Re-appraisal and extension of the Gratton-Vargas two-dimensional analytical snowplow model of plasma focus. III. Scaling theory for high pressure operation and its implications

NASA Astrophysics Data System (ADS)

Auluck, S. K. H.

2016-12-01

Recent work on the revised Gratton-Vargas model (Auluck, Phys. Plasmas 20, 112501 (2013); 22, 112509 (2015) and references therein) has demonstrated that there are some aspects of Dense Plasma Focus (DPF), which are not sensitive to details of plasma dynamics and are well captured in an oversimplified model assumption, which contains very little plasma physics. A hyperbolic conservation law formulation of DPF physics reveals the existence of a velocity threshold related to specific energy of dissociation and ionization, above which, the work done during shock propagation is adequate to ensure dissociation and ionization of the gas being ingested. These developments are utilized to formulate an algorithmic definition of DPF optimization that is valid in a wide range of applications, not limited to neutron emission. This involves determination of a set of DPF parameters, without performing iterative model calculations, that lead to transfer of all the energy from the capacitor bank to the plasma at the time of current derivative singularity and conversion of a preset fraction of this energy into magnetic energy, while ensuring that electromagnetic work done during propagation of the plasma remains adequate for dissociation and ionization of neutral gas being ingested. Such a universal optimization criterion is expected to facilitate progress in new areas of DPF research that include production of short lived radioisotopes of possible use in medical diagnostics, generation of fusion energy from aneutronic fuels, and applications in nanotechnology, radiation biology, and materials science. These phenomena are expected to be optimized for fill gases of different kinds and in different ranges of mass density compared to the devices constructed for neutron production using empirical thumb rules. A universal scaling theory of DPF design optimization is proposed and illustrated for designing devices working at one or two orders higher pressure of deuterium than the current practice of designs optimized at pressures less than 10 mbar of deuterium. These examples show that the upper limit for operating pressure is of technological (and not physical) origin.

Dissociation in victims of childhood abuse or neglect: a meta-analytic review.

PubMed

Vonderlin, Ruben; Kleindienst, Nikolaus; Alpers, Georg W; Bohus, Martin; Lyssenko, Lisa; Schmahl, Christian

2018-04-10

Childhood abuse and neglect are associated with dissociative symptoms in adulthood. However, empirical studies show heterogeneous results depending on the type of childhood abuse or neglect and other maltreatment characteristics. In this meta-analysis, we systematically investigated the relationship between childhood interpersonal maltreatment and dissociation in 65 studies with 7352 abused or neglected individuals using the Dissociative Experience Scale (DES). We extracted DES-scores for abused and non-abused populations as well as information about type of abuse/neglect, age of onset, duration of abuse, and relationship to the perpetrator. Random-effects models were used for data synthesis, and meta-regression was used to predict DES-scores in abused populations from maltreatment characteristics. The results revealed higher dissociation in victims of childhood abuse and neglect compared with non-abused or neglected subsamples sharing relevant population features (MAbuse = 23.5, MNeglect = 18.8, MControl = 13.8) with highest scores for sexual and physical abuse. An earlier age of onset, a longer duration of abuse, and parental abuse significantly predicted higher dissociation scores. This meta-analysis underlines the importance of childhood abuse/neglect in the etiology of dissociation. The identified moderators may inform risk assessment and early intervention to prevent the development of dissociative symptoms.

Effects of Dissociation/Recombination on the Day–Night Temperature Contrasts of Ultra-hot Jupiters

NASA Astrophysics Data System (ADS)

Komacek, Thaddeus D.; Tan, Xianyu

2018-05-01

Secondary eclipse observations of ultra-hot Jupiters have found evidence that hydrogen is dissociated on their daysides. Additionally, full-phase light curve observations of ultra-hot Jupiters show a smaller day-night emitted flux contrast than that expected from previous theory. Recently, it was proposed by Bell & Cowan (2018) that the heat intake to dissociate hydrogen and heat release due to recombination of dissociated hydrogen can affect the atmospheric circulation of ultra-hot Jupiters. In this work, we add cooling/heating due to dissociation/recombination into the analytic theory of Komacek & Showman (2016) and Zhang & Showman (2017) for the dayside-nightside temperature contrasts of hot Jupiters. We find that at high values of incident stellar flux, the day-night temperature contrast of ultra-hot Jupiters may decrease with increasing incident stellar flux due to dissociation/recombination, the opposite of that expected without including the effects of dissociation/recombination. We propose that a combination of a greater number of full-phase light curve observations of ultra-hot Jupiters and future General Circulation Models that include the effects of dissociation/recombination could determine in detail how the atmospheric circulation of ultra-hot Jupiters differs from that of cooler planets.

Superior colliculus resting state networks in post-traumatic stress disorder and its dissociative subtype.

PubMed

Olivé, Isadora; Densmore, Maria; Harricharan, Sherain; Théberge, Jean; McKinnon, Margaret C; Lanius, Ruth

2018-01-01

The innate alarm system (IAS) models the neurocircuitry involved in threat processing in posttraumatic stress disorder (PTSD). Here, we investigate a primary subcortical structure of the IAS model, the superior colliculus (SC), where the SC is thought to contribute to the mechanisms underlying threat-detection in PTSD. Critically, the functional connectivity between the SC and other nodes of the IAS remains unexplored. We conducted a resting-state fMRI study to investigate the functional architecture of the IAS, focusing on connectivity of the SC in PTSD (n = 67), its dissociative subtype (n = 41), and healthy controls (n = 50) using region-of-interest seed-based analysis. We observed group-specific resting state functional connectivity between the SC for both PTSD and its dissociative subtype, indicative of dedicated IAS collicular pathways in each group of patients. When comparing PTSD to its dissociative subtype, we observed increased resting state functional connectivity between the left SC and the right dorsolateral prefrontal cortex (DLPFC) in PTSD. The DLPFC is involved in modulation of emotional processes associated with active defensive responses characterising PTSD. Moreover, when comparing PTSD to its dissociative subtype, increased resting state functional connectivity was observed between the right SC and the right temporoparietal junction in the dissociative subtype. The temporoparietal junction is involved in depersonalization responses associated with passive defensive responses typical of the dissociative subtype. Our findings suggest that unique resting state functional connectivity of the SC parallels the unique symptom profile and defensive responses observed in PTSD and its dissociative subtype. Hum Brain Mapp 39:563-574, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Zero photon dissociation of CS2+ in intense ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Severt, Travis; Betsch, K. J.; Zohrabi, M.; Ablikim, U.; Jochim, Bethany; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

2013-05-01

We measured the dissociation of a CS2+ molecular ion beam in intense laser pulses (<50 fs, <1015 W/cm2), focusing on the zero photon dissociation (ZPD) and above threshold dissociation (ATD) mechanisms. The ZPD mechanism leads to dissociation with the net absorption of zero photons in a strong field. The present work extends the idea of ZPD to more complex molecules than the H2+ discussed in literature. Preliminary data suggests that ZPD is larger than ATD for CS2+ --> C+ + S+. We speculate that a pump-dump process occurs whereby the vibrational wavepacket in the electronic ground state of CS2+ is pumped into the electronic first excited state's continuum by a single photon during the laser pulse. Once this continuum vibrational wavepacket passes the potential barrier in the ground electronic potential, the emission of a second photon is stimulated by the same laser pulse, most likely when the wavepacket moves through the internuclear distance where the two electronic states are in resonance with the driving field. A comparison is made to ZPD and ATD in the isovalent CO2+ species. Curiously, ATD is the favored mechanism in CO2+. The underlying molecular structure and dynamics determining this preference will be discussed. Supported by Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy.

Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

PubMed

Forbert, Harald; Masia, Marco; Kaczmarek-Kedziera, Anna; Nair, Nisanth N; Marx, Dominik

2011-03-23

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.

Gelator-doped liquid-crystal phase grating with multistable and dynamic modes

NASA Astrophysics Data System (ADS)

Lin, Hui-Chi; Yang, Meng-Ru; Tsai, Sheng-Feng; Yan, Shih-Chiang

2014-01-01

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.

