Physics 437: projects in computational physics

Jeff Z.Y. Chen
PHY 355 ext. 5361

Understanding protein folding from polymer models

The current understanding of the characteristics of protein folding is widely based on statistical-physics models of polymers that capture the essential interactions in real protein systems. The reduction of the degrees of freedom of the involved coordinates in such a model, in comparison with the all-atom modelling approach, allows for accumulation of adequate statistics in computer simulations. This type of models has been successfully used to explore the underlying physical mechanism of structural formation, folding dynamics and protein-protein interaction.

David Yevick
PHY 356 ext. 5200

Simulation of pulse propagation and interaction in optical fiber systems

As the speed of optical fiber systems approaches the theoretical fiber bandwidth, the time duration and intensities of the transmitted optical bits are approaching the regime of strong optical nonlinearities. As a result, either the pulse shape must undergo compensation to maintain quasi-linear transmission or nonlinear effects must be exploited by balancing the chromatic dispersion of the different wavelengths in the pulse against the fiber nonlinearities through soliton generation. The objective of this project is to generate a numerical model of high-speed pulse and optical soliton generation and propagation in realistic optical communication systems starting from optical field evolution programs. C++ programming experience would be an asset but is not essential.

Simulation of optical fiber communication systems

System-level simulation tools that allow engineers and scientists to predict bit-error rates based on phenomenological component models are of increasing importance in the design not only of large-scale optical fiber networks but also in setting specifications for optical component design. While many large-scale commercial system simulators currently exist, the ability to design a simple model of an optical fiber link based on observed statistical and physical device-level information is still considered a key asset in many industrial contexts. Students involved in the project would therefore be expected to investigate the properties of current simulators and to implement as far as possible similar functionality for the most basic source-fiber-detector links within an object-oriented visual programming environment. Higher level modeling involving optical fiber networks could also be envisioned as part of or instead of this project for students with prior knowledge in the optical communication or network area.