Modeling ion channel dynamics through reflected stochastic differential equations

Ion channels are membrane proteins that open and close at random and play a vital role in the electrical dynamics of excitable cells. The stochastic nature of the conformational changes these proteins undergo can be significant, however current stochastic modeling methodologies limit the ability to study such systems. Discrete-state Markov chain models are seen as the "gold standard," but are computationally intensive, restricting investigation of stochastic effects to the single-cell level. Continuous stochastic methods that use stochastic differential equations (SDEs) to model the system are more efficient but can lead to simulations that have no biological meaning. In this paper we show that modeling the behavior of ion channel dynamics by a reflected SDE ensures biologically realistic simulations, and we argue that this model follows from the continuous approximation of the discrete-state Markov chain model. Open channel and action potential statistics from simulations of ion channel dynamics using the reflected SDE are compared with those of a discrete-state Markov chain method. Results show that the reflected SDE simulations are in good agreement with the discrete-state approach. The reflected SDE model therefore provides a computationally efficient method to simulate ion channel dynamics while preserving the distributional properties of the discrete-state Markov chain model and also ensuring biologically realistic solutions. This framework could easily be extended to other biochemical reaction networks. © 2012 American Physical Society.

Dermal fibroblast infiltration of poly(ε-caprolactone) scaffolds fabricated by melt electrospinning in a direct writing mode

Melt electrospinning in a direct writing mode is a recent additive manufacturing approach to fabricate porous scaffolds for tissue engineering applications. In this study, we describe porous and cell-invasive poly (ε-caprolactone) scaffolds fabricated by combining melt electrospinning and a programmable x–y stage. Fibers were 7.5 ± 1.6 µm in diameter and separated by interfiber distances ranging from 8 to 133 µm, with an average of 46 ± 22 µm. Micro-computed tomography revealed that the resulting scaffolds had a highly porous (87%), three-dimensional structure. Due to the high porosity and interconnectivity of the scaffolds, a top-seeding method was adequate to achieve fibroblast penetration, with cells present throughout and underneath the scaffold. This was confirmed histologically, whereby a 3D fibroblast-scaffold construct with full cellular penetration was produced after 14 days in vitro. Immunohistochemistry was used to confirm the presence and even distribution of the key dermal extracellular matrix proteins, collagen type I and fibronectin. These results show that melt electrospinning in a direct writing mode can produce cell invasive scaffolds, using simple top-seeding approaches.

Gravity-driven fingering simulations for a thin liquid film flowing down the outside of a vertical cylinder

A numerical study is presented to examine the fingering instability of a gravity-driven thin liquid film flowing down the outer wall of a vertical cylinder. The lubrication approximation is employed to derive an evolution equation for the height of the film, which is dependent on a single parameter, the dimensionless cylinder radius. This equation is identified as a special case of that which describes thin film flow down an inclined plane. Fully three-dimensional simulations of the film depict a fingering pattern at the advancing contact line. We find the number of fingers observed in our simulations to be in excellent agreement with experimental observations and a linear stability analysis reported recently by Smolka & SeGall (Phys Fluids 23, 092103 (2011)). As the radius of the cylinder decreases, the modes of perturbation have an increased growth rate, thus increasing cylinder curvature partially acts to encourage the contact line instability. In direct competition with this behaviour, a decrease in cylinder radius means that fewer fingers are able to form around the circumference of the cylinder. Indeed, for a sufficiently small radius, a transition is observed, at which point the contact line is stable to transverse perturbations of all wavenumbers. In this regime, free surface instabilities lead to the development of wave patterns in the axial direction, and the flow features become perfectly analogous to the two-dimensional flow of a thin film down an inverted plane as studied by Lin & Kondic (Phys Fluids 22, 052105 (2010)). Finally, we simulate the flow of a single drop down the outside of the cylinder. Our results show that for drops with low volume, the cylinder curvature has the effect of increasing drop speed and hence promoting the phenomenon of pearling. On the other hand, drops with much larger volume evolve to form single long rivulets with a similar shape to a finger formed in the aforementioned simulations.

Simplified method for including spatial correlations in mean-field approximations

Biological systems involving proliferation, migration and death are observed across all scales. For example, they govern cellular processes such as wound-healing, as well as the population dynamics of groups of organisms. In this paper, we provide a simplified method for correcting mean-field approximations of volume-excluding birth-death-movement processes on a regular lattice. An initially uniform distribution of agents on the lattice may give rise to spatial heterogeneity, depending on the relative rates of proliferation, migration and death. Many frameworks chosen to model these systems neglect spatial correlations, which can lead to inaccurate predictions of their behaviour. For example, the logistic model is frequently chosen, which is the mean-field approximation in this case. This mean-field description can be corrected by including a system of ordinary differential equations for pair-wise correlations between lattice site occupancies at various lattice distances. In this work we discuss difficulties with this method and provide a simplication, in the form of a partial differential equation description for the evolution of pair-wise spatial correlations over time. We test our simplified model against the more complex corrected mean-field model, finding excellent agreement. We show how our model successfully predicts system behaviour in regions where the mean-field approximation shows large discrepancies. Additionally, we investigate regions of parameter space where migration is reduced relative to proliferation, which has not been examined in detail before, and our method is successful at correcting the deviations observed in the mean-field model in these parameter regimes.

Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions

We define a pair-correlation function that can be used to characterize spatiotemporal patterning in experimental images and snapshots from discrete simulations. Unlike previous pair-correlation functions, the pair-correlation functions developed here depend on the location and size of objects. The pair-correlation function can be used to indicate complete spatial randomness, aggregation or segregation over a range of length scales, and quantifies spatial structures such as the shape, size and distribution of clusters. Comparing pair-correlation data for various experimental and simulation images illustrates their potential use as a summary statistic for calibrating discrete models of various physical processes.

