RNA is a chain of ribonucleotides of four kinds (denoted respectively by the letters A, C, G, U). While being synthesized sequentially from its template dna (transcription), it folds upon itself into intricate higher-...
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ISBN:
(纸本)9783030248857;9783030248864
RNA is a chain of ribonucleotides of four kinds (denoted respectively by the letters A, C, G, U). While being synthesized sequentially from its template dna (transcription), it folds upon itself into intricate higher-dimensional structures in such a way that the free energy is minimized, that is, the more hydrogen bonds between ribonucletoides or larger entropy a structure has, the more likely it is chosen, and furthermore the minimization is done locally. This phenomenon is called cotranscriptional folding (CF). It has turned out to play significant roles in in-vivo computation throughout experiments and recently proven even programmable artificially so as to self-assemble a specific RNA rectangular tile structure in vitro. The next step is to program a computation onto dna in such a way that the computation can be "called" by cotranscriptional folding. In this novel paradigm of computation, what programmers could do is only twofold: designing a template dna and setting environmental parameters. Oritatami is an introductory "toy" model to this paradigm of computation. In this model, programmars are also allowed to employ an arbitrarily large finite alphabet Sigma as well as an arbitrarily complex rule set for binding over Sigma x Sigma. We shall present known architectures of computing in the oritatami model from a simple half-adder to Turing machine along with several programming techniques of use, with hope that they will inspire in-vivo architectures of CF-driven self-assemblable computers, which could be even heritable.
Dynamics dna nanotechnology is currently the most common method for designing molecular circuits, referred to as dna circuits, which can process complex information by utilizing dna strands as information molecules. H...
Dynamics dna nanotechnology is currently the most common method for designing molecular circuits, referred to as dna circuits, which can process complex information by utilizing dna strands as information molecules. However, dna circuits are highly retroactive, that is, they have low modularity, which is a significant limitation in rational circuit design in the field of dnacomputing. A common issue is the significant decrease in the input signal applied to the circuit, which causes serious errors in arithmetic circuits, where fluctuations in the input levels can result in incorrect outcomes. Currently, there is no dna signal generator that can produce a constant input. In this study, we developed a practical design for a constant-signal generator based on a dna strand displacement mechanism to address the issue of decreasing input signals caused by low modularity in dna circuits. Notably, the proposed constant-signal generator had low retroactivity and was therefore highly independent, enabling the maintenance of the desired performance even when dna circuits were connected as loads.
The advent of virtualization technologies and cloud computing has improved application provisioning speed, resource utilization, fault-management, availability using auto-failover and performance optimization using au...
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The advent of virtualization technologies and cloud computing has improved application provisioning speed, resource utilization, fault-management, availability using auto-failover and performance optimization using auto-scaling in distributed computing environments. However, heterogeneous virtualization technologies offered by different service providers with disparate infrastructure and their orchestration and management systems have also increased the complexity of managing distributed applications and vendor lock-in. In this paper we utilize new computing, management and programming models introduced using the DIME network architecture to provide end to end service visibility and control across distributed physical or virtual infrastructure. Resulting decoupling of application and service transaction management from myriad distributed infrastructure management systems at run-time enables policy based, secure, service mobility across physical servers or virtual machines deployed in data enters or public clouds. Using the new architecture we have implemented service self-repair, auto-scaling, live-migration and end-to-end service transaction security independent of server and network security mechanisms.
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