Elucidating the Influence of the Activation Energy on Reaction Rates by Simulations Based on a Simple Particle Model

An application for visualizing the dynamic properties of an equimolar binary mixture of isotropic reactive particles is presented. By introducing a user selectable choice for the activation energy, the application is useful to demonstrate qualitatively that the reaction rate depends on the above choice and on temperature. The application is based on a 2D realistic dynamic model where atoms move because of their thermal energies and the trajectories are determined by solving numerically Newton’s laws according to a Molecular Dynamics (MD) scheme. Collisions are monitored as time progresses, and every time the collision energy is larger than the selected activation energy, a reactive event occurs. By examining the time evolution of the configurations, it is possible to observe that the number of reactive collisions is always smaller than the total number of collisions. However, the number of reactive events increases on raising the temperature and/or by decreasing the activation energy. The above observations, as well as more quantitative analyses of the simulation data, are useful in elucidating the connections existing among particle kinetic energy, temperature, and activation energy of the reaction. The application can be used at different levels of detail and in different instruction levels. Qualitative visual observations of the progress of the reaction are suitable at all levels of instruction. Systematic investigations on the effect of changes of temperature and activation energy, suitable for senior high school and college courses and useful to gain insight into kinetic models and Arrhenius’ law, are also reported

Enhancement of vaccinia virus based oncolysis with histone deacetylase inhibitors

Histone deacetylase inhibitors (HDI) dampen cellular innate immune response by decreasing interferon production and have been shown to increase the growth of vesicular stomatitis virus and HSV. As attenuated tumour-selective oncolytic vaccinia viruses (VV) are already undergoing clinical evaluation, the goal of this study is to determine whether HDI can also enhance the potency of these poxviruses in infection-resistant cancer cell lines. Multiple HDIs were tested and Trichostatin A (TSA) was found to potently enhance the spread and replication of a tumour selective vaccinia virus in several infection-resistant cancer cell lines. TSA significantly decreased the number of lung metastases in a syngeneic B16F10LacZ lung metastasis model yet did not increase the replication of vaccinia in normal tissues. The combination of TSA and VV increased survival of mice harbouring human HCT116 colon tumour xenografts as compared to mice treated with either agent alone. We conclude that TSA can selectively and effectively enhance the replication and spread of oncolytic vaccinia virus in cancer cells. © 2010 MacTavish et al

Critical role of p38 MAPK for regeneration of the sciatic nerve following crush injury in vivo

BACKGROUND The physiological function of p38α, which is an isoform of p38 MAPK, has been investigated previously in several studies using pharmacological inhibitors. However, the results regarding whether p38α promotes or inhibits nerve regeneration in vivo have been controversial. METHODS We generated novel p38α mutant mice (sem mice) with a point mutation in the region encoding the p38α substrate-docking-site, which serves as a limited loss-of-function model of p38α. In the present study, we utilized sem mice and wild-type littermates (wt mice) to investigate the physiological role of p38α in nerve regeneration following crush injuries. RESULTS At four weeks after crush injury, the average axon diameter and the average axon area in sem mice were significantly smaller than those in wt mice. The average myelin sheath thickness in sem mice was reduced compared to wt mice, but no significant difference was observed in the G-ratio between the two groups. The sciatic functional index value demonstrated that functional nerve recovery in sem mice following crush injury was delayed, which is consistent with the histological findings. To investigate the underlying mechanisms of these findings, we examined inflammatory responses of the sciatic nerve by immunohistochemistry and western blotting. At an early phase following crush injury, sem mice showed remarkably lower expression of inflammatory cytokines, such as TNF-α and IL-1β, than wt mice. The expression of Caspase-3 and Tenascin-C were also lower in sem mice. Conversely, at a late phase of the response, sem mice showed considerably higher expression of TNF-α and of IL-1β with lower expression of S-100 than wt mice. CONCLUSIONS This is the first study of the physiological role of p38 MAPK in nerve regeneration that does not rely on the use of pharmacological inhibitors. Our results indicate that p38α insufficiency may cause an inflammatory disorder, resulting in a delay of histological and functional nerve recovery following crush injury. We conclude that p38 MAPK has an important physiological role in nerve regeneration and may be important for controlling both initiation of inflammation and recovery from nerve injury.Naoki Kato, Masahito Matsumoto, Masakazu Kogawa, Gerald J Atkins, David M Findlay, Takahiko Fujikawa, Hiromi Oda and Masato Ogat

Effect of Reynolds number on a normal shock wave-transitional boundary-layer interaction over a curved surface

Funder: Rolls-Royce (GB)Abstract: The interaction between a normal shock wave and a boundary layer is investigated over a curved surface for a Reynolds number range, based on boundary-layer growing length x, of 0.44×106≤Rex≤1.09×106. The upstream boundary layer develops around the leading edge of the model before encountering a M∼1.4 normal shock. This is followed by adverse pressure gradients. The shock position and strength are kept constant as Re is progressively varied. Infra-red thermography is used to determine the nature of the upstream boundary layer. Across the Re range, this is observed to vary from fully laminar to fully turbulent across the entire span. Regardless of the boundary-layer state, the interaction remains benign in nature, without large scale shock-induced separation or unsteadiness. Schlieren images show a pronounced oblique wave developing upstream of the main shock for the laminar cases, this is believed to correspond to the separation and subsequent transition of the laminar shear layer. Downstream of the shock, in the presence of adverse pressure gradients, the boundary-layer growth rate is inversely proportional to Re. Nonetheless, across the entire range of inflow conditions the boundary layer recovers quickly to a healthy turbulent boundary layer. This suggests the upstream boundary-layer state, and its transition mechanism, to have little effect on the outcome of its interaction with a normal shock wave. Graphic abstract

