Max Planck Institute for Dynamics of Complex Technical Systems

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Numerical simulation of large-scale dynamical systems plays a fundamental role in studying a wide range of complex physical phenomena; however, the inherent large-scale nature of the models often leads to unmanageable demands on computational resources. Model reduction aims to reduce this computational burden by generating reduced models that are faster and cheaper to simulate, yet accurately represent the original large-scale system behavior. Model reduction of linear, nonparametric dynamical systems has reached a considerable level of maturity, as reflected by several survey papers and books. However, parametric model reduction has emerged only more recently as an important and vibrant research area, with several recent advances making a survey paper timely. Thus, this paper aims to provide a resource that draws together recent contributions in different communities to survey the state of the art in parametric model reduction methods. Parametric model reduction targets the broad class of problems for which the equations governing the system behavior depend on a set of parameters. Examples include parameterized partial differential equations and large-scale systems of parameterized ordinary differential equations. The goal of parametric model reduction is to generate low-cost but accurate models that characterize system response for different values of the parameters. This paper surveys state-of-the-art methods in projection-based parametric model reduction, describing the different approaches within each class of methods for handling parametric variation and providing a comparative discussion that lends insights to potential advantages and disadvantages in applying each of the methods. We highlight the important role played by parametric model reduction in design, control, optimization, and uncertainty quantification---settings that require repeated model evaluations over different parameter values.

This contribution is concerned with joint angle calculation based on inertial measurement data in the context of human motion analysis. Unlike most robotic devices, the human body lacks even surfaces and right angles. Therefore, we focus on methods that avoid assuming certain orientations in which the sensors are mounted with respect to the body segments. After a review of available methods that may cope with this challenge, we present a set of new methods for: (1) joint axis and position identification; and (2) flexion/extension joint angle measurement. In particular, we propose methods that use only gyroscopes and accelerometers and, therefore, do not rely on a homogeneous magnetic field. We provide results from gait trials of a transfemoral amputee in which we compare the inertial measurement unit (IMU)-based methods to an optical 3D motion capture system. Unlike most authors, we place the optical markers on anatomical landmarks instead of attaching them to the IMUs. Root mean square errors of the knee flexion/extension angles are found to be less than 1° on the prosthesis and about 3° on the human leg. For the plantar/dorsiflexion of the ankle, both deviations are about 1°.

In search for future energy supplies the application of hydrogen as an energy carrier is seen as a prospective issue. However, the implementation of a hydrogen economy is suffering from several unsolved problems. Particularly challenging is the storage of appropriate amounts of hydrogen. In this context the utilization of carbon dioxide–formic acid for hydrogen storing is discussed.

BACKGROUND: Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. So far, software tools providing such methods for both mass-flow (metabolic) as well as signal-flow (signalling and regulatory) networks are lacking. RESULTS: Herein we introduce CellNetAnalyzer, a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks. CONCLUSION: CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis. CellNetAnalyzer is freely available for academic use.

The provision of pure enantiomers is of increasing importance not only for the pharmaceutical industry but also for agrochemistry and biotechnology. In general, there are two rival approaches to provide pure enantiomers. The "chiral" approach is based on developing an asymmetric synthesis of just one of the enantiomers, while the "racemic" approach is based on separating mixtures of the two enantiomers. In the last few years remarkable progress has been achieved in the latter area. This Review focuses in particular on enantioselective crystallization processes and preparative chromatography, including hybrid processes and the incorporation of racemization steps. Several examples from our research are used for illustration purposes.

3,41Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany, 2Institute for Mathematical Optimization, Faculty of Mathematics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany, 3Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Mu¨nchen—German Research Center forEnvironmental Health, Neuherberg, Germany, 4Max Planck Institute for Dynamics and Self-Organization, Go¨ttingen, Germany

We propose a consensus-based distributed voltage control (DVC) that solves the problem of reactive power sharing in autonomous inverter-based microgrids with dominantly inductive power lines and arbitrary electrical topology. Opposed to other control strategies available thus far, the control presented here does guarantee a desired reactive power distribution in steady state while only requiring distributed communication among inverters, i.e., no central computing nor communication unit is needed. For inductive impedance loads and under the assumption of small phase angle differences between the output voltages of the inverters, we prove that the choice of the control parameters uniquely determines the corresponding equilibrium point of the closed-loop voltage and reactive power dynamics. In addition, for the case of uniform time constants of the power measurement filters, a necessary and sufficient condition for local exponential stability of that equilibrium point is given. The compatibility of the DVC with the usual frequency droop control for inverters is shown and the performance of the proposed DVC is compared with the usual voltage droop control via simulation of a microgrid based on the Conseil International des Grands Réseaux Electriques (CIGRE) benchmark medium voltage distribution network.

