EAPSI: Understanding the dynamics of a living cells using algorithms

Fu Szu-Pei, Kearny NJ

Investigators

Abstract

Biopolymers (such as DNA molecules, actin filaments and microtubules) and biomembranes (made of lipids, proteins, and cholesterols) are the most important building blocks of living cells. In recent years much momentum has been built up in the theoretical simulations of biopolymers and biomembranes. Since such simulations take very long computational time, an efficient algorithm is needed (use fast algorithm for generating matrices or better model to reduce the cost). This project will include the development and implementation of state-of-the-art fast numerical algorithms for hydrodynamic interactions, and will be of benefit to scientists and engineers studying DNA dynamics as well as emerging applications of biomimetic membranes. This research will be conducted in collaboration with Dr. Ming-Chih Lai, a noted expert on simulating fluid-structure interactions, at National Chiao Tung University in Hsinchu, Taiwan. In biologically relevant problems the non-local hydrodynamic interactions (HIs) of macromolecules in water are essential to the underlying physics for their dynamics. This project will develop an efficient coarse-grained numerical algorithm with a fast multiple method for HIs between biomembranes and solvents. In previous work it has been demonstrated that this scheme is fast and convergent for capturing Brownian dynamics (BD) of a biopolymer under flow. Based on these results the main focus of this project is to construct such a coarse-grained scheme to simulate the biologically complicated membranes with cholesterols and proteins interacting with different species of lipids. This project will investigate numerical schemes to efficiently calculate the HIs in coarse-grained BD modeling. By comparing with the continuum modeling, results from this investigation will lead to validation and refinement of the proposed numerical schemes. This NSF EAPSI award is funded in collaboration with National Science Council of Taiwan.