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Charles S. Peskin

Publications and source records attributed to Charles S. Peskin.

At least 19 recordsLinked to original sources

A Model of a Buoyancy-Driven Heat Exchanger, with Implications for Optimal Design

In this paper, we introduce a model for a buoyancy-driven, air-to-air heat exchanger. This model, derived from first principles, features a conservative boundary condition at inflow based on the compressible Bernoulli equation, and a dissipative boundary condition at outflow based on pressure continuity. We solve for the steady-state behavior numerically and asymptotically, with excellent agreement between the two, and we study the tradeoff between the efficiency and air flow predicted by the model.

math.NA↗

State change via one-dimensional scattering in quantum mechanics

This study aims to address the nature of state change, measurement, and probabilistic outcomes in non-relativistic quantum mechanics. We consider a pair of particles that interact in a one-dimensional setting via a delta-function potential. One of the particles is confined to a one-dimensional box, and the other particle is free. The free particle is incident from the left with specified energy, and it may cause changes in state of the confined particle before flying away to the left or to the right. We present a formulation and computational scheme that avoids the use of perturbation theory and determines the probability of any such outcome as a function of the initial state of the confined particle and the energy of the incident particle. As demonstrated by a direct comparison, this presented method holds multiple advantages over a standard perturbative method. The problem formulation and corresponding computational scheme may have applications in physical settings which admit one-dimensional scattering, e.g., in the study of quantum wires or quantum dots.

quant-ph↗

Convergence of the Immersed Boundary Method for an Elastically Bound Particle Immersed in a 2D Navier-Stokes Fluid Fluid

The immersed boundary (IB) method has been used as a means to simulate fluid-membrane interactions in a wide variety of biological and engineering applications. Although the numerical convergence of the method has been empirically verified, it is theoretically unproved because of the singular forcing terms present in the governing equations. This paper is motivated by a specific variant of the IB method, in which the fluid is 2 dimensions greater than the dimension of the immersed structure. In these co-dimension 2 problems the immersed boundary is necessarily mollified in the continuous formulation. In this paper we leverage this fact to prove convergence of the IB method as applied to a moving elastically bound particle in a fully non-linear fluid.

math.NA↗

Muscle Crossbridge Theory With Internal Crossbridge Dynamics

We describe in this paper a crossbridge model in which an attached crossbridge behaves like a linear spring with a variable rest length. We assume in particular that the rest length has a linear force-velocity relation, and that the force and rest length are both zero at the moment of crossbridge attachment. Crossbridges that are not attached in our model have a fixed probability per unit time of attachment, and attached crossbridges have a probability per unit time of detachment that is a function of the crossbridge force. This detachment rate is uniquely determined by the requirement that a limiting form of the model should reproduce the force-velocity curve and heat of shortening discovered by A.V.Hill~\cite{AVHILL}, and the detachment rate turns out to be a linearly decreasing function of the crossbridge force. The parameters of the model are determined by a fit to steady-state experimental data; and then an event-driven stochastic simulation methodology is introduced in order to study the behavior of the model in a simulated quick-release experiment. The model explains how the crossbridge can act like a linear spring on a fast time scale but have very different properties on a slower time scale.

physics.bio-ph↗

A model for contractile stress fibers embedded in bulk actomyosin networks

Contractile cytoskeletal structures such as fine actomyosin meshworks and stress fibers are essential force-generators for mechanical phenomena in live cells, including motility, morphogenesis, and mechanosensing. While there have been many studies on the rheology and assembly of individual stress fibers, few mathematical models have explicitly modeled the bulk actomyosin network in which stress fibers are embedded, particularly not in the case of high actin turnover. Generally the extent of the interplay between embedded stress fibers and contractile bulk networks is still not well understood. To address this gap, we design a model of stress fibers embedded in bulk actomyosin networks which utilizes the immersed boundary method, allowing one to consider various stress fiber rheologies in the context of an approximately viscous, compressible, contractile bulk network. We characterize the dynamics of bulk actomyosin networks with and without embedded stress fibers, and simulate a laser ablation experiment to demonstrate the effective long-range interactions between stress fibers as well as how perturbations of stress fibers can result in symmetry breaking of the bulk actomyosin network.

physics.bio-ph↗

An Allosteric Model for the Influence of $\text{H}^+$ and $\text{CO}_2$ on Oxygen-Hemoglobin Binding