Effect of dangling chains on the structure and physical properties of a tightly crosslinked poly(ethylene glycol) network

Major imperfections in crosslinked polymers include loose or dangling chain ends that lower the crosslink d., thereby reducing elastic recovery and increasing the solvent swelling. These imperfections are hard to detect, quantify and control when the network is initiated by free radical reactions. As an alternative approach, the sol-​gel synthesis of a model poly(ethylene glycol) (PEG-​2000) network is described using controlled amts. of bis- and mono-​triethoxy silyl Pr urethane PEG precursors to give silsesquioxane (SSQ, R-​SiO1.5) structures as crosslink junctions with a controlled no. of dangling chains. The effect of the no. of dangling chains on the structure and connectivity of the dried SSQ networks has been detd. by step-​crystn. differential scanning calorimetry. The role that micelle formation plays in controlling the sol-​gel PEG network connectivity has been studied by dynamic light scattering of the bis- and mono-​triethoxy silyl precursors and the networks have been characterized by 29Si solid state NMR, sol fraction and swelling measurements. These show that the dangling chains will increase the mesh size and water uptake. Compared to other end-​linked PEG hydrogels, the SSQ-​crosslinked networks show a low sol fraction and high connectivity, which reduces solvent swelling, degree of crystallinity and the crystal transition temp. The increased degree of freedom in segment movement on the addn. of dangling chains in the SSQ-​crosslinked network facilitates the packing process in crystn. of the dry network and, in the hydrogel, helps to accommodate more water mols. before reaching equil.

A particle based model to simulate microscale morphological changes of plant tissues during drying

Fundamental understanding on microscopic physical changes of plant materials is vital to optimize product quality and processing techniques, particularly in food engineering. Although grid-based numerical modelling can assist in this regard, it becomes quite challenging to overcome the inherited complexities of these biological materials especially when such materials undergo critical processing conditions such as drying, where the cellular structure undergoes extreme deformations. In this context, a meshfree particle based model was developed which is fundamentally capable of handling extreme deformations of plant tissues during drying. The model is built by coupling a particle based meshfree technique: Smoothed Particle Hydrodynamics (SPH) and a Discrete Element Method (DEM). Plant cells were initiated as hexagons and aggregated to form a tissue which also accounts for the characteristics of the middle lamella. In each cell, SPH was used to model cell protoplasm and DEM was used to model the cell wall. Drying was incorporated by varying the moisture content, the turgor pressure, and cell wall contraction effects. Compared to the state of the art grid-based microscale plant tissue drying models, the proposed model can be used to simulate tissues under excessive moisture content reductions incorporating cell wall wrinkling. Also, compared to the state of the art SPH-DEM tissue models, the proposed model better replicates real tissues and the cell-cell interactions used ensure efficient computations. Model predictions showed good agreement both qualitatively and quantitatively with experimental findings on dried plant tissues. The proposed modelling approach is fundamentally flexible to study different cellular structures for their microscale morphological changes at dehydration.

Electromagnetic propulsion and separation by chirality of nanoparticles in liquids

We introduce a new mechanism for the propulsion and separation by chirality of small ferromagnetic particles suspended in a liquid. Under the action of a uniform dc magnetic field H and an ac electric field E isomers with opposite chirality move in opposite directions. Such a mechanism could have a significant impact on a wide range of emerging technologies. The component of the chiral velocity that is odd in H is found to be proportional to the intrinsic orbital and spin angular momentum of the magnetized electrons. This effect arises because a ferromagnetic particle responds to the applied torque as a small gyroscope. © 2012 American Physical Society.

Reduction of amplitude equations by the renormalization group approach

This article elucidates and analyzes the fundamental underlying structure of the renormalization group (RG) approach as it applies to the solution of any differential equation involving multiple scales. The amplitude equation derived through the elimination of secular terms arising from a naive perturbation expansion of the solution to these equations by the RG approach is reduced to an algebraic equation which is expressed in terms of the Thiele semi-invariants or cumulants of the eliminant sequence { Zi } i=1 . Its use is illustrated through the solution of both linear and nonlinear perturbation problems and certain results from the literature are recovered as special cases. The fundamental structure that emerges from the application of the RG approach is not the amplitude equation but the aforementioned algebraic equation. © 2008 The American Physical Society.

Secular series and renormalization group for amplitude equations

We have developed a technique that circumvents the process of elimination of secular terms and reproduces the uniformly valid approximations, amplitude equations, and first integrals. The technique is based on a rearrangement of secular terms and their grouping into the secular series that multiplies the constants of the asymptotic expansion. We illustrate the technique by deriving amplitude equations for standard nonlinear oscillator and boundary-layer problems. © 2008 The American Physical Society.

Surface waves at the interface of a dusty plasma and a metallic wall

Electrostatic surface waves at the interface between a low-temperature nonisothermal dusty plasma and a metallic wall are investigated. The plasma contains massive negatively charged impurity or dust particles. It is shown that the impurities can significantly alter the characteristics and damping of the surface waves by reducing their phase velocity and causing charging-related damping.

Surface waves in strongly irradiated dusty plasmas

High-frequency surface waves at the interface between two dusty plasmas subject to radiation are considered. Ultraviolet radiation with energy flux larger than the photoelectric work function of the dust surface causes photoemission of electrons. The dust charge and the overall charge balance of the plasma are thus modified. The dispersion properties of the surface waves are investigated for three parameter regimes distinguished by the charging mechanisms in the two plasmas. It is shown that photoemission can significantly affect the plasma and the surface waves.