Life cycle of an ideal green solvent from cradle to grave for sustainability studies of green solvents.

BACKGROUND: Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional capabilities. While the structural analysis of metabolic networks is a well-established field, similar methodologies have been scarcely developed and applied to signaling and regulatory networks. RESULTS: We propose formalisms and methods, relying on adapted and partially newly introduced approaches, which facilitate a structural analysis of signaling and regulatory networks with focus on functional aspects. We use two different formalisms to represent and analyze interaction networks: interaction graphs and (logical) interaction hypergraphs. We show that, in interaction graphs, the determination of feedback cycles and of all the signaling paths between any pair of species is equivalent to the computation of elementary modes known from metabolic networks. Knowledge on the set of signaling paths and feedback loops facilitates the computation of intervention strategies and the classification of compounds into activators, inhibitors, ambivalent factors, and non-affecting factors with respect to a certain species. In some cases, qualitative effects induced by perturbations can be unambiguously predicted from the network scheme. Interaction graphs however, are not able to capture AND relationships which do frequently occur in interaction networks. The consequent logical concatenation of all the arcs pointing into a species leads to Boolean networks. For a Boolean representation of cellular interaction networks we propose a formalism based on logical (or signed) interaction hypergraphs, which facilitates in particular a logical steady state analysis (LSSA). LSSA enables studies on the logical processing of signals and the identification of optimal intervention points (targets) in cellular networks. LSSA also reveals network regions whose parametrization and initial states are crucial for the dynamic behavior. We have implemented these methods in our software tool CellNetAnalyzer (successor of FluxAnalyzer) and illustrate their applicability using a logical model of T-Cell receptor signaling providing non-intuitive results regarding feedback loops, essential elements, and (logical) signal processing upon different stimuli. CONCLUSION: The methods and formalisms we propose herein are another step towards the comprehensive functional analysis of cellular interaction networks. Their potential, shown on a realistic T-cell signaling model, makes them a promising tool.

Materials development has historically been driven by human needs and desires, and this is likely to continue in the foreseeable future. The global population is expected to reach ten billion by 2050, which will promote increasingly large demands for clean and high-efficiency energy, personalized consumer products, secure food supplies, and professional healthcare. New functional materials that are made and tailored for targeted properties or behaviors will be the key to tackling this challenge. Traditionally, advanced materials are found empirically or through experimental trial-and-error approaches. As big data generated by modern experimental and computational techniques is becoming more readily available, data-driven or machine learning (ML) methods have opened new paradigms for the discovery and rational design of materials. In this review article, we provide a brief introduction on various ML methods and related software or tools. Main ideas and basic procedures for employing ML approaches in materials research are highlighted. We then summarize recent important applications of ML for the large-scale screening and optimal design of polymer and porous materials, catalytic materials, and energetic materials. Finally, concluding remarks and an outlook are provided.

Large-scale protein signalling networks are useful for exploring complex biochemical pathways but do not reveal how pathways respond to specific stimuli. Such specificity is critical for understanding disease and designing drugs. Here we describe a computational approach--implemented in the free CNO software--for turning signalling networks into logical models and calibrating the models against experimental data. When a literature-derived network of 82 proteins covering the immediate-early responses of human cells to seven cytokines was modelled, we found that training against experimental data dramatically increased predictive power, despite the crudeness of Boolean approximations, while significantly reducing the number of interactions. Thus, many interactions in literature-derived networks do not appear to be functional in the liver cells from which we collected our data. At the same time, CNO identified several new interactions that improved the match of model to data. Although missing from the starting network, these interactions have literature support. Our approach, therefore, represents a means to generate predictive, cell-type-specific models of mammalian signalling from generic protein signalling networks.

Cellular decisions are determined by complex molecular interaction networks. Large-scale signaling networks are currently being reconstructed, but the kinetic parameters and quantitative data that would allow for dynamic modeling are still scarce. Therefore, computational studies based upon the structure of these networks are of great interest. Here, a methodology relying on a logical formalism is applied to the functional analysis of the complex signaling network governing the activation of T cells via the T cell receptor, the CD4/CD8 co-receptors, and the accessory signaling receptor CD28. Our large-scale Boolean model, which comprises 94 nodes and 123 interactions and is based upon well-established qualitative knowledge from primary T cells, reveals important structural features (e.g., feedback loops and network-wide dependencies) and recapitulates the global behavior of this network for an array of published data on T cell activation in wild-type and knock-out conditions. More importantly, the model predicted unexpected signaling events after antibody-mediated perturbation of CD28 and after genetic knockout of the kinase Fyn that were subsequently experimentally validated. Finally, we show that the logical model reveals key elements and potential failure modes in network functioning and provides candidates for missing links. In summary, our large-scale logical model for T cell activation proved to be a promising in silico tool, and it inspires immunologists to ask new questions. We think that it holds valuable potential in foreseeing the effects of drugs and network modifications.

