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  • 1. Cho, Kwang-Hyun
    et al.
    Johansson, Karl Henrik
    KTH, School of Electrical Engineering (EES), Automatic Control.
    Wolkenhauer, Olaf
    A hybrid systems framework for cellular processes2005In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 80, no 3, p. 273-282Article in journal (Refereed)
    Abstract [en]

    With the availability of technologies that allow us to obtain stimulus-response time series data for modeling and system identification, there is going to be an increasing need for conceptual frameworks in which to formulate and test hypotheses about intra- and inter-cellular dynamics, in general and not just dependent on a particular cell line, cell type, organism, or technology. While the semantics can be quite different, biologists and systems scientists use in many cases a similar language (notion of feedback, regulation, etc.). A more abstract system-theoretic framework for signals, systems, and control could provide the biologist with an interface between the domains. Apart from recent examples to identify functional elements and describing them in engineering terms, there have been various more abstract developments to describe dynamics at the cell level in the past. This includes Rosen's (M,R)-systems. This paper presents an abstract and general compact mathematical framework of intracellular dynamics, regulation and regime switching inspired by (M,R)-theory and based on hybrid automata.

  • 2. Jian, Xingxing
    et al.
    Zhou, Shengguo
    Zhang, Cheng
    Hua, Qiang
    In silico identification of gene amplification targets based on analysisof production and growth coupling2016In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324Article in journal (Refereed)
  • 3.
    Koski, Timo
    KTH, Superseded Departments, Mathematics.
    Minimizing stochastic complexity using local search and GLA with applications to classification of bacteria2000In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 57, no 1, p. 37-48Article in journal (Refereed)
    Abstract [en]

    In this paper, we compare the performance of two iterative clustering methods when applied to an extensive data set describing strains of the bacterial family Enterobacteriaceae. In both methods, the classification (i.e. the number of classes and the partitioning) is determined by minimizing stochastic complexity. The first method performs the minimization by repeated application of the generalized Lloyd algorithm (GLA). The second method uses an optimization technique known as local search (LS). The method modifies the current solution by making global changes to the class structure and it, then, performs local fine-tuning to find a local optimum. II is observed that if we fix the number of classes, the LS finds a classification with a lower stochastic complexity value than GLA. In addition, the valiance of the solutions is much smaller for the LS due to its more systematic method of searching. Overall, the two algorithms produce similar classifications but they merge cel tain natural classes with microbiological relevance in different ways.

  • 4. Rosen, Gail
    et al.
    Hasler, Paul
    Smith, Mark T.
    KTH, School of Information and Communication Technology (ICT), Communication Systems, CoS.
    Implementation of a Hebbian chemoreceptor model for diffusive source localization2009In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 96, no 3, p. 223-236Article in journal (Refereed)
    Abstract [en]

    While new approaches to chemical localization have been proposed, animals are still widely used for locating landmines and illegal substances. Existing electronic noses still do not have the necessary sensitivity and accuracy. By modeling a cell's chemical detection system, we can gain insight into the basic "olfactory" system. We use an inspiration from chemotaxis and Hebbian learning to enhance localization and tracking of gradient sources, which can be applied to both chemicals and heat. The eukaryotic receptor clustering model shows improvement over previous prokaryotic chemotaxis-inspired methods that do not take into account receptor clustering. Receptor clustering essentially adapts receptors spatio-temporally. For a mobile simulation. our method locates the source in less convergence time than the other chemotaxis algorithms and insignificantly less time compared to no spatio-temporal filtering (e.g. a single-sensor memoryless case). We then show that local regions of receptor cooperation have the best performance reflecting observations of receptor behavior in biology. To demonstrate the performance of this system in real-time, a stationary 4/8-sensor version of the array is implemented, and the algorithm improves the convergence time, mean, and variance of the Direction-of-Arrival calculation in diffusive, turbulent, and noisy environments.

  • 5. Århem, Peter
    et al.
    Blomberg, Clas
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Ion channel density and threshold dynamics of repetitive firing in a cortical neuron model2007In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 89, no 1-3, p. 117-125Article in journal (Refereed)
    Abstract [en]

    Modifying the density and distribution of ion channels in a neuron (by natural up- and down-regulation, by pharmacological intervention or by spontaneous mutations) changes its activity pattern. In the present investigation, we analyze how the impulse patterns are regulated by the density of voltage-gated channels in a model neuron, based on voltage clamp measurements of hippocampal interneurons. At least three distinct oscillatory patterns, associated with three distinct regions in the Na-K channel density plane, were found. A stability analysis showed that the different regions are characterized by saddle-node, double-orbit, and Hopf bifurcation threshold dynamics, respectively. Single strongly graded action potentials occur in an area outside the oscillatory regions, but less graded action potentials occur together with repetitive firing over a considerable range of channel densities. The presently found relationship between channel densities and oscillatory behavior may be relevance for understanding principal spiking patterns of cortical neurons (regular firing and fast spiking). It may also be of relevance for understanding the action of pharmacological compounds on brain oscillatory activity.

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