Multiphoton Response of Retinal Rod Photoreceptors

Phototransduction is the process by which light is converted into an electrical response in retinal photoreceptors. Rod photoreceptors contain a stack of (about 1000) disc membranes packed with photopigment rhodopsin molecules, which absorb the photons. We present computational experiments which show the profound effect on the response of the distances (how many discs apart) photons happen to be absorbed at. This photon-distribution effect alone can account for much of the observed variability in response

Time-Stepping for Laser Ablation

Nanosecond laser ablation is a popular technique, applied in many areas of science and technology such as medicine, archaeology, chemistry, environmental and materials sciences. We outline a computational model for radiative and collisional processes occurring during ns-laser ablation, and compare the performance of various low and high order time-stepping algorithms

Computational Models for Nanosecond Laser Ablation

Laser ablation in an ambient environment is becoming increasingly important in science and technology. It is used in applications ranging from chemical analysis via mass spectroscopy, to pulsed laser deposition and nanoparticle manufacturing. We describe numerical schemes for a multiphase hydrodynamic model of nanosecond laser ablation expressing energy, momentum, and mass conservation in the target material, as well as in the expanding plasma plume, along with collisional and radiative processes for laser-induced breakdown (plasma formation). Numerical simulations for copper in a helium background gas are presented and the efficiency of various ODE integrators is compared

Hydrodynamic Modeling of ns-Laser Ablation

Laser ablation is a versatile and widespread technique, applied in an increasing number of medical, industrial and analytical applications. A hydrodynamic multiphase model describing nanosecond-laser ablation (ns- LA) is outlined. The model accounts for target heating and mass removal mechanisms as well as plume expansion and plasma formation. A copper target is placed in an ambient environment consisting of helium and irradiated by a nanosecond-laser pulse. The effect of variable laser settings on the ablation process is explored in 1-D numerical simulations

Modeling aerotaxis band formation in Azospirillum brasilense

Background Bacterial chemotaxis, the ability of motile bacteria to navigate gradients of chemicals, plays key roles in the establishment of various plant-microbe associations, including those that benefit plant growth and crop productivity. The motile soil bacterium Azospirillum brasilense colonizes the rhizosphere and promotes the growth of diverse plants across a range of environments. Aerotaxis, or the ability to navigate oxygen gradients, is a widespread behavior in bacteria. It is one of the strongest behavioral responses in A. brasilense and it is essential for successful colonization of the root surface. Oxygen is one of the limiting nutrients in the rhizosphere where density and activity of organisms are greatest. The aerotaxis response of A. brasilense is also characterized by high precision with motile cells able to detect narrow regions in a gradient where the oxygen concentration is low enough to support their microaerobic lifestyle and metabolism. Results Here, we present a mathematical model for aerotaxis band formation that captures most critical features of aerotaxis in A. brasilense. Remarkably, this model recapitulates experimental observations of the formation of a stable aerotactic band within 2 minutes of exposure to the air gradient that were not captured in previous modeling efforts. Using experimentally determined parameters, the mathematical model reproduced an aerotactic band at a distance from the meniscus and with a width that matched the experimental observation. Conclusion Including experimentally determined parameter values allowed us to validate a mathematical model for aerotactic band formation in spatial gradients that recapitulates the spatiotemporal stability of the band and its position in the gradient as well as its overall width. This validated model also allowed us to capture the range of oxygen concentrations the bacteria prefer during aerotaxis, and to estimate the effect of parameter values (e.g. oxygen consumption rate), both of which are difficult to obtain in experiments

Methane hydrate formation and decomposition

Methane hydrates, in arctic permafrost and deep ocean sediments, store vast amounts of methane, which is the primary constituent of natural gas and a potent greenhouse gas

Alloy Solidification with Convection in the Melt

Most models of alloy solidification are severely limited by the assumption of constant density, thus excluding all convective effects. We present a thermodynamicaly consistent model for binary alloy solidification that incorporates energy, species and momentum conservation, constitutional supercooling, as well as temperature, concentration, and pressure dependence of thermophysical parameters. The crucial aspect is the development of an Equation of State capturing the thermochemistry of the phases. A numerical algorithm will also be outlined. 1 Introduction We outline the main features of a macroscopic model for solidification of a binary alloy with convective and diffusive heat and mass transfer. Given a binary melt A 1\Gammax B x and initial and boundary conditions, the goal is to describe macroscopically the evolution of the phases as the melt undergoes solidification, by modeling the heat and mass transfer in the melt and solid. The basic physical assumptions underlying the model ..

Models of Phototransduction in Rod Photoreceptors

ABSTRACT: Phototransduction is the process by which photons of light generate an electrical response in retinal rod and cone photoreceptors, thereby initiating vision. We compare the electrical response in salamander rods from increasingly more (spacialy) detailed models of phototransduction: 0-dimensional (bulk), 1-dimensional (longitudinal), 2-dimensional (axisymmetric), and 3-dimensional (with incisures). We discuss issues of finding physical parameters for simulation and validation of models, and also present some computational experiments for rods with geometry of mouse and human photoreceptors. AMS (MOS) Subject Classification. 92C45, 35K60, 65M99.