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We use TOUGH+/GasH2O to study the effects of a heat sourceburied in the Martian permafrost to evaluate the possibility ofestablishing a wet zone of liquid water, in which terrestrialmicroorganisms could survive and multiply. Analysis of the problemindicates that (1) only a limited permafrost volume (not exceeding 0.35 min radius) is affected, (2) a "wet" zone with limited amounts of liquidwater de-velops (not exceeding 8 and 0.7 kg for a 250 W and a 62.5 Wsource, respectively), (3) the wet zone per-sists for a long time,becomes practically stationary after t = 20 sols because of venting intothe Martian atmosphere, and its thickness is limited and decreases slowlyover time, (4) a "dry" zone (where SG>0.9) evolves, continues toexpand (albeit slowly) with time, but its extent remains limited, and (5)the ice front surrounding the wet zone is self-sharpening. For a range ofinitial conditions investigated, evolution of the liquid water massoccurs at approximately the same rate, reaches roughly the same maximum,and occurs at about the same time (10 to 20 sols; 1 sol = 24.39hours).

Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site-specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

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We develop and present high order mixed finite element discretizations of the time dependent electromagnetic diffusion equations for solving eddy current problems on 3D unstructured grids. The discretizations are based on high order H(grad), H(curl) and H(div) conforming finite element spaces combined with an implicit and unconditionally stable generalized Crank-Nicholson time differencing method. We develop three separate electromagnetic diffusion formulations, namely the E (electric field), H (magnetic field) and the A-{phi} (potential) formulations. For each formulation, we also provide a consistent procedure for computing the secondary variables F (current flux density) and B (magnetic flux density), as these fields are required for the computation of electromagnetic force and heating terms. We verify the error convergence properties of each formulation via a series of numerical experiments on canonical problems with known analytic solutions. The key result is that the different formulations are equally accurate, even for the secondary variables J and B, and hence the choice of which formulation to use depends mostly upon relevance of the Natural and Essential boundary conditions to the problem of interest. In addition, we highlight issues with numerical verification of finite element methods which can lead to false conclusions on the accuracy of the methods.

In this work we report on thevacuum-ultraviolet (VUV) photoionization of small methanol and methanol-water clusters. Clusters of methanol with water are generated via co-expansion of the gas phase constituents in a continuous supersonic jet expansion of methanol and water seeded in Ar. The resulting clusters are investigated by single photon ionization with tunable vacuumultraviolet synchrotron radiation and mass analyzed using reflectron mass spectrometry. Protonated methanol clusters of the form (CH3OH)nH + (n=1-12) dominate the mass spectrum below the ionization energy of the methanol monomer. With an increase in water concentration, small amounts of mixed clusters of the form (CH3OH)n(H2O)H + (n=2-11) are detected. The only unprotonated species observed in this work are the methanol monomer and dimer. Appearance energies are obtained from the photoionization efficiency (PIE) curves for CH3OH +, (CH 3OH)2 +, (CH3OH)nH + (n=1-9), and (CH 3OH)n(H2O)H + (n=2-9 ) as a function of photon energy. With an increase in the water content in the molecular beam, there is an enhancement of photoionization intensity for methanol dimer and protonated methanol monomer at threshold. These results are compared and contrasted to previous experimental observations.

In this paper, we compare constructed records of concentrations of black carbon (BC)--an indicator of anthropogenic aerosols--with observed surface temperature trends in California. Annual average BC concentrations in major air basins in California significantly decreased after about 1990, coincident with an observed statewide surface temperature increase. Seasonal aerosol concentration trends are consistent with observed seasonal temperature trends. These data suggest that the reduction in anthropogenic aerosol concentrations contributed to the observed surface temperature increase. Conversely, high aerosol concentrations may lower surface temperature and partially offset the temperature increase of greenhouse gases.

Beamline 7.2 of the Advanced Light Source (ALS) at theLawrence Berkeley National Laboratory (LBNL) is a beam diagnostics systemthat uses the synchrotron radiation emitted by a dipole magnet. Itconsists of two branches; in the first one the x-ray portion of theradiation is used in a pinhole camera system for measuring the transverseprofile of the beam. The second branch is equipped with an x-ray beamposition monitor (BPM) and with a multipurpose port where the visible andthe far-infrared part of the radiation can be used for variousapplications such as bunch length measurements and IR coherentsynchrotron radiation experiments. The pinhole system has been operatingsuccessfully since the end of 2003. The installation of the second branchhas been completed recently and the results of its commissioning arepresented in this paper together with examples of beam measurementsperformed at BL 7.2.

The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss (i) integration of data clustering and visualization into one framework; (ii) application of data clustering to 3D gene expression data; (iii) evaluation of the number of clusters k in the context of 3D gene expression clustering; and (iv) improvement of overall analysis quality via dedicated post-processing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.

