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Full-Text Articles in Physics
Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore
Toward Improving Understanding Of The Structure And Biophysics Of Glycosaminoglycans, Elizabeth K. Whitmore
Electronic Theses and Dissertations
Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) that mediate PG bioactivities, including signal transduction, tissue morphogenesis, and matrix assembly. To understand GAG function, it is important to understand GAG structure and biophysics at atomic resolution. This is a challenge for existing experimental and computational methods because GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharides. Molecular dynamics (MD) simulations come close to overcoming this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies conformations from unbiased all-atom explicit-solvent MD simulations of short GAG polymers …
Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell
Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell
Faculty Publications
We formulate low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different density and transport coefficients. These equations eliminate the fast isentropic fluctuations in pressure associated with the propagation of sound waves by replacing the equation of state with a local thermodynamic constraint. We demonstrate that the low Mach number model preserves the spatio-temporal spectrum of the slower diffusive fluctuations. We develop a strictly conservative finite-volume spatial discretization of the low Mach number fluctuating equations in both two and three dimensions. We construct several explicit Runge-Kutta temporal integrators that strictly maintain the …