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

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

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

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

Potentiality in Biology

We take the potentialities that are studied in the biological sciences (e.g., totipotency) to be an important subtype of biological dispositions. The goal of this paper is twofold: first, we want to provide a detailed understanding of what biological dispositions are. We claim that two features are essential for dispositions in biology: the importance of the manifestation process and the diversity of conditions that need to be satisfied for the disposition to be manifest. Second, we demonstrate that the concept of a disposition (or potentiality) is a very useful tool for the analysis of the explanatory practice in the biological sciences. On the one hand it allows an in-depth analysis of the nature and diversity of the conditions under which biological systems display specific behaviors. On the other hand the concept of a disposition may serve a unificatory role in the philosophy of the natural sciences since it captures not only the explanatory practice of biology, but of all natural sciences. Towards the end we will briefly come back to the notion of a potentiality in biology

Monoamine Oxidase is a Major Determinant of Redox Balance in Human Atrial Myocardium and is Associated With Postoperative Atrial Fibrillation

BACKGROUND: Onset of postoperative atrial fibrillation (POAF) is a common and costly complication of heart surgery despite major improvements in surgical technique and quality of patient care. The etiology of POAF, and the ability of clinicians to identify and therapeutically target high-risk patients, remains elusive. METHODS AND RESULTS: Myocardial tissue dissected from right atrial appendage (RAA) was obtained from 244 patients undergoing cardiac surgery. Reactive oxygen species (ROS) generation from multiple sources was assessed in this tissue, along with total glutathione (GSHt) and its related enzymes GSH-peroxidase (GPx) and GSH-reductase (GR). Monoamine oxidase (MAO) and NADPH oxidase were observed to generate ROS at rates 10-fold greater than intact, coupled mitochondria. POAF risk was significantly associated with MAO activity (Quartile 1 [Q1]: adjusted relative risk [ARR]=1.0; Q2: ARR=1.8, 95% confidence interval [CI]=0.84 to 4.0; Q3: ARR=2.1, 95% CI=0.99 to 4.3; Q4: ARR=3.8, 95% CI=1.9 to 7.5; adjusted Ptrend=0.009). In contrast, myocardial GSHt was inversely associated with POAF (Quartile 1 [Q1]: adjusted relative risk [ARR]=1.0; Q2: ARR=0.93, 95% confidence interval [CI]=0.60 to 1.4; Q3: ARR=0.62, 95% CI=0.36 to 1.1; Q4: ARR=0.56, 95% CI=0.34 to 0.93; adjusted Ptrend=0.014). GPx also was significantly associated with POAF; however, a linear trend for risk was not observed across increasing levels of the enzyme. GR was not associated with POAF risk. CONCLUSIONS: Our results show that MAO is an important determinant of redox balance in human atrial myocardium, and that this enzyme, in addition to GSHt and GPx, is associated with an increased risk for POAF. Further investigation is needed to validate MAO as a predictive biomarker for POAF, and to explore this enzyme's potential role in arrhythmogenesis

Spectroscopic factors for bound s-wave states derived from neutron scattering lengths

A simple and model-independent method is described to derive neutron single-particle spectroscopic factors of bound s-wave states in $^{A+1}Z = ^{A}Z \otimes n$ nuclei from neutron scattering lengths. Spectroscopic factors for the nuclei ^{13}C, ^{14}C, ^{16}N, ^{17}O, ^{19}O, ^{23}Ne, ^{37}Ar, and ^{41}Ar are compared to results derived from transfer experiments using the well-known DWBA analysis and to shell model calculations. The scattering length of ^{14}C is calculated from the ^{15}C_{g.s.} spectroscopic factor.Comment: 9 pages (uses revtex), no figures, accepted for publication in PRC, uuencoded tex-files and postscript-files available at ftp://is1.kph.tuwien.ac.at/pub/ohu/Thermal.u

The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework

Volume-energy correlations in the slow degrees of freedom of computer-simulated phospholipid membranes

Constant-pressure molecular-dynamics simulations of phospholipid membranes in the fluid phase reveal strong correlations between equilibrium fluctuations of volume and energy on the nanosecond time-scale. The existence of strong volume-energy correlations was previously deduced indirectly by Heimburg from experiments focusing on the phase transition between the fluid and the ordered gel phases. The correlations, which are reported here for three different membranes (DMPC, DMPS-Na, and DMPSH), have volume-energy correlation coefficients ranging from 0.81 to 0.89. The DMPC membrane was studied at two temperatures showing that the correlation coefficient increases as the phase transition is approached