Feynman Lectures on Computation

Feynman, Richard P.; Hey, A J G; Allen, Robin W.

doi:10.1201/9780429500442

Cited by 274 publications

(210 citation statements)

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“…The model has been analyzed from the perspective of non-equilibrium statistical physics. A single RNAP operates as a "tape-copying Turing machine" [45][46][47]; a Turing machine [48] is an ide-alized device conceptualized for abstract 'computation' [49]. Therefore, the general theoretical framework developed here may be of interest also in the theory of computation.…”

Section: Discussionmentioning

confidence: 99%

Biologically motivated asymmetric exclusion process: Interplay of congestion in RNA polymerase traffic and slippage of nascent transcript

et al. 2019

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We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice repesents a DNA strand while each of the particles that hop on it unidirectionally, from site to site, represents a RNA polymerase (RNAP). While walking like a molecular motor along a DNA track in a step-by-step manner, a RNAP simultaneously synthesizes a RNA chain; in each forward step it elongates the nascent RNA molecule by one unit, using the DNA track also as the template. At some special "slippery" position on the DNA, which we represent as a defect on the lattice, a RNAP can lose its grip on the nascent RNA and the latter's consequent slippage results in a final product that is either longer or shorter than the corresponding DNA template. We develope an exclusion model for RNAP traffic where the kinetics of the system at the defect site captures key features of TS events. We demonstrate the interplay of the crowding of RNAPs and TS. A RNAP has to wait at the defect site for longer period in a more congested RNAP traffic, thereby increasing the likelihood of its suffering a larger number of TS events. The qualitative trends of some of our results for a simple special case of our model are consistent with experimental observations. The general theoretical framework presented here will be useful for guiding future experimental queries and for analysis of the experimental data with more detailed versions of the same model.

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Section: Discussionmentioning

confidence: 99%

Biologically motivated asymmetric exclusion process: Interplay of congestion in RNA polymerase traffic and slippage of nascent transcript

et al. 2019

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“…While CMOS fabrication will soon hit a wall due to a combination of economic and technical factors, 1 we are nowhere near the theoretical limits of physical computation [17]. In order to achieve these limits at room temperature we must work in the nanoscale regime, which currently involves various technologies that exploit the quantum-mechanical effects of small devices.…”

Section: Electronic Nanotechnologymentioning

confidence: 99%

NanoFabrics: spatial computing using molecular electronics

Goldstein¹,

Budiu²

Proceedings 28th Annual International Symposium on Computer Architecture

229

217

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The continuation of the remarkable exponential increases in processing power over the recent past faces imminent challenges due in part to the physics of deep-submicron CMOS devices and the costs of both chip masks and future fabrication plants. A promising solution to these problems is offered by an alternative to CMOS-based computing, chemically assembled electronic nanotechnology (CAEN).In this paper we outline how CAEN-based computing can become a reality. We briefly describe recent work in CAEN and how CAEN will affect computer architecture. We show how the inherently reconfigurable nature of CAEN devices can be exploited to provide high-density chips with defect tolerance at significantly reduced manufacturing costs. We develop a layered abstract architecture for CAEN-based computing devices and we present preliminary results which indicate that such devices will be competitive with CMOS circuits.

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“…What is folded is affected by various environmental factors including transcription rate. Polymerases have their own transcription rate: e.g., bacteriophage 3ms/nucleotide (nt) and eukaryote 200ms/nt [14] (less energy would be dissipated at slower transcription [8]). Changing the natural transcription rate, by adjusting, e.g., NTP concentration [19], can impair cotranscriptional processes [2,15] (note that polymerase pausing can also facilitate efficient folding [24] but it is rather a matter of gene design).…”

Section: Introductionmentioning

confidence: 99%

Know When to Fold ’Em: Self-assembly of Shapes by Folding in Oritatami

Demaine

Hendricks

Olsen

et al. 2018

Lecture Notes in Computer Science

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These results serve as a foundation for the study of shape-building in this new model of self-assembly, and have the potential to provide better understanding of cotranscriptional folding in biology, as well as improved abilities of experimentalists to design artificial systems that self-assemble via this complex dynamical process.Note that in [13] in the present proceedings, the authors study a slightly different problem: they show that one can design an oritatami transcript that folds an upscaled version of a non-self-intersecting path (instead of a shape). The initial path may come from the triangular grid or from the square grid. The scale of the resulting path is somewhere in between our scales 3 and 4 according to our definition. Note that the cells are only partially covered by their scheme. Combining their result with our theorem 3, their algorithm provides an oritatami transcript partially covering the upscaled version of any shape at scale 6.

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Feynman Lectures on Computation

Cited by 274 publications

References 0 publications

Biologically motivated asymmetric exclusion process: Interplay of congestion in RNA polymerase traffic and slippage of nascent transcript

Biologically motivated asymmetric exclusion process: Interplay of congestion in RNA polymerase traffic and slippage of nascent transcript

NanoFabrics: spatial computing using molecular electronics

Know When to Fold ’Em: Self-assembly of Shapes by Folding in Oritatami

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