On Bioelectric Algorithms

Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients across their membranes induced by differing concentrations of charged ions. A growing body of research suggests that bioelectric patterns represent an ancient system that plays a key role in guiding many important developmental processes including tissue regeneration, tumor suppression, and embryogenesis. This paper applies techniques from distributed algorithm theory to help better understand how cells work together to form these patterns. To do so, we present the cellular bioelectric model (CBM), a new computational model that captures the primary capabilities and constraints of bioelectric interactions between cells and their environment. We use this model to investigate several important topics from the relevant biology research literature. We begin with symmetry breaking, analyzing a simple cell definition that when combined in single hop or multihop topologies, efficiently solves leader election and the maximal independent set problem, respectively - indicating that these classical symmetry breaking tasks are well-matched to bioelectric mechanisms. We then turn our attention to the information processing ability of bioelectric cells, exploring upper and lower bounds for approximate solutions to threshold and majority detection, and then proving that these systems are in fact Turing complete - resolving an open question about the computational power of bioelectric interactions

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells

NNVA: Neural Network Assisted Visual Analysis of Yeast Cell Polarization Simulation

Complex computational models are often designed to simulate real-world physical phenomena in many scientific disciplines. However, these simulation models tend to be computationally very expensive and involve a large number of simulation input parameters which need to be analyzed and properly calibrated before the models can be applied for real scientific studies. We propose a visual analysis system to facilitate interactive exploratory analysis of high-dimensional input parameter space for a complex yeast cell polarization simulation. The proposed system can assist the computational biologists, who designed the simulation model, to visually calibrate the input parameters by modifying the parameter values and immediately visualizing the predicted simulation outcome without having the need to run the original expensive simulation for every instance. Our proposed visual analysis system is driven by a trained neural network-based surrogate model as the backend analysis framework. Surrogate models are widely used in the field of simulation sciences to efficiently analyze computationally expensive simulation models. In this work, we demonstrate the advantage of using neural networks as surrogate models for visual analysis by incorporating some of the recent advances in the field of uncertainty quantification, interpretability and explainability of neural network-based models. We utilize the trained network to perform interactive parameter sensitivity analysis of the original simulation at multiple levels-of-detail as well as recommend optimal parameter configurations using the activation maximization framework of neural networks. We also facilitate detail analysis of the trained network to extract useful insights about the simulation model, learned by the network, during the training process.Comment: Published at IEEE Transactions on Visualization and Computer Graphic

Liouville mode in Gauge/Gravity Duality

We establish solutions corresponding to AdS4 static charged black holes with inhomogeneous two-dimensional horizon surfaces of constant curvature. Depending on the choice of the 2D constant curvature space, the metric potential of the internal geometry of the horizon satisfies the elliptic wave/elliptic Liouville equations. We calculate the charge diffusion and transport coefficients in the hydrodynamic limit of gauge/gravity duality and observe the exponential suppression in the diffusion coefficient and in the shear viscosity-per-entropy density ratio in the presence of an inhomogeneity on black hole horizons with planar, spherical, and hyperbolic geometry. We discuss the subtleties of the approach developed for a planar black hole with inhomogeneity distribution on the horizon surface in more detail and find, among others, a trial distribution function, which generates values of the shear viscosity-per-entropy density ratio falling within the experimentally relevant range. The solutions obtained are also extended to higher-dimensional AdS space. We observe two different DC conductivities in 4D and higher-dimensional effective strongly coupled dual media and formulate conditions under which the appropriate ratio of different conductivities is qualitatively the same as that observed in an anisotropic strongly coupled fluid. We briefly discuss ways of how the Liouville field could appear in condensed matter physics and outline prospects of further employing the gauge/gravity duality in CMP problems.Comment: 1+22 pages, 1 Fig; v.2: eqs. (2.2), (3.16), (3.18) and (5.2) corrected, Refs. added; v.3: 1+28 pages, expanded version, Refs. added; v.4: published versio

Extracorporeal membrane oxygenation simulation-based training: methods, drawbacks and a novel solution

