Promita Chakraborty

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

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My expertise is in exploring physical, dynamic, scaled models for scientific computing (e.g. for biological and physical systems, nanobiostructures etc).

In my PhD thesis, I have pointed out a new direction of exploration with physical models for polypeptides. I have designed and fabricated Peppytides (www.peppytides.org), the first mechanically flexible, scaled, physical model of the polypeptide chain that accurately demonstrates the molecular dynamics behind protein folding such as degrees of freedom on rotatable bonds, barriers to bond rotation, bond lengths and angles, and short- and long-range (nonbonding) interactions between amino acids. Reported in PNAS here.

Unlike most 3-D printed protein models, Peppytide features a backbone chain that can be folded or unfolded to make at-scale, all of the common protein secondary structure elements, such as alpha helices, beta sheets and turns, and small tertiary structures and protein motifs. See pictures and details of the model in Peppytides website.



Videos

  • May 2015, Peppytide as a tangible molecular interface based on camera-tracking (1 min), work by Xavier Martinez

  • Jan 2014, MAKE Magazine interview (1 min)

  • July 2013, Folding of Peppytides (as published in PNAS supplementary)

  • Dec 2013, Peppytides: Interactive Models of Polypeptide Chains (5 min)



    News (2013-2015):

  • Dec 2015: Guest lecture at Foothill College / Palo Alto High School, Nanoscience course (NANO10: Introduction to Nanoscience & NanoTechnology), a course for advanced students for college credit.

  • Aug 2015: C&EN article reports my work, 3D Print Exchange Helps Chemists Create Their Own Molecular Models.

  • Aug 2015: Interview with Foundry.net, Peppytides.

  • July 2015: Invited lecture at NuLeaf.

  • Jun 16 2015: I am giving an invited talk at the AAAS Pacific Division Meeting 2015.

  • Jun 2015: Received the honor of Maker of Merit Blue Ribbon at National Maker Faire, Washington DC.

  • Jun 2015: I am exhibiting Peppytide 2 and PeppyChain at National Maker Faire. Visit my booth.

  • May 2015: I have exhibited Peppytide 2 and PeppyChain at Maker Faire 2015, San Mateo.

  • March 2015: My invited talk Koc University, Istanbul, Turkey

  • March 2015: My invited talk at University Paris Sud, IBPC, France

  • March 2015: My invited talk at IEEE VR 2015 VARMS (Workshop on Virtual and Augmented Reality for Molecular Science)

  • 11 Feb, 2015> Today at Berkeley Lab news: Berkeley Lab Speakers at AAAS

  • 02 Jul, 2014> Received Berkeley Lab's 2014 Director's Award for Exceptional Achievement.

  • 17 Jun, 2014> Featured in article Lab Contingent Raises User Facility Awareness on Capitol Hill in “Today at Berkeley Lab” news.

  • 10-11 Jun, 2014> Met with Congressional Representatives and their staff and participated in the 4th Annual National User Facility Organization (NUFO) Science Expo, Washington DC, Jun 2014.

  • 22 May, 2014> News coverage in Berkeley Lab's Materials Sciences Division (MSD) website MSD news

  • 22 May, 2014> News coverage in Today at Berkeley Lab (TABL) TABL news

  • 17-18 May, 2014> Exhibiting at Maker Faire Bay Area 2014.
    Summary of exhibit
    Download Flyer

  • 01 May, 2014> Attending Bits-to-Biology workshop @ MIT Media Lab.

  • 26 Apr, 2014> Talk and hands-on with students in grade 7-10 (Johns Hopkins Center for Talented Youth).

  • 12 Apr, 2014> Exhibited at NanoDays, organized by and at Lawrence Hall of Science museum, as "Featured Maker".

  • Invited talk about Peppytides at 248th ACS Meeting in Fall.

  • April 2014> PhD dissertation submitted. Details in publications.

  • March 2014> Accepted to exhibit at MakerFaire Bay Area on May 17 & 18, 2014. Come see me there!

  • 28 Jan, 2014> Peppytide featured as top story in "Science Headlines" in DoE Office of Science Homepage! Plastic Proteins and New Possibilities for Insight

  • 22 Jan, 2014> Peppytide made it to the "Today at Berkeley Lab" news. Link

  • 21 Jan, 2014> Peppytide video in Berkeley Lab website! www.lbl.gov

  • 16 Jan, 2014> Highlighted in MAKE Magazine's "Made On Earth" column (VOL 37, Jan 2014 Issue). (Turning Tides by Laura Kiniry)

  • In News & Highlights corner of Berkeley Lab's Molecular Foundry website. link

  • 07 Jan, 2014> A 1-min interview, and my article in MAKE Magazine, online Projects, on how to make these models. MAKE (article/interview) YouTube (interview)

  • Tweets about Peppytides in Twitter by BerkeleyLab, Berkeley Science Review, PatonGroup, Stratasys

  • 26 Aug, 2013> Peppytide covered in an article in Berkeley Science Review (online) Read it here

  • 13 Aug, 2013> Our paper is now in print; in today's issue of PNAS. Link

  • 29 July, 2013> Our paper has been published online ahead of print today in PNAS! doi: 10.1073/pnas.1305741110. More details in the publications list. Soon to be in print!


    News (2012 and older):

  • Research Associate, Berkeley Lab, Jan 2012.

  • Summer and Fall internship 2011, Berkeley Lab.

  • Session Chair HCI Session, Women In Computing Day, organized by AWC(Association for Women in Computing), April 15, 2011.

  • Grace Hopper Chair for AWC (for the Grace Hopper Celebration Conference 2009, 2010, 2011)



    QuezyLab | Peppytides |

    Molecular Foundry | Berkeley Lab |

    CS@VT | VT| CCT@LSU

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