400 research outputs found
First-principles kinetic Monte Carlo simulations for heterogeneous catalysis, applied to the CO oxidation at RuO2(110)
We describe a first-principles statistical mechanics approach enabling us to
simulate the steady-state situation of heterogeneous catalysis. In a first step
density-functional theory together with transition-state theory is employed to
obtain the energetics of all relevant elementary processes. Subsequently the
statistical mechanics problem is solved by the kinetic Monte Carlo method,
which fully accounts for the correlations, fluctuations, and spatial
distributions of the chemicals at the surface of the catalyst under
steady-state conditions. Applying this approach to the catalytic oxidation of
CO at RuO2(110), we determine the surface atomic structure and composition in
reactive environments ranging from ultra-high vacuum (UHV) to technologically
relevant conditions, i.e. up to pressures of several atmospheres and elevated
temperatures. We also compute the CO2 formation rates (turnover frequencies).
The results are in quantitative agreement with all existing experimental data.
We find that the high catalytic activity of this system is intimately connected
with a disordered, dynamic surface ``phase'' with significant compositional
fluctuations. In this active state the catalytic function results from a
self-regulating interplay of several elementary processes.Comment: 18 pages including 9 figures; related publications can be found at
http://www.fhi-berlin.mpg.de/th/th.htm
The sticking probability of D2O-water on ice: Isotope effects and the influence of vibrational excitation
International audienceThe present study measures the sticking probability of heavy water (D2O) on H2O- and on D2O-ice and probes the influence of selective OD-stretch excitation on D2O sticking on these ices. Molecular beam techniques are combined with infrared laser excitation to allow for precise control of incident angle, translational energy, and vibrational state of the incident molecules. For a translational energy of 69 kJ/mol and large incident angles (θ ≥ 45°), the sticking probability of D2O on H2O-ice was found to be 1% lower than on D2O-ice. OD-stretch excitation by IR laser pumping of the incident D2O molecules produces no detectable change of the D2O sticking probability (<10−3). The results are compared with other gas/surface systems for which the effect of vibrational excitation on trapping has been probed experimentally
Dynamic reconfiguration of human brain networks during learning
Human learning is a complex phenomenon requiring flexibility to adapt
existing brain function and precision in selecting new neurophysiological
activities to drive desired behavior. These two attributes -- flexibility and
selection -- must operate over multiple temporal scales as performance of a
skill changes from being slow and challenging to being fast and automatic. Such
selective adaptability is naturally provided by modular structure, which plays
a critical role in evolution, development, and optimal network function. Using
functional connectivity measurements of brain activity acquired from initial
training through mastery of a simple motor skill, we explore the role of
modularity in human learning by identifying dynamic changes of modular
organization spanning multiple temporal scales. Our results indicate that
flexibility, which we measure by the allegiance of nodes to modules, in one
experimental session predicts the relative amount of learning in a future
session. We also develop a general statistical framework for the identification
of modular architectures in evolving systems, which is broadly applicable to
disciplines where network adaptability is crucial to the understanding of
system performance.Comment: Main Text: 19 pages, 4 figures Supplementary Materials: 34 pages, 4
figures, 3 table
On the statistical mechanics of prion diseases
We simulate a two-dimensional, lattice based, protein-level statistical
mechanical model for prion diseases (e.g., Mad Cow disease) with concommitant
prion protein misfolding and aggregation. Our simulations lead us to the
hypothesis that the observed broad incubation time distribution in
epidemiological data reflect fluctuation dominated growth seeded by a few
nanometer scale aggregates, while much narrower incubation time distributions
for innoculated lab animals arise from statistical self averaging. We model
`species barriers' to prion infection and assess a related treatment protocol.Comment: 5 Pages, 3 eps figures (submitted to Physical Review Letters
Ab initio atomistic thermodynamics and statistical mechanics of surface properties and functions
Previous and present "academic" research aiming at atomic scale understanding
is mainly concerned with the study of individual molecular processes possibly
underlying materials science applications. Appealing properties of an
individual process are then frequently discussed in terms of their direct
importance for the envisioned material function, or reciprocally, the function
of materials is somehow believed to be understandable by essentially one
prominent elementary process only. What is often overlooked in this approach is
that in macroscopic systems of technological relevance typically a large number
of distinct atomic scale processes take place. Which of them are decisive for
observable system properties and functions is then not only determined by the
detailed individual properties of each process alone, but in many, if not most
cases also the interplay of all processes, i.e. how they act together, plays a
crucial role. For a "predictive materials science modeling with microscopic
understanding", a description that treats the statistical interplay of a large
number of microscopically well-described elementary processes must therefore be
applied. Modern electronic structure theory methods such as DFT have become a
standard tool for the accurate description of individual molecular processes.
