Sanjay R. Kharche, Ph.D. Computational Medicine Laboratory. Home of PM3 (Precision Medicine Using Mathematical Modeling) HPC platforms.

Announcing the 2021 workshop: 2021 Workshop.

Kidney disease affects more than 10% of the population in Canada, and treatments are cost and resource intensive. Members of the Kidney Clinical Research Unit (KCRU), within which this lab is based, are aggressively pursuing clinical research to identify effective therapies that can be implemented at various stages of the disease. Clinical research is necessary, but must be thoroughly justified. An integrative approach will help to uncover mechanisms of disease, dialysis treatment, and of pharmacological therapies. We presently have sub-system descriptions (e.g. arrhythmia in small heart tissue preparations, function of a single nephron). However, the effects propagate from one sub-system to another, with the combination of sub-systems giving rise to emergent phenomena. Efforts in multiple projects extends and customizes appropriate sub-system mathematical models to implement available individual characteristics to specify the mechanistic and probablistic basis of disease, to understand non-response to therapy, in view of optimizing treatment strategies.

I am an applied mathematician. I represent poorly understood but very important cell to organ level processes in a mathematical framework as mechanistic models. I use and analyse these models to understand the inter-related dynamics of the complex organisation of electro-mechanical, fluid flow, metabolic and other multi-physics that dictate life functions and failure thereof. In addition to mathematical physiology, I work on computational imaging that is designed to preinform our clinical-imaging research. My work is targeted towards further improvement of healthcare research and practice, but also serves developments in maths, computer science, and software engineering due to the nature of it.

A complementary physical sciences approach will further sharpen the value of our clinical trial outcomes by:

• comprehensively exploiting clinical data (imaging, BP, ECG, blood testing, signals) to the patient's advantage, understand what the processes are;
• generating basic science mechanism based evidence and inform us how and why the therapy may be effective;
• providing decision making tools in the mid-term which will be based on cause-effect mechanism investigations;
• providing a pruning and hypothesis testing platform using the mechanistic and AI systems;
• integrating extant knowledge within our University, Hospitals, as well as worldwide to further increase the pace of our clinical research, be able to share our expertise with other investigators;
• developing a big data (AI) infrastructure geared specifically towards kidney disease patients' data;
• developing an exciting team of investigators with expertise in maths, HPC, imaging techniques, computer science, engineering, clinical sciences; and
• working by collaboration with researchers throughout the world.

To do so, we have the following PM³ platforms:

• PM³-SimVascular, a customized blood flow simulation library for local use.
• PM³-Chaste, a customized cardiac electrophysiology simulation library for local use.
• Virtual Cardiac Physiological Laboratory (VCPL);
• Dynamic blood flow in internal organs simulator;
• CT and MRI simulator.
• Image processing using Slicer3D, Fiji-ImageJ, in house MATLAB programs.