Novel neuronal and astrocytic mechanisms in thalamocortical loop dynamics

In this review, we summarize three sets of findings that have recently been observed in thalamic astrocytes and neurons, and discuss their significance for thalamocortical loop dynamics. (i) A physiologically relevant ‘window’ component of the low–voltage–activated, T–type Ca2+ current (ITwindow) plays an essential part in the slow (less than 1 Hz) sleep oscillation in adult thalamocortical (TC) neurons, indicating that the expression of this fundamental sleep rhythm in these neurons is not a simple reflection of cortical network activity. It is also likely that ITwindow underlies one of the cellular mechanisms enabling TC neurons to produce burst firing in response to novel sensory stimuli. (ii) Both electrophysiological and dye–injection experiments support the existence of gap junction–mediated coupling among young and adult TC neurons. This finding indicates that electrical coupling–mediated synchronization might be implicated in the high and low frequency oscillatory activities expressed by this type of thalamic neuron. (iii) Spontaneous intracellular Ca2+ ([Ca2+]i) waves propagating among thalamic astrocytes are able to elicit large and long–lasting N–methyl–D–aspartate–mediated currents in TC neurons. The peculiar developmental profile within the first two postnatal weeks of these astrocytic [Ca2+]i transients and the selective activation of these glutamate receptors point to a role for this astrocyte–to–neuron signalling mechanism in the topographic wiring of the thalamocortical loop. As some of these novel cellular and intracellular properties are not restricted to thalamic astrocytes and neurons, their significance may well apply to (patho)physiological functions of glial and neuronal elements in other brain areas.

Network evolution and the spatiotemporal dynamics of knowledge sourcing

Knowledge accessing from external organisations is important to firms, especially entrepreneurial ones which often cannot generate internally all the knowledge necessary for innovation. There is, however, a lack of evidence concerning the association between the evolution of firms and the evolution of their networks. The aim of this paper is to begin to fill this gap by undertaking an exploratory analysis of the relationship between the vintage of firms and their knowledge sourcing networks. Drawing on an analysis of firms in the UK, the paper finds some evidence of a U-shaped relationship existing between firm age and the frequency of accessing knowledge from certain sources. Emerging entrepreneurial firms tend to be highly active with regard to accessing knowledge for a range of sources and geographic locations, with the rate of networking dropping somewhat during the period of peak firm growth. For instance, it is found that firms tend to less frequently access knowledge sources such as universities and research institutes in their own region during a stage of peak turnover growth. Overall, the results suggest a complex relationship between the lifecycle of the firm and its networking patterns. It is concluded that policymakers need to become more aware that network formation and utilisation by firms is likely to vary dependent upon their lifecycle position.

The successional dynamics of lightning-initiated canopy gaps in the mangrove forests of Shark River, Everglades National Park, USA

Gap succession is a significant determinant of structure and development in most forest communities. Lightning strikes are an important source of canopy gaps in the mangrove forest of Everglades National Park. I investigated the successional dynamics of lightning-initiated canopy gaps to determine their influence on forest stand structure of the mixed mangrove forests ( Rhizophora mangle, Laguncularia racemosa, and Avicennia germinans ) of the Shark River. I measured gap size, gap shape, light environment, soil characteristics, woody debris, and fiddler crab abundance. I additionally measured the vegetative composition in a chronosequences of gap successional stages (new, recruiting, and growing gaps). I recorded survivorship, recruitment, growth and soil elevation dynamics within a subset of new and growing gaps. I determined the relationship between intact forest soil elevation and site hydrology in order to interpret the effects of lightning disturbance on soil elevation dynamics. ^ Gap size averaged 289 ± 20 m2 (± 1SE) and light transmittance decreased exponentially as gaps filled with saplings. Fine woody debris was highest in recruiting gaps. Soil strength was lower in the gaps than in the forest. The abundance of large and medium fiddler crab burrows increased linearly with total seedling abundance. Soil surface elevation declined in newly formed lightning gaps; this loss was due to a combination of superficial erosion (8.5 mm) and subsidence (60.9 mm). A distinct two-cohort recruitment pattern was evident in the seedling/sapling surveys, suggesting a partitioning of the succession between individuals present before and after lightning strike. In new gaps, the seedling recruitment rate was twice as high as in forest and the sapling population increased. At the growing gap stage, R. mangle seedling mortality was 10 times greater and sapling mortality was 13 times greater than recruitment. Growing gaps had reduced seedling stem elongation, sapling growth and adult growth. However, a few individuals (R. mangle saplings) were able to recruit into the adult life stage. In conclusion, the high density of R. mangle seedlings and saplings imply that lightning strike disturbances in these mangrove forests favor their recruitment over that of A. germinans and L. racemosa. ^