Introduction: Patients under the error-prone and complication-burdened extracorporeal membrane oxygenation (ECMO) are looked after by a highly trained, multidisciplinary team. Simulation-based training (SBT) affords ECMO centers the opportunity to equip practitioners with the technical dexterity required to manage emergencies. The aim of this article is to review ECMO SBT activities and technology followed by a novel solution to current challenges. ECMO simulation: The commonly-used simulation approach is easy-to-build as it requires a functioning ECMO machine and an altered circuit. Complications are simulated through manual circuit manipulations. However, scenario diversity is limited and often lacks physiological and/or mechanical authenticity. It is also expensive to continuously operate due to the consumption of highly specialized equipment. Technological aid: Commercial extensions can be added to enable remote control and to automate circuit manipulation, but do not improve on the realism or cost-effectiveness. A modular ECMO simulator: To address those drawbacks, we are developing a standalone modular ECMO simulator that employs affordable technology for high-fidelity simulation.Peer reviewe

InP membrane based broadband regenerator for silicon-based optical interconnect applications

We demonstrate the use of a Membrane-InP-Switch(MIPS) on-silicon as a signal regenerator. A receiver sensitivity enhancement >2.5dB across the entire C-band and a tripling of Extinction Ratio(ER) for low ER signals at 1Gb/sec is demonstrated

Enhancing Clinical Learning Through an Innovative Instructor Application for ECMO Patient Simulators

© 2018 The Authors. Reprinted by permission of SAGE PublicationsBackground. Simulation-based learning (SBL) employs the synergy between technology and people to immerse learners in highly-realistic situations in order to achieve quality clinical education. Due to the ever-increasing popularity of extracorporeal membrane oxygenation (ECMO) SBL, there is a pressing need for a proper technological infrastructure that enables high-fidelity simulation to better train ECMO specialists to deal with related emergencies. In this article, we tackle the control aspect of the infrastructure by presenting and evaluating an innovative cloud-based instructor, simulator controller, and simulation operations specialist application that enables real-time remote control of fullscale immersive ECMO simulation experiences for ECMO specialists as well as creating custom simulation scenarios for standardized training of individual healthcare professionals or clinical teams. Aim. This article evaluates the intuitiveness, responsiveness, and convenience of the ECMO instructor application as a viable ECMO simulator control interface. Method. A questionnaire-based usability study was conducted following institutional ethical approval. Nineteen ECMO practitioners were given a live demonstration of the instructor application in the context of an ECMO simulator demonstration during which they also had the opportunity to interact with it. Participants then filled in a questionnaire to evaluate the ECMO instructor application as per intuitiveness, responsiveness, and convenience. Results. The collected feedback data confirmed that the presented application has an intuitive, responsive, and convenient ECMO simulator control interface. Conclusion. The present study provided evidence signifying that the ECMO instructor application is a viable ECMO simulator control interface. Next steps will comprise a pilot study evaluating the educational efficacy of the instructor application in the clinical context with further technical enhancements as per participants’ feedback.Peer reviewedFinal Accepted Versio

Model Checking Tap Withdrawal in C. Elegans

We present what we believe to be the first formal verification of a biologically realistic (nonlinear ODE) model of a neural circuit in a multicellular organism: Tap Withdrawal (TW) in \emph{C. Elegans}, the common roundworm. TW is a reflexive behavior exhibited by \emph{C. Elegans} in response to vibrating the surface on which it is moving; the neural circuit underlying this response is the subject of this investigation. Specifically, we perform reachability analysis on the TW circuit model of Wicks et al. (1996), which enables us to estimate key circuit parameters. Underlying our approach is the use of Fan and Mitra's recently developed technique for automatically computing local discrepancy (convergence and divergence rates) of general nonlinear systems. We show that the results we obtain are in agreement with the experimental results of Wicks et al. (1995). As opposed to the fixed parameters found in most biological models, which can only produce the predominant behavior, our techniques characterize ranges of parameters that produce (and do not produce) all three observed behaviors: reversal of movement, acceleration, and lack of response