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ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Computational Synthetic Biology and Regular Papers, Volume 11 Issue 3, December 2014



Section: Special Issue on Computational Synthetic Biology

Introduction to the Special Issue on Computational Synthetic Biology
Chris J. Myers, Herbert Sauro, Anil Wipat
Article No.: 20
DOI: 10.1145/2668126

The goal of this special issue is to introduce the field of computational synthetic biology to engineers and computer scientists. The first article gives an introduction to the key biological principles and experimental techniques that support...

Parallel Networks: Synthetic Biology and Artificial Intelligence
Tara L. Deans
Article No.: 21
DOI: 10.1145/2667229

Synthetic biology has emerged as an important technology for engineering cells to behave in controllable and predictable ways. The promise of this modern technology is dependent on our understanding of cellular complexity to allow us to engineer...

Composable Modular Models for Synthetic Biology
Goksel Misirli, Jennifer Hallinan, Anil Wipat
Article No.: 22
DOI: 10.1145/2631921

Modelling and computational simulation are crucial for the large-scale engineering of biological circuits since they allow the system under design to be simulated prior to implementation in vivo. To support automated, model-driven design it...

Stochastic Model Checking of Genetic Circuits
Curtis Madsen, Zhen Zhang, Nicholas Roehner, Chris Winstead, Chris Myers
Article No.: 23
DOI: 10.1145/2644817

Synthetic genetic circuits have a number of exciting potential applications such as cleaning up toxic waste, hunting and killing tumor cells, and producing drugs and bio-fuels more efficiently. When designing and analyzing genetic circuits,...

Formalizing Modularization and Data Hiding in Synthetic Biology
Harold Fellermann, Maik Hadorn, Rudolf M. Füchslin, Natalio Krasnogor
Article No.: 24
DOI: 10.1145/2667231

Biological systems employ compartmentalization and other co-localization strategies in order to orchestrate a multitude of biochemical processes by simultaneously enabling “data hiding” and modularization. This article presents recent...

A Rule-Based Design Specification Language for Synthetic Biology
Ernst Oberortner, Swapnil Bhatia, Erik Lindgren, Douglas Densmore
Article No.: 25
DOI: 10.1145/2641571

Synthetic Biology is an engineering discipline where parts of DNA sequences are composed into novel, complex systems that execute a desired biological function. Functioning and well-behaving biological systems adhere to a certain set of biological...

Fluigi: Microfluidic Device Synthesis for Synthetic Biology
Haiyao Huang, Douglas Densmore
Article No.: 26
DOI: 10.1145/2660773

One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications. Our incomplete knowledge of the effects of metabolic load and biological “crosstalk” on the host cell make it difficult...

Section: Special Issue on Computational Synthetic Biology

RIMEP2: Evolutionary Design of Reversible Digital Circuits
Fatima Zohra Hadjam, Claudio Moraga
Article No.: 27
DOI: 10.1145/2629534

RIMEP (Reversible Improved Multi Expression Programming), is a system that has been developed for designing reversible digital circuits. This article discloses a new version of RIMEP called “RIMEP2”. The goal was to evolve reversible...

Decomposition of Diagonal Hermitian Quantum Gates Using Multiple-Controlled Pauli Z Gates
Mahboobeh Houshmand, Morteza Saheb Zamani, Mehdi Sedighi, Mona Arabzadeh
Article No.: 28
DOI: 10.1145/2629526

Quantum logic decomposition refers to decomposing a given quantum gate to a set of physically implementable gates. An approach has been presented to decompose arbitrary diagonal quantum gates to a set of multiplexed-rotation gates around z...

A Synthesis Algorithm for 4-Bit Reversible Logic Circuits with Minimum Quantum Cost
Zhiqiang Li, Hanwu Chen, Xiaoyu Song, Marek Perkowski
Article No.: 29
DOI: 10.1145/2629542

This article presents an algorithm which can quickly find the exact minimum solution to almost all of 4-bit reversible functions. We assume minimization of quantum cost (MQC). This algorithm is designed in the most memory-efficient way, or it will...

Realizing Reversible Computing in QCA Framework Resulting in Efficient Design of Testable ALU
Bibhash Sen, Manojit Dutta, Samik Some, Biplab K. Sikdar
Article No.: 30
DOI: 10.1145/2629538

Reversible logic is emerging as a prospective logic design style for implementing ultra-low-power VLSI circuits. It promises low-power consuming circuits by nullifying the energy dissipation in irreversible logic. On the other hand, as a potential...

An Algorithm for Quantum Template Matching
Md. Mazder Rahman, Gerhard W. Dueck, Joseph D. Horton
Article No.: 31
DOI: 10.1145/2629537

Quantum circuits are often generated by decomposing gates from networks with classical reversible gates. Only in rare cases, the results are minimal. Post-optimization methods, such as template matching, are employed to reduce the quantum costs of...