2013 

2.  MontenegroJohnson, T D; Smith, D J; Loghin, D Physics of rheologically enhanced propulsion: different strokes in generalized Stokes Journal Article Physics of Fluids, 25 (8), pp. 081903, 2013, (Highlighted in the Journal Club for Condensed Matter Physics with a commentary by Prof. Thomas R. Powers.). Abstract  BibTeX  Tags: Complex fluid, Finite elements, Microscale propulsion  Links: @article{montenegro2013physics, title = {Physics of rheologically enhanced propulsion: different strokes in generalized Stokes}, author = {T. D. MontenegroJohnson and D. J. Smith and D. Loghin }, url = {http://tomonjon.com/wpcontent/uploads/2016/11/DifferentstrokesingeneralizedStokes.pdf}, doi = {10.1063/1.4818640}, year = {2013}, date = {20130821}, journal = {Physics of Fluids}, volume = {25}, number = {8}, pages = {081903}, abstract = {Shearthinning is an important rheological property of many biological fluids, such as mucus, whereby the apparent viscosity of the fluid decreases with shear. Certain microscopic swimmers have been shown to progress more rapidly through shearthinning fluids, but is this behavior generic to all microscopic swimmers, and what are the physics through which shearthinning rheology affects a swimmer's propulsion? We examine swimmers employing prescribed stroke kinematics in twodimensional, inertialess Carreau fluid: shearthinning “generalized Stokes” flow. Swimmers are modeled, using the method of femlets, by a set of immersed, regularized forces. The equations governing the fluid dynamics are then discretized over a bodyfitted mesh and solved with the finite element method. We analyze the locomotion of three distinct classes of microswimmer: (1) conceptual swimmers comprising sliding spheres employing both one and twodimensional strokes, (2) slipvelocity envelope models of ciliates commonly referred to as “squirmers,” and (3) monoflagellate pushers, such as sperm. We find that morphologically identical swimmers with different strokes may swim either faster or slower in shearthinning fluids than in Newtonian fluids. We explain this kinematic sensitivity by considering differences in the viscosity of the fluid surrounding propulsive and payload elements of the swimmer, and using this insight suggest two reciprocal sliding sphere swimmers which violate Purcell's Scallop theorem in shearthinning fluids. We also show that an increased flow decay rate arising from shearthinning rheology is associated with a reduction in the swimming speed of slipvelocity squirmers. For spermlike swimmers, a gradient of thick to thin fluid along the flagellum alters the force it exerts upon the fluid, flattening trajectories and increasing instantaneous swimming speed.}, note = {Highlighted in the Journal Club for Condensed Matter Physics with a commentary by Prof. Thomas R. Powers.}, keywords = {Complex fluid, Finite elements, Microscale propulsion}, pubstate = {published}, tppubtype = {article} } Shearthinning is an important rheological property of many biological fluids, such as mucus, whereby the apparent viscosity of the fluid decreases with shear. Certain microscopic swimmers have been shown to progress more rapidly through shearthinning fluids, but is this behavior generic to all microscopic swimmers, and what are the physics through which shearthinning rheology affects a swimmer's propulsion? We examine swimmers employing prescribed stroke kinematics in twodimensional, inertialess Carreau fluid: shearthinning “generalized Stokes” flow. Swimmers are modeled, using the method of femlets, by a set of immersed, regularized forces. The equations governing the fluid dynamics are then discretized over a bodyfitted mesh and solved with the finite element method. We analyze the locomotion of three distinct classes of microswimmer: (1) conceptual swimmers comprising sliding spheres employing both one and twodimensional strokes, (2) slipvelocity envelope models of ciliates commonly referred to as “squirmers,” and (3) monoflagellate pushers, such as sperm. We find that morphologically identical swimmers with different strokes may swim either faster or slower in shearthinning fluids than in Newtonian fluids. We explain this kinematic sensitivity by considering differences in the viscosity of the fluid surrounding propulsive and payload elements of the swimmer, and using this insight suggest two reciprocal sliding sphere swimmers which violate Purcell's Scallop theorem in shearthinning fluids. We also show that an increased flow decay rate arising from shearthinning rheology is associated with a reduction in the swimming speed of slipvelocity squirmers. For spermlike swimmers, a gradient of thick to thin fluid along the flagellum alters the force it exerts upon the fluid, flattening trajectories and increasing instantaneous swimming speed. 
