Estimation of the infinitesimal generator by square-root approximation

For the analysis of molecular processes, the estimation of time-scales, i.e., transition rates, is very important. Estimating the transition rates between molecular conformations is -- from a mathematical point of view -- an invariant subspace projection problem. A certain infinitesimal generator acting on function space is projected to a low-dimensional rate matrix. This projection can be performed in two steps. First, the infinitesimal generator is discretized, then the invariant subspace is approxi-mated and used for the subspace projection. In our approach, the discretization will be based on a Voronoi tessellation of the conformational space. We will show that the discretized infinitesimal generator can simply be approximated by the geometric average of the Boltzmann weights of the Voronoi cells. Thus, there is a direct correla-tion between the potential energy surface of molecular structures and the transition rates of conformational changes. We present results for a 2d-diffusion process and Alanine dipeptide

Effect of high glucose concentration on the synthesis of monocyte chemoattractant protein-1 in human peritoneal mesothelial cells: Involvement of protein kinase C

Human peritoneal mesothelial cells (HMC) contribute to the activation and control of inflammatory processes in the peritoneum by their potential to produce various inflammatory mediators. The present study was designed to assess the effect of glucose, the osmotic active compound in most commercially available peritoneal dialysis fluids, on the synthesis of the C-C chemokine monocyte chemoattractant protein-1 (MCP-1) in cultured HMC. The MCP-1 concentration in the cell supernatants was determined by enzyme-linked immunosorbent assay and the MCP-1 mRNA expression was examined using Northern blot analysis. Incubation of HMC with glucose (30-120 mM) resulted in a time- and concentration-dependent increase in MCP-1 protein secretion and mRNA expression. After 24 h the MCP-1 synthesis was increased from 2.8 +/- 0.46 to 4.2 +/- 0.32 ng/10(5) cells (n = 5, p 2001 S. Karger AG. Basel

«Endure and Survive»: Zur medialen Bedeutung des Raumes in The Road und The Last of Us

Die Game Studies zeigen sich als eine relativ neue Forschungsdisziplin, wobei interdisziplinäre Ansätze bestehen, durch welche das neue Medium erforscht wird. Bestand zunächst ein scheinbar zwiespältiges Lager, wonach ein Videospiel entweder als Erzählung oder als Spiel betrachtet wurde, besteht nun weitgehend ein Konsens darüber, dass sich narrative und ludische Elemente nicht ausschliessen müssen. Der Begriff des Raumes erhält in den Game Studies merklich mehr Aufmerksamkeit als in anderen Gebieten wie Literatur- oder Filmwissenschaft. Einerseits zeigt er sich als ein Hilfsmittel, um eine Geschichte zu erzählen, stellt andererseits auch das Spielfeld dar. In der Literatur gibt es verschiedene narrative Strategien, welche mit dem Raum spielen. In der Abenteuerliteratur wird das Fortschreiten im Raum mit dem Erzählen einer Geschichte verbunden – nicht zuletzt deshalb wird diese Formel wohl auch gerne auf das Medium Videospiel übertragen. In einer Geschichte muss der Raum jedoch nicht immer mit dem Fortschreiten einer Erzählung verbunden werden, sondern beschreibt den Kontext, die Figuren und die soziale und geografische Ordnung der Welt.  Bei der Schaffung fiktiver Welten spielt unter anderem die Beziehung zur realen Welt eine wichtige Rolle. Gerade der Raum in Dystopien, also einem postapokalyptischen Setting, bedient auch eine gesellschaftskritische Funktion. Wie wird der Raum in der Literatur und in Videospielen dargestellt? Welche narrative und oder ludischen Funktionen übernimmt er und inwiefern ist die Darstellungsweise und die Funktionalität medial bedingt? Auf diese Fragen versucht der Beitrag innerhalb eines spezifischen Kontextes eine Antwort zu finden. Basierend auf dem 2006 veröffentlichten Roman The Road von Cormac McCarthy und das auf dieser Vorlage basierende, 2013 erschiene Action-Adventure The Last of Us, sollen die Unterschiede und Gemeinsamkeiten der Raumkonzepte sowie deren mediale Bedingungen herausgearbeitet werden

A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models

Dynamical reweighting methods permit to estimate kinetic observables of a stochastic process governed by a target potential $\tilde{V}(x)$ from trajectories that have been generated at a different potential $V(x)$. In this article, we present Girsanov reweighting and Square Root Approximation (SqRA): the first method reweights path probabilities exploiting the Girsanov theorem and can be applied to Markov State Models (MSMs) to reweight transition probabilities; the second method was originally developed to discretize the Fokker-Planck operator into a transition rate matrix, but here we implement it into a reweighting scheme for transition rates. We begin by reviewing the theoretical background of the methods, then present two applications relevant to Molecular Dynamics (MD), highlighting their strengths and weaknesses

