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$20 USD / hour
Flag of UNITED STATES
los angeles, united states
$20 USD / hour
It's currently 2:35 AM here
Joined May 29, 2009
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Jimmy L.

@mrgrumpygill

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$20 USD / hour
Flag of UNITED STATES
los angeles, united states
$20 USD / hour
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Chemical Engineer and Biologist

Graduate school has prepared me to solve any type of problem by quickly dissecting and analyzing every aspect of it. My work focused on the development of mathematical models to describe bacterial behavior. Although creating a complete model to describe bacterial behavior is currently impossible, I realized I could address a number of particular problems through the development of specific computational tools. Because I was the only student performing computational work in my lab, multiple students turned to me for ideas for their projects. Their problems ranged from figuring out which genetic manipulations would optimize biofuel production, to rationalizing which gene configuration would actually help us build a new carbon fixation cycle. Although each of these problems required a different solution, I was able to develop computer programs to address each of their particular needs. Coming from a lab focusing on molecular biology work and being the only graduate student doing theoretical work presented some particular challenges. Because most of my co-workers are biologists, I needed to find a way to translate my own work into a language they would understand. I believe this presented a unique opportunity for personal growth, as I had to learn how those around me thought and approached problems so that I could effectively communicate and collaborate with them. My fondness for multi-disciplinary projects is further accentuated by my undergraduate research experiences. My research endeavors spanned four different departments including the Department of Architecture and the Department of Economics. For example, I created a program to interface with structural simulation software in order to assess the importance of every member in the building. Using this program, the professor I worked with was able to more efficiently analyze the tradeoffs between aesthetics and structural integrity. Outside of school I am an avid beer-brewer and martial arts practitioner holding a Brazilian Jiu-Jitsu (“BJJ”) purple belt and an amateur kickboxing record of 1-0. Through the UCLA BJJ club, I have been able to coach many students and was eventually hired as an instructor for UCLA Recreation. During class, I have trained students with a wide range of athletic proficiencies, and sometimes significant physical constraints. I believe my martial arts training has brought me the opportunity to become a strong leader capable of not only transferring my skills to others, but also motivating them to perform to the best of their potential.

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Experience

Ensemble Modeling for Metabolic Engineering Applications

UCLA
Sep 2009 - Present
Graduate Student Researcher, PI: James C. Liao, Department of Chemical Engineering • Development of computational tools to predict possible outcomes of metabolic engineering • Creation of kinetic (ODE) models of metabolism incorporating 200+ reactions • Experience with whole-genome sequencing (Publication 4) • Deep interaction with experimentalists and understanding of molecular biology techniques

Design of a Self-Sustainable Community

RPI
Jan 2009 - May 2009 (4 months, 1 day)
• Research project resulting in an undergraduate thesis in the Department of Economics • Design of a self-sustaining community (considering labor, nutrition, economics, and hygiene) capable of providing the basic necessities (both physical and psychological) for its population.

Structural Simulation

RPI
Aug 2008 - May 2009 (9 months, 1 day)
• Worked on developing an interactive application to perform iterative structural simulations by interfacing with a structural analysis program (RISA) to determine the effects of removing members from a particular structure

Education

PhD Chemical and Biomolecular Enginerring

University of California, Los Angeles, United States 2009 - 2014
(5 years)

B.S. Biology

Rensselaer Polytechnic Institute, United States 2005 - 2009
(4 years)

B.S. Chemical Engineering

Rensselaer Polytechnic Institute, United States 2005 - 2009
(4 years)

Publications

Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways

Metabolic Engineering
Metabolic pathways in cells must be sufficiently robust to tolerate fluctuations in expression levels and changes in environmental conditions. Perturbations in expression levels may lead to system failure due to the disappearance of a stable steady state. Increasing evidence has suggested that biological networks have evolved such that they are intrinsically robust in their network structure. In this article, we presented Ensemble Modeling for Robustness Analysis (EMRA), which combines a continuation method

Genome sequence of the extreme obligate alkaliphile Bacillus marmarensis strain DSM 21297

Genome Announcements
Whole genome sequence of Bacillus marmarensis strain DSM 21297

Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks

Biotechnology Journal
The ensemble modeling (EM) approach has shown promise in capturing kinetic and regulatory effects in the modeling of metabolic networks. Efficacy of the EM procedure relies on the identification of model parameterizations that adequately describe all observed metabolic phenotypes upon perturbation. In this study, we propose an optimization-based algorithm for the systematic identification of genetic/enzyme perturbations to maximally reduce the number of models retained in the ensemble after each round of mo

Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux

Metabolic Engineering
Dynamic models of metabolism are instrumental for gaining insight and predicting possible outcomes of perturbations. Current approaches start from the selection of lumped enzyme kinetics and determine the parameters within a large parametric space. However, kinetic parameters are often unknown and obtaining these parameters requires detailed characterization of enzyme kinetics. In many cases, only steady-state fluxes are measured or estimated, but these data have not been utilized to construct dynamic model

Conversion of proteins into biofuels by engineering nitrogen flux

Nature Biotechnology
Biofuels are currently produced from carbohydrates and lipids in feedstock. Proteins, in contrast, have not been used to synthesize fuels because of the difficulties of deaminating protein hydrolysates. Here we apply metabolic engineering to generate Escherichia coli that can deaminate protein hydrolysates, enabling the cells to convert proteins to C4 and C5 alcohols at 56% of the theoretical yield. We accomplish this by introducing three exogenous transamination and deamination cycles, which provide an irr

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