Gelator-doped liquid-crystal phase grating with multistable and dynamic modes

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

Lin, Hui-Chi, E-mail: huichilin@nfu.edu.tw; Yang, Meng-Ru; Tsai, Sheng-Feng

2014-01-06

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.

Ultrafast relaxation dynamics of nitric oxide synthase studied by visible broadband transient absorption spectroscopy

NASA Astrophysics Data System (ADS)

Hung, Chih-Chang; Yabushita, Atsushi; Kobayashi, Takayoshi; Chen, Pei-Feng; Liang, Keng S.

2017-09-01

Ultrafast dynamics of endothelial nitric oxide synthase (eNOS) oxygenase domain was studied by transient absorption spectroscopy pumping at Soret band. The broadband visible probe spectrum has visualized the relaxation dynamics from the Soret band to Q-band and charge transfer (CT) band. Supported by two-dimensional correlation spectroscopy, global fitting analysis has successfully concluded the relaxation dynamics from the Soret band to be (1) electronic transition to Q-band (0.16 ps), (2) ligand dissociation and CT (0.94 ps), (3) relaxation of the CT state (4.0 ps), and (4) ligand rebinding (59 ps).

Analysis of Functional Coupling: Mitochondrial Creatine Kinase and Adenine Nucleotide Translocase

PubMed Central

Vendelin, Marko; Lemba, Maris; Saks, Valdur A.

2004-01-01

The mechanism of functional coupling between mitochondrial creatine kinase (MiCK) and adenine nucleotide translocase (ANT) in isolated heart mitochondria is analyzed. Two alternative mechanisms are studied: 1), dynamic compartmentation of ATP and ADP, which assumes the differences in concentrations of the substrates between intermembrane space and surrounding solution due to some diffusion restriction and 2), direct transfer of the substrates between MiCK and ANT. The mathematical models based on these possible mechanisms were composed and simulation results were compared with the available experimental data. The first model, based on a dynamic compartmentation mechanism, was not sufficient to reproduce the measured values of apparent dissociation constants of MiCK reaction coupled to oxidative phosphorylation. The second model, which assumes the direct transfer of substrates between MiCK and ANT, is shown to be in good agreement with experiments—i.e., the second model reproduced the measured constants and the estimated ADP flux, entering mitochondria after the MiCK reaction. This model is thermodynamically consistent, utilizing the free energy profiles of reactions. The analysis revealed the minimal changes in the free energy profile of the MiCK-ANT interaction required to reproduce the experimental data. A possible free energy profile of the coupled MiCK-ANT system is presented. PMID:15240503

Predicting p Ka values from EEM atomic charges

PubMed Central

2013-01-01

The acid dissociation constant p Ka is a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p Ka prediction. We have evaluated the p Ka prediction capabilities of QSPR models based on empirical atomic charges calculated by the Electronegativity Equalization Method (EEM). Specifically, we collected 18 EEM parameter sets created for 8 different quantum mechanical (QM) charge calculation schemes. Afterwards, we prepared a training set of 74 substituted phenols. Additionally, for each molecule we generated its dissociated form by removing the phenolic hydrogen. For all the molecules in the training set, we then calculated EEM charges using the 18 parameter sets, and the QM charges using the 8 above mentioned charge calculation schemes. For each type of QM and EEM charges, we created one QSPR model employing charges from the non-dissociated molecules (three descriptor QSPR models), and one QSPR model based on charges from both dissociated and non-dissociated molecules (QSPR models with five descriptors). Afterwards, we calculated the quality criteria and evaluated all the QSPR models obtained. We found that QSPR models employing the EEM charges proved as a good approach for the prediction of p Ka (63% of these models had R2 > 0.9, while the best had R2 = 0.924). As expected, QM QSPR models provided more accurate p Ka predictions than the EEM QSPR models but the differences were not significant. Furthermore, a big advantage of the EEM QSPR models is that their descriptors (i.e., EEM atomic charges) can be calculated markedly faster than the QM charge descriptors. Moreover, we found that the EEM QSPR models are not so strongly influenced by the selection of the charge calculation approach as the QM QSPR models. The robustness of the EEM QSPR models was subsequently confirmed by cross-validation. The applicability of EEM QSPR models for other chemical classes was illustrated by a case study focused on carboxylic acids. In summary, EEM QSPR models constitute a fast and accurate p Ka prediction approach that can be used in virtual screening. PMID:23574978

Ab initio-informed maximum entropy modeling of rovibrational relaxation and state-specific dissociation with application to the O{sub 2} + O system

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

Kulakhmetov, Marat, E-mail: mkulakhm@purdue.edu; Alexeenko, Alina, E-mail: alexeenk@purdue.edu; Gallis, Michael, E-mail: magalli@sandia.gov

Quasi-classical trajectory (QCT) calculations are used to study state-specific ro-vibrational energy exchange and dissociation in the O{sub 2} + O system. Atom-diatom collisions with energy between 0.1 and 20 eV are calculated with a double many body expansion potential energy surface by Varandas and Pais [Mol. Phys. 65, 843 (1988)]. Inelastic collisions favor mono-quantum vibrational transitions at translational energies above 1.3 eV although multi-quantum transitions are also important. Post-collision vibrational favoring decreases first exponentially and then linearly as Δv increases. Vibrationally elastic collisions (Δv = 0) favor small ΔJ transitions while vibrationally inelastic collisions have equilibrium post-collision rotational distributions. Dissociationmore » exhibits both vibrational and rotational favoring. New vibrational-translational (VT), vibrational-rotational-translational (VRT) energy exchange, and dissociation models are developed based on QCT observations and maximum entropy considerations. Full set of parameters for state-to-state modeling of oxygen is presented. The VT energy exchange model describes 22 000 state-to-state vibrational cross sections using 11 parameters and reproduces vibrational relaxation rates within 30% in the 2500–20 000 K temperature range. The VRT model captures 80 × 10{sup 6} state-to-state ro-vibrational cross sections using 19 parameters and reproduces vibrational relaxation rates within 60% in the 5000–15 000 K temperature range. The developed dissociation model reproduces state-specific and equilibrium dissociation rates within 25% using just 48 parameters. The maximum entropy framework makes it feasible to upscale ab initio simulation to full nonequilibrium flow calculations.« less

[Persistent Perpetrator Contact in a Patient with Dissociative Identity Disorder].

PubMed

Tschöke, Stefan; Eisele, Frank; Steinert, Tilman

2016-05-01

The case of a young woman with still ongoing incest and forced prostitution is presented. The criteria for a dissociative identity disorder (DID) were met. Due to persistent contact to the perpetrator she was repeatedly revictimized. Based on the model of trauma-related dissociation we discuss to what extent she was capable of self-determined decision making as well as therapeutic consequences resulting therefrom. © Georg Thieme Verlag KG Stuttgart · New York.

Dissociative tendencies and individual differences in high hypnotic suggestibility.

PubMed

Terhune, Devin Blair; Cardeña, Etzel; Lindgren, Magnus

2011-03-01

Inconsistencies in the relationship between dissociation and hypnosis may result from heterogeneity among highly suggestible individuals, in particular the existence of distinct highly suggestible subtypes that are of relevance to models of psychopathology and the consequences of trauma. This study contrasted highly suggestible subtypes high or low in dissociation on measures of hypnotic responding, cognitive functioning, and psychopathology. Twenty-one low suggestible (LS), 19 low dissociative highly suggestible (LDHS), and 11 high dissociative highly suggestible (HDHS) participants were administered hypnotic suggestibility scales and completed measures of free recall, working memory capacity, imagery, fantasy-proneness, psychopathology, and exposure to stressful life events. HDHS participants were more responsive to positive and negative hallucination suggestions and experienced greater involuntariness during hypnotic responding. They also exhibited impaired working memory capacity, elevated pathological fantasy and dissociative symptomatology, and a greater incidence of exposure to stressful life events. In contrast, LDHS participants displayed superior object visual imagery. These results provide further evidence for two highly suggestible subtypes: a dissociative subtype characterised by deficits in executive functioning and a predisposition to psychopathology, and a subtype that exhibits superior imagery and no observable deficits in functioning.

