Quadruped Gait Transitions from a Neural Pattern Generator with Arousal Modulated Interactions

A four-channel neural pattern generator is described in which both the frequency and the relative phase of oscillations are controlled by a scalar arousal or GO signal. The generator is used to simulate quadruped gaits; in particular, rapid transitions are simulated in the order - walk, trot, pace, and gallop - that occurs in the cat. Precise switching control is achieved by using an arousal dependent modulation of the model's inhibitory interactions. This modulation generates a different functional connectivity in a single network at different arousal levels.

From Synapse to Self: Spikes, Synchrony, and Attentive Learning by Laminar Thalamocortical Circuits

How do our brains transform the "blooming buzzing confusion" of daily experience into a coherent sense of self that can learn and selectively attend to important information? How do local signals at multiple processing stages, none of which has a global view of brain dynamics or behavioral outcomes, trigger learning at multiple synaptic sites when appropriate, and prevent learning when inappropriate, to achieve useful behavioral goals in a continually changing world? How does the brain allow synaptic plasticity at a remarkably rapid rate, as anyone who has gone to an exciting movie is readily aware, yet also protect useful memories from catastrophic forgetting? A neural model provides a unified answer by explaining and quantitatively simulating data about single cell biophysics and neurophysiology, laminar neuroanatomy, aggregate cell recordings (current-source densities, local field potentials), large-scale oscillations (beta, gamma), and spike-timing dependent plasticity, and functionally linking them all to cognitive information processing requirements.

DC/DC converter 3D assembly for autonomous sensor nodes

This paper reports on the design and the manufacturing of an integrated DCDC converter, which respects the specificity of sensor node network: compactness, high efficiency in acquisition and transmission modes, and compatibility with miniature Lithium batteries. A novel integrated circuit (ASIC) has been designed and manufactured to provide regulated Voltage to the sensor node from miniaturized, thin film Lithium batteries. Then, a 3D integration technique has been used to integrate this ASIC in a 3 layers stack with high efficiency passives components, mixing the wafer level technologies from two different research institutions. Electrical results have demonstrated the feasibility of this integrated system and experiments have shown significant improvements in the case of oscillations in regulated voltage. However, stability of this output voltage toward the input voltage has still to be improved.

Two closely coupled lasers, dynamics & applications

The dynamics of two mutually coupled identical single-mode semi-conductor lasers are theoretically investigated. For small separation and large coupling between the lasers, symmetry-broken one-colour states are shown to be stable. In this case the light output of the lasers have significantly different intensities whilst at the same time the lasers are locked to a single common frequency. For intermediate coupling we observe stable two-colour states, where both single-mode lasers lase simultaneously at two optical frequencies which are separated by up to 150 GHz. For low coupling but possibly large separation, the frequency of the relaxation oscillations of the freerunning lasers defines the dynamics. Chaotic and quasi-periodic states are identified and shown to be stable. For weak coupling undamped relaxation oscillations dominate where each laser is locked to three or more odd number of colours spaced by the relaxation oscillation frequency. It is shown that the instabilities that lead to these states are directly connected to the two colour mechanism where the change in the number of optical colours due to a change in the plane of oscillation. At initial coupling, in-phase and anti-phase one colour states are shown to emerge from “on” uncoupled lasers using a perturbation method. Similarly symmetry-broken one-colour states come from considering one free-running laser initially “on” and the other laser initially “off”. The mechanism that leads to a bi-stability between in-phase and anti-phase one-colour states is understood. Due to an equivariant phase space symmetry of being able to exchange the identical lasers, a symmetric and symmetry-broken variant of all states mentioned above exists and is shown to be stable. Using a five dimensional model we identify the bifurcation structure which is responsible for the appearance of symmetric and symmetry-broken one-colour, symmetric and symmetry-broken two-colour, symmetric and symmetry-broken undamped relaxation oscillations, symmetric and symmetry-broken quasi-periodic, and symmetric and symmetry-broken chaotic states. As symmetry-broken states always exist in pairs, they naturally give rise to bi-stability. Several of these states show multistabilities between symmetric and symmetry-broken variants and among states. Three memory elements on the basis of bi-stabilities in one and two colour states for two coupled single-mode lasers are proposed. The switching performance of selected designs of optical memory elements is studied numerically.

