Stochastic Representations of Ion Channel Kinetics and Exact Stochastic Simulation of Neuronal Dynamics

In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation with a commonly used numerical approximation strategy. The first representation we present is a random time change representation, popularized by Thomas Kurtz, with the second being analogous to a "Gillespie" representation. Exact stochastic algorithms are provided for the different representations, which are preferable to either (a) fixed time step or (b) piecewise constant propensity algorithms, which still appear in the literature. As examples, we provide versions of the exact algorithms for the Morris-Lecar conductance based model, and detail the error induced, both in a weak and a strong sense, by the use of approximate algorithms on this model. We include ready-to-use implementations of the random time change algorithm in both XPP and Matlab. Finally, through the consideration of parametric sensitivity analysis, we show how the representations presented here are useful in the development of further computational methods. The general representations and simulation strategies provided here are known in other parts of the sciences, but less so in the present setting.Comment: 39 pages, 6 figures, appendix with XPP and Matlab cod

Formalizing Theories Of Development: A Fugue On The Orderliness Of Change

This chapter looks at developmental biology as performance. Each animal inherits score (the DNA), mechanisms for interpreting of the score, and mechanisms for improvisation should the score be deficient. Developmental causation is found to be both upwards from the genome, downward from the environment, and laterally between cells. Developmental plasticity, organicism, phenotypic heterogeneity, symbiotic co-development, and cytoplasmic localization are each examples of causation from the environment downward. Stereocomplementary relationships are the key components of most developmental interactions. These interactions can be placed into a formal language of graph theory. Morphogenesis can be depicted in the general structure, where nouns cover tissues, molecules and networks and verbs describe processes such as moves, differentiates, grows and apoptoses. This manner of depicting development emphasizes the distributed nature of causality in morphogenesis and can be annotated with associated information or IDs (e.g. cell types, publications, gene-expression data) that link to external online resources that may be regularly updated. This graph approach portrays dynamic processes as the drivers of developmental momentum, and, since the same processes are used many times during development, they can be viewed as modules whose underlying networks are genomic subroutines

Dynamic Potential-Ph Diagrams Application to Electrocatalysts for Water Oxidation

The construction and use of "dynamic potential-pH diagrams" (DPPDs), that are intended to extend the usefulness of thermodynamic Pourbaix diagrams to include kinetic considerations is described. As an example, DPPDs are presented for the comparison of electrocatalysts for water oxidation, i.e., the oxygen evolution reaction (OER), an important electrochemical reaction because of its key role in energy conversion devices and biological systems (water electrolyses, photoelectrochemical water splitting, plant photosynthesis). The criteria for obtaining kinetic data are discussed and a 3-D diagram, which shows the heterogeneous electron transfer kinetics of an electrochemical system as a function of pH and applied potential is presented. DPPDs are given for four catalysts: IrO(2), Co(3)O(4), Co(3)O(4) electrodeposited in a phosphate medium (Co-Pi) and Pt, allowing a direct comparison of the activity of different electrode materials over a broad range of experimental conditions (pH, potential, current density). In addition, the experimental setup and the factors affecting the accurate collection and presentation of data (e. g., reference electrode system, correction of ohmic drops, bubble formation) are discussed.Ministry of Education, University and Research PRIN 2008PF9TWZ, 2008N7CYL5Universita degli Studi di MilanoNational Science Foundation CHE-0808927Robert A. Welch Foundation F-0021Center for Electrochemistr

Modeling seismic wave propagation and amplification in 1D/2D/3D linear and nonlinear unbounded media

To analyze seismic wave propagation in geological structures, it is possible to consider various numerical approaches: the finite difference method, the spectral element method, the boundary element method, the finite element method, the finite volume method, etc. All these methods have various advantages and drawbacks. The amplification of seismic waves in surface soil layers is mainly due to the velocity contrast between these layers and, possibly, to topographic effects around crests and hills. The influence of the geometry of alluvial basins on the amplification process is also know to be large. Nevertheless, strong heterogeneities and complex geometries are not easy to take into account with all numerical methods. 2D/3D models are needed in many situations and the efficiency/accuracy of the numerical methods in such cases is in question. Furthermore, the radiation conditions at infinity are not easy to handle with finite differences or finite/spectral elements whereas it is explicitely accounted in the Boundary Element Method. Various absorbing layer methods (e.g. F-PML, M-PML) were recently proposed to attenuate the spurious wave reflections especially in some difficult cases such as shallow numerical models or grazing incidences. Finally, strong earthquakes involve nonlinear effects in surficial soil layers. To model strong ground motion, it is thus necessary to consider the nonlinear dynamic behaviour of soils and simultaneously investigate seismic wave propagation in complex 2D/3D geological structures! Recent advances in numerical formulations and constitutive models in such complex situations are presented and discussed in this paper. A crucial issue is the availability of the field/laboratory data to feed and validate such models.Comment: of International Journal Geomechanics (2010) 1-1