Increased Heat Transport in Ultra-hot Jupiter Atmospheres through H2 Dissociation and Recombination

NASA Astrophysics Data System (ADS)

Bell, Taylor J.; Cowan, Nicolas B.

2018-04-01

A new class of exoplanets is beginning to emerge: planets with dayside atmospheres that resemble stellar atmospheres as most of their molecular constituents dissociate. The effects of the dissociation of these species will be varied and must be carefully accounted for. Here we take the first steps toward understanding the consequences of dissociation and recombination of molecular hydrogen (H2) on atmospheric heat recirculation. Using a simple energy balance model with eastward winds, we demonstrate that H2 dissociation/recombination can significantly increase the day–night heat transport on ultra-hot Jupiters (UHJs): gas giant exoplanets where significant H2 dissociation occurs. The atomic hydrogen from the highly irradiated daysides of UHJs will transport some of the energy deposited on the dayside toward the nightside of the planet where the H atoms recombine into H2; this mechanism bears similarities to latent heat. Given a fixed wind speed, this will act to increase the heat recirculation efficiency; alternatively, a measured heat recirculation efficiency will require slower wind speeds after accounting for H2 dissociation/recombination.

The role of impulsivity in the association between childhood trauma and dissociative psychopathology: mediation versus moderation.

PubMed

Somer, Eli; Ginzburg, Karni; Kramer, Lilach

2012-03-30

Previous studies on survivors of childhood trauma documented associations between psychological dysregulation, impulsivity, and both behavioral and emotional manifestations of distress. Yet, the mechanism that links these variables remains unclear. The current study aims to examine the pattern of relations between a history of child abuse, impulsivity and dissociation. More specifically, it examines whether impulsivity serves as a moderator or mediator in the association between childhood trauma and dissociation. Eighty-one inpatients from the acute wards of two psychiatric hospitals participated in this study. Data were collected by clinician-administered questionnaires. A highly significant linear hierarchical regression analysis revealed that both psychiatric comorbidity and childhood trauma made unique contributions to the variance of dissociation. Yet, the significant association between childhood trauma and dissociation decreased when impulsivity was entered into the regression model. Our findings suggest that impulsivity mediates the association between childhood trauma and dissociative psychopathology and imply that the identification and treatment of impulsivity could be a potentially valuable clinical target in individuals with dissociative disorders. Copyright © 2012 Elsevier Ltd. All rights reserved.

Protein-Protein Förster Resonance Energy Transfer Analysis of Nucleosome Core Particles Containing H2A and H2A.Z

PubMed Central

Hoch, Duane A.; Stratton, Jessica J.; Gloss, Lisa M.

2007-01-01

A protein-protein Förster resonance energy transfer (FRET) system, employing probes at multiple positions, was designed to specifically monitor the dissociation of the H2A-H2B dimer from the nucleosome core particle (NCP). Tryptophan donors and Cys-AEDANS acceptors were chosen because, in comparison to fluorophores used in previous NCP FRET studies, they: 1) are smaller and less hydrophobic which should minimize perturbations of histone and NCP structure; and 2) have an R0 of 20 Å, which is much less than the dimensions of the NCP (~50 Å width and ~100 Å diameter). CD and FL equilibrium protein unfolding titrations indicate that the donor and acceptor moieties have minimal effects on the stability of the H2A-H2B dimer and (H3-H4)2 tetramer. NCPs containing the various FRET pairs were reconstituted with the 601 artificial positioning DNA sequence. Equilibrium NaCl-induced dissociation of the modified NCPs showed that the 601 sequence stabilized the NCP to dimer dissociation as compared to previous studies using weaker positioning sequences. This finding implies a significant role for the H2A-H2B dimers in determining the DNA sequence dependence of NCP stability. The free energy of dissociation determined from reversible and well-defined sigmoidal transitions revealed two distinct phases reflecting the dissociation of each H2A-H2B dimer, confirming cooperativity in dimer dissociation. While cooperativity in the association/dissociation of the H2A-H2B dimers has been suggested previously, these data allow its quantitative description. The protein-protein FRET system was then used to study the effects of the histone variant H2A.Z on NCP stability; previous studies have reported both destabilizing and stabilizing effects. Comparison of the H2A and H2A.Z FRET NCP dissociation transitions suggest a slight increase in stability but a significant increase in cooperativity for dimer dissociation from H2A.Z NCPs. Thus, the utility of this protein-protein FRET system to monitor the effects of histone variants on NCP dynamics has been demonstrated, and the system appears equally well-suited for dissection of the kinetic processes of dimer association and dissociation from the NCP. PMID:17597150

Childhood trauma and eating psychopathology: a mediating role for dissociation and emotion dysregulation?

PubMed

Moulton, Stuart J; Newman, Emily; Power, Kevin; Swanson, Vivien; Day, Kenny

2015-01-01

The present study examined the relationship between different forms of childhood trauma and eating psychopathology using a multiple mediation model that included emotion dysregulation and dissociation as hypothesised mediators. 142 female undergraduate psychology students studying at two British Universities participated in this cross-sectional study. Participants completed measures of childhood trauma (emotional abuse, physical abuse, sexual abuse, emotional neglect and physical neglect), eating psychopathology, dissociation and emotion dysregulation. Multiple mediation analysis was conducted to investigate the study's proposed model. Results revealed that the multiple mediation model significantly predicted eating psychopathology. Additionally, both emotion dysregulation and dissociation were found to be significant mediators between childhood trauma and eating psychopathology. A specific indirect effect was observed between childhood emotional abuse and eating psychopathology through emotion dysregulation. Findings support previous research linking childhood trauma to eating psychopathology. They indicate that multiple forms of childhood trauma should be assessed for individuals with eating disorders. The possible maintaining role of emotion regulation processes should also be considered in the treatment of eating disorders. Copyright © 2014 Elsevier Ltd. All rights reserved.

On the Development of a New Nonequilibrium Chemistry Model for Mars Entry

NASA Technical Reports Server (NTRS)

Jaffe, R. L.; Schwenke, D. W.; Chaban, G. M.; Prabhu, D. K.; Johnston, C. O.; Panesi, M.

2017-01-01

This paper represents a summary of results to date of an on-going effort at NASA Ames Research Center to develop a physics-based non-equilibrium model for hypersonic entry into the Martian atmosphere. Our approach is to first compute potential energy surfaces based on accurate solutions of the electronic Schroedinger equation and then use quasiclassical trajectory calculations to obtain reaction cross sections and rate coefficients based on these potentials. We have presented new rate coefficients for N2 dissociation and CO dissociation and exchange reactions. These results illustrate shortcomings with some of the rate coefficients in Parks original T-Tv model for Mars entries and with some of the 30-45 year old shock tube data. We observe that the shock tube experiments of CO + O dissociation did not adequately account for the exchange reaction that leads to formation of C + O2. This reaction is actually the primary channel for CO removal in the shock layer at temperatures below 10,000 K, because the reaction enthalpy for exchange is considerably lower than the comparable value for dissociation.

DSMC simulations of shock tube experiments for the dissociation rate of nitrogen

NASA Astrophysics Data System (ADS)

Bird, G. A.

2012-11-01

The DSMC method has been used to simulate the flow associated with several experiments that led to predictions of the dissociation rate in nitrogen. One involved optical interferometry to determine the density behind strong shock wave and the other involved the measurement of the shock tube end-wall pressure after the reflection of a similar shock wave. DSMC calculations for the un-reflected shock wave were made with the older TCE model that converts rate coefficients to reaction cross-sections, with the newer Q-K model that predicts the rates and with a set of reaction cross-sections for nitrogen dissociation from QCT calculations. A comparison of the resulting density profiles with the measured profile provides a test of the validity of the DSMC chemistry models. The DSMC reaction rates were sampled directly in the DSMC calculation, both far downstream where the flow is in equilibrium and in the non-equilibrium region immediately behind the shock. This permits a critical evaluation of data reduction procedures that were employed to deduce the dissociation rate from the measured quantities.

