Jonathan Coles Email & Phone Number

Zürich, ZH, CH

Zurich, Switzerland

Munich Area, Germany

• Actively developing the molecular dynamics software POLARIS(MD); improved my parallel Fast Multipole Method implementation to support more than 3 million atoms on over 100,000 CPU cores of the LRZ SuperMUC-NG.
• System administrator at the TUM molecular dynamics group, maintaining a computing cluster of 100+ GPUs and 170 TB of storage.
• Currently investigating the effects of including sophisticated physical models on protein interactions using the molecular dynamics program POLARIS(MD).
• Performing molecular dynamics simulations using the GPU accelerated AMBER software. Investigating the binding properties of small proteins to DNA with applications to drug design.

Garching, Bavaria, Germany

Paris Area, France

• Implemented the Fast Multipole Method (FMM) for computing long-range electrostatic and polarization forces in the molecular dynamics program POLARIS(MD).
• Used a hybrid software architecture that combines OpenMP and MPI to run on massively parallel supercomputers using thousands of cores. The force-field in POLARIS(MD) is notable for being completely parameterized from.

Zürich, Switzerland

• Wrote the gravitational lens modeling software GLASS using Python and C.
• Applied GLASS to estimate the age of the Universe and the distribution of dark matter around galaxies.
• Developed a new Monte Carlo sampling algorithm for high-dimensional spaces.
• Developed a parallel, 6D phase-space clustering algorithm to identify dark matter structures within cosmological simulations.
• Assisted in the construction of the zBox4, a custom, in-house computing cluster.
• Performed research in 3D visualization of astrophysical simulations of dark matter.

Developed FPGA motor control software for moving digital tape through a tape drive at high speed. Worked closely with the Director of Hardware. Also provided network and miscellaneous technical support.

Graduate Assistant to the Computer Science Department System Administrator. Helped to maintain the 150+ machine Solaris network. Responsibilities included software upgrades, troubleshooting, and user support.

Tutor in the Computer Science Department Tutoring Center. Helped students with Java/C++ lab and project assignments. The experience taught patience and how to explain new and complex programming techniques to students of all levels.

Osnabrück, Germany

Software developer for the GIS Thuban Project, an interactive geographic data viewer written in Python and C++. I implemented numerous UI components including an interactive map legend, data classification options, and image layer projections. Responsibilities also included providing technical and development support for international users, and writing.

Santa Clara, CA

Continued working with the team developing the reference implementation of the Mobile Information Device Profile (MIDP) preparing for the next software release. Responsibilities included rewriting java packages, addressing software issues, and developing new features.

Cupertino, CA

Worked with a small team developing the reference implementation of the Mobile Information Device Profile (MIDP) for Java ME applets. Responsibilities included addressing existing software issues and developing new graphics code for the next generation release.

Lab instructor for CS 1,2,3 Honors Course Sequence. Responsibilities included conducting class and grading.

Implemented the first version of the Java Debug Wire Protocol for the K Virtual Machine; part of the Java Virtual Machine Micro Edition, which allows any Java debugger to connect to and debug the VM. The Micro Edition is designed to run on small devices such as Palms and cell phones.

Developed software libraries in C to monitor WinSock I/O traffic.

Doctor Of Philosophy (Ph.D.), Theoretical Astrophysics

• Improved estimates of the age of the universe via non-parametric Bayesian modeling of gravitationally lensed quasars. • Performed.

Ba, Ms, Computer Science

MSc. Thesis: Algorithms for Bounding Folkman Numbers Developed a numerical algorithm to solve a combinatorial mathematical question.

Cognitive Science

As part of my undergraduate degree at RIT, I spent one semester semester in Germany taking classes in natural language processing.