We study a general approach to solving conservation laws of the form qt+ f (q, x) x= 0, where the... more We study a general approach to solving conservation laws of the form qt+ f (q, x) x= 0, where the flux function f (q, x) has explicit spatial variation. Finite-volume methods are used in which the flux is discretized spatially, giving a function fi (q) over the i th grid cell and leading to a generalized Riemann problem between neighboring grid cells. A high-resolution wave-propagation algorithm is defined in which waves are based directly on a decomposition of flux differences fi (Qi-1 (Q i-1) into eigenvectors of an approximate Jacobian matrix.
The classical oscillatory shear wave model of Ferry et al.[JD Ferry, WM Sawyer, JN Ashworth, Beha... more The classical oscillatory shear wave model of Ferry et al.[JD Ferry, WM Sawyer, JN Ashworth, Behavior of concentrated polymer solutions under periodic stresses, J. Polym. Sci. 2 (1947) 593–611] is extended for active linear and nonlinear microrheology. In the Ferry protocol, oscillation and attenuation lengths of the shear wave measured from strobe photographs determine storage and loss moduli at each frequency of plate oscillation.
Abstract The presence of small gas fractions is known to affect the turbulence of a flow. In simu... more Abstract The presence of small gas fractions is known to affect the turbulence of a flow. In simulations of complex bubbly flows, computational expense limits the reso0 lution of interface boundaries. Therefore, the straightforward application of known single0phase turbulence models is precluded. In this paper a turbulence model which specifically accounts for the presence of small gas bubbles is constructed and tested. The bubbles are assumed to be small enough so as not to be resolved by the com0 putational grid.
Cellular blebbing occurs when detachment of the underlying cytoskeleton from a portion of the pla... more Cellular blebbing occurs when detachment of the underlying cytoskeleton from a portion of the plasma membrane leads to the formation of protrusions under the influence of cytosol pressure. Blebbing is associated with cellular apoptosis and has been linked to diseased states such as cancer. Multiple phenomena at disparate scales occur during blebbing. At the molecular scale there are biochemical reactions governing actin polymerization, cross-linkage, and formation of membrane adhesion complexes.
A three-dimensional simulation of the formation of metachronal waves in rows of pulmonary cilia i... more A three-dimensional simulation of the formation of metachronal waves in rows of pulmonary cilia is presented. The cilia move in a two-layer fluid model. The fluid layer adjacent to the cilia bases is purely viscous while the tips of the cilia move through a viscoelastic fluid. An overlapping fixed-moving grid formulation is employed to capture the effect of the cilia on the surrounding fluid.
In animal cells, blebs are smooth, quasi-hemispherical protrusions of the plasma membrane that fo... more In animal cells, blebs are smooth, quasi-hemispherical protrusions of the plasma membrane that form when a section of the membrane detaches from the underlying actin cytoskeleton and is inflated by flowing cytosol. The mechanics behind this common cellular activity are not yet clear.
ABSTRACT Many proto-planetary nebulae (PPNs) appear as narrow collimated structures sometimes sho... more ABSTRACT Many proto-planetary nebulae (PPNs) appear as narrow collimated structures sometimes showing multiple, roughly aligned lobes. In addition, many PPN flows have been shown to have short acceleration times. In this paper we explore whether jet or" bullet"(a massive clump) models fit the observations of individual collimated lobes adequately by comparing simulations of both radiatively cooled (stable) jets and bullets.
Abstract In the large scale computation of turbulent bubbly flow limited computer re sources impl... more Abstract In the large scale computation of turbulent bubbly flow limited computer re sources imply that not all phase interfaces and adjoining boundary layers may be resolved. The problem of devising appropriate closure models thus arises. Two closure problems are considered in this report. The computational procedure is assumed to be based upon the center of mass conservation equations.
Realistic numerical simulations of nonlinear internal waves (NLIWs) have been hampered by the nee... more Realistic numerical simulations of nonlinear internal waves (NLIWs) have been hampered by the need to use computationally expensive nonhydrostatic models. In this paper, we show that the solution to the elliptic problem arising from the incompressibility condition can be successfully approximated by a few terms (three at most) of an expansion in powers of the ratio (horizontal grid spacing)/(total depth).
The acoustic spectrum of the mbira, a musical instrument from Africa that produces sound by the v... more The acoustic spectrum of the mbira, a musical instrument from Africa that produces sound by the vibration of cantilevered metal rods, has been measured. It is found that the most prominent overtones present in the spectrum have frequencies that are approximately 5 and 14 times the lowest frequency.
