From Reconfigurability to Evolution in Construction Systems: Spanning the Electronic, Microfluidic and Biomolecular Domains

McCaskill, John S.; Wagler, Patrick F.

doi:10.1007/3-540-44614-1_32

Cited by 13 publications

(9 citation statements)

References 25 publications

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“…The main advantage is in the light programmable, integrated system (operating under steady flow) with no problem dependent pipetting steps. Future reactor configurations can be made re-configurable with evolving DNA-populations to obtain a universal programmable DNA-computer [13].…”

Section: Resultsmentioning

confidence: 99%

<title>DNA computing in microreactors</title>

Wagler¹,

Noort

McCaskill³

2001

BioMEMS and Smart Nanostructures

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Abstract. The goal of this research is to improve the programmability of DNA-based computers. Novel clockable microreactors can be connected in various ways to solve combinatorial optimisation problems, such as Maximum Clique or 3-SAT. This work demonstrates by construction how one micro-reactor design can be programmed optically to solve any instance of Maximum Clique up to its given maximum size (N ). It reports on an implementation of the concept proposed previously [1]. The advantage of this design is that it is generically programmable. This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. Presently, in ongoing research, we are solving a graph for the Maximum Clique problem with N = 6 nodes and have completed the design of a microreactor for N = 20. Furthermore, the design of the DNA solution space will be presented, with solutions encoded in customised word-structured sequences.

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Section: Resultsmentioning

confidence: 99%

<title>DNA computing in microreactors</title>

Wagler¹,

Noort

McCaskill³

2001

BioMEMS and Smart Nanostructures

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“…Whereas natural cells ultimately employ genomic information to regulate the resulting material production network, we envision programmable electronic control by embedding chemtainers into mechanoelectronic microsystems [19,20]. In such devices, dedicated microfluidic channels can be designed for vesicle generation [21], DNA tag insertion, tag and chemtainer trafficking [22], specific or unspecific fusion [23], vesicle rapture and encapsulation [24].…”

Section: Introductionmentioning

confidence: 99%

Programming chemistry in DNA-addressable bioreactors

Fellermann

Cardelli

2014

J. R. Soc. Interface.

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We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by stateof-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis.

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“…[9,10] Through operational feedback and multiple reconfiguration, they can also be iteratively optimised in an evolutionary process. [11] and analysis of the current status inside the microreactor network and enables the dynamic programming of the biosystem using microelectrodes and intelligent feed-back loops. This new approach results in reconfigurable hybrid architectures based on coupled electronic and biomolecular information processing.…”

Section: Introductionmentioning

confidence: 99%

Molecular systems on-chip (MSoC) steps forward for programmable biosystems

Wagler¹,

Tangen²,

Maeke³

et al. 2004

SPIE Proceedings

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This work describes online programmable microfluidic bioprocessing units using digital logic microelectrodes for rapid pipelined translocation of DNA molecules and other charged biopolymers as well as nanoparticles. Fundamentals of the design and fabrication technique both the silicon-PDMS and a polyimide-PDMS based construction (a new method based on conventional printed circuit board materials) of these electronic microfluidic devices and their functions are described as well as the experimental results along with the first proof of principle functionality. The electronically controlled collection, separation and channel transfer of the biomolecules and nanosized beads are monitored by a sensitive fluorescence setup and controlled by a custom-designed hardware for camera-control and feature selection. This hybrid reconfigurable architecture couples electronic and biomolecular information processing via a single module combination of fluidics and electronics and opens new fields of applications not only in DNA computing and molecular diagnostics but also in applications of combinatorial chemistry and lab-on-a-chip biotechnology to the drug discovery process.

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From Reconfigurability to Evolution in Construction Systems: Spanning the Electronic, Microfluidic and Biomolecular Domains

Cited by 13 publications

References 25 publications

<title>DNA computing in microreactors</title>

<title>DNA computing in microreactors</title>

Programming chemistry in DNA-addressable bioreactors

Molecular systems on-chip (MSoC) steps forward for programmable biosystems

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