Here, we discuss the present status of emerging methodologies which attempt to
achieve a (hopefully seamless) match of DFT with concepts from statistical
mechanics or thermodynamics, in order to also address the interplay of the
various molecular processes. The new quality of, and the novel insights that
can be gained by, such techniques is illustrated by how they allow the
description of crystal surfaces in contact with realistic gas-phase
environments.Comment: 24 pages including 17 figures, related publications can be found at
http://www.fhi-berlin.mpg.de/th/paper.htm
Anti-prion drug mPPIg5 inhibits PrP(C) conversion to PrP(Sc).
Prion diseases, also known as transmissible spongiform encephalopathies, are a group of fatal neurodegenerative diseases that include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle and Creutzfeldt-Jakob disease (CJD) in humans. The 'protein only hypothesis' advocates that PrP(Sc), an abnormal isoform of the cellular protein PrP(C), is the main and possibly sole component of prion infectious agents. Currently, no effective therapy exists for these diseases at the symptomatic phase for either humans or animals, though a number of compounds have demonstrated the ability to eliminate PrPSc in cell culture models. Of particular interest are synthetic polymers known as dendrimers which possess the unique ability to eliminate PrP(Sc) in both an intracellular and in vitro setting. The efficacy and mode of action of the novel anti-prion dendrimer mPPIg5 was investigated through the creation of a number of innovative bio-assays based upon the scrapie cell assay. These assays were used to demonstrate that mPPIg5 is a highly effective anti-prion drug which acts, at least in part, through the inhibition of PrP(C) to PrP(Sc) conversion. Understanding how a drug works is a vital component in maximising its performance. By establishing the efficacy and method of action of mPPIg5, this study will help determine which drugs are most likely to enhance this effect and also aid the design of dendrimers with anti-prion capabilities for the future
Predictability of evolutionary trajectories in fitness landscapes
Experimental studies on enzyme evolution show that only a small fraction of
all possible mutation trajectories are accessible to evolution. However, these
experiments deal with individual enzymes and explore a tiny part of the fitness
landscape. We report an exhaustive analysis of fitness landscapes constructed
with an off-lattice model of protein folding where fitness is equated with
robustness to misfolding. This model mimics the essential features of the
interactions between amino acids, is consistent with the key paradigms of
protein folding and reproduces the universal distribution of evolutionary rates
among orthologous proteins. We introduce mean path divergence as a quantitative
measure of the degree to which the starting and ending points determine the
path of evolution in fitness landscapes. Global measures of landscape roughness
are good predictors of path divergence in all studied landscapes: the mean path
divergence is greater in smooth landscapes than in rough ones. The
model-derived and experimental landscapes are significantly smoother than
random landscapes and resemble additive landscapes perturbed with moderate
amounts of noise; thus, these landscapes are substantially robust to mutation.
The model landscapes show a deficit of suboptimal peaks even compared with
noisy additive landscapes with similar overall roughness. We suggest that
smoothness and the substantial deficit of peaks in the fitness landscapes of
protein evolution are fundamental consequences of the physics of protein
folding.Comment: 14 pages, 7 figure
Narrowing the Boundaries of the Genetic Architecture of Schizophrenia
Genetic architecture of a disease comprises the number, frequency, and effect sizes of genetic risk alleles and the way in which they combine together. Before the genomic revolution, the only clue to underlying genetic architecture of schizophrenia came from the recurrence risks to relatives and the segregation patterns within families. From these clues, very simple genetic architectures could be rejected, but many architectures were consistent with the observed family data. The new era of genome-wide association studies can provide further clues to the genetic architecture of schizophrenia. We explore models of genetic architecture by description rather than the mathematics that underpins them. We conclude that the new genome-wide data allow us to narrow the boundaries on the models of genetic architecture that are consistent with the observed data. A genetic architecture of many common variants of moderate (relative risk > approximately 1.2) can be excluded, yet there is evidence that current generation genome-wide chips do tag an important proportion of the genetic variation for schizophrenia and that the underlying causal variants will include common variants of small effect as well as rarer variants of larger effect. Together, these observations imply that the total number of genetic variants is very large—of the order of thousands. The first generation of studies have generated hypotheses that should be testable in the near future and will further narrow the boundaries on genetic architectures that are consistent with empirical data
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