2012 

1.  MontenegroJohnson, T D; Smith, A A; Smith, D J; Loghin, D; Blake, J R Modelling the fluid mechanics of cilia and flagella in reproduction and development Journal Article European Physical Journal E, 35 (10), pp. 111, 2012, ISSN: 1292895X. Abstract  BibTeX  Tags: Cilia, Complex fluid, Microscale propulsion, Symmetrybreaking flow  Links: @article{montenegro2012modelling, title = {Modelling the fluid mechanics of cilia and flagella in reproduction and development}, author = {T. D. MontenegroJohnson and A. A. Smith and D. J. Smith and D. Loghin and J. R. Blake}, url = {http://tomonjon.com/wpcontent/uploads/2016/11/Modellingthefluidmechanicsofciliaandflagellainreproductionanddevelopment.pdf}, doi = {10.1140/epje/i2012121111}, issn = {1292895X}, year = {2012}, date = {20121029}, journal = {European Physical Journal E}, volume = {35}, number = {10}, pages = {111}, abstract = {Cilia and flagella are actively bending slender organelles, performing functions such as motility, feeding and embryonic symmetry breaking. We review the mechanics of viscousdominated microscale flow, including timereversal symmetry, drag anisotropy of slender bodies, and wall effects. We focus on the fundamental force singularity, higherorder multipoles, and the method of images, providing physical insight and forming a basis for computational approaches. Two biological problems are then considered in more detail: 1) leftright symmetry breaking flow in the node, a microscopic structure in developing vertebrate embryos, and 2) motility of microswimmers through nonNewtonian fluids. Our model of the embryonic node reveals how particle transport associated with morphogenesis is modulated by the gradual emergence of cilium posterior tilt. Our model of swimming makes use of force distributions within a bodyconforming finiteelement framework, allowing the solution of nonlinear inertialess Carreau flow. We find that a threesphere model swimmer and a model sperm are similarly affected by shearthinning; in both cases swimming due to a prescribed beat is enhanced by shearthinning, with optimal Deborah number around 0.8. The sperm exhibits an almost perfect linear relationship between velocity and the logarithm of the ratio of zero to infinite shear viscosity, with shearthickening hindering cell progress.}, keywords = {Cilia, Complex fluid, Microscale propulsion, Symmetrybreaking flow}, pubstate = {published}, tppubtype = {article} } Cilia and flagella are actively bending slender organelles, performing functions such as motility, feeding and embryonic symmetry breaking. We review the mechanics of viscousdominated microscale flow, including timereversal symmetry, drag anisotropy of slender bodies, and wall effects. We focus on the fundamental force singularity, higherorder multipoles, and the method of images, providing physical insight and forming a basis for computational approaches. Two biological problems are then considered in more detail: 1) leftright symmetry breaking flow in the node, a microscopic structure in developing vertebrate embryos, and 2) motility of microswimmers through nonNewtonian fluids. Our model of the embryonic node reveals how particle transport associated with morphogenesis is modulated by the gradual emergence of cilium posterior tilt. Our model of swimming makes use of force distributions within a bodyconforming finiteelement framework, allowing the solution of nonlinear inertialess Carreau flow. We find that a threesphere model swimmer and a model sperm are similarly affected by shearthinning; in both cases swimming due to a prescribed beat is enhanced by shearthinning, with optimal Deborah number around 0.8. The sperm exhibits an almost perfect linear relationship between velocity and the logarithm of the ratio of zero to infinite shear viscosity, with shearthickening hindering cell progress. 
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