Dendritic cable with active spines: a modeling study in the spike-diffuse-spike framework

The spike-diffuse-spike (SDS) model describes a passive dendritic tree with active dendritic spines. Spine-head dynamics is modelled with a simple integrate-and-fire process, whilst communication between spines is mediated by the cable equation. Here we develop a computational framework that allows the study of multiple spiking events in a network of such spines embedded in a simple one-dimensional cable. This system is shown to support saltatory waves as a result of the discrete distribution of spines. Moreover, we demonstrate one of the ways to incorporate noise into the spine-head whilst retaining computational tractability of the model. The SDS model sustains a variety of propagating patterns.

Combustion Instability and Active Control: Alternative Fuels, Augmentors, and Modeling Heat Release

Experimental and analytical studies were conducted to explore thermo-acoustic coupling during the onset of combustion instability in various air-breathing combustor configurations. These include a laboratory-scale 200-kW dump combustor and a 100-kW augmentor featuring a v-gutter flame holder. They were used to simulate main combustion chambers and afterburners in aero engines, respectively. The three primary themes of this work includes: 1) modeling heat release fluctuations for stability analysis, 2) conducting active combustion control with alternative fuels, and 3) demonstrating practical active control for augmentor instability suppression. The phenomenon of combustion instabilities remains an unsolved problem in propulsion engines, mainly because of the difficulty in predicting the fluctuating component of heat release without extensive testing. A hybrid model was developed to describe both the temporal and spatial variations in dynamic heat release, using a separation of variables approach that requires only a limited amount of experimental data. The use of sinusoidal basis functions further reduced the amount of data required. When the mean heat release behavior is known, the only experimental data needed for detailed stability analysis is one instantaneous picture of heat release at the peak pressure phase. This model was successfully tested in the dump combustor experiments, reproducing the correct sign of the overall Rayleigh index as well as the remarkably accurate spatial distribution pattern of fluctuating heat release. Active combustion control was explored for fuel-flexible combustor operation using twelve different jet fuels including bio-synthetic and Fischer-Tropsch types. Analysis done using an actuated spray combustion model revealed that the combustion response times of these fuels were similar. Combined with experimental spray characterizations, this suggested that controller performance should remain effective with various alternative fuels. Active control experiments validated this analysis while demonstrating 50-70\% reduction in the peak spectral amplitude. A new model augmentor was built and tested for combustion dynamics using schlieren and chemiluminescence techniques. Novel active control techniques including pulsed air injection were implemented and the results were compared with the pulsed fuel injection approach. The pulsed injection of secondary air worked just as effectively for suppressing the augmentor instability, setting up the possibility of more efficient actuation strategy.