Dissociating 'what' and 'how' in visual form agnosia: a computational investigation.

PubMed

Vecera, S P

2002-01-01

Patients with visual form agnosia exhibit a profound impairment in shape perception (what an object is) coupled with intact visuomotor functions (how to act on an object), demonstrating a dissociation between visual perception and action. How can these patients act on objects that they cannot perceive? Although two explanations of this 'what-how' dissociation have been offered, each explanation has shortcomings. A 'pathway information' account of the 'what-how' dissociation is presented in this paper. This account hypothesizes that 'where' and 'how' tasks require less information than 'what' tasks, thereby allowing 'where/how' to remain relatively spared in the face of neurological damage. Simulations with a neural network model test the predictions of the pathway information account. Following damage to an input layer common to the 'what' and 'where/how' pathways, the model performs object identification more poorly than spatial localization. Thus, the model offers a parsimonious explanation of differential 'what-how' performance in visual form agnosia. The simulation results are discussed in terms of their implications for visual form agnosia and other neuropsychological syndromes.

A Computational Study on the Ground and Excited States of Nickel Silicide.

PubMed

Schoendorff, George; Morris, Alexis R; Hu, Emily D; Wilson, Angela K

2015-09-17

Nickel silicide has been studied with a range of computational methods to determine the nature of the Ni-Si bond. Additionally, the physical effects that need to be addressed within calculations to predict the equilibrium bond length and bond dissociation energy within experimental error have been determined. The ground state is predicted to be a (1)Σ(+) state with a bond order of 2.41 corresponding to a triple bond with weak π bonds. It is shown that calculation of the ground state equilibrium geometry requires a polarized basis set and treatment of dynamic correlation including up to triple excitations with CR-CCSD(T)L resulting in an equilibrium bond length of only 0.012 Å shorter than the experimental bond length. Previous calculations of the bond dissociation energy resulted in energies that were only 34.8% to 76.5% of the experimental bond dissociation energy. It is shown here that use of polarized basis sets, treatment of triple excitations, correlation of the valence and subvalence electrons, and a Λ coupled cluster approach is required to obtain a bond dissociation energy that deviates as little as 1% from experiment.

Dissociative Experiences are Associated with Obsessive-Compulsive Symptoms in a Non-clinical Sample: A Latent Profile Analysis

PubMed Central

BOYSAN, Murat

2014-01-01

Introduction There has been a burgeoning literature considering the significant associations between obsessive-compulsive symptoms and dissociative experiences. In this study, the relationsips between dissociative symtomotology and dimensions of obsessive-compulsive symptoms were examined in homogeneous sub-groups obtained with latent class algorithm in an undergraduate Turkish sample. Method Latent profile analysis, a recently developed classification method based on latent class analysis, was applied to the Dissociative Experiences Scale (DES) item-response data from 2976 undergraduates. Differences in severity of obsessive-compulsive symptoms, anxiety and depression across groups were evaluated by running multinomial logistic regression analyses. Associations between latent class probabilities and psychological variables in terms of obsessive-compulsive sub-types, anxiety, and depression were assessed by computing Pearson’s product-moment correlation coefficients. Results The findings of the latent profile analysis supported further evidence for discontinuity model of dissociative experiences. The analysis empirically justified the distinction among three sub-groups based on the DES items. A marked proportion of the sample (42%) was assigned to the high dissociative class. In the further analyses, all sub-types of obsessive-compulsive symptoms significantly differed across latent classes. Regarding the relationships between obsessive-compulsive symptoms and dissociative symptomatology, low dissociation appeared to be a buffering factor dealing with obsessive-compulsive symptoms; whereas high dissociation appeared to be significantly associated with high levels of obsessive-compulsive symptoms. Conclusion It is concluded that the concept of dissociation can be best understood in a typological approach that dissociative symptomatology not only exacerbates obsessive-compulsive symptoms but also serves as an adaptive coping mechanism. PMID:28360635

Dissociative Experiences are Associated with Obsessive-Compulsive Symptoms in a Non-clinical Sample: A Latent Profile Analysis.

PubMed

Boysan, Murat

2014-09-01

There has been a burgeoning literature considering the significant associations between obsessive-compulsive symptoms and dissociative experiences. In this study, the relationsips between dissociative symtomotology and dimensions of obsessive-compulsive symptoms were examined in homogeneous sub-groups obtained with latent class algorithm in an undergraduate Turkish sample. Latent profile analysis, a recently developed classification method based on latent class analysis, was applied to the Dissociative Experiences Scale (DES) item-response data from 2976 undergraduates. Differences in severity of obsessive-compulsive symptoms, anxiety and depression across groups were evaluated by running multinomial logistic regression analyses. Associations between latent class probabilities and psychological variables in terms of obsessive-compulsive sub-types, anxiety, and depression were assessed by computing Pearson's product-moment correlation coefficients. The findings of the latent profile analysis supported further evidence for discontinuity model of dissociative experiences. The analysis empirically justified the distinction among three sub-groups based on the DES items. A marked proportion of the sample (42%) was assigned to the high dissociative class. In the further analyses, all sub-types of obsessive-compulsive symptoms significantly differed across latent classes. Regarding the relationships between obsessive-compulsive symptoms and dissociative symptomatology, low dissociation appeared to be a buffering factor dealing with obsessive-compulsive symptoms; whereas high dissociation appeared to be significantly associated with high levels of obsessive-compulsive symptoms. It is concluded that the concept of dissociation can be best understood in a typological approach that dissociative symptomatology not only exacerbates obsessive-compulsive symptoms but also serves as an adaptive coping mechanism.

Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies

NASA Astrophysics Data System (ADS)

Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.

2017-03-01

We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Analysis of formation pressure test results in the Mount Elbert methane hydrate reservoir through numerical simulation

USGS Publications Warehouse

Kurihara, M.; Sato, A.; Funatsu, K.; Ouchi, H.; Masuda, Y.; Narita, H.; Collett, T.S.

2011-01-01

Targeting the methane hydrate (MH) bearing units C and D at the Mount Elbert prospect on the Alaska North Slope, four MDT (Modular Dynamic Formation Tester) tests were conducted in February 2007. The C2 MDT test was selected for history matching simulation in the MH Simulator Code Comparison Study. Through history matching simulation, the physical and chemical properties of the unit C were adjusted, which suggested the most likely reservoir properties of this unit. Based on these properties thus tuned, the numerical models replicating "Mount Elbert C2 zone like reservoir" "PBU L-Pad like reservoir" and "PBU L-Pad down dip like reservoir" were constructed. The long term production performances of wells in these reservoirs were then forecasted assuming the MH dissociation and production by the methods of depressurization, combination of depressurization and wellbore heating, and hot water huff and puff. The predicted cumulative gas production ranges from 2.16??106m3/well to 8.22??108m3/well depending mainly on the initial temperature of the reservoir and on the production method.This paper describes the details of modeling and history matching simulation. This paper also presents the results of the examinations on the effects of reservoir properties on MH dissociation and production performances under the application of the depressurization and thermal methods. ?? 2010 Elsevier Ltd.

Mechanistic Study on Electron Capture Dissociation of the Oligosaccharide-Mg2+ Complex

NASA Astrophysics Data System (ADS)

Huang, Yiqun; Pu, Yi; Yu, Xiang; Costello, Catherine E.; Lin, Cheng

2014-08-01

Electron capture dissociation (ECD) has shown great potential in structural characterization of glycans. However, our current understanding of the glycan ECD process is inadequate for accurate interpretation of the complex glycan ECD spectra. Here, we present the first comprehensive theoretical investigation on the ECD fragmentation behavior of metal-adducted glycans, using the cellobiose-Mg2+ complex as the model system. Molecular dynamics simulation was carried out to determine the typical glycan-Mg2+ binding patterns and the lowest-energy conformer identified was used as the initial geometry for density functional theory-based theoretical modeling. It was found that the electron is preferentially captured by Mg2+ and the resultant Mg+• can abstract a hydroxyl group from the glycan moiety to form a carbon radical. Subsequent radical migration and α-cleavage(s) result in the formation of a variety of product ions. The proposed hydroxyl abstraction mechanism correlates well with the major features in the ECD spectrum of the Mg2+-adducted cellohexaose. The mechanism presented here also predicts the presence of secondary, radical-induced fragmentation pathways. These secondary fragment ions could be misinterpreted, leading to erroneous structural determination. The present study highlights an urgent need for continuing investigation of the glycan ECD mechanism, which is imperative for successful development of bioinformatics tools that can take advantage of the rich structural information provided by ECD of metal-adducted glycans.

