Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks

MOTIVATION

Biochemical reaction networks in the form of coupled ordinary differential equations (ODEs) provide a powerful modeling tool for understanding the dynamics of biochemical processes. During the early phase of modeling, scientists have to deal with a large pool of competing nonlinear models. At this point, discrimination experiments can be designed and conducted to obtain optimal data for selecting the most plausible model. Since biological ODE models have widely distributed parameters due to, e.g. biologic variability or experimental variations, model responses become distributed. Therefore, a robust optimal experimental design (OED) for model discrimination can be used to discriminate models based on their response probability distribution functions (PDFs).

RESULTS

In this work, we present an optimal control-based methodology for designing optimal stimulus experiments aimed at robust model discrimination. For estimating the time-varying model response PDF, which results from the nonlinear propagation of the parameter PDF under the ODE dynamics, we suggest using the sigma-point approach. Using the model overlap (expected likelihood) as a robust discrimination criterion to measure dissimilarities between expected model response PDFs, we benchmark the proposed nonlinear design approach against linearization with respect to prediction accuracy and design quality for two nonlinear biological reaction networks. As shown, the sigma-point outperforms the linearization approach in the case of widely distributed parameter sets and/or existing multiple steady states. Since the sigma-point approach scales linearly with the number of model parameter, it can be applied to large systems for robust experimental planning.

AVAILABILITY

An implementation of the method in MATLAB/AMPL is available at http://www.uni-magdeburg.de/ivt/svt/person/rf/roed.html.

CONTACT

flassig@mpi-magdeburg.mpg.de

SUPPLEMENTARY INFORMATION

Supplementary data are are available at Bioinformatics online.

Mass transfer model of triethylamine across the n-decane/water interface derived from dynamic interfacial tension experiments

This publication presents a detailed experimental and theoretical study of mass transfer of triethylamine (TEA) across the n-decane/water interface. In preliminary investigations, the partition of TEA between n-decane and water is determined. Based on the experimental finding that the dissociation of TEA takes place in the aqueous and in the organic phase, we assume that the interfacial mass transfer is mainly affected by adsorption and desorption of ionized TEA molecules at the liquid/liquid interface. Due to the amphiphilic structure of the dissociated TEA molecules, a dynamic interfacial tension measurement technique can be used to experimentally determine the interfacial mass transport. A model-based approach, which accounts for diffusive mass transport in the finite liquid bulk phases and for adsorption and desorption of ionized TEA molecules at the interface, is employed to analyze the experimental data. In the equilibrium state, the interfacial tension of dissociated TEA at the n-decane/water interface can be adequately described by the Langmuir isotherm. The comparison between the theoretical and the experimental dynamic interfacial tension data reveals that an additional activation energy barrier for adsorption and desorption at the interface has to be regarded to accurately describe the mass transport of TEA from the n-decane phase into the aqueous phase. Corresponding adsorption rate constants can be obtained by fitting the theoretical predictions to the experimental data. Interfacial tension measurements of mass transfer from the aqueous into the organic phase are characterized by interfacial instabilities caused by Marangoni convection, which result in an enhancement of the transfer rate across the interface.

Spontaneous oscillations of cell voltage, power density, and anode exit CO concentration in a PEM fuel cell

The spontaneous oscillations of the cell voltage and output power density of a PEMFC (with PtRu/C anode) using CO-containing H(2) streams as anodic fuels have been observed during galvanostatic operating. It is ascribed to the dynamic coupling of the CO adsorption (poisoning) and the electrochemical CO oxidation (reactivating) processes in the anode chamber of the single PEMFC. Accompanying the cell voltage and power density oscillations, the discrete CO concentration oscillations at the anode outlet of the PEMFC were also detected, which directly confirms the electrochemical CO oxidation taking place in the anode chamber during galvanostatic operating.

TRANSWESD: inferring cellular networks with transitive reduction

Motivation: Distinguishing direct from indirect influences is a central issue in reverse engineering of biological networks because it facilitates detection and removal of false positive edges. Transitive reduction is one approach for eliminating edges reflecting indirect effects but its use in reconstructing cyclic interaction graphs with true redundant structures is problematic.

Results: We present TRANSWESD, an elaborated variant of TRANSitive reduction for WEighted Signed Digraphs that overcomes conceptual problems of existing versions. Major changes and improvements concern: (i) new statistical approaches for generating high-quality perturbation graphs from systematic perturbation experiments; (ii) the use of edge weights (association strengths) for recognizing true redundant structures; (iii) causal interpretation of cycles; (iv) relaxed definition of transitive reduction; and (v) approximation algorithms for large networks. Using standardized benchmark tests, we demonstrate that our method outperforms existing variants of transitive reduction and is, despite its conceptual simplicity, highly competitive with other reverse engineering methods.

Contact:klamt@mpi-magdeburg.mpg.de

Supplementary information:Supplementary data are available at Bioinformatics online.

Determination of cluster composition in heteroaggregation of binary particle systems by flow cytometry

Cluster composition in aggregation processes of multiple particle species can be dynamically determined by flow cytometry if particle populations are fluorescently labeled. By flow cytometric single particle analysis, aggregates can be characterized according to the exact amount of constituent particles, allowing the detailed and separate quantification of homo- and heteroaggregation. This contribution demonstrates the application of flow cytometry for the experimental detection of heteroaggregation in a binary particle mixture of oppositely charged polystyrene (PS) particles and Rhodamine-B labeled melamine-formaldehyde (MF-RhB) particles. Experiments with different particle concentration, temperature, mixing mode, ionic strength and particle mixing ratio are presented. Aggregation kinetics are enhanced with increasing particle concentration and temperature as well as by increased shear of mixing. These results represent well-known behavior published in previous investigations and validate the performance of flow cytometry for probing heteroaggregation processes. Physical insight with a novel level of detail is gained by the quantification of de- and restabilization phenomena. At low ionic strength, "raspberry"-type aggregates with PS cores are formed by primary heteroaggregation. At moderate particle number ratios, these aggregates are electrostatically destabilized and form more complex aggregates in a secondary heteroaggregation process. At high particle number ratios (> or =50:1), the raspberry-type aggregates are electrostatically restabilized and secondary heteroaggregation is prevented. The dynamic change of aggregate charge was verified by zeta-potential measurements. The elevation of salt concentration over several orders of magnitude retards aggregation dynamics, since attractive interparticle forces are diminished by an electrostatic double layer. This indicates that heteroaggregation induced by attractive interparticle forces is faster than aggregation due to random Brownian motion. Destabilization at high ionic strength is facilitated by charged ions and no longer by MF-RhB coverage. This results in a species independent one step aggregation process.