Synthetic biology has the potential to revolutionize biotech industry and our everyday lives is already making an impact. Developing synthetic applications requires several steps including design modeling efforts which may be performed by in silico tools. In this work, we have developed two such tools, Eukaryotic Genetic Circuit Design (EuGeneCiD) Modeling (EuGeneCiM) , use optimization concept...

BACKGROUND Positive feedback is a common motif in gene regulatory networks. It can be used in synthetic networks as an amplifier to increase the level of gene expression, as well as a nonlinear module to create bistable gene networks that display hysteresis in response to a given stimulus. Using a synthetic positive feedback-based tetracycline sensor in E. coli, we show that the population dyna...

Differential responses to stimuli can affect how cells succumb to disease. In yeast, DNA damage can create heterogeneous responses. To delineate how a response contributes to a cell's future behavior, we constructed a transcription-based memory circuit that detects DNA repair to isolate subpopulations with heritable damage responses. Strongly responsive cells show multigenerational effects, inc...

Existing research studies on vision and language grounding for robot navigation focus on improving model-free deep reinforcement learning (DRL) models in synthetic environments. However, model-free DRL models do not consider the dynamics in the real-world environments, and they often fail to generalize to new scenes. In this paper, we take a radical approach to bridge the gap between synthetic ...

With the upcoming trend towards built-in test structures and implicit testing, more and more issues of test design need to be resolved during circuit design. A basic requirement for manual as well as for automatic test generation is to assess how accurately a given test strategy will classify good and faulty circuits. Measurement error plays an important role here and must be taken into account...

Time-delay circuitries in which a transcription factor processes independent input parameters can modulate NF-kappaB activation, manage quorum-sensing cross-talk, and control the circadian clock. We have constructed a synthetic mammalian gene network that processes four different input signals to control either immediate or time-delayed transcription of specific target genes. BirA-mediated liga...

Autoregulatory feedback loops occur in the regulation of molecules ranging from ATP to MAP kinases to zinc. Negative feedback loops can increase a system's robustness, while positive feedback loops can mediate transitions between cell states. Recent genome-wide experimental and computational studies predict hundreds of novel feedback loops. However, not all physical interactions are regulatory,...

Gene expression actualizes the organismal phenotypes encoded within the genome in an environment-dependent manner. Among all encoded phenotypes, cell population growth rate (fitness) is perhaps the most important, since it determines how well-adapted a genotype is in various environments. Traditional biological measurement techniques have revealed the connection between the environment and fitn...

Architectural research for Field-Programmable Gate Arrays (FPGAs) tends to use an experimental approach. The benchmark circuits are used not only to compare different architectures, but also to ensure that the FPGA is sufficiently flexible to implement the desired variety of circuits. The most common benchmark circuits used for architectural research are circuits from the Microelectronics Cente...