I AM SUYASH
& I'm a biological

  • Engineer

  • Designer

  • Dreamer

  • Tinkerer

Hi, I'm Suyash Kumar

I'm a student at Duke University. I study Biomedical Engineering & Genome Sciences/Policy, and play around with software development, jazz, electronics, and multimedia.

Creating is not just a job for me, it's a passion.

View my Projects Check out my CV

My Interests

Biomedical Engineering

I've always loved making, tinkering with, and creating useful tools. I combine this passion with my fascisnation with biological systems to explore everything from myoelectric prostheses to molecular engineering. Currently, I seek to leverage biomolecular insights to engineer solutions to complex biological problems via genetic and protein engineering projects in the Gersbach Lab.

Development

I like making neat things using technology. Everything from websites and bioinformatic tools to 3D printed centrifuges and myoelectric prosthetics. I'm a huge fan of the maker movement and am quite involved with DukeMakers on campus. Check out some of my projects below!

Design

I'm a big fan of design. Be it as an engineer, scientist, or artist. As a multimedia project studio consultant (and now student manager) at Duke, I strive to inspire students and their projects using multimedia tools.

Fun

I like a lot of things. I'm a huge fan of music (I jam on piano, flute, and tenor sax), martial arts, good books, philosophy, geocaching, monkey bars, and a whole lot else.

The Projects


-Click around below to find out more.-
Section still in progress.

Microfluidic Devices

Microfluidic devices are comprised up of tiny micron-sized channels through which various fluids flow. These channels can be arranged in functional designs that can prove useful for a variety of purposes--such as reaction encapsulation, mixing/splitting reagents, modelling tissues, and many other modular functions. These functional circuit designs can all be stitched together to create robust platforms for experimentation and molecular engineering. Some notable perks of microfluidics include high-throughput design, small-volume chemistry, and enhanced resolution (much robust single-cell genomic analysis is done using microfluidics). I was first exposed to microfluidic technology when I was working at The Scripps Research Institute on the directed evolution of proteases (where I used a high-throughput droplet based platform to perform the work).

I personally beleive the modular nature of microfluidic technology along with the versatility of the technology will make it an instrumental part of good experimental platforms in the near future.

I've designed and fabricated my own droplet generation microfluidic platforms for use in some of my current protein and genetic engineering work. To learn more about my research, check out my CV!

Design & Fabrication Overview

The chips themselves are first designed in AutoCAD. Then, using photolithography (the same process used to make computer chips) I transfer the designs onto a silicon wafer "master mold." The prodecures used to make this master mold must all be performed in a clean room--a room with constantly filtered air to create a virtually dust free environment (which is why I'm dressed in the white suit in the slider). This silicon master mold (also seen in the slider above) is used to imprint features into a polymer known as PDMS. Once the channel designs are in the PDMS, input/output holes are punched in the PDMS and the PDMS is bonded to a glass slide to complete the device. Below are CAD and finished examples of one of my most simple and traditional droplet generator (generates aqueous compartments in an oil phase).

Glass Flute

I designed and built my first glass flute for the Science Olympiad competition back in high school. Since then, I've made many flutes--including one last spring right here at Duke University (photo credit: the lovely Chrislyn Choo).

Design & Build

Before my first build, I spent time figuring out the physics of instruments (super interesting, by the way). After some more reserach and some calculations, I laid out the design--namely the location and size of the embouchure and tone holes.

I then ordered lengths of glass tubing (usually around 25mm in diameter with 2.4mm wall thickness) that I hand cut to size using a Dremel tool and cermaic/diamond cutting wheel. I then measured and marked all the locations where holes were to be cut. After the first build, I realized that placing all the tone holes in a single line didn't make for a very comfortable playing position. So later, I began offsetting tone holes for better ergonomic design.

Anyway, after marking the hole locations, I used the dremel with the diamond/cermaic bits to first drill and then shape/expand the holes. For the tone holes, I would play the flute to check the tuning as I approached the theoricial size of the hole. I'd incrementally expand the holes until the tuning was just right. At this point, the build's pretty much done! Fairly simple. I also had to locate a suitable cork to plug the left-hand side of the tube.

More Science Olympiad

Placing first at regionals and states, our team made it to nationals for the first time in 2011, where I was ranked top 15. For this event ("Sounds of Music"), we were tasked with building two innovative instruments, writing a duet, performing in front of judges, and giving an interview on the physics of our instruments. It was awesome! I've played regular concert flute ever since I started band back in the 8th grade, and I've always been captured by glass' elegance--so I knew I had to make a glass flute.

3D Printed Myoelectic Hand

A couple of us (members of DukeMakers) started this project because a friend of mine (Ouwen) knew an 11-year old in Durham with Symbrachydactyly (he was born without fingers on his left hand). Since making custom prosthetics for a growing child is often too costly (they occassionally have to be remade as the child grows), we decided to 3D print him an inexpensive hand. We started with customizing designs from the open hand project, and then decided to try incorporating myoelectric control into the function of the hand.

So far, I've been leading the electrical designs and 3D construction. We use a simple electromyography board that smooths and rectifies an incoming signal. In a couple weeks at the end of last semester we had gotten it working fairly robustly (flex a muscle, run a motor) as you can see in the video below (still with a couple kinks). We ended up giving just the 3D printed hand (which is actuated mechanically) to the child for the summer (he loves it), and anticipate working on marrying the electronics and the hand this year. We expect to use newer, more sensitive electromyography tools this semester to create a more robust mechanical hand. Stay tuned for more!