Effect of boiling on deposition of metallic colloids

In this study the relationship between heterogeneous nucleate boiling surfaces and deposition of suspended metallic colloidal particles, popularly known as crud or corrosion products in process industries, on those heterogeneous sites is investigated. Various researchers have reported that hematite is a major constituent of crud which makes it the primary material of interest; however the models developed in this work are irrespective of material choice. Qualitative hypotheses on the deposition process under boiling as proposed by previous researchers have been tested, which fail to provide explanations for several physical mechanisms observed and analyzed. In this study a quantitative model of deposition rate has been developed on the basis of bubble dynamics and colloid-surface interaction potential. Boiling from a heating surface aids in aggregation of the metallic particulates viz. nano-particles, crud particulate, etc. suspended in a liquid, which helps in transporting them to heating surfaces. Consequently, clusters of particles deposit onto the heating surfaces due to various interactive forces, resulting in formation of porous or impervious layers. The deposit layer grows or recedes depending upon variations in interparticle and surface forces, fluid shear, fluid chemistry, etc. This deposit layer in turn affects the rate of bubble generation, formation of porous chimneys, critical heat flux (CHF) of surfaces, activation and deactivation of nucleation sites on the heating surfaces. Several problems are posed due to the effect of boiling on colloidal deposition, which range from research initiatives involving nano-fluids as a heat transfer medium to industrial applications such as light water nuclear reactors. In this study, it is attempted to integrate colloid and surface science with vapor bubble dynamics, boiling heat transfer and evaporation rate. Pool boiling experiments with dilute metallic colloids have been conducted to investigate several parameters impacting the system. The experimental data available in the literature is obtained by flow experiments, which do not help in correlating boiling mechanism with the deposition amount or structure. With the help of experimental evidences and analysis, previously proposed hypothesis for particle transport to the contact line due to hydrophobicity has been challenged. The experimental observations suggest that deposition occurs around the bubble surface contact line and extends underneath area of the bubble microlayer as well. During the evaporation the concentration gradient of a non-volatile species is created, which induces osmotic pressure. The osmotic pressure developed inside the microlayer draws more particles inside the microlayer region or towards contact line. The colloidal escape time is slower than the evaporation time, which leads to the aggregation of particles in the evaporating micro-layer. These aggregated particles deposit onto or are removed from the heating surface, depending upon their total interaction potential. Interaction potential has been computed with the help of surface charge and van der Waals potential for the materials in aqueous solutions. Based upon the interaction-force boundary layer thickness, which is governed by debye radius (or ionic concentration and pH), a simplified quantitative model for the attachment kinetics is proposed. This attachment kinetics model gives reasonable results in predicting attachment rate against data reported by previous researchers. The attachment kinetics study has been done for different pH levels and particle sizes for hematite particles. Quantification of colloidal transport under boiling scenarios is done with the help of overall average evaporation rates because generally waiting times for bubbles at the same position is much larger than growth times. In other words, from a larger measurable scale perspective, frequency of bubbles dictates the rate of collection of particles rather than evaporation rate during micro-layer evaporation of one bubble. The combination of attachment kinetics and colloidal transport kinetics has been used to make a consolidated model for prediction of the amount of deposition and is validated with the help of high fidelity experimental data. In an attempt to understand and explain boiling characteristics, high speed visualization of bubble dynamics from a single artificial large cavity and multiple naturally occurring cavities is conducted. A bubble growth and departure dynamics model is developed for artificial active sites and is validated with the experimental data. The variation of bubble departure diameter with wall temperature is analyzed with experimental results and shows coherence with earlier studies. However, deposit traces after boiling experiments show that bubble contact diameter is essential to predict bubble departure dynamics, which has been ignored previously by various researchers. The relationship between porosity of colloid deposits and bubbles under the influence of Jakob number, sub-cooling and particle size has been developed. This also can be further utilized in variational wettability of the surface. Designing porous surfaces can having vast range of applications varying from high wettability, such as high critical heat flux boilers, to low wettability, such as efficient condensers.

Mixed-layer salinity budget in the tropical Indian Ocean: seasonal cycle based only on observations

The mixed-layer salinity (MLS) budget in the tropical Indian Ocean is estimated from a combination of satellite products and in situ observations over the 2004-2012 period, to investigate the mechanisms controlling the seasonal MLS variability. In contrast with previous studies in the tropical Indian Ocean, our results reveal that the coverage, resolution, and quality of available observations are now sufficient to approach a closed monthly climatology seasonal salt budget. In the South-central Arabian Sea and South-western Tropical Indian Ocean (SCAS and STIO, respectively), where seasonal variability of the MLS is pronounced, the monthly MLS tendency terms are well captured by the diagnostic. In the SCAS region, in agreement with previous results, the seasonal cycle of the MLS is mainly due to meridional advection driven by the monsoon winds. In the STIO, contrasting previous results indicating the control of the meridional advection over the seasonal MLS budget, our results reveal the leading role of the freshwater flux due to precipitation.