A parallel-in-time, multiscale interaction procedure is introduced for systems described at molec... more A parallel-in-time, multiscale interaction procedure is introduced for systems described at molecular scales by time-dependent random variables that obey Langevin dynamics. At larger, kinetic scales, the system is described by a probability distribution function that obeys an associated Fokker-Planck equation. It is assumed that the main quantity of interest is the kinetic-scale probability distribution function, and that molecular time scales are much smaller than those of interest at the kinetic scale.
We revisit a classical topic: response functions of viscoelastic layers in large amplitude oscill... more We revisit a classical topic: response functions of viscoelastic layers in large amplitude oscillatory shear. Motivated by questions concerning protective biological layers, we focus on boundary stresses in a parallel plate geometry with imposed oscillatory strain or stress. These features are gleaned from resolution and analysis of coupled standing waves of deformation and stress.
Many materials undergo reconfiguration of microscopic structure in response to applied stress. Co... more Many materials undergo reconfiguration of microscopic structure in response to applied stress. Computing the mechanical behavior of such materials at the continuum level requires a locally valid stress-strain relation. Due to the dynamic microstructure reconfiguration, such relations are difficult to obtain analytically. Numerical simulation of the microscopic dynamics is an alternative, albeit one that is computationally expensive.
Abstract: A number of approaches to the problem of using adaptive mesh refinement in large eddy s... more Abstract: A number of approaches to the problem of using adaptive mesh refinement in large eddy simulations are considered and tested. These include unstructured and structured adaptive grids, various treatments of the convective terms and a number of flow diagnostic procedures. The approaches are exemplified on a rotating channel flow.
Abstract—We present a computational model of the focusing of an electromagnetically induced press... more Abstract—We present a computational model of the focusing of an electromagnetically induced pressure pulse by an acoustic lens and subsequent shock wave formation. Linear elasticity equations for the lens are solved simultaneously with Euler equations for water considered to be a compressible medium with a Tait equation of state. The model is a two-dimensional axisymmetric computation and a buffer linear elasticity region is used to model the water immediately adjacent to the lens.
Abstract Micro-patterned organic solar cells can exhibit enhanced light absorption properties due... more Abstract Micro-patterned organic solar cells can exhibit enhanced light absorption properties due to a photonic crystal effect [Tumbleston etal, Appl. Phys. Lett. 94, 043305 (2009)]. Here, a three-dimensional model of light absorption and charge carrier transport in micro-patterned materials is presented and applied to the design of organic bulk heterojunction (BHJ) solar cells. Rigorous coupled wave analysis is used to simulate the multiple scattering and absorption of light in a layered solar cell device.
• Transformation from one description to the other• 1925, Heinrich Hencky (TU Delft) introduces t... more • Transformation from one description to the other• 1925, Heinrich Hencky (TU Delft) introduces the idea of describing motion in a coordinate system embedded in the material and deforming with thw material. ZaMM 5: 144-146, Die Bewegungsgleichungen beim nichtstationären Fliessen plasticher Massen• 1950, James Oldroyd derives the transformation law
We present a new multiscale model for complex fluids based on three scales: microscopic, kinetic ... more We present a new multiscale model for complex fluids based on three scales: microscopic, kinetic and continuum. We choose the microscopic level as Kramers' bead–rod model for polymers, which we describe as a system of stochastic differential equations with an implicit constraint formulation. The associated Fokker–Planck equation is then derived, and adiabatic elimination removes the fast momentum coordinates. Approached in this way, the kinetic level reduces to a dispersive drift equation.
Extracorporeal shock wave lithotripsy (ESWL) is a noninvasive medical procedure which uses focuse... more Extracorporeal shock wave lithotripsy (ESWL) is a noninvasive medical procedure which uses focused acoustic shock waves to break up kidney stones into small enough pieces for a patient to pass naturally. The ESWL procedure was first used on patients in 1984 and remains the first treatment choice for most stones under 2.5 cm due to the lower complication rate and shorter hospital stay when compared to other kidney stone removal techniques [6].
Abstract Fluctuation distribution has been recently introduced [2] as an alternative to conventio... more Abstract Fluctuation distribution has been recently introduced [2] as an alternative to conventional upwinding. In contrast to standard upwinding the fluctuation distribution approach extends naturally to multidimensional flow without requiring any splitting along coordinate directions. The technique uses a narrow-stencil, local, piecewise linear reconstruction of the flow field solution. The flow field is updated in time by propagating a subset of the eigenmodes of the convective operator.