Method for metal nanoparticle electrocatalytic amplification

The present invention includes methods, compositions and kits for analyzing a chemical analyte having an electrochemical cell connected to a measuring apparatus. The electrochemical cell contains a solution having one or more nanoparticles, one or more chemical analytes, an indicator. In addition, the electrochemical cell contains one or more electrodes in communication with the solution. One or more electrocatalytic properties are generated by the interaction of the one or more nanoparticles and the liquid sample and measured at the one or more electrodes.Board of Regents, University of Texas Syste

Method and apparatus for nanoparticle electrogenerated chemiluminescence amplification

Methods, compositions and kits for analyzing a chemical analyte using an electrochemical cell connected to a measuring apparatus are provided. The electrochemical cell contains a solution having one or more conductive or redox active NPs (nanoparticles), one or more chemical analytes, and an indicator. In addition, the electrochemical cell contains one or more electrodes in communication with the solution. One or more catalytic ECL properties are generated by the interaction of the one or more conductive or redox active NPs and the liquid sample and measured at the one or more electrodes or with an optical detection system.Board of Regents, University of Texas Syste

Basin Effects in Strong Ground Motion: A Case Study from the 2015 Gorkha, Nepal Earthquake

The term "basin effects" refers to entrapment and reverberation of earthquake waves in soft sedimentary deposits underlain by concave basement rock structures. Basin effects can significantly affect the amplitude, frequency and duration of strong ground motion, while the cone-like geometry of the basin edges gives rise to large amplitude surface waves through seismic wave diffraction and energy focusing, a well-known characteristic of basin effects. In this research, we study the role of basin effects in the mainshock ground motion data recorded at the Kathmandu basin, Nepal during the 2015 Mw7.8 Gorkha earthquake sequence. We specifically try to understand the source of the unusual low frequency reverberating pulse that appeared systematically across the basin, and the unexpected depletion of the ground surface motions from high frequency components, especially away from the basin edges. In order to do that we study the response of a 2D cross section of Kathmandu basin subjected to vertically propagating plane SV waves. Despite the scarcity of geotechnical information and of strong ground motion recordings, we show that an idealized plane-strain elastic model with a simplified layered velocity structure can capture surprisingly well the low frequency components of the basin ground response. We finally couple the 2D elastic simulation with a 1D nonlinear analysis of the shallow basin sediments. The 1D nonlinear approximation shows improved performance over a larger frequency range relative to the first order approximation of a 2D elastic layered basin response.Comment: Geotechnical Earthquake Engineering and Soil Dynamics V, Austin, Texas (2018

Luminescent nanostructured materials for use in electrogenerated chemiluminescence

A nanostructured particulate material, which includes a redox active luminescent organic and/or ionic compound, is provided herein. The nanostructured particulate material may be used for determining the presence of an analyte of interest in a sample by detecting the emitted electromagnetic radiation generated by exposing a reagent mixture, which includes the nanostructured material and the target analyte, to chemical or electrochemical energy.Board of Regents, University of Texas Syste

Nano-Size Layered Manganese-Calcium Oxide as an Efficient and Biomimetic Catalyst for Water Oxidation Under Acidic Conditions: Comparable To Platinum

Inspired by Nature's catalyst, a nano-size layered manganese-calcium oxide showed a low overvoltage for water oxidation in acidic solutions, which is comparable to platinum.Institute for Advanced Studies in Basic Sciences and the National Elite FoundationUS Department of Energy, Office of Basic Energy Sciences, Division of Chemical, Geochemical and Biological Sciences DE-FG02-86ER13622, DE-FG0209ER16119Russian Foundation for Basic Research 11-04-01389a, 12-0492101a, 13-04-92711aMolecular and Cell Biology Programs of the Russian Academy of SciencesCenter for Electrochemistr

Discrete model for laser driven etching and microstructuring of metallic surfaces

We present a unidimensional discrete solid-on-solid model evolving in time using a kinetic Monte Carlo method to simulate micro-structuring of kerfs on metallic surfaces by means of laser-induced jet-chemical etching. The precise control of the passivation layer achieved by this technique is responsible for the high resolution of the structures. However, within a certain range of experimental parameters, the microstructuring of kerfs on stainless steel surfaces with a solution of $\mathrm{H}_3\mathrm{PO}_4$ shows periodic ripples, which are considered to originate from an intrinsic dynamics. The model mimics a few of the various physical and chemical processes involved and within certain parameter ranges reproduces some morphological aspects of the structures, in particular ripple regimes. We analyze the range of values of laser beam power for the appearance of ripples in both experimental and simulated kerfs. The discrete model is an extension of one that has been used previously in the context of ion sputtering and is related to a noisy version of the Kuramoto-Sivashinsky equation used extensively in the field of pattern formation.Comment: Revised version. Etching probability distribution and new simulations adde