Seminar by Promita Chakraborty

Author: Didem Unat
Time: 14:30
Location: ENG 208







Speaker: Promita Chakraborty

Title: Physical Biomodeling and Peppytide Models for Protein Folding 

Date:  30th March ,Monday 2015

Time: 14:30 

Place: ENG 208 

Host: Didem Unat




Abstract: Physical Biomodeling is a new field of study to conceptualize a vision of a CAD-cum-biocomputation-cum-3Dprinting platforms for bringing nano-scale  functions and dynamics of biosystems to be manipulated by hand-held models without compromising on accuracy of scale or function. These guiding principles have been incorporated in a prototype of polypeptide chain for protein folding, called Peppytide, that not only serves as a proof-of-concept, but also is the first of its kind to explore protein folding.


Peppytide is a 3D-printed coarse-grained model of polypeptide chain where the characteristics of polypeptides have been successfully captured and encapsulated through use of parameters like size of atoms, long-range and short-range interactions. The unique thing about this model is that it is foldable by hand into various secondary and tertiary structures of proteins with precision, and hence the first of its kind. The fact that one can then take a measuring scale and accurately quantify the molecule’s various dimensions at its folded capacity, makes it a useful tool for drug designers and other structural biology researchers, as well as for teachers and students in classrooms. Peppytide is the first but crucial step towards a computationally-augmented model.


Physical Biomodeling is an unexplored area of study at the intersection of natural science, computational science and precision physical models. While tremendous advances have been made in computational biology, the cutting-edge 3D printing provides unprecedented opportunities for a third angle into the landscape, thus uncovering this new computational space for modeling that has remained unexplored so far. Physical Biomodeling principles tie together these concepts of form-specific physical-digital interfaces for a seamless design-centric transition from X-ray crystallography type data to CAD-based models to 3D-prints.


This CAD-cum-biocomputation-cum-3Dprinting platform is a futuristic framework to build precise, hand-manipulated systems for biology to take advantage of the advances in biocomputation tools, molecular visualization tools, augmented and virtual reality methods and other 3D immersive techniques. Such blending of methods with interactive physical models might influence scientific modeling in future, the way computational modeling influenced discoveries in science for the past few decades.




Few related talks and publications:


1.      (Invited Talk) Promita Chakraborty. Physical Biomodeling and Peppytide Models for Protein Folding. AAAS Pacific Division Annual Meeting 2015, San Francisco, June 2015, USA (Session: 3D Printing, Arduinos and other Open Source Tech in STEAM Learning)


2.      (Invited Talk) Promita Chakraborty. Physical Biomodeling and Peppytide Models for Protein Folding. VARMS 2015 (1st International Workshop on Virtual and Augmented Reality for Molecular Science at the IEEE Virtual Reality International Conference 2015), March 2015, Arles, France.


3.      (Talk / Co-Organizer) Promita Chakraborty. Physical Biomodeling and foldable, coarse-grained physical model of polypeptide chain. AAAS Annual Meeting 2015, Feb 2015, San Jose, USA. (Session: Emerging Trends in Visualizing Physical Models and Rapid Prototyping for Biological Systems)


4.      Promita Chakraborty. Physical Biomodeling: a new field enabled by 3-D printing in biomodeling. Arxiv, 2015.


5.      Promita Chakraborty. PhD Dissertation. A Computational Framework for Interacting with Physical Molecular Models of the Polypeptide Chain, 2014.


6.      Promita Chakraborty and Ronald N. Zuckermann. MAKE Projects: Peppytides. Jan 2014.


7.      Promita Chakraborty and Ronald N. Zuckermann. Coarse-grained, foldable, physical model of the polypeptide chain. Proc Natl Acad Sci, 110(33):13368 –13373, 2013.



Dr. Promita Chakraborty is a scientist, inventor and computer scientist who has initiated a new field called Physical Biomodeling, an unexplored space of study at the intersection of natural science, computational science and precision physical models. She founded Quezylab, a research-based-company with a vision to connect the macro-physical world to the nano-world without losing accuracy, functionality and dynamics of atomic interactions. With the help of 3D printing technology and her vision for dynamic folding macromolecules, she invented Peppytides and initiated the new field of Physical Biomodeling as a part of her doctoral work. Peppytides is a to-scale physical model of the polypeptide chain that can fold into various motifs and secondary & tertiary structures of proteins. Because of its flexibility and accurate scaling, Peppytides is a model that is first of its kind. She worked as Research Associate at the Molecular Foundry at Berkeley Lab (LBNL) from 2011 to 2014 and initiated Peppytide project as a pioneering work for accurate physical models for protein folding. She coined the terms Peppytides, PeppyChains, and Physical Biomodeling. She received PhD in computer science in 2014 from Department of Computer Science, Virginia Tech, Blacksburg. Recently she has received Berkeley Lab's 2014 Director's Award for Exceptional Achievement for outreach with Peppytides. Her work has been covered in MAKE Magazine and Berkeley Science Review. She received MS in Computer Science from Louisiana State University Baton Rouge, USA, and BS in Mathematics from University of Calcutta, India.