Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3

Time-correlated atomic motions were used to characterize protein domain boundaries from atomic coordinates generated by molecular dynamics simulations. A novel application of the dynamical cross-correlation matrix (DCCM) analysis tool was used to help identify putative protein domains. In implementing this new approach, several DCCM maps were calculated, each using a different coordinate reference frame from which protein domain boundaries and protein domain residue constituents could be identified. Cytochrome P450BM-3, from Bacillus megaterium, was used as the model protein in this study. The analyses indicated that the simulated protein comprises three distinct domain regions; in contrast, only two protein domains were identified in the original crystal structure report. Specifically, the DCCM analyses showed that the F-G helix region was a separate domain entity and not a part of the alpha domain, as previously designated. The simulations demonstrated that the domain motions of the F-G helix region effected both the size and shape of the enzyme active site, and that the dynamics of the F-G helix domain could possibly control access of substrate to the binding pocket

Energy-Dependent Form Factors of the Optical Potential for Intermediate-Energy Protons from a Relativistic Model

This work was supported by the National Science Foundation Grant NSF PHY 78-22774 A02 & A03 and by Indiana Universit

Real time thermal propagtors for massive gauge bosons

We derive Feynman rules for gauge theories exhibiting spontaneous symmetry breaking using the real-time formalism of finite temperature field theory. We also derive the thermal propagators where only the physical degrees of freedom are given thermal boundary conditions. We analyse the abelian Higgs model and find that these new propagators simplify the calculation of the thermal contribution to the self energy.Comment: 7 pages, late

Hubungan antara aktiviti enzim klon Eucalyptus dan kerentanan terhadap serangan penyengat puru, Leptocybe invasa, di selatan China

The activity levels of five defensive enzymes, namely, peroxidase (POD), polyphenol oxidase (PPO), superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL) and catalase (CAT) were assessed in shoots of four commercial Eucalyptus clones (DH201-2, DH32-29, U6, GL9) at ages of 13, 29 and 38 months. Levels were also assessed in healthy and damaged shoots of clone DH201-2 at 15 months, shortly after it was severely attacked by the shoot gall wasp Leptocybe invasa. Foliar levels of these five enzymes did not show any significant increase with age. The level of CAT was found to be significantly higher at ages 29 and 38 months in clone GL9, a clone relatively resistant to L. invasa, than in the three other clones. Clone DH201-2, which was relatively susceptible to L. invasa, had non-significantly lower CAT levels than the rest of the clones at all three ages examined. The levels of the other four enzymes showed no obvious differences between clones and overall activity levels of the five enzymes did not show any clear association with the qualitative ranking susceptibility of the clones to L. invasa. In 15-month-old DH201-2 trees, marked increases in the levels of CAT, SOD and PPO were observed in shoots attacked by L. invasa compared with shoots from healthy trees of the same age, while levels of PAL and POD decreased compared with those in shoots from healthy trees.Aras aktiviti lima enzim pertahanan iaitu peroksidase (POD), polifenol oksidase (PPO), superoksida dismutase (SOD), fenilalanin ammonia-liase (PAL) and katalase (CAT) dinilai dalam pucuk empat klon Eucalyptus komersial (DH201-2, DH32-29, U6, GL9) yang berusia 13 bulan, 29 bulan dan 38 bulan. Aras enzim turut dinilai dalam pucuk yang sihat serta yang rosak bagi klon DH201-2 yang berusia 15 bulan tidak lama selepas ia diserang penyengat puru, Leptocybe invasa. Aras kelima-lima enzim daun tidak menunjukkan peningkatan signifikan dengan usia. Aras CAT lebih tinggi pada klon GL9 yang berusia 29 and 38 bulan. Klon GL9 secara relatifnya lebih rintang terhadap L. invasa berbanding ketiga-tiga klon yang lain. Klon DH201-2 yang agak rentan terhadap L. invasa mempunyai kandungan CAT yang lebih rendah berbanding klon lain yang dikaji. Aras enzim empat lagi enzim tidak menunjukkan perbezaan ketara antara klon. Secara keseluruhannya, aras aktiviti kelima-lima enzim tidak menunjukkan sebarang hubungan yang jelas antara tahap kerentanan kualitatif klon terhadap L. invasa. Pokok DH201-2 yang berusia 15 bulan menunjukkan peningkatan ketara dalam aras CAT, SOD dan PPO bagi pucuk yang diserang L. invasa berbanding pucuk pokok sihat yang sama usianya. Aras PAL and POD pula menurun berbanding pucuk pokok sihat.This study was initiated through a bilateral agreement between South Africa and China, and funded through project 2008B050100014.http://www.frim.gov.my/am201

