Programming custom ASICs for molecular dynamics simulations, including implementing new enhanced sampling algorithms and independently devising a scriptable interface to hardware. Developed high performance distributed workflow system and a number of production tools to enable new drug discovery techniques for our users at scale. Support and maintain multiple tools and packages. Code is deployed at scale across tens of millions of jobs on thousands of nodes.
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Created an algorithm to do error correction and variant calling on data obtained from Oxford Nanopore Technologies' compact MinION nanopore sequencer. By using the raw data available from each read, it is possible to increase de novo accuracy to over 99% and single-base variants can be called with over 99.8% accuracy. The code is available as an easy to install Python package and utility.
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An Arduino attachment board created as part of graduate research, it has 4 channel ADC and DAC converters to allow you to input and output analog voltages easily. What separates it from other such boards is the DC/DC converter on it that allows analog voltages from -10V to +10V to be read and written, even when connected only to the Arduino's +5V supply.
Working with the Golovchenko Group at Harvard University to develop novel methods of trapping and sequencing DNA using nanopores, with DNA sequencing as the ultimate goal. My current research revolves around using two nanopores in close proximity to capture and extend a single strand of DNA, in order to manipulate it freely while maintaining a high signal to noise ratio. Current project started in Fall of 2012.
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Developed a 3D Markov Chain Monte Carlo DNA simulator in Python to extend our group's work with nanopores, capable of incorporating many different physical models and scenarios, including the stretching of DNA under the force applied by a nanopore. The system is currently being used to motivate experimental directions, and future plans include making comprehensive theoretical predictions. Written in Spring of 2013.
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Worked with the Roukes group at Caltech, who were developing a single-molecule NEMS mass spectrometer for protein analysis. Designed and built an ion mobility spectrometer to characterize the quality of the ions generated by the electrospray ionization system being used (based on Bathgate 2004). Dealt with high voltage, high speed, and low current electronics. Worked as a Caltech undergraduate research fellow June-October 2009.
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Developed and implemented an interactive real-time visualization system for multi-terabyte dark matter simulation results, using the parallel computation capability of GPUs and hierarchical data structures. Worked as a Caltech undergraduate research fellow June-August 2008, presented results at the Microsoft eScience Workshop in December 2008. Work done at the Max Planck Institute for Astrophysics in Garching, Germany.
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Spent months working on Team Caltech’s entry to the DARPA Urban Challenge, where autonomous cars raced through an urban environment to complete certain tasks. Did a variety of smaller tasks (lane changes, new radar unit, sensor autocalibration utility), then developed the LIDAR obstacle detection unit on my own, up through to the contest on November 7. Worked as a paid researcher and for academic units, April-November 2007.
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Built a system and wrote a program that uses four omnidirectional microphones in order to calculate the 3D position of audio sources in a room, using cross-correlation and phase closure. Was capable of localizing a person's voice to within a few inches at a distance of twenty feet, robust against background noise and reflections. Presented by a colleague at the 2006 Intel International Science Fair, receiving a Navy Scholarship. Work done in the 2005-2006 school year, junior year of high school.