Challenges and promises of nano and bio communication networks
ABSTRACT In recent years, the importance of interconnects on top-down engineered lithography-based electronic chips has outrun the importance of transistors as a dominant factor of performance. The major challenges in traditional chips are related to delays of non-scalable global interconnects and reliability in general, which leads to the observation that simple scaling will no longer satisfy performance requirements as feature sizes continue to shrink. In addition, the advent of massive-scale multicore architectures, novel silicon and non-silicon manufacturing techniques (such as self-assembly), and an increasing interest in biological components for computing force us to rethink, re-evaluate, and re-design the communication infrastructure and the communication paradigms in the era of nano- and biotechnology. In this paper we present three showcase applications at the forefront of research of bio and nano communication networks. We focus on (1) the signaling and reliability in synthetic bio-circuits, (2) the pattern formation in distributed synthetic bio-networks, and on unstructured nanowire NOC (3). We provide an interdisciplinary and holistic view of such novel communication systems and highlight future challenges and promises.
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ABSTRACT: One of the elementary processes in morphogenesis is the formation of a spatial pattern of tissue structures, starting from almost homogeneous tissue. It will be shown that relatively simple molecular mechanisms based on auto- and cross catalysis can account for a primary pattern of morphogens to determine pattern formation of the tissue. The theory is based on short range activation, long range inhibition, and a distinction between activator and inhibitor concentrations on one hand, and the densities of their sources on the other. While source density is expected to change slowly, e.g. as an effect of cell differentiation, the concentration of activators and inhibitors can change rapidly to establish the primary pattern; this results from auto- and cross catalytic effects on the sources, spreading by diffusion or other mechanisms, and degradation.Employing an approximative equation, a criterium is derived for models, which lead to a striking pattern, starting from an even distribution of morphogens, and assuming a shallow source gradient. The polarity of the pattern depends on the direction of the source gradient, but can be rather independent of other features of source distribution. Models are proposed which explain size regulation (constant proportion of the parts of the pattern irrespective of total size). Depending on the choice of constants, aperiodic patterns, implying a one-to-one correlation between morphogen concentration and position in the tissue, or nearly periodic patterns can be obtained. The theory can be applied not only to multicellular tissues, but also to intracellular differentiation, e.g. of polar cells.The theory permits various molecular interpretations. One of the simplest models involves bimolecular activation and monomolecular inhibition. Source gradients may be substituted by, or added to, sink gradients, e.g. of degrading enzymes. Inhibitors can be substituted by substances required for, and depleted by activation.Sources may be either synthesizing systems or particulate structures releasing activators and inhibitors.Calculations by computer are presented to exemplify the main features of the theory proposed. The theory is applied to quantitative data on hydra — a suitable one-dimensional model for pattern formation — and is shown to account for activation and inhibition of secondary head formation.Biological Cybernetics 01/1972; 12(1):30-39. · 2.07 Impact Factor
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ABSTRACT: This paper identifies non-stationary effects in grid like Network-on-Chip (NoC) traffic and proposes QuaLe, a novel statistical physics-inspired model, that can account for non-stationarity observed in packet arrival processes. Using a wide set of real application traces, we demonstrate the need for a multi-fractal approach and analyze various packet arrival properties accordingly. As a case study, we show the benefits of our multifractal approach in estimating the probability of missing deadlines in packet scheduling for chip multiprocessors (CMPs).NOCS 2010, Fourth ACM/IEEE International Symposium on Networks-on-Chip, Grenoble, France, May 3-6, 2010; 01/2010
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ABSTRACT: Microbial consortia form when multiple species colocalize and communally generate a function that none is capable of alone. Consortia abound in nature, and their cooperative metabolic activities influence everything from biodiversity in the global food chain to human weight gain. Here, we present an engineered consortium in which the microbial members communicate with each other and exhibit a "consensus" gene expression response. Two colocalized populations of Escherichia coli converse bidirectionally by exchanging acyl-homoserine lactone signals. The consortium generates the gene-expression response if and only if both populations are present at sufficient cell densities. Because neither population can respond without the other's signal, this consensus function can be considered a logical AND gate in which the inputs are cell populations. The microbial consensus consortium operates in diverse growth modes, including in a biofilm, where it sustains its response for several days.Proceedings of the National Academy of Sciences 11/2007; 104(44):17300-4. · 9.74 Impact Factor