A woman with dermatitis and dissociative periods.

PubMed

Wise, T N; Reading, A J

1975-01-01

A nineteen year old female with pustular eczema and dissociative spells is presented. The patient has a three year history of severe dermatitis beginning shortly after her marriage. Central dynamic issues appear to be difficulty separating from her mother and an ambivalent identification with a hostile father. The patient also describes fugue-like episodes which occur with emerging aggressive feelings. Psychological testing supported these hypotheses. The relevant literature describing the correlation between aggression and skin disease is reviewed. A final uniform formulation was tentatively proposed that this patient, in addition to a strong genetic component for atopic dermatitis, had her illness abetted by inability to cope with aggressive affects.

Imaging Agonist-Induced D2/D3 Receptor Desensitization and Internalization In Vivo with PET/fMRI.

PubMed

Sander, Christin Y; Hooker, Jacob M; Catana, Ciprian; Rosen, Bruce R; Mandeville, Joseph B

2016-04-01

This study investigated the dynamics of dopamine receptor desensitization and internalization, thereby proposing a new technique for non-invasive, in vivo measurements of receptor adaptations. The D2/D3 agonist quinpirole, which induces receptor internalization in vitro, was administered at graded doses in non-human primates while imaging with simultaneous positron emission tomography (PET) and functional magnetic resonance imaging (fMRI). A pronounced temporal divergence between receptor occupancy and fMRI signal was observed: occupancy remained elevated while fMRI responded transiently. Analogous experiments with an antagonist (prochlorperazine) and a lower-affinity agonist (ropinirole) exhibited reduced temporal dissociation between occupancy and function, consistent with a mechanism of desensitization and internalization that depends upon drug efficacy and affinity. We postulated a model that incorporates internalization into a neurovascular-coupling relationship. This model yielded in vivo desensitization/internalization rates (0.2/min for quinpirole) consistent with published in vitro measurements. Overall, these results suggest that simultaneous PET/fMRI enables characterization of dynamic neuroreceptor adaptations in vivo, and may offer a first non-invasive method for assessing receptor desensitization and internalization.

Imaging Agonist-Induced D2/D3 Receptor Desensitization and Internalization In Vivo with PET/fMRI

PubMed Central

Sander, Christin Y; Hooker, Jacob M; Catana, Ciprian; Rosen, Bruce R; Mandeville, Joseph B

2016-01-01

This study investigated the dynamics of dopamine receptor desensitization and internalization, thereby proposing a new technique for non-invasive, in vivo measurements of receptor adaptations. The D2/D3 agonist quinpirole, which induces receptor internalization in vitro, was administered at graded doses in non-human primates while imaging with simultaneous positron emission tomography (PET) and functional magnetic resonance imaging (fMRI). A pronounced temporal divergence between receptor occupancy and fMRI signal was observed: occupancy remained elevated while fMRI responded transiently. Analogous experiments with an antagonist (prochlorperazine) and a lower-affinity agonist (ropinirole) exhibited reduced temporal dissociation between occupancy and function, consistent with a mechanism of desensitization and internalization that depends upon drug efficacy and affinity. We postulated a model that incorporates internalization into a neurovascular-coupling relationship. This model yielded in vivo desensitization/internalization rates (0.2/min for quinpirole) consistent with published in vitro measurements. Overall, these results suggest that simultaneous PET/fMRI enables characterization of dynamic neuroreceptor adaptations in vivo, and may offer a first non-invasive method for assessing receptor desensitization and internalization. PMID:26388148

Exploring evidence of a dissociative subtype in PTSD: Baseline symptom structure, etiology, and treatment efficacy for those who dissociate.

PubMed

Burton, Mark S; Feeny, Norah C; Connell, Arin M; Zoellner, Lori A

2018-05-01

With the inclusion of a dissociative subtype, recent changes to the DSM-5 diagnosis of posttraumatic stress disorder (PTSD) have emphasized the role of dissociation in the experience and treatment of the disorder. However, there is a lack of research exploring the clinical impact for highly dissociative groups receiving treatment for PTSD. The current study examined the presence and clinical impact of a dissociative subtype in a sample of individuals receiving treatment for chronic PTSD. This study used latent transition analyses (LTA), an expanded form of latent profile analyses (LPA), to examine latent profiles of PTSD and dissociation symptoms before and after treatment for individuals (N = 200) receiving prolonged exposure (PE) or sertraline treatment for chronic PTSD. The best fitting LTA model was one with a 4-class solution at both pretreatment and posttreatment. There was a latent class at pretreatment with higher levels of dissociative symptoms. However, this class was also marked by higher reexperiencing symptoms, and membership was not predicted by chronic child abuse. Further, although those in the class were less likely to transition to the responder class overall, this was not the case for exposure-based treatment specifically. These findings are not in line with the dissociative-subtype theoretical literature that proposes those who dissociate represent a clinically distinct group that may respond worse to exposure-based treatments for PTSD. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Simulating the effect of hydrate dissociation on wellhead stability during oil and gas development in deepwater

NASA Astrophysics Data System (ADS)

Li, Qingchao; Cheng, Yuanfang; Zhang, Huaiwen; Yan, Chuanliang; Liu, Yuwen

2018-02-01

It is well known that methane hydrate has been identified as an alternative resource due to its massive reserves and clean property. However, hydrate dissociation during oil and gas development (OGD) process in deep water can affect the stability of subsea equipment and formation. Currently, there is a serious lack of studies over quantitative assessment on the effects of hydrate dissociation on wellhead stability. In order to solve this problem, ABAQUS finite element software was used to develop a model and to evaluate the behavior of wellhead caused by hydrate dissociation. The factors that affect the wellhead stability include dissociation range, depth of hydrate formation and mechanical properties of dissociated hydrate region. Based on these, series of simulations were carried out to determine the wellhead displacement. The results revealed that, continuous dissociation of hydrate in homogeneous and isotropic formations can causes the non-linear increment in vertical displacement of wellhead. The displacement of wellhead showed good agreement with the settlement of overlying formations under the same conditions. In addition, the shallower and thicker hydrate formation can aggravate the influence of hydrate dissociation on the wellhead stability. Further, it was observed that with the declining elastic modulus and Poisson's ratio, the wellhead displacement increases. Hence, these findings not only confirm the effect of hydrate dissociation on the wellhead stability, but also lend support to the actions, such as cooling the drilling fluid, which can reduce the hydrate dissociation range and further make deepwater operations safer and more efficient.

General Reynolds analogy on curved surfaces in hypersonic rarefied gas flows with non-equilibrium chemical reactions

NASA Astrophysics Data System (ADS)

Xingxing, Chen; Zhihui, Wang; Yongliang, Yu

2016-11-01

Hypersonic chemical non-equilibrium gas flows around blunt nosed bodies are studied in the present paper to investigate the Reynolds analogy relation on curved surfaces. With a momentum and energy transfer model being applied through boundary layers, influences of molecular dissociations and recombinations on skin frictions and heat fluxes are separately modeled. Expressions on the ratio of Cf / Ch (skin friction coefficient to heat flux) are presented along the surface of circular cylinders under the ideal dissociation gas model. The analysis indicates that molecular dissociations increase the linear distribution of Cf / Ch, but the nonlinear Reynolds analogy relation could ultimately be obtained in flows with larger Reynolds numbers and Mach numbers, where the decrease of wall heat flux by molecular recombinations signifies. The present modeling and analyses are also verified by the DSMC calculations on nitrogen gas flows.