A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure.

Independent individual addressing of multiple neutral atom qubits with a micromirror-based beam steering system

We demonstrate a scalable approach to addressing multiple atomic qubits for use in quantum information processing. Individually trapped 87Rb atoms in a linear array are selectively manipulated with a single laser guided by a microelectromechanical beam steering system. Single qubit oscillations are shown on multiple sites at frequencies of ≃3.5 MHz with negligible crosstalk to neighboring sites. Switching times between the central atom and its closest neighbor were measured to be 6-7 μs while moving between the central atom and an atom two trap sites away took 10-14 μs. © 2010 American Institute of Physics.

Plasmon-induced electrical conduction in molecular devices.

Metal nanoparticles (NPs) respond to electromagnetic waves by creating surface plasmons (SPs), which are localized, collective oscillations of conduction electrons on the NP surface. When interparticle distances are small, SPs generated in neighboring NPs can couple to one another, creating intense fields. The coupled particles can then act as optical antennae capturing and refocusing light between them. Furthermore, a molecule linking such NPs can be affected by these interactions as well. Here, we show that by using an appropriate, highly conjugated multiporphyrin chromophoric wire to couple gold NP arrays, plasmons can be used to control electrical properties. In particular, we demonstrate that the magnitude of the observed photoconductivity of covalently interconnected plasmon-coupled NPs can be tuned independently of the optical characteristics of the molecule-a result that has significant implications for future nanoscale optoelectronic devices.

Atmospheric neutrino oscillation analysis with subleading effects in Super-Kamiokande I, II, and III

We present a search for nonzero θ13 and deviations of sin2θ23 from 0.5 in the oscillations of atmospheric neutrino data from Super-Kamiokande I, II, and III. No distortions of the neutrino flux consistent with nonzero θ13 are found and both neutrino mass hierarchy hypotheses are in agreement with the data. The data are best fit at Δm2=2.1×10-3eV2, sin2θ13=0.0, and sin2θ23=0.5. In the normal (inverted) hierarchy θ13 and Δm2 are constrained at the one-dimensional 90% C.L. to sin2θ13<0.04(0.09) and 1.9(1.7)×10 -3<Δm2<2.6(2.7)×10-3eV2. The atmospheric mixing angle is within 0.407≤sin2θ23≤0.583 at 90% C.L. © 2010 The American Physical Society.

A von Bertalanffy Based Model for the Estimation of Oyster (Crassostrea virginica) Growth on Restored Oyster Reefs in Chesapeake Bay

A model to estimate the mean monthly growth of Crassostrea virginica oysters in Chesapeake Bay was developed. This model is based on the classic von Bertalanffy growth function, however the growth constant is changed every monthly timestep in response to short term changes in temperature and salinity. Using a dynamically varying growth constant allows the model to capture seasonal oscillations in growth, and growth responses to changing environmental conditions that previous applications of the von Bertalanffy model do not capture. This model is further expanded to include an estimation of Perkinsus marinus impacts on growth rates as well as estimations of ecosystem services provided by a restored oyster bar over time. The model was validated by comparing growth estimates from the model to oyster shell height observations from a variety of restoration sites in the upper Chesapeake Bay. Without using the P. marinus impact on growth, the model consistently overestimates mean oyster growth. However, when P. marinus effects are included in the model, the model estimates match the observed mean shell height closely for at least the first 3 years of growth. The estimates of ecosystem services suggested by this model imply that even with high levels of mortality on an oyster reef, the ecosystem services provided by that reef can still be maintained by growth for several years. Because larger oyster filter more water than smaller ones, larger oysters contribute more to the filtration and nutrient removal ecosystem services of the reef. Therefore a reef with an abundance of larger oysters will provide better filtration and nutrient removal. This implies that if an oyster restoration project is trying to improve water quality through oyster filtration, it is important to maintain the larger older oysters on the reef.

Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming.

Transient overexpression of defined combinations of master regulator genes can effectively induce cellular reprogramming: the acquisition of an alternative predicted phenotype from a differentiated cell lineage. This can be of particular importance in cardiac regenerative medicine wherein the heart lacks the capacity to heal itself, but simultaneously contains a large pool of fibroblasts. In this study we determined the cardio-inducing capacity of ten transcription factors to actuate cellular reprogramming of mouse embryonic fibroblasts into cardiomyocyte-like cells. Overexpression of transcription factors MYOCD and SRF alone or in conjunction with Mesp1 and SMARCD3 enhanced the basal but necessary cardio-inducing effect of the previously reported GATA4, TBX5, and MEF2C. In particular, combinations of five or seven transcription factors enhanced the activation of cardiac reporter vectors, and induced an upregulation of cardiac-specific genes. Global gene expression analysis also demonstrated a significantly greater cardio-inducing effect when the transcription factors MYOCD and SRF were used. Detection of cross-striated cells was highly dependent on the cell culture conditions and was enhanced by the addition of valproic acid and JAK inhibitor. Although we detected Ca(2+) transient oscillations in the reprogrammed cells, we did not detect significant changes in resting membrane potential or spontaneously contracting cells. This study further elucidates the cardio-inducing effect of the transcriptional networks involved in cardiac cellular reprogramming, contributing to the ongoing rational design of a robust protocol required for cardiac regenerative therapies.

Calcium dependent CAMTA1 in adult stem cell commitment to a myocardial lineage.

The phenotype of somatic cells has recently been found to be reversible. Direct reprogramming of one cell type into another has been achieved with transduction and over expression of exogenous defined transcription factors emphasizing their role in specifying cell fate. To discover early and novel endogenous transcription factors that may have a role in adult-derived stem cell acquisition of a cardiomyocyte phenotype, mesenchymal stem cells from human and mouse bone marrow and rat liver were co-cultured with neonatal cardiomyocytes as an in vitro cardiogenic microenvironment. Cell-cell communications develop between the two cell types as early as 24 hrs in co-culture and are required for elaboration of a myocardial phenotype in the stem cells 8-16 days later. These intercellular communications are associated with novel Ca(2+) oscillations in the stem cells that are synchronous with the Ca(2+) transients in adjacent cardiomyocytes and are detected in the stem cells as early as 24-48 hrs in co-culture. Early and significant up-regulation of Ca(2+)-dependent effectors, CAMTA1 and RCAN1 ensues before a myocardial program is activated. CAMTA1 loss-of-function minimizes the activation of the cardiac gene program in the stem cells. While the expression of RCAN1 suggests involvement of the well-characterized calcineurin-NFAT pathway as a response to a Ca(2+) signal, the CAMTA1 up-regulated expression as a response to such a signal in the stem cells was unknown. Cell-cell communications between the stem cells and adjacent cardiomyocytes induce Ca(2+) signals that activate a myocardial gene program in the stem cells via a novel and early Ca(2+)-dependent intermediate, up-regulation of CAMTA1.

Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.

Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises from the binding of a regulatory protein to a promoter in the chromosomal DNA. In this study, we focus on two minimal oscillators based on activator titration and repressor titration to understand the key parameters that are important for oscillations and for overcoming binary noise. We show that the rate of unbinding from the DNA, despite traditionally being considered a fast parameter, needs to be slow to broaden the space of oscillatory solutions. The addition of multiple, independent DNA binding sites further expands the oscillatory parameter space for the repressor-titration oscillator and lengthens the period of both oscillators. This effect is a combination of increased effective delay of the unbinding kinetics due to multiple binding sites and increased promoter ultrasensitivity that is specific for repression. We then use stochastic simulation to show that multiple binding sites increase the coherence of oscillations by mitigating the binary noise. Slow values of DNA unbinding rate are also effective in alleviating molecular noise due to the increased distance from the bifurcation point. Our work demonstrates how the number of DNA binding sites and slow unbinding kinetics, which are often omitted in biophysical models of gene circuits, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.

