Heterogenous Cryo EM Reconstruction

In collaboration with Prof. John (Jack) E. Johnson at The Scripps Research Institute, we have worked on computational problems in the structural biology of viruses since about 1990. The current focus is on single-particle cryo electron microscopy (cryo EM). This technique collects transmission electron microscopy images on a large number of individual instances of the particle. Since the information from different particles is not mixed (as it is in x-ray crystallography or nuclear magnetic resonance), it is possible to study the heterogeneity of the particles. We have developed a statistical description of the heterogeneity and algorithms and software for estimating the heterogeneity from the image data. We are currently working to improve the algorithms and software in order to achieve higher spatial resolution in the 3-D information that is obtained. We are currently trying to take a more fundamental physics-oriented approach for the case where the heterogeneity is due to statistical physics motions of the particles in the ensemble. Eleven Ph.D. students have completed thesis research in the area of computational structural biology and the work is currently being continued by Christina L. Lau who is a Ph.D. student in ECE.

In collaboration with Prof. Uli Weisner, we have investigated the geometry of nanoscale silica particles using the same software that was developed for the structural biology of viruses!  This work is presently being pursued by Dong June Jang who is a Ph.D. student in Prof. Wiesner’s group in Materials Science and Engineering.

Printed and Cleanroom Electronics

In collaboration with Prof. Amit Lal and Prof. Ben Davaji, we are exploring the applications of Artificial Intelligence and Machine Learning (AI/ML) to electronics fabrication, both nanoscale electronics fabricated in the Cornell NanoScale Science and Technology Facility and millimeter scale printed electronics.  A focus is AI/ML digital twins of the tools with the eventual goal of doing design both of the layout and of the process parameters for each tool in the fabrication process.  The work started with a DARPA Physics in AI contract and has continued with five SEMI contracts.

AI/ML for Lipid Nanoparticle Synthesis

In collaboration with a large pharmaceutical company, we are using Artificial Intelligence and Machine Learning (AI/ML) to describe and improve the synthesis of Lipid Nano Particles (LNPs) for the delivery of mRNA cargo.

Past Projects


Pharmacokinetics of Alcohol

In collaboration with Prof. Sean J. O’Connor, we have investigated the pharmacokinetics of alcohol (ethanol) in human subjects.  The goal was to develop mathematical models describing the pharmacokinetcs, develop algorithms and software to determine the parameters in the models from human subject data, and to use the models to predict what would happen when human subjects were given alcohol.

Other Projects

Other projects include speech signal processing, the dynamics of blood flow in the cerebral cortex, and statistical image processing based on analogies with lattice field theories in statistical physics.

Information about publications is here.