A continuum method for modeling surface tension

We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

/pdf/the-martini-force-field-coarse-grained-model-for-3l11ncr3fg.pdf

The MARTINI force field : Coarse grained model for biomolecular simulations

This paper is concerned with the mathematical structure of the immersed boundary (IB) method, which is intended for the computer simulation of fluid–structure interaction, especially in biological fluid dynamics. The IB formulation of such problems, derived here from the principle of least action, involves both Eulerian and Lagrangian variables, linked by the Dirac delta function. Spatial discretization of the IB equations is based on a fixed Cartesian mesh for the Eulerian variables, and a moving curvilinear mesh for the Lagrangian variables. The two types of variables are linked by interaction equations that involve a smoothed approximation to the Dirac delta function. Eulerian/Lagrangian identities govern the transfer of data from one mesh to the other. Temporal discretization is by a second-order Runge–Kutta method. Current and future research directions are pointed out, and applications of the IB method are briefly discussed. Introduction The immersed boundary (IB) method was introduced to study flow patterns around heart valves and has evolved into a generally useful method for problems of fluid–structure interaction. The IB method is both a mathematical formulation and a numerical scheme. The mathematical formulation employs a mixture of Eulerian and Lagrangian variables. These are related by interaction equations in which the Dirac delta function plays a prominent role. In the numerical scheme motivated by the IB formulation, the Eulerian variables are defined on a fixed Cartesian mesh, and the Lagrangian variables are defined on a curvilinear mesh that moves freely through the fixed Cartesian mesh without being constrained to adapt to it in any way at all.

/pdf/the-immersed-boundary-method-xfkx3wd291.pdf

The immersed boundary method

Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the Peclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.

/pdf/microfluidics-fluid-physics-at-the-nanoliter-scale-4bpahtd8qa.pdf

Microfluidics: Fluid physics at the nanoliter scale

Here, we describe a biomimetic microsystem that reconstitutes the critical functional alveolar-capillary interface of the human lung. This bioinspired microdevice reproduces complex integrated organ-level responses to bacteria and inflammatory cytokines introduced into the alveolar space. In nanotoxicology studies, this lung mimic revealed that cyclic mechanical strain accentuates toxic and inflammatory responses of the lung to silica nanoparticles. Mechanical strain also enhances epithelial and endothelial uptake of nanoparticulates and stimulates their transport into the underlying microvascular channel. Similar effects of physiological breathing on nanoparticle absorption are observed in whole mouse lung. Mechanically active "organ-on-a-chip" microdevices that reconstitute tissue-tissue interfaces critical to organ function may therefore expand the capabilities of cell culture models and provide low-cost alternatives to animal and clinical studies for drug screening and toxicology applications.

http://science.sciencemag.org/content/sci/328/5986/1662.full.pdf

Reconstituting Organ-Level Lung Functions on a Chip

Airway collapse and reopening due to mechanical ventilation exerts mechanical stress on airway walls and injures surfactant-compromised lungs. The reopening of a collapsed airway was modeled experimentally and computationally by the progression of a semi-infinite bubble in a narrow fluid-occluded channel. The extent of injury caused by bubble progression to pulmonary epithelial cells lining the channel was evaluated. Counterintuitively, cell damage increased with decreasing opening velocity. The presence of pulmonary surfactant, Infasurf, completely abated the injury. These results support the hypotheses that mechanical stresses associated with airway reopening injure pulmonary epithelial cells and that pulmonary surfactant protects the epithelium from this injury. Computational simulations identified the magnitudes of components of the stress cycle associated with airway reopening (shear stress, pressure, shear stress gradient, or pressure gradient) that may be injurious to the epithelial cells. By comparing these magnitudes to the observed damage, we conclude that the steep pressure gradient near the bubble front was the most likely cause of the observed cellular damage.

https://www.physiology.org/doi/pdf/10.1152/japplphysiol.00764.2002

Mechanisms of surface-tension-induced epithelial cell damage in a model of pulmonary airway reopening.

We investigate the flow induced by a localized insoluble surfactant on a thin film. This problem is intended to model the behaviour of the lung's thin-film lining after an aerosol droplet lands on its surface. The surfactant-induced surface-tension gradients drive convection (Marangoni convection) within the film, disrupting the film surface and causing the surfactant to spread. The surfactant may also spread on the film's surface by surface diffusion without inducing convection. Gravity provides a restoring force that decreases film disturbances.Lubrication theory is employed to derive equations that describe the evolution of the film thickness and surfactant concentration. A nonlinear surface-tension equation of state describes the relationship between the surfactant concentration and the surface tension. Solutions of the evolution equations are found numerically using the method of lines and analytically under limiting cases of small and large surface diffusivity. The results elucidate the behaviour of the thin-film/surfactant system.We find that surface-tension-induced convection creates film disturbances that increase the film thickness near the surfactant's leading edge, and thins the film in the central region. Surface diffusion causes more rapid spreading of the surfactant, and decreases the film disturbances. Gravity decreases the film disturbances by creating bi-directional flow in the form of a ring vortex. This behaviour may have implications for the delivery of medications or toxins by aerosol inhalation.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0022112090002257

The dynamics of a localized surfactant on a thin film

We studied airway opening in a benchtop model intended to mimic bronchial walls held in apposition by airway lining fluid. We measured the relationship between the airway opening velocity (U) and t...

Effects of surface tension and viscosity on airway reopening.

https://www.cell.com/biophysj/pdf/S0006-3495(98)77562-9.pdf

Donald P. Gaver

Papers

Mechanisms of surface-tension-induced epithelial cell damage in a model of pulmonary airway reopening.

The dynamics of a localized surfactant on a thin film

Effects of surface tension and viscosity on airway reopening.

A Theoretical Model Study of the Influence of Fluid Stresses on a Cell Adhering to a Microchannel Wall

Modeling Biofilm Processes Using the Immersed Boundary Method