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Yefei Li, Zhi-Pan Liu
Seeking for active MnOx material as artificial water splitting catalyst has been a long history since the discovery of PSII system in Nature. To date, the highest activity MnOx catalyst reported for oxygen evolution reaction (OER) is however not common MnO2 polymorphs (α-, β-, δ-MnO2), but nascent δ-MnO2 layer produced in situ from spinel under electrochemical conditions with unknown active site structure. Here with the stochastic surface walking (SSW) pathway sampling method, we for the first time resolve the atomic-level mechanism of spinel-to-layer Mn3O4 solid phase transition in aqueous electrolyte...
January 15, 2018: Journal of the American Chemical Society
Nathaniel H Merrill, Todd Guilfoos
We introduce a model that incorporates two important elements to estimating welfare gains from groundwater management: stochasticity and a spatial stock externality. We estimate welfare gains resulting from optimal management under uncertainty as well as a gradual stock externality that produces the dynamics of a large aquifer being slowly exhausted. This groundwater model imposes an important aspect of a depletable natural resource without the extreme assumption of complete exhaustion that is necessary in a traditional single cell (bathtub) model of groundwater extraction...
January 1, 2018: American Journal of Agricultural Economics
Ross Wilson, J Haxby Abbott
OBJECTIVE: To describe the construction and preliminary validation of a new population-based microsimulation model developed to analyse the health and economic burden and cost-effectiveness of treatments for knee osteoarthritis (OA) in New Zealand (NZ). METHOD: We developed the New Zealand Management of Osteoarthritis (NZ-MOA) model, a discrete-time state-transition microsimulation model of the natural history of radiographic knee OA. In this article, we report on the model structure, derivation of input data, validation of baseline model parameters against external data sources, and validation of model outputs by comparison of the predicted population health loss with previous estimates...
January 10, 2018: Osteoarthritis and Cartilage
Xiaoan Yan, Minping Jia, Wan Zhang, Lin Zhu
Periodic transient impulses are key indicators of rolling element bearing defects. Efficient acquisition of impact impulses concerned with the defects is of much concern to the precise detection of bearing defects. However, transient features of rolling element bearing are generally immersed in stochastic noise and harmonic interference. Therefore, in this paper, a new optimal scale morphology analysis method, named adaptive multiscale combination morphological filter-hat transform (AMCMFH), is proposed for rolling element bearing fault diagnosis, which can both reduce stochastic noise and reserve signal details...
January 10, 2018: ISA Transactions
Pei-Yang Chen, Mark E Tuckerman
Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions...
January 14, 2018: Journal of Chemical Physics
Jinxian Li, Weiqiang Li, Zhen Jin
The spread of an infectious disease may depend on the structure of the network. To study the influence of the structure parameters of the network on the spread of the epidemic, we need to put these parameters into the epidemic model. The method of moment closure introduces structure parameters into the epidemic model. In this paper, we present a new moment closure epidemic model based on the approximation of third-order motifs in networks. The order of a motif defined in this paper is determined by the number of the edges in the motif, rather than by the number of nodes in the motif as defined in the literature...
January 9, 2018: Mathematical Biosciences
Matan Danino, Nadav M Shnerb
A fundamental problem in the fields of population genetics, evolution, and community ecology, is the fate of a single mutant, or invader, introduced in a finite population of wild types. For a fixed-size community of N individuals, with Markovian, zero-sum dynamics driven by stochastic birth-death events, the mutant population eventually reaches either fixation or extinction. The classical analysis, provided by Kimura and his coworkers, is focused on the neutral case, [where the dynamics is only due to demographic stochasticity (drift)], and on time-independent selective forces (deleterious/beneficial mutation)...
January 9, 2018: Journal of Theoretical Biology
Chi Xue, Nigel Goldenfeld
The "kill the winner" hypothesis is an attempt to address the problem of diversity in biology. It argues that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. We develop a stochastic model for the kill the winner paradigm and show that the stable coexistence state of the deterministic kill the winner model is destroyed by demographic stochasticity, through a cascade of extinction events. We formulate an individual-level stochastic model in which predator-prey coevolution promotes the high diversity of the ecosystem by generating a persistent population flux of species...
December 29, 2017: Physical Review Letters
Aashutosh Mistry, Kandler Smith, Partha P Mukherjee
Lithium-ion battery electrodes exhibit complex interplay among multiple electrochemically coupled transport processes, which rely on the underlying functionality and relative arrangement of different constituent phases. The electrochemically inactive solid phases (e.g., conductive additive and binder, referred to as the secondary phase) while beneficial for improved electronic conductivity and mechanical integrity, may partially block the electrochemically active sites and introduce additional transport resistances in the pore (electrolyte) phase...
January 12, 2018: ACS Applied Materials & Interfaces
Robin Shannon, David R Glowacki
The chemical master equation is a powerful theoretical tool for analysing the kinetics of complex multi-well potential energy surfaces in a wide range of different domains of chemical kinetics spanning combustion, atmospheric chemistry, gas-surface chemistry, solution phase chemistry, and biochemistry. There are two well-established methodologies for solving the chemical master equation: a stochastic "kinetic Monte Carlo" approach and a matrix-based approach. In principle, the results yielded by both approaches are identical; the decision of which approach is better suited to a particular study depends on the details of the specific system under investigation...
