CV

John Saeger
john.saeger@gmail.com
zyenz.blogspot.com
github.com/aequorea
linkedin.com/in/john-saeger


Experience

  Software engineer
  2018 - present

Showed how "pointerizing" code in C can result in improved performance on some x86_64 platforms. In days of old this was a popular way to speed up C code, but for a considerable period of time, computer architectures and compilers were such that it was of little or no benefit. As an optimization technique it went "out of style." In a modest way, it looks like it's working again on some modern x86_64 machines.
(https://zyenz.blogspot.com/2019/02/fast-pointers.html)

Wrote a "pointerized" hybrid quicksort in C that's pretty fast on some x86_64 machines.
(https://github.com/aequorea/phtest)

  Protein designer
  2013 - 2018

Wrote a speculative plan for an HIV vaccine.
(https://zyenz.blogspot.com/2018/07/hiv-vaccine-strategy.html)

Described a prospective method for evolving sharply focused antibodies.
(https://zyenz.blogspot.com/2018/06/sharp-antibodies.html)

Designed a prospective HIV microbicide.
(https://zyenz.blogspot.com/2017/11/HIV-microbicide.html)

Wrote glycodesign software in python to support the above designs.
(https://zyenz.blogspot.com/2017/11/glycodesign.html)

  Doctoral student at ETH Zürich
  Advisor: Viola Vogel
  2007 - 2012

Used computational and experimental studies to infer the fluorescence properties of GFP in various mechanical states using engineered GFP mutants designed to mimic the structures seen in computer simulations.

Devised a method for measuring the length of long polymeric molecules using fluorescence lifetime (FLIM) measurements of fluorescence resonant energy transfer (FRET).

Average arrival time based FLIM imaging software was written in C.
(https://www.research-collection.ethz.ch/handle/20.500.11850/153705)

  Research assistant at University of Washington and ETH Zürich
  2000 - 2007

Studied lipid self-assembly at the air-water interface. Simulated a variety of small proteins using steered molecular dynamics.

  z26 -- An Atari 2600 emulator
  1997-2011

Under DOS it was the fastest and most accurate 2600 emulator. It was like an embedded project because most of the hardware was controlled directly. It started out as pure x86 assembly language, but over time, was completely written in C using SDL as the I/O library.
(www.whimsey.com/z26)

  Computers
  1976 - 2000

Worked in the computer industry doing hardware and software consulting and development that was mainly communications related. Developed numerous hardware and software products for Nova compatible computers running the IRIS operating system. Co-founder Starburst Data Systems, Inc.

During this time there were three significant embedded systems. One called picoNET was a network controller that implemented the lower level parts of the AppleTalk network protocol on a device for the Nova compatible computers. It used a 68701 controller.

The second was Boxtops Bisync. It was a stand-alone product that converted asynchronous data to bisynchronous and which implemented the 2780 and 3780 communications protocols. This is how it was done before the internet became what it is now. It used a z180. I ported the Small-C compiler so I could have a high-level language for the firmware development.

The third is the Palomino battery charger. It was used by police, firefighters and other emergency workers to keep their radios going. It was designed to make the best of bad batteries. It could charge a battery with a shorted cell without overheating. Charge termination was based on the derivative of the voltage. It used a PIC16C71 microcontroller.
(https://github.com/aequorea/palomino)

  Geology lab helper at California Institute of Technology
  1972

Worked in C.C. Patterson's geochemistry lab. Helped prepare samples in clean room and collected mass spectroscopy data from ultra-pure samples of lead. This was after he had produced the first reliable measurement of the age of the earth, during the get the lead out of gasoline period.


Publications

The talin-integrin interface under mechanical stress
2014 Mol Biosyst, dx.doi.org/10.1039/c4mb00341a

GFP's Mechanical Intermediate States
2012 PLoS ONE, dx.doi.org/10.1371/journal.pone.0046962

Mechanosensitive fluorescent probes
2012 ETH doctoral thesis, dx.doi.org/10.3929/ethz-a-007577672

Education

ETH Zürich, Dr. sc., Health Science and Technology, 2012
University of Washington, MS, Physics, 2007
University of Washington, BS, Physics, 2001
Harvey Mudd College, --- , Physics, 1976
Pasadena City College, --- , Physics, 1974
La Cañada High School, Diploma, 1972


Honors and Awards

2004 - Graduate School Top Scholar Award


(20190222)