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- Florencio Balboa Usabiaga, John B. Bell, +4 authors Charles S. Peskin
- Multiscale Modeling & Simulation
- 2012

Florencio Balboa, John B. Bell, Rafael Delgado-Buscalioni, Aleksandar Donev, ∗ Thomas Fai, Boyce Griffith, and Charles S. Peskin 1Departamento de F́ısica Teórica de la Materia Condensada, Univeridad Autónoma de Madrid, Madrid 28049, Spain 2Center for Computational Science and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 3Courant… (More)

- Thomas G. Fai, Boyce E. Griffith, Yoichiro Mori, Charles S. Peskin
- SIAM J. Scientific Computing
- 2013

We present a general variable viscosity and variable density immersed boundary method that is first-order accurate in the variable density case and, for problems possessing sufficient regularity, second-order accurate in the constant density case. The viscosity and density are considered material properties and are defined by a dynamically updated… (More)

Aleksandar Donev, ∗ Andy Nonaka, Yifei Sun, 3 Thomas G. Fai, Alejandro L. Garcia, and John B. Bell Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 Center for Computational Science and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 Leon H. Charney Division of Cardiology, Department of Medicine, New… (More)

- Shashank Shekhar, Lian Zhu, Linas Mazutis, Allyson E. Sgro, Thomas G. Fai, Marija Podolski
- Molecular biology of the cell
- 2014

Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative… (More)

We study diffusive mixing in the presence of thermal fluctuations under the assumption of large Schmidt number. In this regime we obtain a limiting equation that contains a diffusive stochastic drift term with diffusion coefficient obeying a Stokes-Einstein relation, in addition to the expected advection by a random velocity. The overdamped limit correctly… (More)

- Andy Nonaka, Yifei Sun, +5 authors A. L. Gar
- 2014

Continuing on our previous work [1], we develop semi-implicit numerical methods for solving low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different densities and transport coefficients. We treat viscous dissipation implicitly using a recently-developed variable-coefficient… (More)

A model for diffusion in liquids that couples the dynamics of tracer particles to a fluctuating Stokes equation for the fluid is investigated in the limit of large Schmidt number. In this limit, the concentration of tracers is shown to satisfy a closed-form stochastic advection-diffusion equation that is used to investigate the collective diffusion of… (More)

- Thomas G. Fai, Boyce E. Griffith, Yoichiro Mori, Charles S. Peskin
- SIAM J. Scientific Computing
- 2014

We analyze the stability and convergence of first-order accurate and second-order accurate timestepping schemes for the Navier-Stokes equations with variable viscosity. These schemes are characterized by a mixed implicit/explicit treatment of the viscous term, in which a numerical parameter, λ, determines the degree of splitting between the implicit and… (More)

We consider a generalization of the classical Art Gallery Problem, where instead of a light source, the guards, called k-transmitters, model a wireless device with a signal that can pass through at most k walls. We show it is NP-hard to compute a minimum cover of point 2transmitters, point k-transmitters, and edge 2-transmitters in a simple polygon. The… (More)

- Chen-Hung Wu, Thomas G. Fai, Paul J. Atzberger, Charles S. Peskin
- SIAM J. Scientific Computing
- 2015

We develop computational methods for the simulation of osmotic swelling phenomena relevant to microscopic vesicles containing transformable solute molecules. We introduce Stochastic Immersed Boundary Methods (SIBM) that can capture osmotically driven fluid transport through semi-permeable elastic membranes subject to thermal fluctuations. We also develop… (More)