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Zhen Zhang
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Articles
Conference Papers
Articles
(18)
Article
STAMINA 2.0: Improving Scalability of Infinite-State Stochastic Model Checking
Lecture Notes in Computer Science (2022)
Riley Roberts, Thakur Neupane, Lukas Buecherl, Chris J. Myers, et al.
Stochastic model checking (SMC) is a formal verification technique for the analysis of systems with probabilistic behavior. Scalability has been ...
Article
Scaling Up Livelock Verification for Network-on-Chip Routing Algorithms
Lecture Notes in Computer Science (2022)
Landon Taylor and Zhen Zhang
As an efficient interconnection network, Network-on-Chip (NoC) provides significant flexibility for increasingly prevalent many-core systems. It is desirable to deploy ...
Article
Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA
ACS Synthetic Biology (2021)
Lukas Buecherl, Riley Roberts, Pedro Fontanarrosa, Payton J. Thomas, et al.
In synthetic biology, combinational circuits are used to program cells for various new applications like biosensors, drug delivery systems, and ...
Article
Probabilistic Verification for Reliability of a Two-by-Two Network-on-Chip System
Lecture Notes in Computer Science (2021)
Riley Roberts, Benjamin Lewis, Arnd Hartmanns, Prabal Basu, et al.
Modern network-on-chip (NoC) systems face reliability issues due to process and environmental variations. The power supply noise (PSN) in the ...
Article
A Computational Metabolic Model for Engineered Production of Resveratrol in ...
ACS Synthetic Biology (2021)
Michael Cotner, Jixun Zhan and Zhen Zhang
Although engineered microbial production of natural compounds provides a promising alternative method to plant production and extraction, the process can ...
Article
Probabilistic Verification for Reliable Network-on-Chip System Design
Lecture Notes in Computer Science (2019)
Benjamin Lewis, Arnd Hartmanns, Prabal Basu, Rajesh Jayashankara Shridevi, et al.
The design of modern network-on-chip (NoC) systems faces reliability challenges due to process and environmental variations. Peak power supply noise ...
Article
STAMINA: Stochastic Approximate Model-Checker for Infinite-State Analysis
Lecture Notes in Computer Science (2019)
Thackur Neupane, Chris J. Myers, Curtis Madsen, Hao Zheng, et al.
Stochastic model checking is a technique for analyzing systems that possess probabilistic characteristics. However, its scalability is limited as probabilistic ...
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Article
Synthetic Biology Open Language (SBOL) Version 2.3
Journal of Integrative Bioinformatics (2019)
Curtis Madsen, Angel Goñi Moreno, Umesh P, Zachary Palchick, et al.
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to ...
Article
Approximation Techniques for Stochastic Analysis of Biological Systems
Automated Reasoning for Systems Biology and Medicine (2019)
Thakur Neupane, Zhen Zhang, Curtis Madsen, Hao Zheng, et al.
There has been an increasing demand for formal methods in the design process of safety-critical synthetic genetic circuits. Probabilistic model ...
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Article
IBIOSIM 3: A Tool for Model-Based Genetic Circuit Design
ACS Synthetic Biology (2018)
Leandro Watanabe, Tramy Nguyen, Michael Zhang, Zach Zundel, et al.
The iBioSim tool has been developed to facilitate the design of genetic circuits via a model-based design strategy. This paper ...
Article
A Validator and Converter for the Synthetic Biology Open Language
ACS Synthetic Biology (2016)
Zach Zundel, Meher Samineni, Zhen Zhang and Chris J. Myers
This paper presents a new validation and conversion utility for the Synthetic Biology Open Language (SBOL). This utility can be ...
Article
Sharing Structure and Function in Biological Desing with SBOL 2 ...
ACS Synthetic Biology (2016)
Nicholas Roehner, Jacob Beal, Kevin Clancy, Bryan Bartley, et al.
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and ...
Article
An improved fault-tolerant routing algorithm for a Network-on-Chip derived with ...
Science of Computer Programming (2016)
Zhen Zhang, Wendelin Serwe, Jian Wu, Tomohiro Yoneda, et al.
A fault-tolerant routing algorithm in Network-on-Chip (NoC) architectures provides adaptivity for on-chip communications. Adding fault-tolerance adaptivity to a routing algorithm ...
Article
libSBOLj 2.0: A Java Library to Support SBOL 2 ...
IEEE Life Science Letters (2015)
Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Goksel Misirli, et al.
The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL ...
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Article
Generating Systems Biology Markup Language Models from the Synthetic Biology ...
ACS Synthetic Biology (2015)
Nicholas Roehner, Zhen Zhang, Tramy Nguyen and Chris J. Myers
In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. ...
Article
Synthetic Biology Open Language (SBOL) Version 2.0.0
Journal of Integrative Bioinformatics (2015)
Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, et al.
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to ...
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Article
Stochastic Model Checking of Genetic Circuits
ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Computational Synthetic Biology and Regular Papers (2014)
Curtis Madsen, Zhen Zhang, Nicholas Roehner, Chris Winstead, et al.
Synthetic genetic circuits have a number of exciting potential applications such as cleaning up toxic waste, hunting and killing tumor ...
Article
Compositional Model Checking of Concurrent Systems
IEEE Transactions on Computers (2014)
Hao Zheng, Zhen Zhang, Chris J. Myers, Emmanuel Rodriguez, et al.
This paper presents a compositional framework to address the state explosion problem in model checking of concurrent systems. This framework ...
Conference Papers
(4)
Article
Formal Analysis of a Fault-Tolerant Routing Algorithm for a Network-on-Chip
Formal Methods for Industrial Critical System (2014)
Zhen Zhang, Wendeling Serwe, Jian Wu, Tomohiro Yoneda, et al.
A fault-tolerant routing algorithm in Network-on-Chip architectures provides adaptivity for on-chip communications. Adding fault-tolerance adaptivity to a routing algorithm increases ...
Article
Utilizing Stochastic Model Checking to Analyze Genetic Circuits
IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (2012)
Curtis Madsen, Chris J. Myers, Nicholas Roehner, Chris Winstead, et al.
When designing and analyzing genetic circuits, researchers are often interested in the probability of the system reaching a given state ...
Article
A Fault-Tolerant Routing Algorithm for a Network-on-Chip Using a Link ...
VirtualWorldwide Forum for PhD researchers in Electronic Design Automantion (2011)
Jian Wu, Zhen Zhang and Chris Myers
Adaptive routing is a sensible approach to enhance fault-tolerance in Network-on-Chip (NoC) architectures, but can cause deadlock if implemented improperly. ...
Article
Performance Analysis of Two Synchronizers
20th UK Asynchronous Forum (2008)
Zhen Zhang and Jim Garside
Synchronizers are necessary when importing signals into any clocked domain. As multiple different clocks become increasingly common on chips, synchronizers ...
