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- Brookhaven National LaboratoryUS215 papers
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6 papers · 1 filter
Fan-out in Gene Regulatory Networks
Kyung Hyuk Kim, Herbert M. Sauro
In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors a…
TinkerCell: Modular CAD Tool for Synthetic Biology
Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between c…
A Generic Rate Equation for modeling Enzymatic Reactions under Living Conditions
L. W. Lee, L. Yin, X. M. Zhu +1
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetri…
Metabolic Network Modelling: Including Stochastic Effects
P. Ao
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation…
Robustness, Stability and Efficiency of Phage lambda Gene Regulatory Network: Dynamical Structure Analysis
X. -M. Zhu, L. Yin, L. Hood +1
Based on our physical and biological studies we have recently developed a mathematical framework for the analysis of nonlnear dynamics. We call this framework the dynamical structu…
Calculating Biological Behaviors of Epigenetic States in Phage lambda Life Cycle
X. -M. Zhu, L. Yin, L. Hood +1
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at…