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PDRA position at MIT Media Lab on pattern formation in engineered bacteria

The Mediated Matter Group at MIT Media Lab is seeking a highly motivated and experienced researcher to conduct independent research to develop: a) A computer-aided design (CAD) software environment to simulate pattern formation and emergence informed by synthetically engineered cell behavior. b) A computer-aided design environment to infer regulatory networks for engineered cells based on user-defined constraints.

Job Title: Postdoctoral Associate
Institution: Massachusetts institute of Technology
Department: Architecture Program: Media Arts & Sciences
Sub-unit: MIT Media Lab
Job Function: Research
Time Status: Full-time
Location: USA – MA – Cambridge
Posted: May 15, 2017 (no closing date listed)

Contact: Prof Neri Oxman 

Description: The Mediated Matter Group focuses on Nature-inspired Design and Design-inspired Nature. We conduct research at the intersection of computational design, digital fabrication, materials science, and synthetic biology, and apply that knowledge to design across scales from the micro scale to the building scale. We create biologically inspired and engineered design fabrication tools, technologies, and structures aiming to enhance the relation between natural and man-made environments. Our research area, entitled Material Ecology, integrates computational form-finding strategies with biologically inspired fabrication. This design approach enables the mediation between objects and the environment; between humans and objects; and between humans and environment. For more information, please visit (http://matter.media.mit.edu/).

The Mediated Matter Group is seeking a highly motivated and experienced researcher to conduct independent research to develop: a) A computer-aided design (CAD) software environment to simulate pattern formation and emergence informed by synthetically engineered cell behavior. b) A computer-aided design environment to infer regulatory networks for engineered cells based on user-defined constraints. Designers often specify the final form of a material object using computer-aided design tools to generate a design file that can be used to build a part to specification. Here, the goal is to develop a framework with the objective to bring this capability to biological design and engineering. In this new computational design environment, a final form or pattern-formation logic is specified and is subsequently used to design a progenitor cell that can differentiate and grow into the specified form.

Sub-goals of this research are: to explore the possible design space of engineered cells encoding developmental circuits, and to generalize the CAD environment to make predictions towards regulatory networks required to generate predefined patterns and shapes.

This is a long-term funded position for up to two years with the possibility of renewal.

 

Start Date: ASAP with flexibility.

Duties & Responsibilities:

The postdoctoral associate will lead the development of the computer-aided design environment for engi- neered cell-based modelling of embryogenesis, pattern formation and rule-set inference. The CAD environment should be made to support the simulation of pattern formation processes that emerge from specifically engineered cells. This entails the development and application of mathematical modeling tools for, and the visual representation of, physical cell-to-cell interactions, differentiation, quorum signaling, reaction to signaling, as well as visual cell response. The CAD environment should further be able to infer rule-sets for the development of cells engineered to grow into user-specified patterns. This can include design, simulation, and parameterization of pattern formation processes. The development process will involve new data structures, parallel algorithms and adapted mathematical models to obtain more efficient and flexible simulations of cellular pattern formation. Further, the candidate will be responsible for the integration of these modules in an interactive environment with user-interface, the documentation of the developed methods, and regular reports on progress towards goals.

This research will be conducted in collaboration with the Synthetic Biology Center at MIT and the MIT De- partment of Mechanical Engineering. The position reports to the Director of The Mediated Matter Group (Prof. Neri Oxman) and the Director of the Voigt Lab (Prof. Christopher Voigt). The candidate will be responsible for managing the scientific and technical challenges and activities related to this effort, including interactions with other relevant colleagues and/or teams.

Basic Qualifications:

The candidate should hold a PhD degree in the biological sciences, such as systems biology, developmental biology, or a related discipline, with a good understanding of modelling in synthetic biology, biophysical processes, and general mathematical modelling. Experiences in computer science, computational physics, and user interface development for mathematical modelling tools are a plus, as is a good graphic sensibility. The candidate should have experience with simulation of cells and cell populations, and should also have a profound understanding of numerical methods for the discretization of complex dynamic systems. Experience in computer vision related methods for the evaluation pattern formation processes is a plus. Additional qualifications include:

• Demonstrated success in leading and working in cross-disciplinary team.

• Comfortable in a fast-paced environment and able to adjust workload based upon changing priorities.

• Flexible and cooperative spirit with strong commitment to team efforts.

• Strong oral, writing, and presentation skills.

• Innate optimism and a can-do attitude.

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The Synthetic Biology Strategic Research Initiative provides a hub for anyone interested in Synthetic Biology at the University of Cambridge, including researchers, commercial partners and external collaborators. 

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