Max A. Fahrenkopf
- Carnegie Mellon University
- Department of Chemical Engineering
- 5000 Forbes Avenue
- Doherty Hall, Room 4200
- Pittsburgh, PA 15213
|2009 — 2014||Ph.D., Chemical Engineering, Carnegie Mellon University|
|2005 — 2009||B.S., Chemical Engineering, University of Wyoming|
Optimation of gel free DNA separation and stability of non-linear thermodynamic systems
Length-based separation is critical step in DNA sequencing. One of my research focuses is to develop an efficient design procedure for rapid, gel-free DNA separation platforms on bench-top capillary electrophoresis and microfluidic platforms. The gel-free DNA separation is achieved using a novel separation technique called micelle end-labeled free solution electrophoresis (ELFSE) that leads to rapid separations and easy to use reagents. The optimal designs for micelle ELFSE are found by solving non-convex non-linear programming problems using global optimization codes such as BARON. Proper formulation of the mathematical model describing the DNA separation process leads to solve times that are around one second for each design problem. Our formalism allows for efficient characterization of many different DNA separation platforms which is useful for trade-off analysis.
Stochastic simulation of polymer dynamics is a useful tool for design of novel DNA separation techniques. Unfortunately these simulations are very computationally expensive. Course simulation techniques such as projective integration may offer significant speed up but require certain stability properties to be satisfied for viability. Stability of non-linear systems is difficult to show in most cases. We utilize a thermodynamics based approach that leverages the second law to help us build a Lyapunov function which can be used to derive stability conditions of non-linear systems. This approach is fairly general and is applicable to range of systems including oil-reservoirs, flash drums and distillation.
Peer Reviewed Publications
M. A. Fahrenkopf, B. E. Ydstie, T. Mukherjee, J. W. Schneider "Modeling and Global Optimization of DNA Separation" Comp. & Chem. Eng. - Accepted Jan 2014
M. A. Fahrenkopf, B. E. Ydstie, T. Mukherjee, J. W. Schneider "Optimal Design of Microfluidic Devices for Rapid DNA Separations" Presented at Computer Applications in Biotechnology, Dec 2013
M. A. Fahrenkopf, J. W. Schneider, B. E. Ydstie "Projective Integration with an Adaptive Projection Horizon" Presented at Dynamics and Control of Process Systems, Dec 2013