Promita Chakraborty

"We cannot teach people anything; we can only help them discover it within themselves." - Galileo Galilei

Research

Long term vision

Her vision is to understand whether the shape and dynamics in the biological systems can govern the rules of computing. See About for details.

To develop a new field of study that she calls Physical Scientific Computing and Modeling. Her first project in this is Peppytide for the Protein Folding Problem. This field will explore open scientific problems using accurate and dynamic physical models.

 

Current research interest

Physical Scientific Computing and Modeling; Physical Biomodeling; Peppytide

(1) Interfacing ACCURATE physical models of polypeptides with the computing tools of protein folding, (2) Back-end connectivity of interactive physical polypeptides with supercomputers and clouds, (3) understanding how very small peptides fold at the atomic level, (4) understanding design principles of proteins from first principles, (5) building other physical biomolecules, (6) building better biocomputation tools for protein folding, (7) developing related technology for biosystems with a focus on facilitating innovation and insight.

 

Molecular Foundry @ Berkeley Lab (May 2011 - July 2014)

Made models for polypeptide folding. Coined the named Peppytide for the model. Details in the paper, "Coarse-grained, foldable, physical model of the polypeptide chain ", PNAS, 2013. (Used CoCreate CAD modeling, Python, R, 3D Printing)

 

Summer Internship 2009 @ Berkeley Lab (LBNL)

Benchmarking parallel biology codes using CRAY-XT5 supercomputer.

 

Virginia Tech, Blacksburg (Aug 2008 - May 2011)

Came up with the idea for Peppytide and Physical Biomodeling for proteins and other macromolecules. Prototyped BioTable for that as a first step (using Python and OpenCV). Presented 3 posters about these ideas.

(Aug 2008 - Apr 2009) Also worked in an existing project called JigCell that mathematically models (using Partial Differential Equation) cell division and other Computational Cell Biology mechanisms (presented posters) (using Java).

 

Past research @ Center for Computation and Technology (Louisiana State University) CCT (LSU) - (2005-2008)

Started working in molecular dynamics for proteins and amino acids in Grid Computing environments.

This work includes her analysis on the performance and behavior of a parallelized Molecular Dynamics code on LONI (Louisiana Optical Network Interface) grid. First stage of the project included parallelizing a Molecular Dynamics code, using C++ and MPICH-g2, and profiling both the serial and parallel code; in the subsequent stages, showed the benefit of distributing a job over grid during submission over submitting it on a single node.

The work was a part of: (1) work package 1 of the Cybertools Project, (2) UCoMS project.

See publications for more details.

Taught undergraduate Physics Lab (Fall 2005).

 

Indian Statistical Institute, Kolkata (ISI) at the Advanced Computing and Microelectronics Unit (2003-2005)

Explored cellular communication algorithms and GPS networking. (2004-2005)

Worked on Algorithms and Data Structure Lecture notes. (2003-2004)

 



QuezyLab | Peppytides |

Molecular Foundry | Berkeley Lab |

CS@VT | VT| CCT@LSU

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