Strategies for mimicking the primary events of bacterial photosynthesis: Structure, function, and mechanism

Some of the possible implications of the photochemistry of photosynthesis for artificial systems are presented. A major aspect of this paper involves the special conditions required to prevent the undesirable charge recombination via the excited triplet state of the primary donor. If a multi-jump model is operative in the primary events of photosynthesis, then artificial model systems are relatively easy to synthesize. Such systems prevent back reactions via a series of downhill chemical reactions. Each downhill step in energy results in an increase in charge separation distance. The annihilation reactions, even to the less energetic triplet state, involve intermediate states uphill in energy and consequently are greatly diminished. However, if superexchange is a correct explanation of photosynthesis, then model systems have not been developed that properly mimic the natural process. In particular, the triplet back reaction can occur due to the lack of any thermal activation barrier. In nature this downhill back reaction appears to be prevented by carefully balancing the energetics using four molecules in the electron transport system. If this is the case, artificial photosynthesis would also require fine tuning of the coupling and energetics with three or four molecules making duplication more difficult to achieve. 10 refs

Dynamics of Primordial Black Hole Formation

We present a numerical investigation of the gravitational collapse of horizon-size density fluctuations to primordial black holes (PBHs) during the radiation-dominated phase of the Early Universe. The collapse dynamics of three different families of initial perturbation shapes, imposed at the time of horizon crossing, is computed. The perturbation threshold for black hole formation, needed for estimations of the cosmological PBH mass function, is found to be $\delta_{\rm c} \approx 0.7$ rather than the generally employed $\delta_{\rm c} \approx 1/3$, if $\delta$ is defined as \Delta M/\mh, the relative excess mass within the initial horizon volume. In order to study the accretion onto the newly formed black holes, we use a numerical scheme that allows us to follow the evolution for long times after formation of the event horizon. In general, small black holes (compared to the horizon mass at the onset of the collapse) give rise to a fluid bounce that effectively shuts off accretion onto the black hole, while large ones do not. In both cases, the growth of the black hole mass owing to accretion is insignificant. Furthermore, the scaling of black hole mass with distance from the formation threshold, known to occur in near-critical gravitational collapse, is demonstrated to apply to primordial black hole formation.Comment: 10 pages, 8 figures, revtex style, submitted to PR

Perspectives on distributed computing : thirty people, four user types, and the distributed computing user experience.

This report summarizes the methodology and results of a user perspectives study conducted by the Community Driven Improvement of Globus Software (CDIGS) project. The purpose of the study was to document the work-related goals and challenges facing today's scientific technology users, to record their perspectives on Globus software and the distributed-computing ecosystem, and to provide recommendations to the Globus community based on the observations. Globus is a set of open source software components intended to provide a framework for collaborative computational science activities. Rather than attempting to characterize all users or potential users of Globus software, our strategy has been to speak in detail with a small group of individuals in the scientific community whose work appears to be the kind that could benefit from Globus software, learn as much as possible about their work goals and the challenges they face, and describe what we found. The result is a set of statements about specific individuals experiences. We do not claim that these are representative of a potential user community, but we do claim to have found commonalities and differences among the interviewees that may be reflected in the user community as a whole. We present these as a series of hypotheses that can be tested by subsequent studies, and we offer recommendations to Globus developers based on the assumption that these hypotheses are representative. Specifically, we conducted interviews with thirty technology users in the scientific community. We included both people who have used Globus software and those who have not. We made a point of including individuals who represent a variety of roles in scientific projects, for example, scientists, software developers, engineers, and infrastructure providers. The following material is included in this report: (1) A summary of the reported work-related goals, significant issues, and points of satisfaction with the use of Globus software; (2) A method for characterizing users according to their technology interactions, and identification of four user types among the interviewees using the method; (3) Four profiles that highlight points of commonality and diversity in each user type; (4) Recommendations for technology developers and future studies; (5) A description of the interview protocol and overall study methodology; (6) An anonymized list of the interviewees; and (7) Interview writeups and summary data. The interview summaries in Section 3 and transcripts in Appendix D illustrate the value of distributed computing software--and Globus in particular--to scientific enterprises. They also document opportunities to make these tools still more useful both to current users and to new communities. We aim our recommendations at developers who intend their software to be used and reused in many applications. (This kind of software is often referred to as 'middleware.') Our two core recommendations are as follows. First, it is essential for middleware developers to understand and explicitly manage the multiple user products in which their software components are used. We must avoid making assumptions about the commonality of these products and, instead, study and account for their diversity. Second, middleware developers should engage in different ways with different kinds of users. Having identified four general user types in Section 4, we provide specific ideas for how to engage them in Section 5

CIM-EARTH: Community Integrated Model of Economic and Resource Trajectories for Humankind.