The IceCube neutrino detector is a cubic kilometer TeV to PeV neutrino detector under construction at the geographic South Pole. The dominant population of neutrinos detected in IceCube is due to meson decay in cosmic-ray air showers. These atmospheric neutrinos are relatively well understood and serve as a calibration and verification tool for the new detector. In 2006, the detector was approximately 10% completed, and we report on data acquired from the detector in this configuration. We observe an atmospheric neutrino signal consistent with expectations, demonstrating that the IceCube detector is capable of identifying neutrino events. In the first 137.4 days of livetime, 234 neutrino candidates were selected with an expectation of 211 {+-} 76.1(syst.) {+-} 14.5(stat.) events from atmospheric neutrinos.

Previous analyses have assumed that wedge absorbers are triangularly shaped with equal angles for the two faces. In this case, to linear order, the energy loss depends only on the position in the direction of the face tilt, and is independent of the incoming angle. One can instead construct an absorber with entrance and exit faces facing rather general directions. In this case, the energy loss can depend on both the position and the angle of the particle in question. This paper demonstrates that and computes the effect to linear order.

We present here the design and construction of an all niobium superconducting RF injector to generate high average current, high brightness electron beam. A 1/2 cell superconducting cavity has been designed, built, and tested. A cryostat has been built to cool the cavity to {approx}2 K. The RF system can deliver up to 500 W at 1.3 GHz to the cavity. A mode-locked Nd:YVO{sub 4} laser, operating at 266 nm with 0.15 W average power, phase locked to the RF, will irradiate a laser cleaned Nb surface at the back wall of the cavity. Description of critical components and their status are presented in the paper. Based on DC measurements, QE of up to 10{sup 4} can be expected from such cavity.

Success in the application of the action and phase analysis to find linear errors at RHIC Interaction Regions [1] has encouraged the creation of a technique based on the action and phase analysis to find non linear errors. In this paper we show the first attempt to measure the sextupole components at RHIC interaction regions using the action and phase method. Experiments done by intentionally activating sextupoles in RHIC and in SPS [2] will also be analyzed with this method. First results have given values for the sextupole errors that at least have the same order of magnitude as the values found by an alternate technique during the RHIC 2001 run [3].

Beam induced electron multipacting may be among the main reasons for the vacuum pressure rise when circulating high intensity ion and proton beams in RHIC. Latest simulation results are benchmarked with recent experimental observations for RHIC, and compared to other general computer codes. The influence of the electron multipacting to the vacuum properties is also discussed.

As one of the most critical system for RHIC operation, the beam abort kicker system has to be highly available, reliable, and stable for the entire operating range. Along with the RHIC commission and operation, consistent efforts have been spend to cope with immediate issues as well as inherited design issues. Major design changes have been implemented to achieve the higher operating voltage, longer high voltage hold-off time, fast retriggering and redundant triggering, and improved system protection, etc. Recent system test has demonstrated for the first time that both blue ring and yellow ring beam abort systems have achieved more than 24 hours hold off time at desired operating voltage. In this paper, we report break down, thyratron reverse arcing, and to build a fast re-trigger system to reduce beam spreading in event of premature discharge.

A future muon collider or neutrino factory requires fast acceleration to minimize muon decay. We have previously described an FFAG ring that accelerated muons from 10 to 20 GeV in energy. The ring achieved its large momentum acceptance using a low-emittance lattice with a small dispersion. In this paper, we present an update on that ring. We have used design tools that more accurately represent the ring's behavior at large momentum offsets. We have also improved the dynamic aperture from the earlier design.

During the summer of 2002, eight superconducting helical spin rotators were installed into RHIC in order to control the polarization directions independently at the STAR and PHENIX experiments. Without the rotators, the orientation of polarization at the interaction points would only be vertical. With four rotators around each of the two experiments, we can rotate either or both beams from vertical into the horizontal plane through the interaction region and then back to vertical on the other side. This allows independent control for each beam with vertical, longitudinal, or radial polarization at the experiment. In this paper, we present results from the first run using the new spin rotators at PHENIX.

Deuteron and gold beams have been accelerated to a collision energy of {radical}s = 200 GeV/u in the Relativistic Heavy Ion Collider (RHIC), providing the first asymmetric-species collisions of this complex. Necessary changes for this mode of operation include new ramping software and asymmetric crossing angle geometries. This paper reviews machine performance, problem encountered and their solutions, and accomplishments during the 16 weeks of ramp-up and operations.