Ionospheric Turbulence Near the Upper Hybrid Layer: Theory and Experiment

The thesis presents experimental results, simulations, and theory on turbulence excited in magnetized plasmas near the ionosphere’s upper hybrid layer. The results include: The first experimental observations of super small striations (SSS) excited by the High-Frequency Auroral Research Project (HAARP) The first detection of high-frequency (HF) waves from the HAARP transmitter over a distance of 16x10^3 km The first simulations indicating that upper hybrid (UH) turbulence excites electron Bernstein waves associated with all nearby gyroharmonics Simulation results that indicate that the resulting bulk electron heating near the upper hybrid (UH) resonance is caused primarily by electron Bernstein waves parametrically excited near the first gyroharmonic. On the experimental side we present two sets of experiments performed at the HAARP heating facility in Alaska. In the first set of experiments, we present the first detection of super-small (cm scale) striations (SSS) at the HAARP facility. We detected density structures smaller than 30 cm for the first time through a combination of satellite and ground based measurements. In the second set of experiments, we present the results of a novel diagnostic implemented by the Ukrainian Antarctic Station (UAS) in Verdansky. The technique allowed the detection of the HAARP signal at a distance of nearly 16 Mm, and established that the HAARP signal was injected into the ionospheric waveguide by direct scattering off of dekameter-scale density structures induced by the heater. On the theoretical side, we present results of Vlasov simulations near the upper hybrid layer. These results are consistent with the bulk heating required by previous work on the theory of the formation of descending artificial ionospheric layers (DIALs), and with the new observations of DIALs at HAARP’s upgraded effective radiated power (ERP). The simulations that frequency sweeps, and demonstrate that the heating changes from a bulk heating between gyroharmonics, to a tail acceleration as the pump frequency is swept through the fourth gyroharmonic. These simulations are in good agreement with experiments. We also incorporate test particle simulations that isolate the effects of specific wave modes on heating, and we find important contributions from both electron Bernstein waves and upper hybrid waves, the former of which have not yet been detected by experiments, and have not been previously explored as a driver of heating. In presenting these results, we analyzed data from HAARP diagnostics and assisted in planning the second round of experiments. We integrated the data into a picture of experiments that demonstrated the detection of SSS, hysteresis effects in simulated electromagnetic emission (SEE) features, and the direct scattering of the HF pump into the ionospheric waveguide. We performed simulations and analyzed simulation data to build the understanding of collisionless heating near the upper hybrid layer, and we used these simulations to show that bulk electron heating at the upper hybrid layer is possible, which is required by current theories of DAIL formation. We wrote a test particle simulation to isolate the effects of electron Bernstein waves and upper hybrid layers on collisionless heating, and integrated this code to work with both the output of Vlasov simulations and the input for simulations of DAIL formation.

Spatio-temporal filtering properties of a dendritic cable with active spines: a modeling study in the spike-diffuse-spike framework

The spike-diffuse-spike (SDS) model describes a passive dendritic tree with active dendritic spines. Spine-head dynamics is modeled with a simple integrate-and-fire process, whilst communication between spines is mediated by the cable equation. In this paper we develop a computational framework that allows the study of multiple spiking events in a network of such spines embedded on a simple one-dimensional cable. In the first instance this system is shown to support saltatory waves with the same qualitative features as those observed in a model with Hodgkin-Huxley kinetics in the spine-head. Moreover, there is excellent agreement with the analytically calculated speed for a solitary saltatory pulse. Upon driving the system with time varying external input we find that the distribution of spines can play a crucial role in determining spatio-temporal filtering properties. In particular, the SDS model in response to periodic pulse train shows a positive correlation between spine density and low-pass temporal filtering that is consistent with the experimental results of Rose and Fortune [1999, Mechanisms for generating temporal filters in the electrosensory system. The Journal of Experimental Biology 202, 1281-1289]. Further, we demonstrate the robustness of observed wave properties to natural sources of noise that arise both in the cable and the spine-head, and highlight the possibility of purely noise induced waves and coherent oscillations.

Quasispecies dynamics and treatment outcome during early hepatitis C infection in a cohort of HIV-infected men

Hepatitis C virus (HCV) is emerging as one of the leading causes of morbidity and mortality in individuals infected with HIV and has overtaken AIDS-defining illnesses as a cause of death in HIV patient populations who have access to highly active antiretroviral therapy. For many years, the clonal analysis was the reference method for investigating viral diversity. In this thesis, a next generation sequencing (NGS) approach was developed using 454 pyrosequencing and Illumina-based technology. A sequencing pipeline was developed using two different NGS approaches, nested PCR, and metagenomics. The pipeline was used to study the viral populations in the sera of HCV-infected patients from a unique cohort of 160 HIV-positive patients with early HCV infection. These pipelines resulted in an improved understanding of HCV quasispecies dynamics, especially regarding studying response to treatment. Low viral diversity at baseline correlated with sustained virological response (SVR) while high viral diversity at baseline was associated with treatment failure. The emergence of new viral strains following treatment failure was most commonly associated with emerging dominance of pre-existing minority variants rather than re-infection. In the new era of direct-acting antivirals, next generation sequencing technologies are the most promising tool for identifying minority variants present in the HCV quasispecies populations at baseline. In this cohort, several mutations conferring resistance were detected in genotype 1a treatment-naïve patients. Further research into the impact of baseline HCV variants on SVR rates should be carried out in this population. A clearer understanding of the properties of viral quasispecies would enable clinicians to make improved treatment choices for their patients.