Direct alkaline alcohol fuel cells (DAAFCs) have attracted increasing interest over the past decade because of their favourable reaction kinetics in alkaline media, higher energy densities achievable and the easy handling of the liquid fuels. In this review, principles and mechanisms of DAAFCs in alcohol oxidation and oxygen reduction are discussed. Despite the high energy densities available during the oxidation of polycarbon alcohols they are difficult to oxidise. Apart from methanol, the complete oxidation of other polycarbon alcohols to CO2 has not been achieved with current catalysts. Different types of catalysts, from conventional precious metal catalyst of Pt and Pt alloys to other lower cost Pd, Au and Ag metal catalysts are compared. Non precious metal catalysts, and lanthanum, strontium oxides and perovskite-type oxides are also discussed. Membranes like the ones used as polymer electrolytes and developed for DAAFCs are reviewed. Unlike conventional proton exchange membrane fuel cells, anion exchange membranes are used in present DAAFCs. Fuel cell performance with DAAFCs using different alcohols, catalysts and membranes, as well as operating parameters are summarised. In order to improve the power output of the DAAFCs, further developments in catalysts, membrane materials and fuel cell systems are essential.

A large German research consortium mainly within the Max Planck Society ("MaxSynBio") was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom-up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non-living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.

Apoptosis is an important physiological process crucially involved in development and homeostasis of multicellular organisms. Although the major signaling pathways have been unraveled, a detailed mechanistic understanding of the complex underlying network remains elusive. We have translated here the current knowledge of the molecular mechanisms of the death-receptor-activated caspase cascade into a mathematical model. A reduction down to the apoptotic core machinery enables the application of analytical mathematical methods to evaluate the system behavior within a wide range of parameters. Using parameter values from the literature, the model reveals an unstable status of survival indicating the need for further control. Based on recent publications we tested one additional regulatory mechanism at the level of initiator caspase activation and demonstrated that the resulting system displays desired characteristics such as bistability. In addition, the results from our model studies allowed us to reconcile the fast kinetics of caspase 3 activation observed at the single cell level with the much slower kinetics found at the level of a cell population.

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Abstract The ability to accurately model and simulate chemical processes has been paramount to the growing success and efficiency in process design and operation. These improvements usually come with increasing complexity of the underlying models leading to substantial computational effort in their use. It may also occur that the structure of the model is sometimes unknown making optimization and study difficult. To circumvent these issues, mathematically simpler models, commonly known as surrogate models, have been designed and used to successfully replace these complex, underlying models with much success. This technique has seen increasing use within the chemical process engineering field and this article summarizes some popular surrogates and their recent use in this area.

Robustness, a relative insensitivity to perturbations, is a key characteristic of living cells. However, the specific structural characteristics that are responsible for robust performance are not clear, even in genetic circuits of moderate complexity. Formal sensitivity analysis allows the investigation of robustness and fragility properties of mathematical models representing regulatory networks, but it yields only local properties with respect to a particular choice of parameter values. Here, we show that by systematically investigating the parameter space, more global properties linked to network structure can be derived. Our analysis focuses on the genetic oscillator responsible for generating circadian rhythms in Drosophila as a prototypic dynamical cellular system. Analysis of two mathematical models of moderate complexity shows that the tradeoff between robustness and fragility is largely determined by the regulatory structure. Rank-ordered sensitivities, for instance, allow the correct identification of protein phosphorylation as an influential process determining the oscillator's period. Furthermore, sensitivity analysis confirms the theoretical insight that hierarchical control might be important for achieving robustness. The complex feedback structures encountered in vivo, however, do not seem to enhance robustness per se but confer robust precision and adjustability of the clock while avoiding catastrophic failure.

This article describes the subroutine library SLICOT that provides Fortran 77 implementations of numerical algorithms for computations in systems and control theory. Around a nucleus of basic numerical linear algebra subroutines, this library builds methods for the design and analysis of linear control systems. A brief history of the library is given together with a description of the current version of the library and the on-going activities to complete and improve the library in several aspects. 1 Introduction Systems and control theory are disciplines widely used to describe, control, and optimize industrial and economical processes. There is now a huge amount of theoretical results available which has lead to a variety of methods and algorithms used throughout industry and academia. Although based on theoretical results, these methods often fail when applied to real-life problems, which often tend to be ill-posed or of high dimensions. This failing is frequently due to the lack of...