How to mesh up Ewald sums (I): A theoretical and numerical comparison of various particle mesh routines

Standard Ewald sums, which calculate e.g. the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the Fast Fourier Transformation (FFT). In this article we investigate three algorithms for the FFT-accelerated Ewald sum, which attracted a widespread attention, namely, the so-called particle-particle-particle-mesh (P3M), particle mesh Ewald (PME) and smooth PME method. We present a unified view of the underlying techniques and the various ingredients which comprise those routines. Additionally, we offer detailed accuracy measurements, which shed some light on the influence of several tuning parameters and also show that the existing methods -- although similar in spirit -- exhibit remarkable differences in accuracy. We propose combinations of the individual components, mostly relying on the P3M approach, which we regard as most flexible.Comment: 18 pages, 8 figures included, revtex styl

Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were genetically evaluated using a powerful microsatellite marker suite to determine if they are genetically distinct. Specifically, this study evaluates the genetic structure, characterizes the genetic diversity, estimates effective population size, and measures inbreeding of Atlantic sturgeon in the James River. The results indicate that fall and spring spawning James River Atlantic sturgeon groups are genetically distinct (overall FST = 0.048, F’ST = 0.181) with little admixture between the groups. The observed levels of genetic diversity and effective population sizes along with the lack of detected inbreeding all indicated that the James River has two genetically healthy populations of Atlantic sturgeon. The study also demonstrates that samples from adult Atlantic sturgeon, with proper sample selection criteria, can be informative when creating reference population databases. The presence of two genetically-distinct spawning groups of Atlantic sturgeon within the James River raises concerns about the current genetic assignment used by managers. Other nearby rivers may also have dual spawning groups that either are not accounted for or are pooled in reference databases. Our results represent the second documentation of genetically distinct dual spawning groups of Atlantic sturgeon in river systems along the U.S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history

The optimal P3M algorithm for computing electrostatic energies in periodic systems

We optimize Hockney and Eastwood's Particle-Particle Particle-Mesh (P3M) algorithm to achieve maximal accuracy in the electrostatic energies (instead of forces) in 3D periodic charged systems. To this end we construct an optimal influence function that minimizes the RMS errors in the energies. As a by-product we derive a new real-space cut-off correction term, give a transparent derivation of the systematic errors in terms of Madelung energies, and provide an accurate analytical estimate for the RMS error of the energies. This error estimate is a useful indicator of the accuracy of the computed energies, and allows an easy and precise determination of the optimal values of the various parameters in the algorithm (Ewald splitting parameter, mesh size and charge assignment order).Comment: 31 pages, 3 figure

Territorial defense in a network: Audiences only matter to male fiddler crabs primed for confrontation

This is the author accepted manuscript. The final version is available from Oxford University Press via the DOI in this recordTerritorial contests often occur in the presence of conspecifics not directly involved in the interaction. Actors may alter their behavior in the presence of this audience, an “audience effect,” and audiences themselves may alter their behavior as a result of observing an interaction, a “bystander effect.” Previous work has documented these effects by looking at each in isolation, but to our knowledge, none has investigated their interaction; something that is more likely to represent a realistic scenario for species where individuals aggregate spatially. We therefore have a somewhat limited understanding of the extent and direction of these potentially complex indirect social effects on behavior. Here, we examined how audience and bystander effects work in tandem to modify resident male aggressive behavior towards intruders in European fiddler crabs, Afruca tangeri. We found that male crabs with an audience showed greater aggressive behavior towards an intruder compared with males without an audience, but only if they had acted as a bystander to an aggressive signaling interaction prior to the intrusion. Indeed, bystanding during aggressive interactions elevated aggressive responses to intruders maximally if there was an audience present. Our results suggest that bystanding had a priming effect on territory-holding males, potentially by providing information on the immediate level of competition in the local neighborhood, and that same-sex audiences only matter if males have been primed. This study highlights the fundamental importance of considering broader interaction networks in studying real-world dyadic interactions and of including nonvertebrate taxonomic groups in these studiesDanish Council for Independent Research/Natural SciencesDFFLeverhulme Trust Early Careers Fellowshi

Selected new developments in computational chemistry.

Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry

Assessing Operational Total Lightning Visualization Products

In May 2003, NASA's Short-term Prediction Research and Transition (SPoRT) program successfully provided total lightning data from the North Alabama Lightning Mapping Array (NALMA) to the National Weather Service (NWS) office in Huntsville, Alabama. The major accomplishment was providing the observations in real-time to the NWS in the native Advanced Weather Interactive Processing System (AWIPS) decision support system. Within days, the NALMA data were used to issue a tornado warning initiating seven years of ongoing support to the NWS' severe weather and situational awareness operations. With this success, SPoRT now provides real-time NALMA data to five forecast offices as well as working to transition data from total lightning networks at Kennedy Space Center and the White Sands Missile Range to the surrounding NWS offices. The only NALMA product that has been transitioned to SPoRT's partner NWS offices is the source density product, available at a 2 km resolution in 2 min intervals. However, discussions with users of total lightning data from other networks have shown that other products are available, ranging from spatial and temporal variations of the source density product to the creation of a flash extent density. SPoRT and the Huntsville, Alabama NWS are evaluating the utility of these variations as this has not been addressed since the initial transition in 2003. This preliminary analysis will focus on what products will best support the operational warning decision process. Data from 19 April 2009 are analyzed. On this day, severe thunderstorms formed ahead of an approaching cold front. Widespread severe weather was observed, primarily south of the Tennessee River with multiple, weak tornadoes, numerous severe hail reports, and wind. This preliminary analysis is the first step in evaluation which product(s) are best suited for operations. The ultimate goal is selecting a single product for use with all total lightning networks to streamline training and science sharing

Kant's philosophy of the aesthetic and the philosophy of praxis

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2012 Association for Economic and Social Analysis.This essay seeks to reconstruct the terms for a more productive engagement with Kant than is typical within contemporary academic cultural Marxism, which sees him as the cornerstone of a bourgeois model of the aesthetic. The essay argues that, in the Critique of Judgment, the aesthetic stands in as a substitute for the missing realm of human praxis. This argument is developed in relation to Kant's concept of reflective judgment that is in turn related to a methodological shift toward inductive and analogical procedures that help Kant overcome the dualisms of the first two Critiques. This reassessment of Kant's aesthetic is further clarified by comparing it with and offering a critique of Terry Eagleton's assessment of the Kantian aesthetic as synonymous with ideology

Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates.

Human immunodeficiency virus type 1 protease is inhibited in vitro by zinc ions at neutral pH. The binding site of these ions is not known; however, experimental data suggest that binding may occur in the active site. To examine the possibility of zinc binding in the active site, molecular dynamics simulations in the presence and absence of zinc have been carried out to 200 psec. The results are compared with the 2.8-A crystallographic structures of a synthetic HIV-1 protease, and a zinc binding site at the catalytic aspartate residues (Asp-25, Asp-25') is proposed. Molecular dynamics simulations show that the zinc ion remains stably bound in this region, coordinating the carboxylate side chains of both aspartate residues. Interaction with zinc does not disrupt the dimeric structure of the protein or significantly alter the structure of the active site. These data are consistent with experimental studies of HIV-1 protease inhibition by zinc and give strong evidence that this is the binding site that leads to inactivation

ELECTRON MICROSCOPY OF PLASMA-CELL TUMORS OF THE MOUSE : I. MPC-1 and X5563 Tumors

An electron microscope study was made of a series of transplanted MPC-1 plasma-cell tumors carried by BALB/c mice. Large numbers of particles similar in morphology to virus particles were present inside the endoplasmic reticulum of tumor plasma cells. Very few particles were seen outside the cells or in ultracentrifuged preparations of the plasma or ascites fluid. In very early tumors particles were occasionally seen free in the cytoplasm adjacent to finely granular material. In general, the distribution of these particles inside endoplasmic reticulum is similar in early and late tumors. A few transplanted X5563 tumors of C3H mice were also examined. Large numbers of particles were found in the region of the Golgi apparatus in late X5663 tumors. A newly described cytoplasmic structure of plasma cells, here called a "granular body," appears to be associated with the formation of the particles. Particles present in MPC-1 tumors are exclusively of a doughnut form, whereas some of those in the inclusions of the late X5563 tumors show a dense center. Normal plasma cells, produced by inoculation of a modified Freund adjuvant into BALB/c mice. have been compared morphologically with tumor plasma cells of both tumor lines