Nonlinear Optics and Carrier Dynamics in Nanostructured and Two-Dimensional Materials

Understanding and measuring the interaction of light with sub-wavelength structures and atomically thin materials is of critical importance for the development of next generation photonic devices.  One approach to achieve the desired optical properties in a material is to manipulate its mesoscopic structure or its composition in order to affect the properties of the light-matter interaction.  There has been tremendous recent interest in so called two-dimensional materials, consisting of only a single to a few layers of atoms arranged in a planar sheet.  These materials have demonstrated great promise as a platform for studying unique phenomena arising from the low-dimensionality of the material and for developing new types of devices based on these effects.  A thorough investigation of the optical and electronic properties of these new materials is essential to realizing their potential.  In this work we present studies that explore the nonlinear optical properties and carrier dynamics in nanoporous silicon waveguides, two-dimensional graphite (graphene), and atomically thin black phosphorus. We first present an investigation of the nonlinear response of nanoporous silicon optical waveguides using a novel pump-probe method. A two-frequency heterodyne technique is developed in order to measure the pump-induced transient change in phase and intensity in a single measurement. The experimental data reveal a characteristic material response time and temporally resolved intensity and phase behavior matching a physical model dominated by free-carrier effects that are significantly stronger and faster than those observed in traditional silicon-based waveguides.  These results shed light on the large optical nonlinearity observed in nanoporous silicon and demonstrate a new measurement technique for heterodyne pump-probe spectroscopy. Next we explore the optical properties of low-doped graphene in the terahertz spectral regime, where both intraband and interband effects play a significant role. Probing the graphene at intermediate photon energies enables the investigation of the nonlinear optical properties in the graphene as its electron system is heated by the intense pump pulse. By simultaneously measuring the reflected and transmitted terahertz light, a precise determination of the pump-induced change in absorption can be made. We observe that as the intensity of the terahertz radiation is increased, the optical properties of the graphene change from interband, semiconductor-like absorption, to a more metallic behavior with increased intraband processes. This transition reveals itself in our measurements as an increase in the terahertz transmission through the graphene at low fluence, followed by a decrease in transmission and the onset of a large, photo-induced reflection as fluence is increased.  A hybrid optical-thermodynamic model successfully describes our observations and predicts this transition will persist across mid- and far-infrared frequencies.  This study further demonstrates the important role that reflection plays since the absorption saturation intensity (an important figure of merit for graphene-based saturable absorbers) can be underestimated if only the transmitted light is considered. These findings are expected to contribute to the development of new optoelectronic devices designed to operate in the mid- and far-infrared frequency range.  Lastly we discuss recent work with black phosphorus, a two-dimensional material that has recently attracted interest due to its high mobility and direct, configurable band gap (300 meV to 2eV), depending on the number of atomic layers comprising the sample. In this work we examine the pump-induced change in optical transmission of mechanically exfoliated black phosphorus flakes using a two-color optical pump-probe measurement. The time-resolved data reveal a fast pump-induced transparency accompanied by a slower absorption that we attribute to Pauli blocking and free-carrier absorption, respectively. Polarization studies show that these effects are also highly anisotropic - underscoring the importance of crystal orientation in the design of optical devices based on this material. We conclude our discussion of black phosphorus with a study that employs this material as the active element in a photoconductive detector capable of gigahertz class detection at room temperature for mid-infrared frequencies.

