The computing power unleashed by biomolecule based massively parallel MEK162

The computing power unleashed by biomolecule based massively parallel MEK162 computational units continues to be the focus of many interdisciplinary studies that couple state of the art ideas from mathematical logic theoretical computer science bioengineering and nanotechnology to fulfill some computational task. we discuss the impact of mathematical modeling and simulation in the field of synthetic biology and on computing. The impact of the emergence of gene regulatory networks and the potential of proteins acting as “circuit wires” around the problem of interconnecting molecular computing device subunits is also highlighted. Should computing devices be envisioned as a replacement for the current state of the art silicon based computers? Since the inception of the first DNA based computing device by Leonard Adleman (Adleman 1994 in 1994 many scientific investigations have been carried out and it seems that when it comes to computing “problem-specific” molecular computing devices (MCDs) take precedence over all purpose computing devices. Based on the environment in which the computation takes place MCDs can be broadly classified fallotein into computers (mainly based on DNA RNA proteins hybrid structures or artificial chemistries) and computing devices. As described by Adleman the MCDs that belong to the first category make use of replication of the DNA subunits while computational models that aim at harnessing the whole protein translational machinery of a living cell and employ gene regulation by proteins comprise the second category (Bogunia-Kubik and Sugisaka 2002 Studies in the realm of MCDs have successfully demonstrated individual subunits that can compute both fundamental and moderately complex mathematical problems; however the realization of the truly massively parallel MCD can only be possible when these individual subunits can be efficiently circuited collectively (Sprinzak and Elowitz 2005 Simpson 2004 Making proteins act as MEK162 the information carrying “wire” inside a circuit recent studies (Benenson et al. 2004 Yaakov et al. 2001 Hinze et al. 2008 have brought forth the notion of implementing MCDs like a massively parallel and fully autonomous problem-specific MEK162 automaton. For example the autonomous system as MEK162 explained by Yaakov and co-workers (Yaakov et al. 2001 uses ATP restriction nuclease and ligase as MEK162 the “hardware.” Two times stranded DNA molecules act as the input and the automaton processes the input molecule via a cascade of restriction hybridization and ligation cycles producing a detectable output molecule that encodes the automaton’s final state and thus the computational result. The computing overall performance for an output resulting from five transitions was reported to be on the order of 109 transitions per second. Related work (Benenson et al. 2004 defined a modular sturdy and versatile MCD with the capacity of reasonable evaluation of mRNA disease indications and handled administration of biologically energetic ssDNA substances. The MCD was reported to use at concentrations near 1012 substances per microliter. These and various other studies in books exemplify the rising use of smart diagnostic processing devices in medication delivery genetic anatomist and biochemical sensing (Rinaudo et al. 2007 Bogunia-Kubik and Sugisaka 2002 McDaniel and Weiss 2005 Processing BOOLEAN AND ARITHMETIC Features As opposed to the processing devices talked about above MCDs utilize the normally occurring translational legislation system from the web host organism. Sincesystems need to go through yet another step of proteins translation these are suggested to become implicitly slower than DNA structured MCDs. Nevertheless the use of mistake correction mechanisms normally applied in the evolutionarily optimized transcription legislation equipment of living cells makes the entire computation better quality and therefore justifies the trade-off with quickness (Baker et al. 2006 A recently available theoretical study executed by Cory and Perkins (Cory and Perkins 2008 provides laid the concentrate on the usage of a transcriptional regulatory system to solve simple arithmetic operations. The analysis displays how different parametrizations of a straightforward chemical kinetic style of transcription legislation can provide rise to these different functions. The precision of such theoretical arithmetic computations predicated on the transcription regulatory MEK162 system would depend on the.