We study a general approach to solving conservation laws of the form qt+ f (q, x) x= 0, where the... more We study a general approach to solving conservation laws of the form qt+ f (q, x) x= 0, where the flux function f (q, x) has explicit spatial variation. Finite-volume methods are used in which the flux is discretized spatially, giving a function fi (q) over the i th grid cell and leading to a generalized Riemann problem between neighboring grid cells. A high-resolution wave-propagation algorithm is defined in which waves are based directly on a decomposition of flux differences fi (Qi-1 (Q i-1) into eigenvectors of an approximate Jacobian matrix.
The classical oscillatory shear wave model of Ferry et al.[JD Ferry, WM Sawyer, JN Ashworth, Beha... more The classical oscillatory shear wave model of Ferry et al.[JD Ferry, WM Sawyer, JN Ashworth, Behavior of concentrated polymer solutions under periodic stresses, J. Polym. Sci. 2 (1947) 593–611] is extended for active linear and nonlinear microrheology. In the Ferry protocol, oscillation and attenuation lengths of the shear wave measured from strobe photographs determine storage and loss moduli at each frequency of plate oscillation.
Abstract The presence of small gas fractions is known to affect the turbulence of a flow. In simu... more Abstract The presence of small gas fractions is known to affect the turbulence of a flow. In simulations of complex bubbly flows, computational expense limits the reso0 lution of interface boundaries. Therefore, the straightforward application of known single0phase turbulence models is precluded. In this paper a turbulence model which specifically accounts for the presence of small gas bubbles is constructed and tested. The bubbles are assumed to be small enough so as not to be resolved by the com0 putational grid.
Cellular blebbing occurs when detachment of the underlying cytoskeleton from a portion of the pla... more Cellular blebbing occurs when detachment of the underlying cytoskeleton from a portion of the plasma membrane leads to the formation of protrusions under the influence of cytosol pressure. Blebbing is associated with cellular apoptosis and has been linked to diseased states such as cancer. Multiple phenomena at disparate scales occur during blebbing. At the molecular scale there are biochemical reactions governing actin polymerization, cross-linkage, and formation of membrane adhesion complexes.
A three-dimensional simulation of the formation of metachronal waves in rows of pulmonary cilia i... more A three-dimensional simulation of the formation of metachronal waves in rows of pulmonary cilia is presented. The cilia move in a two-layer fluid model. The fluid layer adjacent to the cilia bases is purely viscous while the tips of the cilia move through a viscoelastic fluid. An overlapping fixed-moving grid formulation is employed to capture the effect of the cilia on the surrounding fluid.
In animal cells, blebs are smooth, quasi-hemispherical protrusions of the plasma membrane that fo... more In animal cells, blebs are smooth, quasi-hemispherical protrusions of the plasma membrane that form when a section of the membrane detaches from the underlying actin cytoskeleton and is inflated by flowing cytosol. The mechanics behind this common cellular activity are not yet clear.
ABSTRACT Many proto-planetary nebulae (PPNs) appear as narrow collimated structures sometimes sho... more ABSTRACT Many proto-planetary nebulae (PPNs) appear as narrow collimated structures sometimes showing multiple, roughly aligned lobes. In addition, many PPN flows have been shown to have short acceleration times. In this paper we explore whether jet or" bullet"(a massive clump) models fit the observations of individual collimated lobes adequately by comparing simulations of both radiatively cooled (stable) jets and bullets.
Abstract In the large scale computation of turbulent bubbly flow limited computer re sources impl... more Abstract In the large scale computation of turbulent bubbly flow limited computer re sources imply that not all phase interfaces and adjoining boundary layers may be resolved. The problem of devising appropriate closure models thus arises. Two closure problems are considered in this report. The computational procedure is assumed to be based upon the center of mass conservation equations.
Realistic numerical simulations of nonlinear internal waves (NLIWs) have been hampered by the nee... more Realistic numerical simulations of nonlinear internal waves (NLIWs) have been hampered by the need to use computationally expensive nonhydrostatic models. In this paper, we show that the solution to the elliptic problem arising from the incompressibility condition can be successfully approximated by a few terms (three at most) of an expansion in powers of the ratio (horizontal grid spacing)/(total depth).
The acoustic spectrum of the mbira, a musical instrument from Africa that produces sound by the v... more The acoustic spectrum of the mbira, a musical instrument from Africa that produces sound by the vibration of cantilevered metal rods, has been measured. It is found that the most prominent overtones present in the spectrum have frequencies that are approximately 5 and 14 times the lowest frequency.
