355 research outputs found
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 from
trajectories that have been generated at a different potential . 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
Recommended from our members
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
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, PdCoO and PtCoO as a new family of
electrocatalysts for the HER in acidic media. We show that in PdCoO 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 from 2
to 5 mA/cm and by reducing the Tafel slope down to 38 mV/decade,
leading to overpotentials < 15 mV for 10 mA/cm, superior
to bulk platinum. The greatly improved activity is attributed to the in-situ
stabilization of a -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
Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux
Abstract
Molecular dynamics (MD) are extremely complex, yet understanding the slow components of
their dynamics is essential to understanding their macroscopic properties. To achieve this, one
models the MD as a stochastic process and analyses the dominant eigenfunctions of the
associated Fokker–Planck operator, or of closely related transfer operators. So far, the
calculation of the discretized operators requires extensive MD simulations. The square-root
approximation of the Fokker–Planck equation is a method to calculate transition rates as a
ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be
calculated without a simulation. In a previous work we still used MD simulations to determine
the flux. Here, we propose several methods to calculate the exact or approximate flux for
various grid types, and thus estimate the rate matrix without a simulation. Using model
potentials we test computational efficiency of the methods, and the accuracy with which they
reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate
matrices with up to O(106) states can be obtained within seconds on a single
high-performance compute server if regular grids are used
Microarray-Based Gene Expression Profiling Suggests adaptation of Lung Epithelial Cells Subjected to Chronic Cyclic Strain
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