• Interdisciplinary Bio Central
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• v.3 no.3
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• pp.10.1-10.8
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• 2011

Introduction: Hash functions are computer algorithms that protect information and secure transactions. In response to the NIST's "International Call for Hash Function", we developed a biological hash function using the computing capabilities of bacteria. We designed a DNA-based XOR logic gate that allows bacterial colonies arranged in a series on an agar plate to perform hash function calculations. Results and Discussion: In order to provide each colony with adequate time to process inputs and perform XOR logic, we designed and successfully demonstrated a system for time-delayed bacterial growth. Our system is based on the diffusion of ${\ss}$-lactamase, resulting in destruction of ampicillin. Our DNA-based XOR logic gate design is based on the op-position of two promoters. Our results showed that $P_{lux}$ and $P_{OmpC}$ functioned as expected individually, but $P_{lux}$ did not behave as expected in the XOR construct. Our data showed that, contrary to literature reports, the $P_{lux}$ promoter is bidirectional. In the absence of the 3OC6 inducer, the LuxR activator can bind to the $P_{lux}$ promoter and induce backwards transcription. Conclusion and Prospects: Our system of time delayed bacterial growth allows for the successive processing of a bacterial hash function, and is expected to have utility in other synthetic biology applications. While testing our DNA-based XOR logic gate, we uncovered a novel function of $P_{lux}$. In the absence of autoinducer 3OC6, LuxR binds to $P_{lux}$ and activates backwards transcription. This result advances basic research and has important implications for the widespread use of the $P_{lux}$ promoter.

• Interdisciplinary Bio Central
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• v.4 no.3
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• pp.10.1-10.12
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• 2012

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

• Proceedings of the KIEE Conference
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• 1997.07a
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• pp.12-14
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• 1997

The analysis of eigenvalue and eigenvector is a crucial procedure for many electromagnetic computation problems. However, eigenpair computation is timing-consuming task. Thus, its parallelization is required for designing large-scale and precision three-dimensional electromagnetic machines. In this paper, the Davidson method is parallelized on a cluster of workstations. Performance of the parallelization scheme is reported. This scheme is applied to a ridged waveguide design problem.

• Journal of Industrial Technology
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• v.17
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• pp.255-260
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• 1997

The analysis of eigenvalue and eigenvector is a crucial procedure for many electromagnetic computation problems. Although it is always the case in practice that only selected eigenpairs are needed, computation of eigenpair still seems to be a time-consuming task. In order to compute the eigenpair more quickly, there are two resorts: one is to select a good algorithm with care and another is to use parallelization technique to improve the speed of the computing. In this paper, one of the best eigensolver, the Davidson method, is parallelized on a cluster of workstations. We apply this scheme to a ridged waveguide design problem and obtain promising linear speedup and scalability.

• Korean Journal of Logic
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• v.9 no.2
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• pp.99-116
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• 2006

There has been several proposals to resolve the gentle murder paradox; Forrester claims that the paradox shows that the deontic closure principle should be abandoned, while Sinnott-Armstrong claims that the paradoxical result arises from the scope ambiguity. However, I shall argue, the gentle murder paradox hinges on the logical structure of adverbial expressions. Although Davidson shows an insightful way of understanding logical structure of adverbs, there has been misunderstandings concerning the nature of his account. Especially what is called neo-Davidsonian event semantics is based upon combination of two fundamentally conflicting ideas. I shall propose a new way of understanding Davidson's account, on the basis of which I continue to give a new diagnosis of the gentle murder paradox.

• Korean Journal of Logic
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• v.16 no.2
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• pp.131-154
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• 2013

Michael Williams, in his paper, rejects the wide-accepted view that Donald Davidson's radical interpretation is a truth conditional account of meaning, and suggests a claim that robust truth in fact does not play any role in Davidson's interpretation and thus interpretation can be in accord with the deflationary theory of truth. In this paper, I will first research the right understanding on the explanatory relations in radical interpretation between truth and meaning, and on that ground, will evaluate the adequacy of Williams' suggestion. My diagnosis is that the acceptability of Williams' idea depends on how we regard the several factors which are crucial for interpretation. Especially I will argue that whether truth condition is regarded as deflationary or inflationary makes difference to the way of understanding radical interpretation, hence the room for taking radical interpretation as deflationary can be in two different ways. Furthermore I will show the same argument can be applied to Williams' another claim that Paul Horwich's use theory of meaning is similar to Davidson's account.

• Bulletin of the Society of Naval Architects of Korea
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• v.4 no.1
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• pp.35-48
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• 1967

• Transactions of the Korean Society of Mechanical Engineers
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• v.19 no.3
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• pp.741-750
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• 1995

The turbulent buoyancy-driven flow in 2-dimensional enclosed cavities heated from the vertical side is numerically calculated for both cases of a Rayleigh number of 5*10$^{10}$ for air and 2.5*10$^{10}$ for water. Three different turbulence models are considered : standard k-.epsilon. model of Ozoe and low-Reynolds-number model of Lam and Bremhorst, and another low-Reynolds-number model of Davidson. The results indicate that the use of low-Reynolds number models is recommended for the indoor airflow computation, and the results from Davidson model are reasonably close to the reported experimental data. A sensitivity study shows that the amounts of wall-heat transfer and the velocity profiles with the Lam and Bremhorst model largely depend on the choice of the wall function for .epsilon..

• Journal of the Korean Chemical Society
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• v.36 no.2
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• pp.329-334
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• 1992

Ultrasonic absorption was measured in bovine serum albumin (BSA) aqueous solution (50 g/l) in the frequency range from 100 kHz to 1600 MHz at neutral pH. Three experimental techniques were used to cover the wide frequency range : plano-concave resonator, conventional Bragg reflection, and high-resolution Bragg reflection methods. The absorption spectrum at neutral pH fitted the relaxation curve well using the distribution function of a mirror image of Davidson-Cole function. The relaxaition behavior was interpreted in terms of various degree of hydration of BSA molecules.

• Proceedings of the Korean Society of Rheology Conference
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• 2001.09a
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• pp.152.5-153
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• 2001

(No abstract, see full-text)