In the physiology of oxygen-hemoglobin binding, an important role is played by the influence of $\text{H}^+$ and $\text{CO}_2$ on the affinity of hemoglobin for $\text{O}_2$. Here we extend the allosteric model of hemoglobin to include these effects. We assume purely allosteric modulation, i.e., that the modulatory effects of $\text{H}^+$ and $\text{CO}_2$ on oxygen binding occur only because of their influence on the T $\leftrightarrow$ R transition, in which all four subunits of the hemoglobin molecule participate simultaneously. We assume, moreover, that these modulatory influences occur only through the interaction of $\text{H}^+$ and $\text{CO}_2$ with the amino group at the N-terminal of each of the four polypeptide chains of the hemoglobin molecule. We fit the model to experimental data and obtain reasonable agreement with the observed shifts in oxygen-hemoglobin binding that occur when the concentrations of $\text{H}^+$ and $\text{CO}_2$ are changed.

physics.bio-ph↗

Simulating Cardiac Fluid Dynamics in the Human Heart

Cardiac fluid dynamics fundamentally involves interactions between complex blood flows and the structural deformations of the muscular heart walls and the thin, flexible valve leaflets. There has been longstanding scientific, engineering, and medical interest in creating mathematical models of the heart that capture, explain, and predict these fluid-structure interactions. However, existing computational models that account for interactions among the blood, the actively contracting myocardium, and the cardiac valves are limited in their abilities to predict valve performance, resolve fine-scale flow features, or use realistic descriptions of tissue biomechanics. Here we introduce and benchmark a comprehensive mathematical model of cardiac fluid dynamics in the human heart. A unique feature of our model is that it incorporates biomechanically detailed descriptions of all major cardiac structures that are calibrated using tensile tests of human tissue specimens to reflect the heart's microstructure. Further, it is the first fluid-structure interaction model of the heart that provides anatomically and physiologically detailed representations of all four cardiac valves. We demonstrate that this integrative model generates physiologic dynamics, including realistic pressure-volume loops that automatically capture isovolumetric contraction and relaxation, and predicts fine-scale flow features. None of these outputs are prescribed; instead, they emerge from interactions within our comprehensive description of cardiac physiology. Such models can serve as tools for predicting the impacts of medical devices or clinical interventions. They also can serve as platforms for mechanistic studies of cardiac pathophysiology and dysfunction, including congenital defects, cardiomyopathies, and heart failure, that are difficult or impossible to perform in patients.

q-bio.TO↗

A Fourier spectral immersed boundary method with exact translation invariance, improved boundary resolution, and a divergence-free velocity field

This paper introduces a new immersed boundary (IB) method for viscous incompressible flow, based on a Fourier spectral method for the fluid solver and on the nonuniform fast Fourier transform (NUFFT) algorithm for coupling the fluid with the immersed boundary. The new Fourier spectral immersed boundary (FSIB) method gives improved boundary resolution in comparison to the standard IB method. The interpolated velocity field, in which the boundary moves, is analytically divergence-free. The FSIB method is gridless and has the meritorious properties of volume conservation, exact translation invariance, conservation of momentum, and conservation of energy. We verify these advantages of the FSIB method numerically both for the Stokes equations and for the Navier-Stokes equations in both two and three space dimensions. The FSIB method converges faster than the IB method. In particular, we observe second-order convergence in various problems for the Navier-Stokes equations in three dimensions. The FSIB method is also computationally efficient with complexity of $O(N^3\log(N))$ per time step for $N^3$ Fourier modes in three dimensions.

physics.flu-dyn↗

Optimal fenestration of the Fontan circulation

In this paper, we develop a pulsatile compartmental model of the Fontan circulation and use it to explore the effects of a fenestration added to this physiology. A fenestration is a shunt between the systemic and pulmonary veins that is added either at the time of Fontan conversion or at a later time for the treatment of complications. This shunt increases cardiac output and decreases systemic venous pressure. However, these hemodynamic benefits are achieved at the expense of a decrease in the arterial oxygen saturation. The model developed this paper incorporates fenestration size as a parameter and describes both blood flow and oxygen transport. It is calibrated to clinical data from Fontan patients, and we use it to study the impact of a fenestration on several hemodynamic variables. In certain scenarios corresponding to high-risk Fontan physiology, we demonstrate the existence of an optimal fenestration size that maximizes oxygen delivery to the systemic tissues.