Development and application of computational aerothermodynamics flowfield computer codes

NASA Technical Reports Server (NTRS)

Venkatapathy, Ethiraj

1993-01-01

Computations are presented for one-dimensional, strong shock waves that are typical of those that form in front of a reentering spacecraft. The fluid mechanics and thermochemistry are modeled using two different approaches. The first employs traditional continuum techniques in solving the Navier-Stokes equations. The second-approach employs a particle simulation technique (the direct simulation Monte Carlo method, DSMC). The thermochemical models employed in these two techniques are quite different. The present investigation presents an evaluation of thermochemical models for nitrogen under hypersonic flow conditions. Four separate cases are considered. The cases are governed, respectively, by the following: vibrational relaxation; weak dissociation; strong dissociation; and weak ionization. In near-continuum, hypersonic flow, the nonequilibrium thermochemical models employed in continuum and particle simulations produce nearly identical solutions. Further, the two approaches are evaluated successfully against available experimental data for weakly and strongly dissociating flows.

Chemical Thermodynamics of Aqueous Atmospheric Aerosols: Modeling and Microfluidic Measurements

NASA Astrophysics Data System (ADS)

Nandy, L.; Dutcher, C. S.

2017-12-01

Accurate predictions of gas-liquid-solid equilibrium phase partitioning of atmospheric aerosols by thermodynamic modeling and measurements is critical for determining particle composition and internal structure at conditions relevant to the atmosphere. Organic acids that originate from biomass burning, and direct biogenic emission make up a significant fraction of the organic mass in atmospheric aerosol particles. In addition, inorganic compounds like ammonium sulfate and sea salt also exist in atmospheric aerosols, that results in a mixture of single, double or triple charged ions, and non-dissociated and partially dissociated organic acids. Statistical mechanics based on a multilayer adsorption isotherm model can be applied to these complex aqueous environments for predictions of thermodynamic properties. In this work, thermodynamic analytic predictive models are developed for multicomponent aqueous solutions (consisting of partially dissociating organic and inorganic acids, fully dissociating symmetric and asymmetric electrolytes, and neutral organic compounds) over the entire relative humidity range, that represent a significant advancement towards a fully predictive model. The model is also developed at varied temperatures for electrolytes and organic compounds the data for which are available at different temperatures. In addition to the modeling approach, water loss of multicomponent aerosol particles is measured by microfluidic experiments to parameterize and validate the model. In the experimental microfluidic measurements, atmospheric aerosol droplet chemical mimics (organic acids and secondary organic aerosol (SOA) samples) are generated in microfluidic channels and stored and imaged in passive traps until dehydration to study the influence of relative humidity and water loss on phase behavior.

Preliminary Measurements on the Mechanical Properties of Clathrate Hydrates with Implications for the Internal Dynamics of Icy Satellites

NASA Astrophysics Data System (ADS)

Choukroun, M.; Barmatz, M. B.; Castillo, J. C.; Sotin, C.

2008-12-01

Surface features potentially associated with cryovolcanism have been identified on Titan, and the processes taking place beneath the surface are likely associated with the dissociation of clathrate hydrates and the release of methane. On Enceladus, the South Pole plume discovered by the Cassini-Huygens mission contains a large proportion of volatiles, in amounts consistent with models of clathrate hydrates dissociation at depth (Kieffer et al., Science 314, 1764-1766, 2006). The stability of clathrate hydrates is relatively well constrained in pure and mixed gas systems (e.g., Sloan, Clathrate hydrates of natural gases, Marcel Dekker, New York, 1998). Recent measurements of clathrate destabilization in presence of ammonia, a likely component of Titan's interior, led to the development of a new model of cryovolcanism (Choukroun et al., Lunar Planet. Sci. Conf., #1837, Houston, 2008). Internal dynamics relies on ice convection at depth on Titan and Enceladus (e.g., Tobie et al., Icarus 175, 496-502, 2005), and on relatively large tidal stresses on Enceladus. Clathrates are expected to destabilize when subject to stress (Durham et al., J. Geophys. Res. 108 (B4), 2182, 2003). Therefore, addressing the mechanical properties of clathrate hydrates in these environments is a necessary step toward better understanding cryovolcanic processes. We have developed a new apparatus for growing clathrate hydrates samples with controlled geometry, composition, and grain size. This system consists of a high-pressure autoclave and a cooling system and supports gas pressures up to 500 bars, and temperatures within the range -50 - 150 °C. We have started the production of clathrate hydrates of CH4, CO2, and N2 with this system, with the purpose to test their mechanical properties using an Instron compression system (Castillo-Rogez et al., submitted to J. Geophys. Res.; Castillo-Rogez et al., this meeting). We will present initial measurements on the creep response and on the viscoelastic response of clathrate hydrates as a function of frequency. These measurements will provide new information on the behavior of clathrate hydrates during dynamic motions within icy satellites.

Heat aggregation studies of phycobilisomes, ferritin, insulin, and immunoglobulin by dynamic light scattering.

PubMed

Singh, B P; Bohidar, H B; Chopra, S

1991-10-15

Dynamic laser light scattering studies on the heat aggregation behavior of phycobilisomes (PBS), ferritin, insulin, and immunoglobulin (IgG) in dilute aqueous solutions has been reported. Except for PBS, results are reported for heat aggregation trends in these proteins for three different pH environments (4.0, 7.5, 9.1). For PBS, studies were performed only in the neutral buffer medium (pH 7.5). The experiments were performed in the very dilute concentration regime (between 0.23 and 1.8 gL-1). For all these samples heat aggregation and dissociation trends were found to be linear with temperature. Upon temperature reversal (self-cooling), hysteresis-like behavior observed in insulin was found to be predominantly large at pH 7.5. PBS, ferritin, and IgG showed no such behavior at any of three pH values, and retraced their path of aggregation while dissociating on temperature reversal. Heat aggregation and dissociation processes in ferritin were found to be independent of pH. The IgG samples showed smooth aggregation tendency only up to 35 degrees C in the buffer media pH 4.0 and 9.1, whereas for pH 7.0 the same could be observed until 60 degrees C. Low polydispersity in the correlation spectra was observed in case of all these samples.

Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

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

Cao, Haining; Kim, Seungchul; Lee, Kwang-Ryeol, E-mail: krlee@kist.re.kr

2016-03-28

Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathwaymore » for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.« less

The atmosphere of a dirty-clathrate cometary nucleus - A two-phase, multifluid model

NASA Astrophysics Data System (ADS)

Marconi, M. L.; Mendis, D. A.

1983-10-01

The dynamical and thermal structure of a dirty-clathrate cometary nucleus' gas atmosphere is presently given a self-consistent, transonic multifluid solution in which, although the heavy neutron and ion species are treated as a single fluid in the collision-dominated region, the photoproduced H is treated separately. The thermal profile of the atmosphere thus obtained is entirely different from those predicted by the earlier, single-fluid models as well as the multifluid models which assumed equipartition of energy between electrons and ions. While the electron gas, like the neutrals and the ions, cools due to expansion, its main mode of energy loss in the inner coma is by way of inelastic collisions with the predominant H2O molecule. The high electron temperature in the outer coma also decreases the efficiency of electron removal by dissociative recombination, thereby increasing electron density throughout the coma.

Quantum anharmonic oscillator plus delta-function potential: a molecular view of pairing formation and breaking in the coordinate space

NASA Astrophysics Data System (ADS)

Sumaryada, Tony; Maha Putra, Bima; Pramudito, Sidikrubadi

2017-05-01

We propose an alternative way to describe the pairing formation and breaking via a quantum anharmonic oscillator with a delta-function potential model. Unlike BCS theory, which describes the pairing formation in the momentum space, this model works in the coordinate space and is able to give a molecular view of pairing formation and breaking in the coordinate space. By exploring the dynamical interplay between the intrinsic factor (dissociation energy) and external factor (pairing strength) of this system additional information was gained, including the critical pairing strength and critical scattering length, which might relate to the BCS-BEC crossover phenomena and halo state formation. Although only the energetic aspect of pairing is described by this model, its simplicity and pedagogical steps might help undergraduate students to understand the pairing problem in a simple way.

