Research > Bio-Transport


The functioning and survival of biological systems in physiological and pathological situations is extremely complex and involves interactions of various forces, chemical reactions and physical transport processes at multiple scales. At the macro-scale, starting from the supply of oxygenated blood to the various organs, and return of venous fluid to the lungs for cyclical detoxification, numerous multi-scale phenomena occur in every biological system, including the human body. At the cell level, the shear stress on the endothelium and platelets can cause local atherosclerosis through local plaque deposition, resulting in catastrophic consequences. Inside the cell, numerous physical and chemical processes continuously take place, impacted by the DNA and genetic structure of the cell. The cell itself can be classified as a unit biological factory, which is responsible for cell differentiation, cell replication, and cell death. In normal physiological circumstances, the cell and the organs work harmoniously for system survival and growth. However, these mechanisms are interrupted and lead to abnormal behavior through propagation of disease, cell morphing, cell death and organ failure.

Our goal is to develop multi-scale simulation tools ranging from macro-scale transport of bodily fluids (blood, nutrients, drugs, particles in lungs) to the modeling of an individual cell's behavior through a variety of computational tools that range from continuum-based partial-differential equations to atomistic simulations focusing on individual atoms and molecules. At the intermediate (meso) scale, several models (e.g., lattice Boltzmann method, discrete event simulation methods, dissipative particle dynamics) can be used to bridge the continuum flow processes with the finer-scale processes. On the geometry side as well, the human vascular network is huge consisting of large vessels transitioning to smaller capillaries through branching of the large vessels. Determining the transport processes in physiological and pathological situations can lead to understanding of disease arrest and drug delivery, as well as surgical planning.

In addition to the normal physiological operation, several external forces can be imposed on the biological system to treat several diseases. Examples include laser surgery of the eye, thermal treatment of tumors using acoustic and radio-frequency fields and waves, cell damage due to electromagnetic fields and light effects on cell development. An understanding of these phenomena using multi-physics simulations is challenging and requires extensive data on cell and tissue properties. Modeling can be done at the continuum level as well as the cell level by solving the appropriate equations.

In all of the above simulations, extensive use of parallel computing will be needed. The computational approaches can range from solving partial-differential equations to lattice Boltzmann equations to atomistic-level molecular dynamics simulations. All these approaches can be coupled with each other using multi-scale methods with feedback between individual approaches. The problems can involve hundreds of millions of grid points (or atoms), and the algorithms can be run on several tens to hundreds of CPU nodes.