Experimentally driven verification of synthetic biological circuits

Download

Date

2012-04-03

Author

Yordanov, Boyan
Appleton, Evan
Ganguly, Rishi
Aydın Göl, Ebru
Carr, Swati B
Bhatia, Swapnil
Haddock, Traci
Belta, Calin
Densmore, Douglas

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

127
views

0
downloads

We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits. Our back-end synthesis tool automatically generates genetic-regulatory network (GRN) topology realizing the specifications with assigned biological "parts" from a database. We describe experimental procedures to acquire characterization data for the assigned parts and construct mathematical models capturing all possible behaviors of the generated GRN. We delineate algorithms to create finite abstractions of these models, and novel analysis techniques inspired from model-checking to verify behavioral specifications using Linear Temporal Logic (LTL) formulae.

Subject Keywords

Genetics, Proteins, Trajectory, Regulators, Inverters, Analytical models, Computational modeling

URI

https://hdl.handle.net/11511/41473

DOI

https://doi.org/10.1109/date.2012.6176468

Collections

Department of Computer Engineering, Conference / Seminar

Suggestions

OpenMETU
Core

Data driven verification of synthetic gene networks Aydın Göl, Ebru; Belta, Calin (2014-03-10) Automatic design of synthetic gene networks with specific functions is an emerging field in synthetic biology. Quantitative evaluation of gene network designs is a missing feature of the existing automatic design tools. In this work, we address this issue and present a framework to probabilistically analyze the dynamic behavior of a gene network against specifications given in a rich and high level language. Given a gene network built from primitive DNA parts, and given experimental data for the parts, the ...
Development of a closely coupled approach for solution of static and dynamic aeroelastic problems Başkut, Erkut; Seber, Güçlü; Department of Aerospace Engineering (2010) In this thesis a fluid-structure coupling procedure which consists of a commercial flow solver, FLUENT, a finite element structural solver, MSC/NASTRAN, and the coupling interface between the two disciplines is developed in order to solve static and dynamic aeroelastic problems. The flow solver relies on inviscid Euler equations with finite volume discretization. In order to perform faster computations, multiple processors are parallelized. Closely coupled approach is used to solve the coupled field aeroela...
Experimental Analysis and FPGA Implementation of the Real Valued Time Delay Neural Network Based Digital Predistortion Yesil, Soner; Sen, Cansu; Yılmaz, Ali Özgür (2019-01-01) This paper presents an FPGA implementation of the Real Valued Time Delay Neural Network (RVTDNN) based digital predistortion with a very low resource utilization and high throughput. The implementation exploits efficient utilization of FPGA primitives and approximation of activation functions that can be realized with simple logic operations. The proposed modifications and constraints on the algorithms have been decided and verified based on a closed-loop adaptive hardware setup including RFHIC RWP03040-1H ...
Fuzzy Hybrid Systems modeling with application in decision making and control Boutalis, Yiannis; Moor, Thomas; Schmidt, Klaus Verner (2012-11-28) Hybrid Systems are systems containing both discrete event and continuous variable components. Many recent contributions address crisp situations, where ambiguity or subjectivity in the measured data is absent. In this paper, we propose Fuzzy Hybrid Systems to account for inaccurate measurements and uncertain dynamics. We present a strategy to determine the most appropriate control actions in a sampled data setting. The proposed approach is based on three basic steps that are performed in each sampling perio...
Numerical study on effects of computational domain length on flow field in standing wave thermoacoustic couple MERGEN, SÜHAN; Yıldırım, Ender; TÜRKOĞLU, HAŞMET (Elsevier BV, 2019-03-01) For the analysis of thermoacoustic (TA) devices, computational methods are commonly used. In the computational studies found in the literature, the flow domain has been modelled differently by different researchers. A common approach in modelling the flow domain is to truncate the computational domain around the stack, instead of modelling the whole resonator to save computational time. However, where to truncate the domain is not clear. In this study, we have investigated how the simulation results are aff...

Citation Formats

B. Yordanov et al., “Experimentally driven verification of synthetic biological circuits,” 2012, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/41473.