A quantum dynamical study of the He++2He-->He2++He reaction

NASA Astrophysics Data System (ADS)

Xie, Junkai; Poirier, Bill; Gellene, Gregory I.

2003-11-01

The temperature dependent rate of the He++2He→He2++He three-body association reaction is studied using two complementary quantum dynamical models. Model I presumes a two-step, reverse Lindemann mechanism, where the intermediate energized complex, He2+*, is interpreted as the rotational resonance states of He2+. The energy and width of these resonances are determined via "exact" quantum calculation using highly accurate potential-energy curves. Model II uses an alternate quantum rate expression as the thermal average of the cumulative recombination probability, N(E). This microcanonical quantity is computed approximately, over the He2+ space only, with the third-body interaction modeled using a special type of absorbing potential. Because Model II implicitly incorporates both the two-step reverse Lindemann mechanism, and a one-step, reverse collision induced dissociation mechanism, the relative importance of the two formation mechanisms can be estimated by a comparison of the Model I and Model II results. For T<300 K, the reaction is found to be dominated by the two-step mechanism, and a formation rate in good agreement with the available experimental results is obtained with essentially no adjustable parameters in the theory. Interestingly, a nonmonotonic He2+ formation rate is observed, with a maximum identified near 25 K. This maximum is associated with just two reaction intermediate resonance states, the lowest energy states that can contribute significantly to the formation kinetics.

A Comparison of Linear versus Non-Linear Models of Aversive Self-Awareness, Dissociation, and Non-Suicidal Self-Injury among Young Adults

ERIC Educational Resources Information Center

Armey, Michael F.; Crowther, Janis H.

2008-01-01

Research has identified a significant increase in both the incidence and prevalence of non-suicidal self-injury (NSSI). The present study sought to test both linear and non-linear cusp catastrophe models by using aversive self-awareness, which was operationalized as a composite of aversive self-relevant affect and cognitions, and dissociation as…

Analysis of single-molecule fluorescence spectroscopic data with a Markov-modulated Poisson process.

PubMed

Jäger, Mark; Kiel, Alexander; Herten, Dirk-Peter; Hamprecht, Fred A

2009-10-05

We present a photon-by-photon analysis framework for the evaluation of data from single-molecule fluorescence spectroscopy (SMFS) experiments using a Markov-modulated Poisson process (MMPP). A MMPP combines a discrete (and hidden) Markov process with an additional Poisson process reflecting the observation of individual photons. The algorithmic framework is used to automatically analyze the dynamics of the complex formation and dissociation of Cu2+ ions with the bidentate ligand 2,2'-bipyridine-4,4'dicarboxylic acid in aqueous media. The process of association and dissociation of Cu2+ ions is monitored with SMFS. The dcbpy-DNA conjugate can exist in two or more distinct states which influence the photon emission rates. The advantage of a photon-by-photon analysis is that no information is lost in preprocessing steps. Different model complexities are investigated in order to best describe the recorded data and to determine transition rates on a photon-by-photon basis. The main strength of the method is that it allows to detect intermittent phenomena which are masked by binning and that are difficult to find using correlation techniques when they are short-lived.

Shot through with voices: Dissociation mediates the relationship between varieties of inner speech and auditory hallucination proneness

PubMed Central

Alderson-Day, Ben; McCarthy-Jones, Simon; Bedford, Sarah; Collins, Hannah; Dunne, Holly; Rooke, Chloe; Fernyhough, Charles

2014-01-01

Inner speech is a commonly experienced but poorly understood phenomenon. The Varieties of Inner Speech Questionnaire (VISQ; McCarthy-Jones & Fernyhough, 2011) assesses four characteristics of inner speech: dialogicality, evaluative/motivational content, condensation, and the presence of other people. Prior findings have linked anxiety and proneness to auditory hallucinations (AH) to these types of inner speech. This study extends that work by examining how inner speech relates to self-esteem and dissociation, and their combined impact upon AH-proneness. 156 students completed the VISQ and measures of self-esteem, dissociation and AH-proneness. Correlational analyses indicated that evaluative inner speech and other people in inner speech were associated with lower self-esteem and greater frequency of dissociative experiences. Dissociation and VISQ scores, but not self-esteem, predicted AH-proneness. Structural equation modelling supported a mediating role for dissociation between specific components of inner speech (evaluative and other people) and AH-proneness. Implications for the development of “hearing voices” are discussed. PMID:24980910

Thermal dissociation and relaxation in vinyl fluoride, 1,1-difluoroethane and 1,3,5-triazine

NASA Astrophysics Data System (ADS)

Xu, Hui

This study reports measurements of the thermal dissociation of 1,1-difluoroethane in the shock tube. The experiments employ laser schlieren measurements of rate for the dominant HF elimination using 10% 1,1-difluoroethane in Kr over 1500--2000 K and 43 < P < 424 torr. The product vinyl then dissociates affecting the late density gradient. We include a laser schlieren study (1717--2332 K, 75 < P < 482 torr in 10% and 4% vinyl fluoride in Kr) of this dissociation. This latter work also includes a set of experiments using shock-tube time-of-flight mass-spectrometry (4% vinyl fluoride in neon, 1500--1980 K, 500 < P < 1300 torr), which confirm the theoretical expectation that the only reaction in vinyl fluoride is HF elimination. The relaxation experiments (1--20% C2H3F in Kr, 415--1975 K, 5 < P < 50 torr, and 2% and 5% C2H4F2 in Kr, 700--1350 K, 6 < P < 22 torr) exhibit very rapid relaxation, and incubation delays should be negligible in dissociation. A RRKM model of dissociation in 1,1-difluoroethane based on a G3B3 calculation of barrier and other properties fits the experiments but requires a very large down of 1600cm-1 . Dissociation of vinyl fluoride has two parallel HF eliminations both three-center and four-center with nearly equal barriers. An RRKM fit to the observed falloff again requires an unusually large down and the experiments actually support a slightly reduced barrier. Both 1,3,5-triazine and pyrazine relax extremely rapidly with energy transfer in a few collisions, any incubation delay can be confidently discounted in dissociation. 1,3,5-triazine dissociation experiments show fall-off with a clear pressure dependence. The three body product dissociation mechanism models this dissociation perfectly. Experimental data agree well with an RRKM calculation using a down of 1200cm-1 and a barrier E0 = 84.66 kcal/mol. Dyakov et al. suggested lower barrier of E0 = 81 kcal/mole. The new RRKM calculation using this barrier seems a better fit to the experiments. The falloff is now fit well with a down of the more usual form 126(T/298) 0-9 cm-1.

Understanding the free energy barrier and multiple timescale dynamics of charge separation in organic photovoltaic cells.

PubMed

Yan, Yaming; Song, Linze; Shi, Qiang

2018-02-28

By employing several lattice model systems, we investigate the free energy barrier and real-time dynamics of charge separation in organic photovoltaic (OPV) cells. It is found that the combined effects of the external electric field, entropy, and charge delocalization reduce the free energy barrier significantly. The dynamic disorder reduces charge carrier delocalization and results in the increased charge separation barrier, while the effect of static disorder is more complicated. Simulation of the real-time dynamics indicates that the free charge generation process involves multiple time scales, including an ultrafast component within hundreds of femtoseconds, an intermediate component related to the relaxation of the hot charge transfer (CT) state, and a slow component on the time scale of tens of picoseconds from the thermally equilibrated CT state. Effects of hot exciton dissociation as well as its dependence on the energy offset between the Frenkel exciton and the CT state are also analyzed. The current results indicate that only a small energy offset between the band gap and the lowest energy CT state is needed to achieve efficient free charge generation in OPV devices, which agrees with recent experimental findings.