q-bio.TO↗

The hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow

In swimming microorganisms and the cell cytoskeleton, inextensible fibers resist bending and twisting, and interact with the surrounding fluid to cause or resist large-scale fluid motion. In this paper, we develop a novel numerical method for the simulation of cylindrical fibers by extending our previous work on inextensible bending fibers [Maxian et al., Phys. Rev. Fluids 6 (1), 014102] to fibers with twist elasticity. In our "Euler" model, twist is a scalar function that measures the deviation of the fiber cross section relative to a twist-free frame, the fiber exerts only torque parallel to the centerline on the fluid, and the perpendicular components of the rotational fluid velocity are discarded in favor of the translational velocity. In the first part of this paper, we justify this model by comparing it to another commonly-used "Kirchhoff" formulation where the fiber exerts both perpendicular and parallel torque on the fluid, and the perpendicular angular fluid velocity is required to be consistent with the translational fluid velocity. We then develop a spectral numerical method for the hydrodynamics of the Euler model. We define hydrodynamic mobility operators using integrals of the Rotne-Prager-Yamakawa tensor, and evaluate these integrals through a novel slender-body quadrature, which requires on the order of 10 points along the fiber to obtain several digits of accuracy. We demonstrate that this choice of mobility removes the unphysical negative eigenvalues in the translation-translation mobility associated with asymptotic slender body theories, and ensures strong convergence of the fiber velocity and weak convergence of the fiber constraint forces. We pair the spatial discretization with a semi-implicit temporal integrator to confirm the negligible contribution of twist elasticity to the relaxation dynamics of a bent fiber and study the instability of a twirling fiber.

math.NA↗

An Analysis of the Numerical Stability of the Immersed Boundary Method

We present a numerical stability analysis of the immersed boundary(IB) method for a special case which is constructed so that Fourier analysis is applicable. We examine the stability of the immersed boundary method with the discrete Fourier transforms defined differently on the fluid grid and the boundary grid. This approach gives accurate theoretical results about the stability boundary since it takes the effects of the spreading kernel of the immersed boundary method on the numerical stability into account. In this paper, the spreading kernel is the standard 4-point IB delta function. A three-dimensional incompressible viscous flow and a no-slip planar boundary are considered. The case of a planar elastic membrane is also analyzed using the same analysis framework and it serves as an example of many possible generalizations of our theory. We present some numerical results and show that the observed stability behaviors are consistent with what are predicted by our theory.

math.NA↗

Computer simulation of surgical interventions for the treatment of refractory pulmonary hypertension

This paper describes computer models of three interventions used for treating refractory pulmonary hypertension (RPH). These procedures create either an atrial septal defect, a ventricular septal defect, or, in the case of a Potts shunt, a patent ductus arteriosus. The aim in all three cases is to generate a right-to-left shunt, allowing for either pressure or volume unloading of the right side of the heart in the setting of right ventricular failure, while maintaining cardiac output. These shunts are created, however, at the expense of introducing de-oxygenated blood into the systemic circulation, thereby lowering the systemic arterial oxygen saturation. The models developed in this paper are based on compartmental descriptions of human hemodynamics and oxygen transport. An important parameter included in our models is the cross-sectional area of the surgically created defect. Numerical simulations are performed to compare different interventions and various shunt sizes and to assess their impact on hemodynamic variables and oxygen saturations. We also create a model for exercise and use it to study exercise tolerance in simulated pre-intervention and post-intervention RPH patients.

q-bio.TO↗

Gaussian-Like Immersed Boundary Kernels with Three Continuous Derivatives and Improved Translational Invariance

The immersed boundary (IB) method is a general mathematical framework for studying problems involving fluid-structure interactions in which an elastic structure is immersed in a viscous incompressible fluid. In the IB formulation, the fluid described by Eulerian variables is coupled with the immersed structure described by Lagrangian variables via the use of the Dirac delta function. From a numerical standpoint, the Lagrangian force spreading and the Eulerian velocity interpolation are carried out by a regularized, compactly supported discrete delta function, which is assumed to be a tensor product of a single-variable immersed-boundary kernel. IB kernels are derived from a set of postulates designed to achieve approximate grid translational invariance, interpolation accuracy and computational efficiency. In this note, we present new 5-point and 6-point immersed-boundary kernels that are $\mathscr{C}^3$ and yield a substantially improved translational invariance compared to other common IB kernels.

math.NA↗

Models for plasma kinetics during simultaneous therapeutic plasma exchange and extracorporeal membrane oxygenation

This paper focuses on the derivation and simulation of mathematical models describing new plasma fraction in blood for patients undergoing simultaneous extracorporeal membrane oxygenation and therapeutic plasma exchange. Models for plasma exchange with either veno-arterial or veno-venous extracorporeal membrane oxygenation are considered. Two classes of models are derived for each case, one in the form of an algebraic delay equation and another in the form of a system of delay differential equations. In special cases, our models reduce to single compartment ones for plasma exchange that have been validated with experimental data. We also show that the algebraic delay equations are forward Euler discretizations of the delay differential equations, with timesteps equal to transit times through model compartments. Numerical simulations are performed to compare different model types, to investigate the impact of plasma device port switching on the efficiency of the exchange process, and to study the sensitivity of the models to their parameters.

math.DS↗

An immersed boundary method with subgrid resolution and improved numerical stability applied to slender bodies in Stokes flow

