Bayesian ensemble refinement by replica simulations and reweighting

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraint should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" (BioEn) method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.Comment: Paper submitted to The Journal of Chemical Physics (15 pages, 4 figures); updated references; expanded discussions of related formalisms, error treatment, and ensemble refinement with and without replicas; appendi

Hydrodynamics of Diffusion in Lipid Membrane Simulations

By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon nanotubes in membranes. The resulting Oseen correction allows us to extract infinite-system diffusion coefficients and membrane surface viscosities from membrane simulations despite the logarithmic divergence of apparent diffusivities with increasing box width. The hydrodynamic theory of diffusion applies also to membranes with asymmetric leaflets and embedded proteins, and to a complex plasma-membrane mimetic

The Brauer characters of the sporadic simple Harada-Norton group and its automorphism group in characteristics 2 and 3

We determine the 2-modular and 3-modular character tables of the sporadic simple Harada-Norton group and its automorphism group.Comment: 29 page

Public Pensions and Capital Accumulation: The Case of Brazil

We use an OLG model to study the effects of the generous public sector pension system in Brazil. In our model there are two types of workers, one working in the private sector, the other working in the public sector. Public workers produce infrastructure or education services. We find that reducing generosity of the public sector pensions has large effects on capital accumulation and steady state income.pension reform, capital accumulation

Red list and checklist of the true bugs (Heteroptera) of Berlin

Es wird eine Checkliste und Rote Liste der Wanzen (Insecta: Heteroptera) Berlins vorgelegt. Die Liste umfasst 502 Wanzenarten, die gegenwärtig in Berlin vorkommen oder die seit Mitte des 19. Jahrhunderts wenigstens einmal hier gefunden wurden. 88 Arten (18 %) werden als (regional) verschollen oder ausgestorben betrachtet und 271 Arten (54 %) als nicht bedroht. Sieben Arten sind Neobiota und 11 sind seit 2005 das erste Mal in Berlin nachgewiesen worden. Die wenigen publizierten Arbeiten der letzten Jahre und das Fehlen systematischer Untersuchungen erschweren die Einschätzung der Häufigkeit vieler Arten und ihre Klassifizierung hinsichtlich des Rote-Liste-Status. Besonders bedroht sind Arten von Feuchtgebieten, von fließenden und stehenden Gewässern, Uferbereichen, sowie Arten des Offenlandes. Die Ursachen liegen wie seit Jahren in der zunehmenden Bebau-ung, Zerstörung, Degradierung und Isolation der Standorte und in der Eutrophierung der Lebensräume.A list of 502 Heteroptera species that are currently known from Berlin or at least found once since the mid-19th century is given. 88 species (18 %) are considered (regionally) extinct and 271 species (54 %) of least concern. Seven species are non-indigenous and 11 species are recorded for the first time in Berlin since 2005. The few publications on Heteroptera in the last years and the lack of systematic studies on this group make it difficult to evaluate the frequency of the species and the classification of the threat. Species are particularly endangered in wetlands, extensive dry or wet grasslands, open lands and also in running and still waters. The drivers are urban sprawl, habitat loss, degradation and isolation as well as eutrophication

Auswirkungen von Steueränderungen im Bereich Entfernungspauschale und Werbungskosten : ein Mikrosimulationsmodell

Die vorliegende Arbeit dokumentiert ein neues Mikrosimulationsmodell für Werbungskosten, das im Auftrag des Bundesministeriums der Finanzen entwickelt wurde und das die Schwierigkeiten bisheriger erfahrungsbasierter Werbungskostenmodelle durch Einsatz moderner statistischer Verfahren überwindet. Das neue Modell erweist sich als flexibles, leicht zu handhabendes Instrument zur Quantifizierung der kurzfristigen Aufkommens und Verteilungswirkungen von Steuerreformen. Wir wenden es zur Analyse der Effekte wichtiger Änderungen des Einkommensteuergesetzes ab 1. Januar 2007 sowie einer Reihe von Alternativvorschlägen für die Abzugsfähigkeit von Werbungskosten aus nichtselbständiger Arbeit an.To overcome a lack of information in official income tax statistcs, we developed a statistical matching approach for adding additional data from the German Socio-Economic Panel (GSOEP) to the most recent official income tax statistics data as of 2002. Based on a representative dataset of more than 35000 original tax report extracts, we implemented a microsimulation model that calculates the fiscal impact of changes in the area of tax deductible income related expenses, in particular tax deductible expenses for traveling from home to work and the lump sum deductible for all income related expenses. The new model allows a more detailed simulation of the fiscal impact of changes in the German income tax law than previously possible

Kinetic energy flow in Nb(400 A MeV) + Nb: evidence for hydrodynamic compression of nuclear matter

A kinetic-energy—flow analysis of multiplicity-selected collisions of 93Nb(Elab=400A MeV)+93Nb is performed on the basis of the nuclear fluid dynamical model. The effects of finite particle numbers on the flow tensor are explicitly taken into account. Strong sidewards peaks are predicted in dN/dcosθF, the distribution of event by event flow angles. This is in qualitative agreement with recent data from the "Plastic Ball" electronic detection system. Cascade simulations fail to reproduce the data

Biosynthesis of fucoxanthin and diadinoxanthin and function of initial pathway genes in Phaeodactylum tricornutum

The biosynthesis pathway to diadinoxanthin and fucoxanthin was elucidated in Phaeodactylum tricornutum by a combined approach involving metabolite analysis identification of gene function. For the initial steps leading to β-carotene, putative genes were selected from the genomic database and the function of several of them identified by genetic pathway complementation in Escherichia coli. They included genes encoding a phytoene synthase, a phytoene desaturase, a ζ-carotene desaturase, and a lycopene β-cyclase. Intermediates of the pathway beyond β-carotene, present in trace amounts, were separated by TLC and identified as violaxanthin and neoxanthin in the enriched fraction. Neoxanthin is a branching point for the synthesis of both diadinoxanthin and fucoxanthin and the mechanisms for their formation were proposed. A single isomerization of one of the allenic double bounds in neoxanthin yields diadinoxanhin. Two reactions, hydroxylation at C8 in combination with a keto-enol tautomerization and acetylation of the 3′-HO group results in the formation of fucoxanthin

Viscous fluid dynamical calculation of the reaction 12C(85 MeV/nucleon) + 197Au

Proton spectra have been calculated for the reaction 12C(85 MeV/nucleon) + 197Au using a three-dimensional hydrodynamical model with viscosity and thermal conductivity and final thermal breakup. The theoretical results are compared to recent data. It is shown that the predicted flow effects are not observable as a result of the impact parameter averaging inherent in the inclusive proton spectra. In contrast, angular distributions of medium mass nuclei (A>3) in nearly central collisions can provide signatures for flow effects