L. Elam, M. Quiñones Frías, Y. Zhang. A. A. Rodal, and T. G. Fai, Fast solver for diffusive transport times on dynamic intracellular networks, Submitted (arXiv).
Y. Zhang and T.G. Fai, Influence of the endothelial surface layer on the wall-induced migration of red blood cells, PLOS Comput. Biol., in press (arXiv).
S.J. Zhang, L.A. Lowe, P. Anees, Y. Krishnan, T.G. Fai, J.W. Szostak, and A. Wang, Passive endocytosis in model protocells, Proc. Natl. Acad. Sci. U.S.A., in press (bioRxiv).
G. Kelly, N. Bizmark, B. Chakraborty, S.S. Datta, and T.G. Fai, Modeling the transition between localized and extended deposition in flow networks through packings of glass beads, Phys. Rev. Lett., 130, 128204, 2023 (link, arXiv).
S. J. Del Signore, M. G. Mitzner, A. M. Silveira, T. G. Fai, and A. A. Rodal, An approach for quantitative mapping of synaptic periactive zone architecture and organization, Mol. Biol. Cell, 34(6), ar51, 2023 (link, bioRxiv).
Featured in Condensed Matter Physics Journal Club. (link, highlight)
G. Kelly and T.G. Fai, Multiscale model of clogging in microfluidic devices with grid-like geometries, Proc. R. Soc. A, 478(2261), 20220119, 2022 (link, arXiv).
Y. Park, P. Singh, and T.G. Fai, Coarse-grained stochastic model of myosin-driven vesicles into dendritic spines, SIAM J Appl Math, 82(3), 793-820, 2022 (link, arXiv).
T. G. Fai and Y. Park, Global asymptotic stability of an active disassembly model of flagellar length control, J Math Biol, 84, 8, 2022 (link, arXiv).
J.M. Taylor, T.G. Fai, E.G. Virga, X. Zheng, and P. Palffy-Muhoray, Cavity volume and free energy in many-body systems, J Nonlinear Sci., 31, 87, 2021 (link, arXiv).
S.J. Del Signore, C.F. Kelley, E.M. Messelaar, T. Lemos, M.F. Marchan, B. Ermanoska, M. Mund, T.G. Fai, M. Kaksonen, A.A. Rodal, An autoinhibitory clamp of actin assembly constrains and directs synaptic endocytosis, eLife, 10, e69597, 2021 (link, bioRxiv).
T. G. Fai, J. M. Taylor, E. G. Virga, X. Zheng, and P. Palffy-Muhoray, Leaky cell model of hard spheres. J. Chem. Phys., 154, 104505, 2021 (link, arXiv).
T.G. Fai, L. Mohapatra, P. Kar, J. Kondev, and A. Amir, Length regulation of multiple flagella that self-assemble from a shared pool of components. eLife, 8, e42599, 2019 (link).
T. Ruiz-Herrero, T.G. Fai, and L. Mahadevan, Dynamics of growth and form in prebiotic vesicles. Phys. Rev. Lett., 123, 038102, 2019 (link, arXiv).
Featured in Nature Reviews Physics. (link, highlight)
T.G. Fai and C. Rycroft, Lubricated Immersed Boundary Method in Two Dimensions, J. Comput. Phys., 356, 319-339, 2018 (link, arXiv).
Movies comparing the standard and lubricated immersed boundary methods:
Channel flow, standard IB method (colors represent pressure)
Channel flow, lubricated IB method
Wall-induced migration, standard IB method (dotted line is 2 gridpoints from wall)
Wall-induced migration, lubricated IB method
S. Cannon, T.G. Fai, J. Iwerks, U. Leopold and C. Schmidt, Edge and point 2-transmitter art gallery problems, Comput. Geom., 68, 89-100, 2018 (link, arXiv).
T.G. Fai, R. Kusters, J. Harting, C. Rycroft, and L. Mahadevan, Active elastohydrodynamics of vesicles in narrow, blind constrictions, Phys. Rev. Fluids, 2, 113601, 2017 (link, arXiv)
T.G. Fai, A. Leo-Macias, D.L. Stokes and C.S. Peskin, An image-based model of the spectrin cytoskeleton for red blood cell simulation, PLOS Comput. Biol., 11(6), e1005790, 2017 (link).
Movie of cytoskeleton dynamics
Simulated extension by optical tweezers
C.-H. Wu, T.G. Fai, P.J. Atzberger, and C.S. Peskin, Simulation of osmotic swelling by the stochastic immersed boundary method, SIAM J. Sci. Comput., 37(4), B660-B688, 2015 (link, preprint).
S. Shekhar, L. Zhu, L. Mazutis, A.E. Sgro, T.G. Fai, M. Podolski, Quantitative biology: where modern biology meets physical sciences, Mol. Biol. Cell, 25(22), 3482-3485, 2014 (link).
A. Donev, A.J. Nonaka, Y. Sun, T.G. Fai, A.L. Garcia, and J.B. Bell, Low Mach number fluctuating hydrodynamics of diffusively mixing fluids. Comm. App. Math. and Comp. Sci., 9(1), 47-105, 2014 (link, arXiv).
T.G. Fai, B.E. Griffith, Y. Mori, and C.S. Peskin, Immersed Boundary Method for Variable Viscosity and Variable Density Problems using Fast Constant-Coefficient Linear Solvers II: Theory, SIAM J. Sci. Comput., 36:3, B589-B621, 2014 (link, preprint).
Movies from internal gravity waves in a stratified fluid:
Traveling wave packet, mass density perturbation (left) and energy density (right)
Cross-shaped density (left) and energy (right) resulting from localized disturbance at origin with a fixed frequency
Traveling wave packet in the nonlinear regime with variable viscosity
A. Donev, T.G. Fai, E. Vanden-Eijnden, A reversible mesoscopic model of diffusion in liquids: From giant fluctuations to Fick’s law, J. Stat. Mech., P04004, 2014 (link, arXiv).
T.G. Fai, B.E. Griffith, Y. Mori, and C.S. Peskin. Immersed Boundary Method for Variable Viscosity and Variable Density Problems using Fast Constant-Coefficient Linear Solvers I: Numerical Method and Results, SIAM J. Sci. Comput., 35:5, B1132-B1161, 2013 (link, preprint).
Movies from red blood cell simulations:
Flow through capillary, center of mass frame with fluid tracers