Weak coupling of acoustic-like phonons and magnon dynamics in incommensurate spin ladder compound Sr14Cu24O41

Intriguing lattice dynamics has been predicted for aperiodic crystals that contain incommensurate substructures. Here we report inelastic neutron scattering measurements of phonon and magnon dispersions in Sr14Cu24O41, which contains incommensurate one-dimensional (1D) chain and two-dimensional (2D) ladder substructures. Two distinct acoustic phonon-like modes, corresponding to the sliding motion of one sublattice against the other, are observed for atomic motions polarized along the incommensurate axis. In the long wavelength limit, it is found that the sliding mode shows a remarkably small energy gap of 1.7-1.9 meV, indicating very weak interactions between the two incommensurate sublattices. The measurements also reveal a gapped and steep linear magnon dispersion of the ladder sublattice. The high group velocity of this magnon branch and weak coupling with acoustic phonons can explain the large magnon thermal conductivity in Sr14Cu24O41 crystals. In addition, the magnon specific heat is determined from the measured total specific heat and phonon density of states, and exhibits a Schottky anomaly due to gapped magnon modes of the spin chains. These findings offer new insights into the phonon and magnon dynamics and thermal transport properties of incommensurate magnetic crystals that contain low-dimensional substructures.

Optical emission of strained direct-band-gap Ge quantum well embedded inside InGaAs alloy layers

We studied the optical properties of a strain-induced direct-band-gap Ge quantum well embedded in InGaAs. We showed that the band offsets depend on the electronegativity of the layer in contact with Ge, leading to different types of optical transitions in the heterostructure. When group-V atoms compose the interfaces, only electrons are confined in Ge, whereas both carriers are confined when the interface consists of group-III atoms. The different carrier confinement results in different emission dynamics behavior. This study provides a solution to obtain efficient light emission from Ge.

Bridging the Scale Gap from Leaf to Canopy in Biosphere-Atmosphere Gas and Particle Exchanges

Terrestrial ecosystems, occupying more than 25% of the Earth's surface, can serve as

`biological valves' in regulating the anthropogenic emissions of atmospheric aerosol

particles and greenhouse gases (GHGs) as responses to their surrounding environments.

While the signicance of quantifying the exchange rates of GHGs and atmospheric

aerosol particles between the terrestrial biosphere and the atmosphere is

hardly questioned in many scientic elds, the progress in improving model predictability,

data interpretation or the combination of the two remains impeded by

the lack of precise framework elucidating their dynamic transport processes over a

wide range of spatiotemporal scales. The diculty in developing prognostic modeling

tools to quantify the source or sink strength of these atmospheric substances

can be further magnied by the fact that the climate system is also sensitive to the

feedback from terrestrial ecosystems forming the so-called `feedback cycle'. Hence,

the emergent need is to reduce uncertainties when assessing this complex and dynamic

feedback cycle that is necessary to support the decisions of mitigation and

adaptation policies associated with human activities (e.g., anthropogenic emission

controls and land use managements) under current and future climate regimes.