Kinetic Energy Density Study of Some Representative Semilocal Kinetic Energy Functionals

There is a number of explicit kinetic energy density functionals for non-interacting electron systems that are obtained in terms of the electron density and its derivatives. These semilocal functionals have been widely used in the literature. In this work we present a comparative study of the kinetic energy density of these semilocal functionals, stressing the importance of the local behavior to assess the quality of the functionals. We propose a quality factor that measures the local differences between the usual orbital-based kinetic energy density distributions and the approximated ones, allowing to ensure if the good results obtained for the total kinetic energies with these semilocal functionals are due to their correct local performance or to error cancellations. We have also included contributions coming from the laplacian of the electron density to work with an infinite set of kinetic energy densities. For all the functionals but one we have found that their success in the evaluation of the total kinetic energy are due to global error cancellations, whereas the local behavior of their kinetic energy density becomes worse than that corresponding to the Thomas-Fermi functional.Comment: 12 pages, 3 figure

Temperature dependence of binary and ternary recombination of H3+ ions with electron

We study binary and the recently discovered process of ternary He-assisted recombination of H3+ ions with electrons in a low temperature afterglow plasma. The experiments are carried out over a broad range of pressures and temperatures of an afterglow plasma in a helium buffer gas. Binary and He-assisted ternary recombination are observed and the corresponding recombination rate coefficients are extracted for temperatures from 77 K to 330 K. We describe the observed ternary recombination as a two-step mechanism: First, a rotationally-excited long-lived neutral molecule H3* is formed in electron-H3+ collisions. Second, the H3* molecule collides with a helium atom that leads to the formation of a very long-lived Rydberg state with high orbital momentum. We present calculations of the lifetimes of H3* and of the ternary recombination rate coefficients for para and ortho-H3+. The calculations show a large difference between the ternary recombination rate coefficients of ortho- and para-H3+ at temperatures below 300 K. The measured binary and ternary rate coefficients are in reasonable agreement with the calculated values.Comment: 15 page

Relativistically extended Blanchard recurrence relation for hydrogenic matrix elements

General recurrence relations for arbitrary non-diagonal, radial hydrogenic matrix elements are derived in Dirac relativistic quantum mechanics. Our approach is based on a generalization of the second hypervirial method previously employed in the non-relativistic Schr\"odinger case. A relativistic version of the Pasternack-Sternheimer relation is thence obtained in the diagonal (i.e. total angular momentum and parity the same) case, from such relation an expression for the relativistic virial theorem is deduced. To contribute to the utility of the relations, explicit expressions for the radial matrix elements of functions of the form $r^\lambda$ and $\beta r^\lambda$ ---where $\beta$ is a Dirac matrix--- are presented.Comment: 21 pages, to be published in J. Phys. B: At. Mol. Opt. Phys. in Apri

Theory of x-ray absorption by laser-aligned symmetric-top molecules

We devise a theory of x-ray absorption by symmetric-top molecules which are aligned by an intense optical laser. Initially, the density matrix of the system is composed of the electronic ground state of the molecules and a thermal ensemble of rigid-rotor eigenstates. We formulate equations of motion of the two-color (laser plus x rays) rotational-electronic problem. The interaction with the laser is assumed to be nonresonant; it is described by an electric dipole polarizability tensor. X-ray absorption is approximated as a one-photon process. It is shown that the equations can be separated such that the interaction with the laser can be treated independently of the x rays. The laser-only density matrix is propagated numerically. After each time step, the x-ray absorption is calculated. We apply our theory to study adiabatic alignment of bromine molecules (Br2). The required dynamic polarizabilities are determined using the ab initio linear response methods coupled-cluster singles (CCS), second-order approximate coupled-cluster singles and doubles (CC2), and coupled-cluster singles and doubles (CCSD). For the description of x-ray absorption on the sigma_g 1s --> sigma_u 4p resonance, a parameter-free two-level model is used for the electronic structure of the molecules. Our theory opens up novel perspectives for the quantum control of x-ray radiation.Comment: 14 pages, 4 figures, 1 table, RevTeX4, revise

Cluster-based density-functional approach to quantum transport through molecular and atomic contacts

We present a cluster-based density-functional approach to model charge transport through molecular and atomic contacts. The electronic structure of the contacts is determined in the framework of density functional theory, and the parameters needed to describe transport are extracted from finite clusters. A similar procedure, restricted to nearest-neighbor interactions in the electrodes, has been presented by Damle et al. [Chem. Phys. 281, 171 (2002)]. Here, we show how to systematically improve the description of the electrodes by extracting bulk parameters from sufficiently large metal clusters. In this way we avoid problems arising from the use of nonorthogonal basis functions. For demonstration we apply our method to electron transport through Au contacts with various atomic-chain configurations and to a single-atom contact of Al.Comment: 18 pages, 13 figure