A parallel-in-time, multiscale interaction procedure is introduced for systems described at molec... more A parallel-in-time, multiscale interaction procedure is introduced for systems described at molecular scales by time-dependent random variables that obey Langevin dynamics. At larger, kinetic scales, the system is described by a probability distribution function that obeys an associated Fokker-Planck equation. It is assumed that the main quantity of interest is the kinetic-scale probability distribution function, and that molecular time scales are much smaller than those of interest at the kinetic scale.
We revisit a classical topic: response functions of viscoelastic layers in large amplitude oscill... more We revisit a classical topic: response functions of viscoelastic layers in large amplitude oscillatory shear. Motivated by questions concerning protective biological layers, we focus on boundary stresses in a parallel plate geometry with imposed oscillatory strain or stress. These features are gleaned from resolution and analysis of coupled standing waves of deformation and stress.
Many materials undergo reconfiguration of microscopic structure in response to applied stress. Co... more Many materials undergo reconfiguration of microscopic structure in response to applied stress. Computing the mechanical behavior of such materials at the continuum level requires a locally valid stress-strain relation. Due to the dynamic microstructure reconfiguration, such relations are difficult to obtain analytically. Numerical simulation of the microscopic dynamics is an alternative, albeit one that is computationally expensive.
Abstract: A number of approaches to the problem of using adaptive mesh refinement in large eddy s... more Abstract: A number of approaches to the problem of using adaptive mesh refinement in large eddy simulations are considered and tested. These include unstructured and structured adaptive grids, various treatments of the convective terms and a number of flow diagnostic procedures. The approaches are exemplified on a rotating channel flow.
Abstract—We present a computational model of the focusing of an electromagnetically induced press... more Abstract—We present a computational model of the focusing of an electromagnetically induced pressure pulse by an acoustic lens and subsequent shock wave formation. Linear elasticity equations for the lens are solved simultaneously with Euler equations for water considered to be a compressible medium with a Tait equation of state. The model is a two-dimensional axisymmetric computation and a buffer linear elasticity region is used to model the water immediately adjacent to the lens.
Abstract Micro-patterned organic solar cells can exhibit enhanced light absorption properties due... more Abstract Micro-patterned organic solar cells can exhibit enhanced light absorption properties due to a photonic crystal effect [Tumbleston etal, Appl. Phys. Lett. 94, 043305 (2009)]. Here, a three-dimensional model of light absorption and charge carrier transport in micro-patterned materials is presented and applied to the design of organic bulk heterojunction (BHJ) solar cells. Rigorous coupled wave analysis is used to simulate the multiple scattering and absorption of light in a layered solar cell device.
• Transformation from one description to the other• 1925, Heinrich Hencky (TU Delft) introduces t... more • Transformation from one description to the other• 1925, Heinrich Hencky (TU Delft) introduces the idea of describing motion in a coordinate system embedded in the material and deforming with thw material. ZaMM 5: 144-146, Die Bewegungsgleichungen beim nichtstationären Fliessen plasticher Massen• 1950, James Oldroyd derives the transformation law
We present a new multiscale model for complex fluids based on three scales: microscopic, kinetic ... more We present a new multiscale model for complex fluids based on three scales: microscopic, kinetic and continuum. We choose the microscopic level as Kramers' bead–rod model for polymers, which we describe as a system of stochastic differential equations with an implicit constraint formulation. The associated Fokker–Planck equation is then derived, and adiabatic elimination removes the fast momentum coordinates. Approached in this way, the kinetic level reduces to a dispersive drift equation.
Extracorporeal shock wave lithotripsy (ESWL) is a noninvasive medical procedure which uses focuse... more Extracorporeal shock wave lithotripsy (ESWL) is a noninvasive medical procedure which uses focused acoustic shock waves to break up kidney stones into small enough pieces for a patient to pass naturally. The ESWL procedure was first used on patients in 1984 and remains the first treatment choice for most stones under 2.5 cm due to the lower complication rate and shorter hospital stay when compared to other kidney stone removal techniques [6].
Abstract Fluctuation distribution has been recently introduced [2] as an alternative to conventio... more Abstract Fluctuation distribution has been recently introduced [2] as an alternative to conventional upwinding. In contrast to standard upwinding the fluctuation distribution approach extends naturally to multidimensional flow without requiring any splitting along coordinate directions. The technique uses a narrow-stencil, local, piecewise linear reconstruction of the flow field solution. The flow field is updated in time by propagating a subset of the eigenmodes of the convective operator.
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