The interplay between tectonics, sediment dynamics and gateways evolution in the Danube system from the Pannonian Basin to the western Black Sea

Understanding the natural evolution of a river–delta–sea system is important to develop a strong scientific basis for efficient integrated management plans. The distribution of sediment fluxes is linked with the natural connection between sediment source areas situated in uplifting mountain chains and deposition in plains, deltas and, ultimately, in the capturing oceans and seas. The Danube River–western Black Sea is one of the most active European systems in terms of sediment re-distribution that poses significant societal challenges. We aim to derive the tectonic and sedimentological background of human-induced changes in this system and discuss their interplay. This is obtained by analysing the tectonic and associated vertical movements, the evolution of relevant basins and the key events affecting sediment routing and deposition. The analysis of the main source and sink areas is focused in particular on the Miocene evolution of the Carpatho-Balkanides, Dinarides and their sedimentary basins including the western Black Sea. The vertical movements of mountains chains created the main moments of basin connectivity observed in the Danube system. Their timing and effects are observed in sediments deposited in the vicinity of gateways, such as the transition between the Pannonian/Transylvanian and Dacian basins and between the Dacian Basin and western Black Sea. The results demonstrate the importance of understanding threshold conditions driving rapid basins connectivity changes superposed over the longer time scale of tectonic-induced vertical movements associated with background erosion and sedimentation. The spatial and temporal scale of such processes is contrastingly different and challenging. The long-term patterns interact with recent or anthropogenic induced modifications in the natural system and may result in rapid changes at threshold conditions that can be quantified and predicted. Their understanding is critical because of frequent occurrence during orogenic evolution, as commonly observed in the Mediterranean area and discussed elsewhere.

Adipocyte size fluctuation, mechano-active lipid droplets and caveolae

International audience

Slot Film Cooling: A Comprehensive Experimental Characterization

When components of a propulsion system are exposed to elevated flow temperatures there is a risk for catastrophic failure if the components are not properly protected from the thermal loads. Among several strategies, slot film cooling is one of the most commonly used, yet poorly understood active cooling techniques. Tangential injection of a relatively cool fluid layer protects the surface(s) in question, but the turbulent mixing between the hot mainstream and cooler film along with the presence of the wall presents an inherently complex problem where kinematics, thermal transport and multimodal heat transfer are coupled. Furthermore, new propulsion designs rely heavily on CFD analysis to verify their viability. These CFD models require validation of their results, and the current literature does not provide a comprehensive data set for film cooling that meets all the demands for proper validation, namely a comprehensive (kinematic, thermal and boundary condition data) data set obtained over a wide range of conditions. This body of work aims at solving the fundamental issue of validation by providing high quality comprehensive film cooling data (kinematics, thermal mixing, heat transfer). 3 distinct velocity ratios (VR=uc/u∞) are examined corresponding to wall-wake (VR~0.5), min-shear (VR ~ 1.0), and wall-jet (VR~2.0) type flows at injection, while the temperature ratio TR= T∞/Tc is approximately 1.5 for all cases. Turbulence intensities at injection are 2-4% for the mainstream (urms/u∞, vrms/u∞,), and on the order of 8-10% for the coolant (urms/uc, vrms/uc,). A special emphasis is placed on inlet characterization, since inlet data in the literature is often incomplete or is of relatively low quality for CFD development. The data reveals that min-shear injection provides the best performance, followed by the wall-jet. The wall-wake case is comparably poor in performance. The comprehensive data suggests that this relative performance is due to the mixing strength of each case, as well as the location of regions of strong mixing with respect to the wall. Kinematic and thermal data show that strong mixing occurs in the wall-jet away from the wall (y/s>1), while strong mixing in the wall-wake occurs much closer to the wall (y/s<1). Min-shear cases exhibit noticeably weaker mixing confined to about y/s=1. Additionally to these general observations, the experimental data obtained in this work is analyzed to reveal scaling laws for the inlets, near-wall scaling, detecting and characterizing coherent structures in the flow as well as to provide data reduction strategies for comparison to CFD models (RANS and LES).

