Top transport in electroweak baryogenesis

In non-supersymmetric models of electroweak baryogenesis the top quark plays a crucial role. Its CP-violating source term can be calculated in the WKB approximation. We point out how to resolve certain discrepancies between computations starting from the Dirac equation and the Schwinger--Keldysh formalism. We also improve on the transport equations, keeping the W-scatterings at finite rate. We apply these results to a model with one Higgs doublet, augmented by dimension-6 operators, where our refinements lead to an increase in the baryon asymmetry by a factor of up to about 5.Comment: 17 pages, 3 figures, references adde

VITESS 3 Virtual Instrumentation Tool for the European Spallation Source

VITESS is a software widely used for simulation of neutron scattering experiments. Although originally motivated by instrument design for the European Spallation Source, all major neutron sources are available. Existing as well as future instruments on reactor or spallation sources can be designed and optimized, or simulated in a virtual experiment to prepare a measurement, including basic data evaluation. This note gives an overview of the VITESS software concept and usage. New developments are presented, including a 3D visualization of instruments and neutron trajectories, a numerical optimization routine and a parallelization tool allowing to split VITESS simulations on a computer cluste

Dose, exposure time, and resolution in Serial X-ray Crystallography

The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 0.7 nm should be possible with short exposures.Comment: 19 pages, 7 figures, 1 tabl

An Unrecognized Source of PCB Contamination in Schools and Other Buildings

An investigation of 24 buildings in the Greater Boston Area revealed that one-third (8 of 24) contained caulking materials with polychlorinated biphenyl (PCB) content exceeding 50 ppm by weight, which is the U.S. Environmental Protection Agency (U.S. EPA) specified limit above which this material is considered to be PCB bulk product waste. These buildings included schools and other public buildings. In a university building where similar levels of PCB were found in caulking material, PCB levels in indoor air ranged from 111 to 393 ng/m(3); and in dust taken from the building ventilation system, < 1 ppm to 81 ppm. In this building, the U.S. EPA mandated requirements for the removal and disposal of the PCB bulk product waste as well as for confirmatory sampling to ensure that the interior and exterior of the building were decontaminated. Although U.S. EPA regulations under the Toxic Substances Control Act stipulate procedures by which PCB-contaminated materials must be handled and disposed, the regulations apparently do not require that materials such as caulking be tested to determine its PCB content. This limited investigation strongly suggests that were this testing done, many buildings would be found to contain high levels of PCBs in the building materials and potentially in the building environment. The presence of PCBs in schools is of particular concern given evidence suggesting that PCBs are developmental toxins

Production of Gravitational Waves in the nMSSM

During a strongly first-order phase transition gravitational waves are produced by bubble collisions and turbulent plasma motion. We analyze the relevant characteristics of the electroweak phase transition in the nMSSM to determine the generated gravitational wave signal. Additionally, we comment on correlations between the production of gravitational waves and baryogenesis. We conclude that the gravitational wave relic density in this model is generically too small to be detected in the near future by the LISA experiment. We also consider the case of a "Standard Model" with dimension-six Higgs potential, which leads to a slightly stronger signal of gravitational waves.Comment: 29 pages, 7 figures; published version, some comments adde

DNA binding shifts the redox potential of the transcription factor SoxR

Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from Escherichia coli and Pseudomonas aeruginosa. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR–DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property

CP violation Beyond the MSSM: Baryogenesis and Electric Dipole Moments

We study electroweak baryogenesis and electric dipole moments in the presence of the two leading-order, non-renormalizable operators in the Higgs sector of the MSSM. Significant qualitative and quantitative differences from MSSM baryogenesis arise due to the presence of new CP-violating phases and to the relaxation of constraints on the supersymmetric spectrum (in particular, both stops can be light). We find: (1) spontaneous baryogenesis, driven by a change in the phase of the Higgs vevs across the bubble wall, becomes possible; (2) the top and stop CP-violating sources can become effective; (3) baryogenesis is viable in larger parts of parameter space, alleviating the well-known fine-tuning associated with MSSM baryogenesis. Nevertheless, electric dipole moments should be measured if experimental sensitivities are improved by about one order of magnitude.Comment: 33 pages, 6 figure

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach

Adherence and Concordance between Serious Illness Care Planning Conversations and Oncology Clinician Documentation among Patients with Advanced Cancer

Background:Serious illness conversations are part of advance care planning (ACP) and focus on prognosis, values, and goals in patients who are seriously ill. To be maximally effective, such conversations must be documented accurately and be easily accessible. Objectives:The two coprimary objectives of the study were to assess concordance between written documentation and recorded audiotaped conversations, and to evaluate adherence to the Serious Illness Conversation Guide questions. Methods:Data were obtained as part of a trial in patients with advanced cancer. Clinicians were trained to use a guide to conduct and document serious illness conversations. Conversations were audiotaped. Two researchers independently compared audiorecordings with the corresponding documentation in an electronic health record (EHR) template and free-text progress notes, and rated the degree of concordance and adherence. Results:We reviewed a total of 25 audiorecordings. Clinicians addressed 87% of the conversation guide elements. Prognosis was discussed least frequently, only in 55% of the patients who wanted that information. Documentation was fully concordant with the conversation 43% of the time. Concordance was best when documenting family matters and goals, and least frequently concordant when documenting prognostic communication. Most conversations (64%) were documented in the template, a minority (28%) only in progress notes and two conversations (8%) were not documented. Concordance was better when the template was used (62% vs. 28%). Conclusion:Clinicians adhered well to the conversation guide. However, key information elicited was documented and fully concordant less than half the time. Greater concordance was observed when clinicians used a prespecified template. The combined use of a guide and EHR template holds promise for ACP conversations