Estimation of the infinitesimal generator by square-root approximation

For the analysis of molecular processes, the estimation of time-scales, i.e., tran- sition rates, is very important. Estimating the transition rates between molecular conformations is - from a mathematical point of view - an invariant subspace projec- tion problem. A certain infinitesimal generator acting on function space is projected to a low-dimensional rate matrix. This projection can be performed in two steps. First, the infinitesimal generator is discretized, then the invariant subspace is ap- proximated and used for the subspace projection. In our approach, the discretization will be based on a Voronoi tessellation of the conformational space. We will show that the discretized infinitesimal generator can simply be approximated by the ge- ometric average of the Boltzmann weights of the Voronoi cells. Thus, there is a direct correlation between the potential energy surface of molecular structures and the transition rates of conformational changes. We present results for a 2d-diffusion process and Alanine dipeptide

Acceptance and timeliness of standard vaccination in children with chronic neurological deficits in north-western Switzerland

There are no special recommendations for basic vaccinations in patients with chronic neurological deficits distinct from the nationwide advocated schedule in Switzerland. Reports describing adverse neurological events possibly related to vaccinations have attracted public attention. It is unclear if patients with chronic neurological deficits are more reluctantly vaccinated compared to healthy children. We therefore investigated the acceptance of vaccinations in such patients and healthy controls in a retrospective case-control study. At the University Children's Hospital, Basel, Switzerland we investigated 100 patients with chronic neurological deficits and 200 age-matched healthy controls regarding the issue of vaccination rates and ages. The total number of administered vaccinations against diphtheria, tetanus, pertussis, polio, Haemophilus influenzae type b (Hib), mumps, measles, rubella and hepatitis B were significantly lower in patients compared to healthy controls ( P <0.01 for each of the respective vaccines). Patients had an increased risk to receive the third pertussis, diphtheria, and tetanus vaccinations (relative risks (RR) for late vaccination 1.53, 1.53, and 1.54 respectively, P <0.01 for all comparisons), the second (RR=1.60, P <0.05) and third Hib vaccinations (RR=1.52, P <0.05), and the third polio vaccination (RR=1.43, P <0.05) later than controls. Conclusion:Children with chronic neurological deficits received fewer vaccinations than healthy controls. In addition, patients received vaccinations later than healthy children. Hence, it may be assumed that children with chronic neurological deficits are at an increased risk to acquire preventable infections. Therefore, vaccination should be promoted as part of the consultation during a routine appointment with the specialis

Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopic analysis

Abstract. Manganese (Mn)-rich natural rock coatings, so-called rock varnishes, are discussed controversially regarding their genesis. Biogenic and abiogenic mechanisms, as well as a combination of both, have been proposed to be responsible for the Mn oxidation and deposition process. We conducted scanning transmission X-ray microscopy - near edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS) measurements to examine the abundance and spatial distribution of the different oxidation states of Mn within these nano- to micrometer thick crusts. Such microanalytical measurements of thin and hard rock crusts require sample preparation with minimal contamination risk. Focused ion beam (FIB) slicing, a well-established technique in geosciences, was used in this study to obtain 100–200 nm thin slices of the samples for X-ray transmission spectroscopy. However, even though this preparation is suitable to investigate element distributions and structures in rock samples, we observed that, using standard parameters, modifications of the Mn oxidation states occur in the surfaces of the FIB slices. Based on our results, the preparation technique likely causes the reduction of Mn4+ to Mn2+/3+. We draw attention to this issue, since FIB slicing, SEM imaging, and other preparation and visualization techniques operating in the keV range are well-established in geosciences, but researchers are often unaware of the potential for reduction of Mn and possibly other elements in the samples’ surface layers

Rational Strain Engineering in Delafossite Oxides for Highly Efficient Hydrogen Evolution Catalysis in Acidic Media

The rational design of hydrogen evolution reaction (HER) electrocatalysts which are competitive with platinum is an outstanding challenge to make power-to-gas technologies economically viable. Here, we introduce the delafossites PdCrO$_2$, PdCoO$_2$ and PtCoO$_2$ as a new family of electrocatalysts for the HER in acidic media. We show that in PdCoO$_2$ the inherently strained Pd metal sublattice acts as a pseudomorphic template for the growth of a strained (by +2.3%) Pd rich capping layer under reductive conditions. The surface modification continuously improves the electrocatalytic activity by simultaneously increasing the exchange current density j$_0$ from 2 to 5 mA/cm$^2_{geo}$ and by reducing the Tafel slope down to 38 mV/decade, leading to overpotentials $\eta_{10}$ < 15 mV for 10 mA/cm$^2_{geo}$, superior to bulk platinum. The greatly improved activity is attributed to the in-situ stabilization of a $\beta$-palladium hydride phase with drastically enhanced surface catalytic properties with respect to pure or nanostructured palladium. These findings illustrate how operando induced electrodissolution can be used as a top-down design concept for rational surface and property engineering through the strain-stabilized formation of catalytically active phases