Role of Landau quantization on the neutron-drip transition in magnetar crusts

The role of a strong magnetic field on the neutron-drip transition in the crust of a magnetar is studied. The composition of the crust and the neutron-drip threshold are determined numerically for different magnetic field strengths using the experimental atomic mass measurements from the 2012 Atomic Mass Evaluation complemented with theoretical masses calculated from the Brussels-Montreal Hartree-Fock-Bogoliubov nuclear mass model HFB-24. The equilibrium nucleus at the neutron-drip point is found to be independent of the magnetic field strength. As demonstrated analytically, the neutron-drip density and pressure increase almost linearly with the magnetic field strength in the strongly quantizing regime for which electrons lie in the lowest Landau level. For weaker magnetic fields, the neutron-drip density exhibits typical quantum oscillations. In this case, the neutron-drip density can be either increased by about 14% or decreased by 25% depending on the magnetic field strength. These variations are shown to be almost universal, independently of the nuclear mass model employed. These results may have important implications for the physical interpretation of timing irregularities and quasiperiodic oscillations detected in soft gamma-ray repeaters and anomalous x-ray pulsars, as well as for the cooling of strongly magnetized neutron stars.

A multi-scale atomistic-continuum modelling of crack propagation in a two-dimensional macroscopic plate

A novel multi-scale seamless model of brittle-crack propagation is proposed and applied to the simulation of fracture growth in a two-dimensional Ag plate with macroscopic dimensions. The model represents the crack propagation at the macroscopic scale as the drift-diffusion motion of the crack tip alone. The diffusive motion is associated with the crack-tip coordinates in the position space, and reflects the oscillations observed in the crack velocity following its critical value. The model couples the crack dynamics at the macroscales and nanoscales via an intermediate mesoscale continuum. The finite-element method is employed to make the transition from the macroscale to the nanoscale by computing the continuum-based displacements of the atoms at the boundary of an atomic lattice embedded within the plate and surrounding the tip. Molecular dynamics (MD) simulation then drives the crack tip forward, producing the tip critical velocity and its diffusion constant. These are then used in the Ito stochastic calculus to make the reverse transition from the nanoscale back to the macroscale. The MD-level modelling is based on the use of a many-body potential. The model successfully reproduces the crack-velocity oscillations, roughening transitions of the crack surfaces, as well as the macroscopic crack trajectory. The implications for a 3-D modelling are discussed.

A two-dimensional numerical investigation of the oscillatory flow behaviour in rectangular fire compartments with a single horizontal ceiling vent

This paper presents a comparison of fire field model predictions with experiment for the case of a fire within a compartment which is vented (buoyancydriven) to the outside by a single horizontal ceiling vent. Unlike previous work, the mathematical model does not employ a mixing ratio to represent vent temperatures but allows the model to predict vent temperatures a priori. The experiment suggests that the flow through the vent produces oscillatory behaviour in vent temperatures with puffs of smoke emerging from the fire compartment. This type of flow is also predicted by the fire field model. While the numerical predictions are in good qualitative agreement with observations, they overpredict the amplitudes of the temperature oscillations within the vent and also the compartment temperatures. The discrepancies are thought to be due to three-dimensional effects not accounted for in this model as well as using standard ‘practices’ normally used by the community with regards to discretization and turbulence models. Furthermore, it is important to note that the use of the k–ε turbulence model in a transient mode, as is used here, may have a significant effect on the results. The numerical results also suggest that a linear relationship exists between the frequency of vent temperature oscillation (n) and the heat release rate (Q0) of the type n∝Q0.290, similar to that observed for compartments with two horizontal vents. This relationship is predicted to occur only for heat release rates below a critical value. Furthermore, the vent discharge coefficient is found to vary in an oscillatory fashion with a mean value of 0.58. Below the critical heat release rate the mean discharge coefficient is found to be insensitive to fire size.