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Promita Chakraborty

Publications and source records attributed to Promita Chakraborty.

3 recordsLinked to original sources

Physical Biomodeling: a new field enabled by 3-D printing in biomodeling

Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research over the last couple of decades. Now 3D printing technology opens the door for a new field, Physical Biomodeling, at the intersection of experimental data, computational biology and physical modeling for study of biological systems, such as protein folding at nano-scale. Here I explore this new domain of precision physical modeling and correlate it with existing visualization and computational systems and future possibilities. Dynamic physical models can be designed to-scale that can serve as research tools in future along with existing biocomputational tools and databases, adding a third angle to tackle unsolved scientific problems.

cs.OH

PeppyChains: Simplifying the assembly of 3D-printed generic protein models

Peppytides is a coarse-grained, accurate, physical model of the polypeptide chain. I have shared instructions to make your own polypeptide chain and STL files of Peppytides in MAKE magazine in Jan 2014 issue. However, Peppytides involves a lot of steps and assembly of units. People were asking me, 'Is there any easier way to make these models?'. I have been at several workshops, hands-on sessions, talks and a science events with Peppytides. From the feedback that I got everywhere, most of the makers, teachers and students want something that is 3D-Print-&-Go, or at least easier to make, even at the cost of some features. I have designed a new version of the model, named PeppyChains, in which the backbone chain of the model can be 3d-printed as a single unit. PeppyChains design eliminates the assembling of parts to form the backbone chain, but with the cost of losing the ability to use bias-magnets to favor certain phi/psi angles in the backbone. I have been demonstrating PeppyChains at various talks and workshops along with Peppytides, and I have received requests for making the STL file public. On popular demand, here I am sharing this STL and providing the step-by-step instructions to make PeppyChains. Just add the hydrogen-bond magnets, paint and color-code the atoms, and you are ready to go! No drilling. No time consuming assembly.

q-bio.OT