Kinetic and Structural Analysis of the Mg2+ -binding Site of the Guanine Nucleotide-binding Protein p21 H-ras.

The coordination and binding of the Mg2+ ion in the nucleotide−binding site of p21 have been investigated using site−directed mutagenesis, kinetic methods, and phosphorous NMR. Mg2+ in the p21.nucleotide.Mg2+ complex appears to be in fast equilibrium with the solvent. The dissociation constant between Mg2+ and the p21.GDP complex was determined to be 2.8 microM. It decreases 30− or 16−fold on substituting Ser−17 or Asp−57 with alanine, respectively, whereas the T35A mutation has no effect. All three mutations influence the dissociation constants and the association and dissociation rate constants of the interaction between guanine nucleotides and p21, but to a different degree. We conclude that Thr−35 is only complexed to Mg2+ in the GTP conformation and both Asp−57 and Ser−17 appear to be critical for both GDP and GTP binding. 31P NMR spectra of the GDP and Gpp(NH)p (guanosine−5'−(beta,gamma−imido)triphosphate) complexes of mutated p21 show a remarkable perturbation of the guanine nucleotide− binding site compared to wild−type protein. The mutant proteins show reduced GTPase rates, which are not stimulated by the GTPase−activating protein GAP. p21(S17A) has been reported to function just as p21(S17N) as a dominant negative inhibitor of normal p21. We find that it inhibits oncogenic p21−induced survival of primary neuron

Jet thermalization in QCD kinetic theory

We perform numerical studies in QCD kinetic theory to investigate the energy and angular profiles of a high energy parton - as a proxy for a jet produced heavy ion collisions - passing through a Quark-Gluon Plasma (QGP). We find that the fast parton loses energy to the plasma mainly via a radiative turbulent gluon cascade that transport energy locally from the jet down to the temperature scale where dissipation takes place. In this first stage, the angular structure of the turbulent cascade is found to be relatively collimated. However, when the lost energy reaches the plasma temperature is it rapidly transported to large angles w.r.t. the jet axis and thermalizes. We investigate the contribution of the soft jet constituents to the total jet energy. We show that for jet opening angles of about 0.3 rad or smaller the effect is negligible. Conversely, larger opening angles become more and more sensitive to the thermal component of the jet and thus to medium response. Our result showcase the importance of the jet cone size in mitigating or enhancing the details of dissipation in jet quenching observables.Comment: 41 pages, 11 figures

Initial Planetesimal Sizes and the Size Distribution of Small Kuiper Belt Objects

The Kuiper Belt is a remnant from the early solar system and its size distribution contains many important constraints that can be used to test models of planet formation and collisional evolution. We show, by comparing observations with theoretical models, that the observed Kuiper Belt size distribution is well matched by coagulation models, which start with an initial planetesimal population with radii of about 1 km, and subsequent collisional evolution. We find that the observed size distribution above R ~ 30 km is primordial, i.e., it has not been modified by collisional evolution over the age of the solar system, and that the size distribution below R ~ 30 km has been modified by collisions and that its slope is well matched by collisional evolution models that use published strength laws. We investigate in detail the resulting size distribution of bodies ranging from 0.01 km to 30 km and find that its slope changes several times as a function of radius before approaching the expected value for an equilibrium collisional cascade of material strength dominated bodies for R ≾0.1 km. Compared to a single power-law size distribution that would span the whole range from 0.01 km to 30 km, we find in general a strong deficit of bodies around R ~ 10 km and a strong excess of bodies around 2 km in radius. This deficit and excess of bodies are caused by the planetesimal size distribution left over from the runaway growth phase, which left most of the initial mass in small planetesimals while only a small fraction of the total mass is converted into large protoplanets. This excess mass in small planetesimals leaves a permanent signature in the size distribution of small bodies that is not erased after 4.5 Gyr of collisional evolution. Observations of the small Kuiper Belt Object (KBO) size distribution can therefore test if large KBOs grew as a result of runaway growth and constrained the initial planetesimal sizes. We find that results from recent KBO occultation surveys and the observed KBO size distribution can be best matched by an initial planetesimal population that contained about equal mass per logarithmic mass bin in bodies ranging from 0.4 km to 4 km in radius. We further find that we cannot match the observed KBO size distribution if most of the planetesimal mass was contained in bodies that were 10 km in radius or larger simply because their resulting size distribution cannot be sufficiently depleted over 4.5 Gyr to match observations

Aureochrome 1 illuminated: structural changes of a transcription factor probed by molecular spectroscopy.