The immersed boundary method is a numerical and mathematical formulation for solving fluid-structure interaction problems. It relies on solving fluid equations on an Eulerian fluid grid and interpolating the resulting velocity back onto immersed structures. To resolve slender fibers, the grid spacing must be on the order of the fiber radius, and thus the number of required grid points along the filament must be of the same order as the aspect ratio. Simulations of slender bodies using the IB method can therefore be intractable. A technique is presented to address this problem in the context of Stokes flow. The velocity of the structure is split into a component coming from the underlying fluid grid, which is coarser than normally required, and a component proportional to the force (a drag term). The drag coefficient is set so that a single sphere is represented exactly on a grid of arbitrary meshwidth. Implicit treatment of the drag term removes some of the stability restrictions normally associated with the IB method. This comes at a loss of accuracy, although tests are conducted that show 1-2 digits of relative accuracy can be obtained on coarser grids. After its accuracy and stability are tested, the method is applied to two real world examples: fibers in shear flow and a suspension of fibers. These examples show that the method can reproduce existing results and make reasonable predictions about the viscosity of an aligned fiber suspension.

math.NA↗

Modeling the Mitral Valve

This work is concerned with modeling and simulation of the mitral valve, one of the four valves in the human heart. The valve is composed of leaflets, the free edges of which are supported by a system of chordae, which themselves are anchored to the papillary muscles inside the left ventricle. First, we examine valve anatomy and present the results of original dissections. These display the gross anatomy and information on fiber structure of the mitral valve. Next, we build a model valve following a design-based methodology, meaning that we derive the model geometry and the forces that are needed to support a given load, and construct the model accordingly. We incorporate information from the dissections to specify the fiber topology of this model. We assume the valve achieves mechanical equilibrium while supporting a static pressure load. The solution to the resulting differential equations determines the pressurized configuration of the valve model. To complete the model we then specify a constitutive law based on a stress-strain relation consistent with experimental data that achieves the necessary forces computed in previous steps. Finally, using the immersed boundary method, we simulate the model valve in fluid in a computer test chamber. The model opens easily and closes without leak when driven by physiological pressures over multiple beats. Further, its closure is robust to driving pressures that lack atrial systole or are much lower or higher than normal.

q-bio.TO↗

An Immersed Boundary Method with Divergence-Free Velocity Interpolation and Force Spreading

The Immersed Boundary (IB) method is a mathematical framework for constructing robust numerical methods to study fluid-structure interaction in problems involving an elastic structure immersed in a viscous fluid. The IB formulation uses an Eulerian representation of the fluid and a Lagrangian representation of the structure. The Lagrangian and Eulerian frames are coupled by integral transforms with delta function kernels. The discretized IB equations use approximations to these transforms with regularized delta function kernels to interpolate the fluid velocity to the structure, and to spread structural forces to the fluid. It is well-known that the conventional IB method can suffer from poor volume conservation since the interpolated Lagrangian velocity field is not generally divergence-free, and so this can cause spurious volume changes. In practice, the lack of volume conservation is especially pronounced for cases where there are large pressure differences across thin structural boundaries. The aim of this paper is to greatly reduce the volume error of the IB method by introducing velocity-interpolation and force-spreading schemes with the properties that the interpolated velocity field in which the structure moves is at least C1 and satisfies a continuous divergence-free condition, and that the force-spreading operator is the adjoint of the velocity-interpolation operator. We confirm through numerical experiments in two and three spatial dimensions that this new IB method is able to achieve substantial improvement in volume conservation compared to other existing IB methods, at the expense of a modest increase in the computational cost. Further, the new method provides smoother Lagrangian forces (tractions) than traditional IB methods. The method presented here is restricted to periodic computational domains. Its generalization to non-periodic domains is important future work.

math.NA↗

The Influence of Spatial Variation in Chromatin Density Determined by X-ray Tomograms on the Time to Find DNA Binding Sites

In this work we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory sensory neurons is determined from soft X-ray tomography reconstructions of five nuclei. We show that there is a division of the nuclear space into regions of low-density euchromatin and high-density heterochromatin. Volume exclusion experienced by a diffusing protein caused by this varying density of chromatin is modeled by a repulsive potential. The value of the potential at a given point in space is chosen to be proportional to the density of chromatin at that location. The constant of proportionality, called the volume exclusivity, provides a model parameter that determines the strength of volume exclusion. Numerical simulations demonstrate that the mean time for a protein to locate a binding site localized in euchromatin is minimized for a finite, non-zero volume exclusivity. For binding sites in heterochromatin, the mean time is minimized when the volume exclusivity is zero (the protein experiences no volume exclusion). An analytical theory is developed to explain these results. The theory suggests that for binding sites in euchromatin there is an optimal level of volume exclusivity that balances a reduction in the volume searched in finding the binding site, with the height of effective potential barriers the protein must cross during the search process.

q-bio.SC↗