A study of electrochemical transport and diffuse charge dynamics using a Langevin equation

This thesis aims to develop new numerical and computational tools to study electrochemical transport and diffuse charge dynamics at small scales. Previous efforts at modeling electrokinetic phenomena at scales where the noncontinuum effects become significant have included continuum models based on the Poisson-Nernst-Planck equations and atomic simulations using molecular dynamics algorithms. Neither of them is easy to use or conducive to electrokinetic transport modeling in strong confinement or over long time scales. This work introduces a new approach based on a Langevin equation for diffuse charge dynamics in nanofluidic devices, which incorporates features from both continuum and atomistic methods. The model is then extended to include steric effects resulting from finite ion size, and applied to the phenomenon of double layer charging in a symmetric binary electrolyte between parallel-plate blocking electrodes, between which a voltage is applied. Finally, the results of this approach are compared to those of the continuum model based on the Poisson-Nernst-Planck equations.

Three-dimensional kinetic simulations of active suspensions: effect of chemotaxis and steric interaction

In this work, the effects of chemotaxis and steric interactions in active suspensions are analyzed by extending the kinetic model proposed by Saintillan and Shelley [1, 2]. In this model, a conservation equation for the active particle configuration is coupled to the Stokes equation for the flow arising from the force dipole exerted by the particles on the fluid. The fluid flow equations are solved spectrally and the conservation equation is solved by second-order finite differencing in space and second-order Adams-Bashforth time marching. First, the dynamics in suspensions of oxytactic run-and-tumble bacteria confined in thin liquid films surrounded by air is investigated. These bacteria modify their tumbling behavior by making temporal comparisons of the oxygen concentration, and, on average, swim towards high concentrations of oxygen. The kinetic model proposed by Saintillan and Shelley [1, 2] is modified to include run-and-tumble effects and oxygentaxis. The spatio-temporal dynamics of the oxygen and bacterial concentration are analyzed. For small film thicknesses, there is a weak migration of bacteria to the boundaries, and the oxygen concentration is high inside the film as a result of diffusion; both bacterial and oxygen concentrations quickly reach steady states. Above a critical film thickness (approximately 200 micron), a transition to chaotic dynamics is observed and is characterized by turbulent-like 3D motion, the formation of bacterial plumes, enhanced oxygen mixing and transport into the film, and hydrodynamic velocities of magnitudes up to 7 times the single bacterial swimming speed. The simulations demonstrate that the combined effects of hydrodynamic interactions and oxygentaxis create collective three-dimensional instabilities which enhances oxygen availability for the bacteria. Our simulation results are consistent with the experimental findings of Sokolov et al. [3], who also observed a similar transition with increasing film thickness. Next, the dynamics in concentrated suspensions of active self-propelled particles in a 3D periodic domain are analyzed. We modify the kinetic model of Saintillan and Shelley [1, 2] by including an additional nematic alignment torque proportional to the local concentration in the equation for the rotational velocity of the particles, causing them to align locally with their neighbors (Doi and Edwards [4]). Large-scale three- dimensional simulations show that, in the presence of such a torque both pusher and puller suspensions are unstable to random fluctuations and are characterized by highly nematic structures. Detailed measures are defined to quantify the degree and direction of alignment, and the effects of steric interactions on pattern formation will be presented. Our analysis shows that steric interactions have a destabilizing effect in active suspensions.

Mode locking in a spatially extended neuron model: active soma and compartmental tree

Understanding the mode-locked response of excitable systems to periodic forcing has important applications in neuroscience. For example it is known that spatially extended place cells in the hippocampus are driven by the theta rhythm to generate a code conveying information about spatial location. Thus it is important to explore the role of neuronal dendrites in generating the response to periodic current injection. In this paper we pursue this using a compartmental model, with linear dynamics for each compartment, coupled to an active soma model that generates action potentials. By working with the piece-wise linear McKean model for the soma we show how the response of the whole neuron model (soma and dendrites) can be written in closed form. We exploit this to construct a stroboscopic map describing the response of the spatially extended model to periodic forcing. A linear stability analysis of this map, together with a careful treatment of the non-differentiability of the soma model, allows us to construct the Arnol'd tongue structure for 1:q states (one action potential for q cycles of forcing). Importantly we show how the presence of quasi-active membrane in the dendrites can influence the shape of tongues. Direct numerical simulations confirm our theory and further indicate that resonant dendritic membrane can enlarge the windows in parameter space for chaotic behavior. These simulations also show that the spatially extended neuron model responds differently to global as opposed to point forcing. In the former case spatio-temporal patterns of activity within an Arnol'd tongue are standing waves, whilst in the latter they are traveling waves.