We measure the deflagration behavior of energetic materials at extreme conditions (up to 520K and 1 GPa) in the LLNL High Pressure Strand Burner, thereby obtaining reaction rate data for prediction of violence of thermal explosions. The apparatus provides both temporal pressure history and flame time-of-arrival information during deflagration, allowing direct calculation of deflagration rate as a function of pressure. Samples may be heated before testing. Here we report the deflagration behavior of several HMX-based explosives at pressures of 10-600 MPa and temperatures of 300-460 K. We find that formulation details are very important to overall deflagration behavior. Formulations with high binder content (>15 wt%) deflagrate smoothly over the entire pressure range regardless of particle size, with a larger particle size distribution leading to a slower reaction. The deflagration follows a power law function with the pressure exponent being unity. Formulations with lower binder content ({le} 10% or less by weight) show physical deconsolidation at pressures over 100-200 MPA, with transition to a rapid erratic deflagration 10-100 times faster. High temperatures have a relatively minor effect on the deflagration rate until the HMX {beta} {yields} {delta} phase transition occurs, after which the deflagration rate increases by more than a factor …

Fixed target studies of small branching ratio decay processes require intense beams and smooth spills. Longitudinal structure arises through collective effects, well below the coasting beam stability threshold. These structures have been observed at the Brookhaven AGS and dependence on intensity and momentum spread measured. Measurements and amelioration techniques have been developed and will be described.

As part of a future upgrade to the Relativistic Heavy Ion Collider (RHIC), electron cooling is foreseen to decrease ion beam emittances. Within the electron cooling section, the ''hot'' ion beam is immersed in a ''cold'' electron beam. The cooling effect is further enhanced by a solenoid field in the cooling section, which forces the electrons to spiral around the field lines with a (Larmor) radius of 10 micrometers, reducing the effective transverse temperature by orders of magnitude. Studies of the effect of solenoid field errors on electron beam temperatures are reported.

The human breast comprises three lineages: the luminal epithelial lineage, the myoepithelial lineage, and the mesenchymal lineage. It has been widely accepted that human breast neoplasia pertains only to the luminal epithelial lineage. In recent years, however, evidence has accumulated that neoplastic breast epithelial cells may be substantially more plastic in their differentiation repertoire than previously anticipated. Thus, along with an increasing availability of markers for the myoepithelial lineage, at least a partial differentiation towards this lineage is being revealed frequently. It has also become clear that conversions towards the mesenchymal lineage actually occur, referred to as epithelial to mesenchymal transitions. Indeed, some of the so-called myofibroblasts surrounding the tumor may indeed have an epithelial origin rather than a mesenchymal origin. Because myoepithelial cells, epithelial to mesenchymal transition-derived cells, genuine stromal cells and myofibroblasts share common markers, we now need to define a more ambitious set of markers to distinguish these cell types in the microenvironment of the tumors. This is necessary because the different microenvironments may confer different clinical outcomes. The aim of this commentary is to describe some of the inherent complexities in defining cellular phenotypes in the microenvironment of breast cancer and to expand wherever possible on …

A predictive framework for supersymmetry at the TeV scale is presented, which incorporates the Ciafaloni-Pomarol mechanism for the dynamical determination of the \mu parameter of the MSSM. It is replaced by (\lambda S), where S is a singlet field, and the axion becomes a heavy pseudoscalar, G, by adding a mass, m_G, by hand. The explicit breaking of Peccei-Quinn (PQ) symmetry is assumed to be sufficiently weak at the TeV scale that the only observable consequence is the mass m_G. Three models for the explicit PQ breaking are given; but the utility of this framework is that the predictions for all physics at the electroweak scale are independent of the particular model for PQ breaking. Our framework leads to a theory similar to the MSSM, except that \mu is predicted by the Ciafaloni-Pomarol relation, and there are light, weakly-coupled states in the spectrum. The production and cascade decay of superpartners at colliders occurs as in the MSSM, except that there is one extra stage of the cascade chain, with the next-to-LSP decaying to its"superpartner" and \tilde{s}, dramatically altering the collider signatures for supersymmetry. The framework is compatible with terrestrial experiments and astrophysical observations for a wide range of m_G and<s>. …

We present the design and performance of a home-built high-pressure and high-temperature reactor equipped with a high-resolution scanning tunneling microscope (STM) for catalytic studies. In this design, the STM body, sample, and tip are placed in a small high pressure reactor ({approx}19 cm{sup 3}) located within an ultrahigh vacuum (UHV) chamber. A sealable port on the wall of the reactor separates the high pressure environment in the reactor from the vacuum environment of the STM chamber and permits sample transfer and tip change in UHV. A combination of a sample transfer arm, wobble stick, and sample load-lock system allows fast transfer of samples and tips between the preparation chamber, high pressure reactor, and ambient environment. This STM reactor can work as a batch or flowing reactor at a pressure range of 10{sup -13} to several bars and a temperature range of 300-700 K. Experiments performed on two samples both in vacuum and in high pressure conditions demonstrate the capability of in situ investigations of heterogeneous catalysis and surface chemistry at atomic resolution at a wide pressure range from UHV to a pressure higher than 1 atm.