With the goal to improve the predictions for the biosphere-atmosphere exchange

of biologically active gases and atmospheric aerosol particles, the main focus of this

dissertation is on revising and up-scaling the biotic and abiotic transport processes

from leaf to canopy scales. The validity of previous modeling studies in determining

iv

the exchange rate of gases and particles is evaluated with detailed descriptions of their

limitations. Mechanistic-based modeling approaches along with empirical studies

across dierent scales are employed to rene the mathematical descriptions of surface

conductance responsible for gas and particle exchanges as commonly adopted by all

operational models. Specically, how variation in horizontal leaf area density within

the vegetated medium, leaf size and leaf microroughness impact the aerodynamic attributes

and thereby the ultrane particle collection eciency at the leaf/branch scale

is explored using wind tunnel experiments with interpretations by a porous media

model and a scaling analysis. A multi-layered and size-resolved second-order closure

model combined with particle

uxes and concentration measurements within and

above a forest is used to explore the particle transport processes within the canopy

sub-layer and the partitioning of particle deposition onto canopy medium and forest

oor. For gases, a modeling framework accounting for the leaf-level boundary layer

eects on the stomatal pathway for gas exchange is proposed and combined with sap

ux measurements in a wind tunnel to assess how leaf-level transpiration varies with

increasing wind speed. How exogenous environmental conditions and endogenous

soil-root-stem-leaf hydraulic and eco-physiological properties impact the above- and

below-ground water dynamics in the soil-plant system and shape plant responses

to droughts is assessed by a porous media model that accommodates the transient

water

ow within the plant vascular system and is coupled with the aforementioned

leaf-level gas exchange model and soil-root interaction model. It should be noted

that tackling all aspects of potential issues causing uncertainties in forecasting the

feedback cycle between terrestrial ecosystem and the climate is unrealistic in a single

dissertation but further research questions and opportunities based on the foundation

derived from this dissertation are also brie

y discussed.

Photochemical dynamics of laser-irradiated semiconductor nanostructures

Thesis (Ph.D.)--University of Washington, 2016-08

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.

Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50 ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5-7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants. The data described here are related to the research article entitled "The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels" (Schadzek et al., 2015) [1].

Neuronal networks with gap junctions: A study of piece-wise linear planar neuron models

The presence of gap junction coupling among neurons of the central nervous systems has been appreciated for some time now. In recent years there has been an upsurge of interest from the mathematical community in understanding the contribution of these direct electrical connections between cells to large-scale brain rhythms. Here we analyze a class of exactly soluble single neuron models, capable of producing realistic action potential shapes, that can be used as the basis for understanding dynamics at the network level. This work focuses on planar piece-wise linear models that can mimic the firing response of several different cell types. Under constant current injection the periodic response and phase response curve (PRC) is calculated in closed form. A simple formula for the stability of a periodic orbit is found using Floquet theory. From the calculated PRC and the periodic orbit a phase interaction function is constructed that allows the investigation of phase-locked network states using the theory of weakly coupled oscillators. For large networks with global gap junction connectivity we develop a theory of strong coupling instabilities of the homogeneous, synchronous and splay state. For a piece-wise linear caricature of the Morris-Lecar model, with oscillations arising from a homoclinic bifurcation, we show that large amplitude oscillations in the mean membrane potential are organized around such unstable orbits.

Automated Feedback for 'Fill in the Gap' Programming Exercises

Timely feedback is a vital component in the learning process. It is especially important for beginner students in Information Technology since many have not yet formed an effective internal model of a computer that they can use to construct viable knowledge. Research has shown that learning efficiency is increased if immediate feedback is provided for students. Automatic analysis of student programs has the potential to provide immediate feedback for students and to assist teaching staff in the marking process. This paper describes a “fill in the gap” programming analysis framework which tests students’ solutions and gives feedback on their correctness, detects logic errors and provides hints on how to fix these errors. Currently, the framework is being used with the Environment for Learning to Programming (ELP) system at Queensland University of Technology (QUT); however, the framework can be integrated into any existing online learning environment or programming Integrated Development Environment (IDE)