Climate change is a global problem with local climatic and economic impacts. Mitigation policies can be applied on large geographic scales, such as a carbon cap-and-trade program for the entire U.S., on medium geographic scales, such as the NOx program for the northeastern U.S., or on smaller scales, such as statewide renewable portfolio standards and local gasoline taxes. To enable study of the environmental benefits, transition costs, capitalization effects, and other consequences of mitigation policies, we are developing dynamic general equilibrium models capable of incorporating important climate impacts. This report describes the economic framework we have developed and the current Community Integrated Model of Economic and Resource Trajectories for Humankind (CIM-EARTH) instance

Gravitational couplings of the inflaton in extended inflation

We discuss a new extended inflationary scenario evading the difficulties of the original model. Our model can thermalize the energy in the bubble walls by the necessary epoch, and establish a Robertson-Walker frame in the bubble clusters. The essential new ingredient in our model is the observation that the coupling of inflaton to the Jordan-Brans-Dicke field is expected to be different from that of visible matter. 13 refs., 1 fig

Section on prospects for dark matter detection of the white paper on the status and future of ground-based TeV gamma-ray astronomy.

This is a report on the findings of the dark matter science working group for the white paper on the status and future of TeV gamma-ray astronomy. The white paper was commissioned by the American Physical Society, and the full white paper can be found on astro-ph (arXiv:0810.0444). This detailed section discusses the prospects for dark matter detection with future gamma-ray experiments, and the complementarity of gamma-ray measurements with other indirect, direct or accelerator-based searches. We conclude that any comprehensive search for dark matter should include gamma-ray observations, both to identify the dark matter particle (through the characteristics of the gamma-ray spectrum) and to measure the distribution of dark matter in galactic halos

2006 XSD Scientific Software Workshop report.

In May of 2006, a committee was formed to assess the fundamental needs and opportunities in scientific software for x-ray data reduction, analysis, modeling, and simulation. This committee held a series of discussions throughout the summer, conducted a poll of the members of the x-ray community, and held a workshop. This report details the findings and recommendations of the committee. Each experiment performed at the APS requires three crucial ingredients: the powerful x-ray source, an optimized instrument to perform measurements, and computer software to acquire, visualize, and analyze the experimental observations. While the APS has invested significant resources in the accelerator, investment in other areas such as scientific software for data analysis and visualization has lagged behind. This has led to the adoption of a wide variety of software with variable levels of usability. In order to maximize the scientific output of the APS, it is essential to support the broad development of real-time analysis and data visualization software. As scientists attack problems of increasing sophistication and deal with larger and more complex data sets, software is playing an ever more important role. Furthermore, our need for excellent and flexible scientific software can only be expected to increase, as the upgrade of the APS facility and the implementation of advanced detectors create a host of new measurement capabilities. New software analysis tools must be developed to take full advantage of these capabilities. It is critical that the APS take the lead in software development and the implementation of theory to software to ensure the continued success of this facility. The topics described in this report are relevant to the APS today and critical for the APS upgrade plan. Implementing these recommendations will have a positive impact on the scientific productivity of the APS today and will be even more critical in the future

Laue diffraction protein crystallography at the National Synchrotron Light Source

A new facility for the study of protein crystal structure using Laue diffraction has been established at the X26 beam line of the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory. The characteristics of the beam line and diffraction apparatus are described. Selected results of some of the initial experiments are discussed briefly by beam line users to illustrate the scope of the experimental program. Because the Laue method permits the recording of large data sets in a single shot, one goal in establishing this facility has been to develop the means to study time-resolved structures within protein crystals. Systems being studied include: the reactions catalyzed by trypsin; photolysis of carbonmonoxy myoglobin; and the photocycle of photoactive yellow protein