State transitions by molecules

Sakamoto, Kensaku; Kiga, Daisuke; Komiya, Ken; Gouzu, Hidetaka; Yokoyama, Shigeyuki; Ikeda, Shuji; Sugiyama, Hiroshi; Hagiya, Masami

doi:10.1016/s0303-2647(99)00035-0

Cited by 99 publications

(60 citation statements)

References 11 publications

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“…The above approach differs in the type of programming from previous experimental approaches to DNA computing in vitro (Adleman, 1994;Guarnieri et al, 1996;Sakamoto et al, 1999;Ouyang et al, 1997;Liu et al, 2000;Faulhammer et al, 2000) and in vivo (Khodor and Gifford, 1999). Instead of programming by a manual series of biochemical pipetting operations, the entire fluid flow is held constant and a single light pattern determines the program.…”

Section: Discussionmentioning

confidence: 99%

Optically programming DNA computing in microflow reactors

McCaskill¹

2001

Biosystems

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The programmability and the integration of biochemical processing protocols are addressed for DNA computing using photochemical and microsystem techniques. A magnetically switchable selective transfer module (STM) is presented which implements the basic sequence-specific DNA filtering operation under constant flow. Secondly, a single steady flow system of STMs is presented which solves an arbitrary instance of the maximal clique problem of given maximum size N. Values of N up to about 100 should be achievable with current lithographic techniques. The specific problem is encoded in an initial labeling pattern of each module with one of 2N DNA oligonucleotides, identical for all instances of maximal clique. Thirdly, a method for optically programming the DNA labeling process via photochemical lithography is proposed, allowing different problem instances to be specified. No hydrodynamic switching of flows is required during operation -the STMs are synchronously clocked by an external magnet. An experimental implementation of this architecture is under construction and will be reported elsewhere.

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Section: Discussionmentioning

confidence: 99%

Optically programming DNA computing in microflow reactors

McCaskill¹

2001

Biosystems

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“…For this, we need to design a biomolecular device, where multiple copies of the same or distinct devices can simultaneously compute without interfering with each other. These needs can be satisfied by a number of known biomolecular computing device designs including tiling assemblies (Winfree, 1998a), Whiplash PCR machines (Sakamoto et al, 1999) and hybridization chain reactions (Dirks and Pierce, 2004).…”

Section: The Challenges Of a Molecular Implementation Of Process Algebramentioning

confidence: 99%

“…Whiplash PCR (WPCR) machines (Sakamoto et al, 1999) appear to be an ideal candidate for a molecular implementation of process algebra. Recall that WPCR machines are DNA devices composed of a single strand of DNA containing a distinct program (via segments of the DNA that encode computational rewrite rules) and a current state (via a short segment at the 3 end of the strand).…”

Section: Implementation Of a Molecular Process Algebraic System Via Mmentioning

confidence: 99%

“…The concept of WPCR machines was introduced by Hagiya et al (Sakamoto et al, 1999) in 1997. Winfree was the first to coin the name of Whiplash PCR machines for these biomolecular state transitioning systems and adopt it to a wider range of problems (Winfree, 1998b).…”

Section: Previous Work On Molecular Computers Capable Of Executing Prmentioning

confidence: 99%

“…We addressed that issue in an earlier paper (Reif and Majumder, 2008) that provided an isothermal design, but this involved a rather complicated construction. Hence, in this paper, for simplicity, we adapt the design methodology of the original WPCR machines (Sakamoto et al, 1999) for the molecular implementation of process algebra.…”

Section: Previous Work On Molecular Computers Capable Of Executing Prmentioning

confidence: 99%

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Design of a Biomolecular Device That Executes Process Algebra

Majumder

Reif

2009

Lecture Notes in Computer Science

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Process algebras are widely used for defining the formal semantics of concurrent communicating processes. This paper considers stochastic π-calculus which is a particularly expressive kind of process algebra providing a specification of probabilities of process behavior such as stochastic delays, communication and branching, as well as rates of execution. In this paper, we implement stochastic π-calculus at the molecular scale, providing a design for a DNA-based biomolecular device that executes the stochastic π-calculus. Designing this device is challenging due to the requirement that a specific pair of processes must be able to communicate repeatedly; this appears to rule out the use of many of the usual classes of DNA computation (e.g., tiling selfassembly or hybridization chain reactions) that allow computational rule molecules to float freely in solution within a test tube. Our design of the molecular stochastic π-calculus system makes use of a modified form of Whiplash-PCR (WPCR) machines.In our machine which we call π-WPCR machine, we connect (via a tethering DNA nanostructure) a number of DNA strands, each of which corresponds to a π-WPCR

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Immobilization of Biomolecules on Mesoporous Structured Materials

Vinu

Gokulakrishnan

Mori

et al. 2007

Bio‐inorganic Hybrid Nanomaterials

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Various functional systems have been developed using artificially constructed structures and synthesized compounds, and the nanotechnology based on them has recently received much attention. However, current nanoscale technologies are still highly inferior to those seen in natural systems. The efficiency of the energy conversion that occurs in mitochondrial and photosynthetic systems far exceeds that obtained in artificial systems. A dog can smell and a bat can hear far more sensitively than most artificial sensors. The information processing exhibited by the brain and nervous systems is much more sophisticated than that exhibited by current computers. Nature developed superior nanotechnologies to our own several billion years ago. Therefore, the use of biomaterials for the development of various functional systems can be a very practical approach to reaching several goals in current nanotechnologies.Unfortunately, biomolecules in most cases give their best performance under ambient conditions and are not mechanically and thermally strong enough to be used in harsh conditions. In order to overcome such difficulties, hybridization of biomolecules with supporting materials such as lipid assemblies, polymers and inorganic materials has been proposed to attain both biological functions and mechanical stability . Biomolecules are frequently immobilized on silica supports through a sol-gel process. As advanced silica structures, mesoporous silica molecular sieves and related materials have received much attention as inorganic supports for biomolecules [31][32][33][34][35][36][37][38][39][40]. Mesoporous silica materials are chemically and mechanically stable and resistant to microbial attack. In addition, chemical modification to introduce organic functional groups to the inner silica pore wall is highly possible. Outstanding properties of the mesoporous structure also lie in their high specific surface area and huge specific pore volume, which are definitely advantageous for the efficient accommodation of biomolecules. In addition, the narrow pore size distribution could provide reliable immobilization of biomolecules. According to the j113 Bio-inorganic Hybrid Nanomaterials. Edited

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State transitions by molecules

Cited by 99 publications

References 11 publications

Optically programming DNA computing in microflow reactors

Optically programming DNA computing in microflow reactors

Design of a Biomolecular Device That Executes Process Algebra

Immobilization of Biomolecules on Mesoporous Structured Materials

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