Zoltan A. Tuza

An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system

In this paper, we develop an experimentally validated MATLAB software toolbox as an accompaniment to an in vitro cell-free biomolecular “breadboard” system. The toolbox gives insight into the dynamics of unmeasured states in the cell-free system, accounting especially for resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid ill-conditioning. The toolbox provides a general framework for experiment planning and predictive modeling for synthetic biomolecular circuits in cell-free systems, accelerating our capacity to rationally design circuits from well characterized parts.

COMPUTING ALL SPARSE KINETIC STRUCTURES FOR A LORENZ SYSTEM USING OPTIMIZATION

In this paper, all possible sparse chemical reaction network structures of a classical 3-dimensional Lorenz system are computed assuming a given chemical complex set. The original non-kinetic equations are transformed into kinetic form using two different approaches: firstly, using a state-dependent time-rescaling and secondly, by applying the theory of X-factorable systems. Using the notions of core reactions and core complexes, an effective optimization-based computation approach is proposed for the calculation of all structurally different sparse reaction graphs. The resulting structures are briefly analyzed and compared from a structural point of view.

Using LMS-100 laser rangefinder for indoor metric map building

The design and implementation of a scan matching based map building method is described in this paper. The brand new LMS-100 laser rangefinder was used and evaluated for point measurement and metric map building. The official driver of the rangefinder was migrated to Linux in order to be integrated into the applied software framework. The measurement results were compared to data obtained by the widely used LMS-200 device. Both sensors were mounted on a commercially available PowerBot differentially driven mobile robot. It is shown that for indoor robotic applications, the LMS-100 is similarly well-usable to the LMS-200 with significant advantages in compactness and power consumption. Furthermore, from a map-building point of view, the LMS-100 performs better in dense environments with obstacles having complex reflective surfaces.

Developing an integrated software environment for mobile robot navigation and control

A flexible modular robotic software environment based on the popular MRPT toolkit is reported in this paper that is able to integrate path planning, navigation and control algorithms easily from several sources. The different modules (which are responsible for SLAM, trajectory tracking, sensor and actuator handling, visualization etc.) communicate with each other via a carefully developed network based protocol set that ensures transparency and robust operation. The system can also be used as a simulation environment and it is capable of comparative benchmarking of different navigation algorithms. Laser scanner based map building and navigation of an autonomous wheelchair is shown as application examples to illustrate the features of the developed software environment.

Computing all possible graph structures describing linearly conjugate realizations of kinetic systems

In this paper an algorithm is given to determine all possible structurally different linearly conjugate realizations of a given kinetic polynomial system. The solution is based on the iterative search for constrained dense realizations using linear programming. Since there might exist exponentially many different reaction graph structures, we cannot expect to have a polynomial-time algorithm, but we can organize the computation in such a way that polynomial time is elapsed between displaying any two consecutive realizations. The correctness of the algorithm is proved, and possibilities of a parallel implementation are discussed. The operation of the method is shown on two illustrative examples.

A resource dependent protein synthesis model for evaluating synthetic circuits

Reliable in silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow Model and among other things describes the movement of RNA-polymerase and ribosomes on mRNA and DNA templates, respectively. By analyzing the convergence properties of this model based upon geometric considerations, we present additional insights into the dynamic mechanisms of the process of protein synthesis. Further, we demonstrate how this model can be used to evaluate the performance of synthetic gene circuits under different loading scenarios.

Resource usage and gene circuit performance characterization in a cell-free breadboard

The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as the complexity of synthetic circuits increases, the benefits—in cost savings and design cycle time—of a more traditional engineering approach can be significant. We have recently developed an in vitro ‘breadboard’ prototyping platform based on E. coli cell extract that allows biocircuits to operate in an environment considerably simpler than but functionally similar to in vivo. The simplicity of the cell-free transcription-translation breadboard makes it a promising tool for rapid biocircuit design and testing, as well as for probing the fundamentals of gene circuit functions that are normally masked by cellular complexity. In this work we characterize the cell-free breadboard using real-time and simultaneous measurements of transcriptional and translational activities of a small set of reporter genes and a transcriptional activation cascade. We determine the effects of promoter strength, gene and nucleoside triphosphate concentrations on biocircuits properties, and we isolate contributions of the essential components—core RNA polymerase, housekeeping sigma factor, and ribosomes—to overall performance. Importantly, we show how limits on essential resources, particularly those involved in translation steps, manifest themselves in the form of reduced expression in the presence of orthogonal genes as load processes.

Determining biochemical reaction network structures for kinetic polynomial models with uncertain coefficients

A numerical method is proposed in this paper for the computation of dense and sparse reaction network structures for kinetic polynomial models with uncertain parameters represented as intervals. The problem is traced back to mixed integer linear programming.

Computing core reactions of uncertain polynomial kinetic systems

Kinetic systems form a wide nonlinear system class with good descriptive power that can efficiently be used for the dynamical modeling of non-negative models emerging not only in (bio)chemistry but in other important scientific and engineering fields as well. The directed graph structure assigned to kinetic models give us important information about the qualitative dynamical properties of the system. In this paper we extend the previous results for computing structurally invariant directed edges (called core reactions) for uncertain kinetic polynomial models, where the uncertainty is represented as a multi-dimensional interval in the space of monomial coefficients. We show that the computation can be put into the framework of linear programming. Using illustrative examples we demonstrate the properties of the computed structures and the potential application of the method in the support of structural identification of biochemical networks.

Analysis-based parameter estimation of an in vitro transcription-translation system

Recent advances in measurement technology provide us with rich source of data for estimating parameters in biomolecular circuit models, particularly in simplified in vitro transcription-translation systems, so-called molecular “bread-boards”. In this paper, we elaborate on a mass action type dynamic model for such an in vitro system and detail a parameter estimation procedure that may be used with time series data containing information about both transcriptional and translational stages of gene expression. The identification process is supported by structural identifiability analysis to ensure proper model structure. Statistical analysis and validation of the estimated parameter set help us to understand the characteristics of point estimation results.