Understanding the free energy barrier and multiple timescale dynamics of charge separation in organic photovoltaic cells

NASA Astrophysics Data System (ADS)

Yan, Yaming; Song, Linze; Shi, Qiang

2018-02-01

By employing several lattice model systems, we investigate the free energy barrier and real-time dynamics of charge separation in organic photovoltaic (OPV) cells. It is found that the combined effects of the external electric field, entropy, and charge delocalization reduce the free energy barrier significantly. The dynamic disorder reduces charge carrier delocalization and results in the increased charge separation barrier, while the effect of static disorder is more complicated. Simulation of the real-time dynamics indicates that the free charge generation process involves multiple time scales, including an ultrafast component within hundreds of femtoseconds, an intermediate component related to the relaxation of the hot charge transfer (CT) state, and a slow component on the time scale of tens of picoseconds from the thermally equilibrated CT state. Effects of hot exciton dissociation as well as its dependence on the energy offset between the Frenkel exciton and the CT state are also analyzed. The current results indicate that only a small energy offset between the band gap and the lowest energy CT state is needed to achieve efficient free charge generation in OPV devices, which agrees with recent experimental findings.

On low temperature glide of dissociated <1 1 0> dislocations in strontium titanate

NASA Astrophysics Data System (ADS)

Ritterbex, Sebastian; Hirel, Pierre; Carrez, Philippe

2018-05-01

An elastic interaction model is presented to quantify low temperature plasticity of SrTiO3 via glide of dissociated <1 1 0>{1 1 0} screw dislocations. Because <1 1 0> dislocations are dissociated, their glide, controlled by the kink-pair mechanism at T < 1050 K, involves the formation of kink-pairs on partial dislocations, either simultaneously or sequentially. Our model yields results in good quantitative agreement with the observed non-monotonic mechanical behaviour of SrTiO3. This agreement allows to explain the experimental results in terms of a (progressive) change in <1 1 0>{1 1 0} glide mechanism, from simultaneous nucleation of two kink-pairs along both partials at low stress, towards nucleation of single kink-pairs on individual partials if resolved shear stress exceeds a critical value of 95 MPa. High resolved shear stress allows thus for the activation of extra nucleation mechanisms on dissociated dislocations impossible to occur under the sole action of thermal activation. We suggest that stress condition in conjunction with core dissociation is key to the origin of non-monotonic plastic behaviour of SrTiO3 at low temperatures.

The dissociation of subjective measures of mental workload and performance

NASA Technical Reports Server (NTRS)

Yeh, Y. H.; Wickens, C. D.

1984-01-01

Dissociation between performance and subjective workload measures was investigated in the theoretical framework of the multiple resources model. Subjective measures do not preserve the vector characteristics in the multidimensional space described by the model. A theory of dissociation was proposed to locate the sources that may produce dissociation between the two workload measures. According to the theory, performance is affected by every aspect of processing whereas subjective workload is sensitive to the amount of aggregate resource investment and is dominated by the demands on the perceptual/central resources. The proposed theory was tested in three experiments. Results showed that performance improved but subjective workload was elevated with an increasing amount of resource investment. Furthermore, subjective workload was not as sensitive as was performance to differences in the amount of resource competition between two tasks. The demand on perceptual/central resources was found to be the most salient component of subjective workload. Dissociation occurred when the demand on this component was increased by the number of concurrent tasks or by the number of display elements. However, demands on response resources were weighted in subjective introspection as much as demands on perceptual/central resources. The implications of these results for workload practitioners are described.

Theoretical study on the cooperative exciton dissociation process based on dimensional and hot charge-transfer state effects in an organic photocell

NASA Astrophysics Data System (ADS)

Shimazaki, Tomomi; Nakajima, Takahito

2016-06-01

This paper discusses the exciton dissociation process at the donor-acceptor interface in organic photocells. In our previous study, we introduced a local temperature to handle the hot charge-transfer (CT) state and calculated the exciton dissociation probability based on the 1D organic semiconductor model [T. Shimazaki and T. Nakajima, Phys. Chem. Chem. Phys. 17, 12538 (2015)]. Although the hot CT state plays an essential role in exciton dissociations, the probabilities calculated are not high enough to efficiently separate bound electron-hole pairs. This paper focuses on the dimensional (entropy) effect together with the hot CT state effect and shows that cooperative behavior between both effects can improve the exciton dissociation process. In addition, we discuss cooperative effects with site-disorders and external-electric-fields.

A general mechanism for competitor-induced dissociation of molecular complexes

PubMed Central

Paramanathan, Thayaparan; Reeves, Daniel; Friedman, Larry J.; Kondev, Jane; Gelles, Jeff

2014-01-01

The kinetic stability of non-covalent macromolecular complexes controls many biological phenomena. Here we find that physical models of complex dissociation predict that competitor molecules will in general accelerate the breakdown of isolated bimolecular complexes by occluding rapid rebinding of the two binding partners. This prediction is largely independent of molecular details. We confirm the prediction with single-molecule fluorescence experiments on a well-characterized DNA strand dissociation reaction. Contrary to common assumptions, competitor–induced acceleration of dissociation can occur in biologically relevant competitor concentration ranges and does not necessarily implyternary association of competitor with the bimolecular complex. Thus, occlusion of complex rebinding may play a significant role in a variety of biomolecular processes. The results also show that single-molecule colocalization experiments can accurately measure dissociation rates despite their limited spatio temporal resolution. PMID:25342513

The dissociative post-traumatic stress disorder (PTSD) subtype: A treatment outcome cohort study in veterans with PTSD.

PubMed

Haagen, Joris F G; van Rijn, Allison; Knipscheer, Jeroen W; van der Aa, Niels; Kleber, Rolf J

2018-06-01

Dissociation is a prevalent phenomenon among veterans with post-traumatic stress disorder (PTSD) that may interfere with the effectiveness of treatment. This study aimed to replicate findings of a dissociative PTSD subtype, to identify corresponding patterns in coping style, symptom type, and symptom severity, and to investigate its impact on post-traumatic symptom improvement. Latent profile analysis (LPA) was applied to baseline data from 330 predominantly (97%) male treatment-seeking veterans (mean age 39.5 years) with a probable PTSD. Multinomial logistic models were used to identify predictors of dissociative PTSD. Eighty veterans with PTSD that commenced with psychotherapy were invited for a follow-up measure after 6 months. The majority (n = 64, 80% response rate) completed the follow-up measure. Changes in post-traumatic stress between baseline and follow-up were explored as a continuous distal outcome. Latent profile analysis revealed four distinct patient profiles: 'low' (12.9%), 'moderate' (33.2%), 'severe' (45.1%), and 'dissociative' (8.8%) PTSD. The dissociative PTSD profile was characterized by more severe pathology levels, though not post-traumatic reactions symptom severity. Veterans with dissociative PTSD benefitted equally from PTSD treatment as veterans with non-dissociative PTSD with similar symptom severity. Within a sample of veterans with PTSD, a subsample of severely dissociative veterans was identified, characterized by elevated severity levels on pathology dimensions. The dissociative PTSD subtype did not negatively impact PTSD treatment. The present findings confirmed the existence of a distinct subgroup veterans that fit the description of dissociative PTSD. Patients with dissociative PTSD subtype symptoms uniquely differed from patients with non-dissociative PTSD in the severity of several psychopathology dimensions. Dissociative and non-dissociative PTSD patients with similar post-traumatic severity levels showed similar levels of improvement after PTSD treatment. The observational design and small sample size caution interpretation of the treatment outcome data. The IES-R questionnaire does not assess all PTSD DSM-IV diagnostic criteria (14 of 17), although it is considered a valid measure for an indication of PTSD. © 2018 The British Psychological Society.

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

PubMed Central

Schramm, Vern L.

2017-01-01

Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein’s dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states. PMID:21675920

UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture.

PubMed

Soorkia, Satchin; Dehon, Christophe; Kumar, S Sunil; Pedrazzani, Mélanie; Frantzen, Emilie; Lucas, Bruno; Barat, Michel; Fayeton, Jacqueline A; Jouvet, Christophe

2014-04-03

Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ-σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.