Vertices Site

dukevertices.com

Vertices is Duke's student-run undergraduate research publication. Undergraduate research features, projects, and programs are all published in Vertices. I helped set them up with a website! Check it out

Computer Build

I planned and executed this build right before I had to leave my dorm for winter break. It's essentially a low-cost server for me to mess around with/learn things with. At the same time, I put in a good graphics card that allows me to effectively mine scrypt cryptocoins as a bit of a hobby. This way, the computer slowly pays for itself by mining these cryptocurriencies (litecoin, dogecoin, etc. Similar to bitcoin). As I earn the cost of components back, I'll start ramping up computational work donations to BOINC (a distributed computing project that uses crowdsourced computing resources to solve problems in science). So I see it as a fun way to pursue some of my computational/server side interests while also giving back to science. Oh and get a cheap/subsidzed computer. Woo! It had also been a while since I built a computer (the last one being a high powered one for my Science Olympiad team for data anaylysis) so I had a great time with this build. I may upgrade/add parts in the future as things progress. Here's a look at the components I used: http://pcpartpicker.com/p/2fRR5

DNA2RVD

This was a simple quick little computational tool I recently wrote for some of my work in lab. This essentially simplifies verification of targeted TALE proteins (these are modular proteins that can be synthesized to target almost any arbitrary region in the genome). Once the portion of the TALE protein one is verifying is sequenced, just throw the DNA sequence into the box and hit go. The repeat variable diresidue (RVD) sequence will instantly be parsed and printed out below. To date I haven't seen an easily accessible tool to do this.

I wrote this quickly over winter break, and it was my first real experience dealing with the Java swing libraries. From a web design perspective, they're a bit shoddy, but I was able to get what I needed done! I'm looking forward to teaching myself more backend web technologies (Rails, python, etc) such that I can make apps like these more accessible as web apps.

>For now, you can download the .jar app here.

Also, as soon as I finish commenting up some of the code, I'll throw this up on Github so stay tuned.

3D Printing Challenge

Duke's Innovation Co-Lab recently put together a 3D printing challenge that really jump started my exploration into the wonderful world of 3D Printing. Before the challenge, I had only started toying around with the Multimedia Project Studio's Makerbot 2 (starting out with Keychains and such). Inspired by the challenge and captured by the power of the platform, I started designing and printing out various items I found useful--from bottle openers to lab reaction racks and modular rail systems. I went on to design a simple 3D Printed centrifuge that attaches to a Dremel tool--which won first place! (Thanks to the Co-Lab for hosting the challenge and for the Makerbot Mini prize)!

The idea behind the entry was to create an ultra low cost centrifuge that can be used for hands on science exposure in local middle/high schools while also providing a cheap and rugged alternative to traditional centerfuges for performing field blood and lab work in rural areas. I'm hoping to start rolling out these as part of science experiment kits to local schools, where I hope they'll help inspire the next generation of explorers and innovators.

Above: The dual rotor version of my 3D Printed centrifuge design.

3D Printing

After the past semester at Duke, I've been hooked on 3D Printing. I started out printing keychains and other small trinkets, while slowly building my CAD and printer troubleshooting skills as the semester progressed. Inspired by the 3D printing challenge and captured by the power of the platform, I started designing and printing out various items I found useful--from bottle openers to lab reaction racks and modular rail systems. I went on to design a simple 3D Printed centrifuge that attaches to a Dremel tool--which won first place in the Innovation Co-Lab's 3D printing challenge! I won a Makerbot mini which I'm oh so excited to play with as soon as it ships (thanks Co-Lab)! Still lots (and lots) to learn, and I'm so excited to do so and so grateful to Duke for the opportunity to learn more.

You can check out some of the other stuff I printed last semester in the images below or in the slider above! Of note there is: a modular reaction rack (for performing reactions in lab without having to reach all over the place--unites an ice bucket, a PCR tube rack, and a microcentrifuge rack all in one modular unit).

I've since become very involved in DukeMakers--Duke's organization for makers/builders/hackers. We're working on building an accessible MakerSpace at Duke while supporting home-grown maker projects and talent.

Above: The dual rotor version of my 3D Printed centrifuge design.

Current Work

Just as a quick note, the most updated version of me and my work will always be my CV which can be found here.

This past summer, I worked at the Howard Hughes Medical Institute's Janelia farm research campus (HHMI's JFRC. Gotta love acronyms, right?). As a Janelia Undergraduate Scholar, I have a fellowship to utilize genetic engineering tools and advanced imaging tools (under development) to ask questions about embryogenesis and neurogenesis

I'll be working in a relativly new model system called Parhyale hawaiensis.

After working at Janelia this summer, I've grown a keen interest in neuroscience and the union between neuroscience and engineering!

At Duke, I work in the Gersbach lab on genetic engineering and protein engineering related projects. I'm focusing on two projects at the moment:
Engineering tools for Targeted Epigenetic Modifications
Epigenetic chemical markers can be attached to DNA and modify its expression rate and functional consequence. They can be heritable, can be environmentally influenced, and have recently be found to be more important than once thought for determining certain traits. I'm working with Dewran to develop a set of targeted tools that can alter the epigenetic state of DNA at desired loci. Potential applications include genetic reprogramming of cells (ie turning a skin cell into a neuron) and targeted cellular therapies (silencing malicious genes, etc).

Say hello to me

Suyash Kumar