Hydrodynamic limit of a B.G.K. like model on domains with boundaries and analysis of kinetic boundary conditions for scalar multidimensional conservation laws

In this paper we study the hydrodynamic limit of a B.G.K. like kinetic model on domains with boundaries via $BV_{loc}$ theory. We obtain as a consequence existence results for scalar multidimensional conservation laws with kinetic boundary conditions. We require that the initial and boundary data satisfy the optimal assumptions that they all belong to $L^1\cap L^\infty$ with the additional regularity assumptions that the initial data are in $BV_{loc}$. We also extend our hydrodynamic analysis to the case of a generalized kinetic model to account for forces effects and we obtain as a consequence the existence theory for conservation laws with source terms and kinetic boundary conditions

Prediction of enzyme kinetic parameters based on statistical learning

Values of enzyme kinetic parameters are a key requisite for the kinetic modelling of biochemical systems. For most kinetic parameters, however, not even an order of magnitude is known, so the estimation of model parameters from experimental data remains a major task in systems biology. We propose a statistical approach to infer values for kinetic parameters across species and enzymes making use of parameter values that have been measured under various conditions and that are nowadays stored in databases. We fit the data by a statistical regression model in which the substrate, the combination enzyme-substrate and the combination organism-substrate have a linear effect on the logarithmic parameter value. As a result, we obtain predictions and error ranges for unknown enzyme parameters. We apply our method to decadic logarithmic Michaelis-Menten constants from the BRENDA database and confirm the results with leave-one-out crossvalidation, in which we mask one value at a time and predict it from the remaining data. For a set of 8 metabolites we obtain a standard prediction error of 1.01 for the deviation of the predicted values from the true values, while the standard deviation of the experimental values is 1.16. The method is applicable to other types of kinetic parameters for which many experimental data are available

NIKEL: Electronics and data acquisition for kilopixels kinetic inductance camera

A prototype of digital frequency multiplexing electronics allowing the real time monitoring of microwave kinetic inductance detector (MKIDs) arrays for mm-wave astronomy has been developed. Thanks to the frequency multiplexing, it can monitor simultaneously 400 pixels over a 500 MHz bandwidth and requires only two coaxial cables for instrumenting such a large array. The chosen solution and the performances achieved are presented in this paper.Comment: 21 pages, 14 figure

Inference of the Kinetic Ising Model with Heterogeneous Missing Data

We consider the problem of inferring a causality structure from multiple binary time series by using the Kinetic Ising Model in datasets where a fraction of observations is missing. We take our steps from a recent work on Mean Field methods for the inference of the model with hidden spins and develop a pseudo-Expectation-Maximization algorithm that is able to work even in conditions of severe data sparsity. The methodology relies on the Martin-Siggia-Rose path integral method with second order saddle-point solution to make it possible to calculate the log-likelihood in polynomial time, giving as output a maximum likelihood estimate of the couplings matrix and of the missing observations. We also propose a recursive version of the algorithm, where at every iteration some missing values are substituted by their maximum likelihood estimate, showing that the method can be used together with sparsification schemes like LASSO regularization or decimation. We test the performance of the algorithm on synthetic data and find interesting properties when it comes to the dependency on heterogeneity of the observation frequency of spins and when some of the hypotheses that are necessary to the saddle-point approximation are violated, such as the small couplings limit and the assumption of statistical independence between couplings

Electronics and data acquisition demonstrator for a kinetic inductance camera

A prototype of digital frequency multiplexing electronics allowing the real time monitoring of kinetic inductance detector (KIDs) arrays for mm-wave astronomy has been developed. It requires only 2 coaxial cables for instrumenting a large array. For that, an excitation comb of frequencies is generated and fed through the detector. The direct frequency synthesis and the data acquisition relies heavily on a large FPGA using parallelized and pipelined processing. The prototype can instrument 128 resonators (pixels) over a bandwidth of 125 MHz. This paper describes the technical solution chosen, the algorithm used and the results obtained

Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule F\"orster resonance energy transfer (smFRET) provides access to enzymatically important timescales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings - such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.Comment: 17 pages, 6 figure

Kinetic research on heterogeneously catalysed processes: a questionnaire on the state-of-the-art in industry

On the initiative of the Working Party `Chemical Engineering in the Applications of Catalysis¿ of the European Federation of Chemical Engineering an assessment of the issues in the determination and application of kinetic data within the European industry was performed. The basis of the analysis consisted of a questionnaire put together by researchers from Dow, DSM, Shell and Eindhoven University of Technology. The 24 companies, which have responded to the questionnaire, can be classified into four groups: chemical, oil, engineering contractors and catalyst manufacturers. From the overall input it appears that there are three, equally important, utilisation areas for kinetic data: process development, process optimisation and catalyst development. There is a wide variety of kinetic data sources. Most of the respondents make use of test units which were primarily designed for development and optimisation. Avoiding transport limitation is, certainly in the case of short range projects or for complex feedstocks, not always taken care of. With respect to the modelling approaches, a common philosophy is `as simple as possible¿. Most of the respondents state that `in principle¿ one should strive for intrinsic kinetics, but the majority nevertheless does for various reasons not separate all transport phenomena from reaction kinetics. Kinetic models are mostly simple first or nth order or Langmuir-Hinshelwood type expressions. More complex kinetic models are scarcely used. Three areas were frequently identified to offer opportunities for improvement. Gathering of kinetic data is too costly and time consuming. There is no systematic approach at all for determination and application of kinetics in case of unstable catalytic performance. Furthermore, the software available for the regression of kinetic data to rate equations based on mechanistic schemes as well as software to model reactors are insufficiently user friendly. The majority of the respondents state that the problems indicated should be solved by cooperation, e.g., between companies, between industry and academia and between the catalysis and the chemical engineering community. A workshop on the above topics was held in December 1996 with 15 companies and 6 academics attending. More information can be obtained from the secretariat of the Working Party