January 12, 2018: Journal of Physical Chemistry. A
Yijin Ren, Can Wang, Zhi Chen, Elaine Allan, Henny C van der Mei, Henk J Busscher
Phenotypically-heterogeneous micro-environments emerge as biofilms mature across different environments. Phenotypic-heterogeneity in biofilm sub-populations not obeying quorum sensing-dictated, collective group-behavior, may be considered as a strategy allowing non-conformists to survive hostile conditions. Heterogeneous phenotype development has been amply studied with respect to gene expression and genotypic changes, but 'biofilm genes' responsible for pre-programmed development of heterogeneous micro-environments in biofilms have never been discovered...
January 9, 2018: FEMS Microbiology Reviews
Daniel S Calovi, Alexandra Litchinko, Valentin Lecheval, Ugo Lopez, Alfonso Pérez Escudero, Hugues Chaté, Clément Sire, Guy Theraulaz
The development of tracking methods for automatically quantifying individual behavior and social interactions in animal groups has open up new perspectives for building quantitative and predictive models of collective behavior. In this work, we combine extensive data analyses with a modeling approach to measure, disentangle, and reconstruct the actual functional form of interactions involved in the coordination of swimming in Rummy-nose tetra (Hemigrammus rhodostomus). This species of fish performs burst-and-coast swimming behavior that consists of sudden heading changes combined with brief accelerations followed by quasi-passive, straight decelerations...
January 11, 2018: PLoS Computational Biology
Alessandro Bertucci, Junling Guo, Nicolas Oppmann, Agata Glab, Francesco Ricci, Frank Caruso, Francesca Cavalieri
Transcription factor DNA binding activity is of pivotal importance in living systems because of its primary involvement in the regulation of genetic machinery. The analysis of transient expression levels of transcription factors in response to a certain cell status is a powerful means for investigating cellular dynamics at the biomolecular level. Herein, a DNA-based molecular switch that enables probing of transcription factor DNA binding activity is directly used in living cells. We demonstrate that the DNA nanoswitch allows for dynamic fluorescence imaging of NF-κB and quantification of downstream gene silencing in real time...
January 11, 2018: Nanoscale
Michael P Hart, Oliver Hobert
During development and adulthood, brain plasticity is evident at several levels, from synaptic structure and function to the outgrowth of dendrites and axons. Whether and how sex impinges on neuronal plasticity is poorly understood. Here we show that the sex-shared GABA (γ-aminobutyric acid)-releasing DVB neuron in Caenorhabditis elegans displays experience-dependent and sexually dimorphic morphological plasticity, characterized by the stochastic and dynamic addition of multiple neurites in adult males. These added neurites enable synaptic rewiring of the DVB neuron and instruct a functional switch of the neuron that directly modifies a step of male mating behaviour...
January 10, 2018: Nature
Ya D Sergeyev, D E Kvasov, M S Mukhametzhanov
Global optimization problems where evaluation of the objective function is an expensive operation arise frequently in engineering, decision making, optimal control, etc. There exist two huge but almost completely disjoint communities (they have different journals, different conferences, different test functions, etc.) solving these problems: a broad community of practitioners using stochastic nature-inspired metaheuristics and people from academia studying deterministic mathematical programming methods. In order to bridge the gap between these communities we propose a visual technique for a systematic comparison of global optimization algorithms having different nature...
January 11, 2018: Scientific Reports
Binu Mani Tripathi, Mincheol Kim, Yongwon Kim, Eunji Byun, Ji-Woong Yang, Jinho Ahn, Yoo Kyung Lee
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth...
January 11, 2018: Scientific Reports
Anna Lintunen, Stefan Mayr, Yann Salmon, Hervé Cochard, Teemu Hölttä
It is not well understood what determines the degree of supercooling of apoplastic sap in trees, although it determines the number and duration of annual freeze-thaw cycles in a given environment. We studied the linkage between apoplastic ice nucleation temperature, tree water status, and conduit size. We used branches of 10 gymnosperms and 16 angiosperms collected from an arboretum in Helsinki (Finland) in winter and spring. Branches with lower relative water content froze at lower temperatures, and branch water content was lower in winter than in spring...
January 2018: Ecology and Evolution
Devin W Goodsman, Brian H Aukema, Nate G McDowell, Richard S Middleton, Chonggang Xu
Phenology models are becoming increasingly important tools to accurately predict how climate change will impact the life histories of organisms. We propose a class of integral projection phenology models derived from stochastic individual-based models of insect development and demography. Our derivation, which is based on the rate summation concept, produces integral projection models that capture the effect of phenotypic rate variability on insect phenology, but which are typically more computationally frugal than equivalent individual-based phenology models...
January 2018: Ecology and Evolution
Anja Lück, Lukas Klimmasch, Peter Großmann, Sebastian Germerodt, Christoph Kaleta
Organisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms' metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation...
January 10, 2018: Scientific Reports
Jorge M Serrador, Brian M Deegan, Maria C Geraghty, Scott J Wood
Age-related loss of vestibular function can result in decrements in gaze stabilization and increased fall risk in the elderly. This study was designed to see if low levels of electrical stochastic noise applied transcutaneously to the vestibular system can improve a gaze stabilization reflex in young and elderly subject groups. Ocular counter-rolling (OCR) using a video-based technique was obtained in 16 subjects during low frequency passive roll tilts. Consistent with previous studies, there was a significant reduction in OCR gains in the elderly compared to the young group...
January 10, 2018: Scientific Reports
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