A simple sum rule for the thermal gluon spectral function and applications

In this paper, we derive a simple sum rule satisfied by the gluon spectral function at finite temperature. This sum rule is useful in order to calculate exactly some integrals that appear frequently in the photon or dilepton production rate by a quark gluon plasma. Using this sum rule, we rederive simply some known results and obtain some new results that would be extremely difficult to justify otherwise. In particular, we derive an exact expression for the collision integral that appears in the calculation of the Landau-Pomeranchuk-Migdal effect.Comment: 24 latex pages, 2 postscript figure

Heavy ion fusion program at Argonne

Argonne's Heavy Ion Fusion (HIF) program is trying for two major achievements during the coming 4 to 5 years. The primary objective is to demonstrate accelerator operation in areas that are especially important for the use of heavy ion accelerator systems as drivers in inertial fusion power plants. These demonstrations comprise reliable operation of a front end (source, preaccelerator, and rf linac to approx. 10 MeV) with adequate output beam current and emittance; tolerable emittance growth during further acceleration in an rf linac (including frequency transition, with simulated linac-beam combination, and intense beam stripping); strong debunching; multiturn injection with minimal beam loss and tolerable phase space dilution; beam compression; and efficient focusing. The second objective is to demonstrate efficient stopping of intense ion beams in material at conditions relevant to fusion pellet implosion. For this purpose, the apparatus of the primary (accelerator) demonstration would be modified to include a synchrotron accelerating the 220 MeV Xe/sup +8/ from the linac to 10 GeV

The Lamé Class of Lorenz Curves.

In this paper, the class of Lamé Lorenz curves is studied. This family has the advantage of modeling inequality with a single parameter. The family has a double motivation: it can be obtain from an economic model and from simple transformations of classical Lorenz curves. The underlying cumulative distribution functions have a simple closed form, and correspond to the Singh-Maddala and Dagum distributions, which are well known in the economic literature. The Lorenz order is studied and several inequality and polarization measures are obtained, including Gini, Donaldson-Weymark-Kakwani, Pietra and Wolfson indices. Some extensions of the Lamé family are obtained. Fitting and estimation methods under two different data configuration are proposed. Empirical applications with real data are given. Finally, some relationships with other curves are included.The authors thank to Ministerio de Econom a y Competitividad, project ECO2010-15455, for partial support. The second author thanks to the Ministerio de Educaci on (FPU AP-2010-4907) for partial support. We are grateful for the constructive suggestions provided by the reviewers, which improved the paper

Hard-Loop Effective Action for Anisotropic Plasmas

We generalize the hard-thermal-loop effective action of the equilibrium quark-gluon plasma to a non-equilibrium system which is space-time homogeneous but for which the parton momentum distribution is anisotropic. We show that the manifestly gauge-invariant Braaten-Pisarski form of the effective action can be straightforwardly generalized and we verify that it then generates all n-point functions following from collisionless gauge-covariant transport theory for a homogeneous anisotropic plasma. On the other hand, the Taylor-Wong form of the hard-thermal-loop effective action has a more complicated generalization to the anisotropic case. Already in the simplest case of anisotropic distribution functions, it involves an additional term that is gauge invariant by itself, but nontrivial also in the static limit.Comment: 12 pages. Version 3: typo in (15) corrected, note added discussing metric conventions use