Aureochrome 1 from Vaucheria frigida is a recently identified blue-light receptor that acts as a transcription factor. The protein comprises a photosensitive light-, oxygen- and voltage-sensitive (LOV) domain and a basic zipper (bZIP) domain that binds DNA rendering aureochrome 1 a prospective optogenetic tool. Here, we studied the photoreaction of full-length aureochrome 1 by molecular spectroscopy. The kinetics of the decay of the red-shifted triplet state and the blue-shifted signaling state were determined by time-resolved UV/Vis spectroscopy. It is shown that the presence of the bZIP domain further prolongs the lifetime of the LOV390 signaling state in comparison to the isolated LOV domain whereas bound DNA does not influence the photocycle kinetics. The light-dark Fourier transform infrared (FTIR) difference spectrum shows the characteristic features of the flavin mononucleotide chromophore except that the S-H stretching vibration of cysteine 254, which is involved in the formation of the thio-adduct state, is significantly shifted to lower frequencies compared to other LOV domains. The presence of the target DNA influences the light-induced FTIR difference spectrum of aureochrome 1. Vibrational bands that can be assigned to arginine and lysine side chains as well to the phosphate backbone, indicate crucial changes in interactions between transcription factor and DNA

Jet pumps for thermoacoustic applications: design guidelines based on a numerical parameter study

The oscillatory flow through tapered cylindrical tube sections (jet pumps) is characterized by a numerical parameter study. The shape of a jet pump results in asymmetric hydrodynamic end effects which cause a time-averaged pressure drop to occur under oscillatory flow conditions. Hence, jet pumps are used as streaming suppressors in closed-loop thermoacoustic devices. A two-dimensional axisymmetric computational fluid dynamics model is used to calculate the performance of a large number of conical jet pump geometries in terms of time-averaged pressure drop and acoustic power dissipation. The investigated geometrical parameters include the jet pump length, taper angle, waist diameter and waist curvature. In correspondence with previous work, four flow regimes are observed which characterize the jet pump performance and dimensionless parameters are introduced to scale the performance of the various jet pump geometries. The simulation results are compared to an existing quasi-steady theory and it is shown that this theory is only applicable in a small operation region. Based on the scaling parameters, an optimum operation region is defined and design guidelines are proposed which can be directly used for future jet pump design.Comment: The following article has been accepted by the Journal of the Acoustical Society of America. After it is published, it will be found at http://scitation.aip.org/JAS

Transversal inhomogeneities in dilute vibrofluidized granular fluids

The spontaneous symmetry breaking taking place in the direction perpendicular to the energy flux in a dilute vibrofluidized granular system is investigated, using both a hydrodynamic description and simulation methods. The latter include molecular dynamics and direct Monte Carlo simulation of the Boltzmann equation. A marginal stability analysis of the hydrodynamic equations, carried out in the WKB approximation, is shown to be in good agreement with the simulation results. The shape of the hydrodynamic profiles beyond the bifurcation is discussed

Resilience of Micropollutant and Biological Effect Removal in an Aerated Horizontal Flow Treatment Wetland

The performance of an aerated horizontal subsurface flow treatment wetland was investigated before, during and after a simulated aeration failure. Conventional wastewater parameters (e.g., carbonaceous biological oxygen demand, total nitrogen, and Escherichia coli) as well as selected micropollutants (caffeine, ibuprofen, naproxen, benzotriazole, diclofenac, acesulfame, and carbamazepine) were investigated. Furthermore, the removal of biological effects was investigated using in vitro bioassays. The six bioassays selected covered environmentally relevant endpoints (indicative of activation of aryl hydrocarbon receptor, AhR; binding to the peroxisome proliferator-activated receptor gamma, PPARγ; activation of estrogen receptor alpha, ERα; activation of glucocorticoid receptor, GR; oxidative stress response, AREc32; combined algae test, CAT). During the aeration interruption phase, the water quality deteriorated to a degree comparable to that of a conventional (non-aerated) horizontal subsurface flow wetland. After the end of the aeration interruption, the analytical and biological parameters investigated recovered at different time periods until their initial treatment performance. Treatment efficacy for conventional parameters was recovered within a few days, but no complete recovery of treatment efficacy could be observed for bioassays AhR, AREc32 and CAT in the 21 days following re-start of the aeration system. Furthermore, the removal efficacy along the flow path for most of the chemicals and bioassays recovered as it was observed in the baseline phase. Only for the activation of AhR and AREc32 there was a shift of the internal treatment profile from 12.5% to 25% (AhR) and 50% (AREc32) of the fractional length

Microfluidics: From Crystallization to Serial Time-Resolved Crystallography

Capturing protein structural dynamics in real-time has tremendous potential in elucidating biological functions and providing information for structure-based drug design. While time-resolved structure determination has long been considered inaccessible for a vast majority of protein targets, serial methods for crystallography have remarkable potential in facilitating such analyses. Here, we review the impact of microfluidic technologies on protein crystal growth and X-ray diffraction analysis. In particular, we focus on applications of microfluidics for use in serial crystallography experiments for the time-resolved determination of protein structural dynamics

Travelling waves in pipe flow

A family of three-dimensional travelling waves for flow through a pipe of circular cross section is identified. The travelling waves are dominated by pairs of downstream vortices and streaks. They originate in saddle-node bifurcations at Reynolds numbers as low as 1250. All states are immediately unstable. Their dynamical significance is that they provide a skeleton for the formation of a chaotic saddle that can explain the intermittent transition to turbulence and the sensitive dependence on initial conditions in this shear flow.Comment: 4 pages, 5 figure