Temporal dynamics in an immunological synapse:role of thermal fluctuations in signaling

The article analyzes the contribution of stochastic thermal fluctuations in the attachment times of the immature T-cell receptor TCR: peptide-major-histocompatibility-complex pMHC immunological synapse bond. The key question addressed here is the following: how does a synapse bond remain stabilized in the presence of high-frequency thermal noise that potentially equates to a strong detaching force? Focusing on the average time persistence of an immature synapse, we show that the high-frequency nodes accompanying large fluctuations are counterbalanced by low-frequency nodes that evolve over longer time periods, eventually leading to signaling of the immunological synapse bond primarily decided by nodes of the latter type. Our analysis shows that such a counterintuitive behavior could be easily explained from the fact that the survival probability distribution is governed by two distinct phases, corresponding to two separate time exponents, for the two different time regimes. The relatively shorter timescales correspond to the cohesion:adhesion induced immature bond formation whereas the larger time reciprocates the association:dissociation regime leading to TCR:pMHC signaling. From an estimate of the bond survival probability, we show that, at shorter timescales, this probability PΔ(τ) scales with time τ as a universal function of a rescaled noise amplitude DΔ2, such that PΔ(τ)∼τ-(ΔD+12),Δ being the distance from the mean intermembrane (T cell:Antigen Presenting Cell) separation distance. The crossover from this shorter to a longer time regime leads to a universality in the dynamics, at which point the survival probability shows a different power-law scaling compared to the one at shorter timescales. In biological terms, such a crossover indicates that the TCR:pMHC bond has a survival probability with a slower decay rate than the longer LFA-1:ICAM-1 bond justifying its stability.

The effect of slow passage in the pulse-pumped quantum dot laser

In recent years, quantum-dot (QD) semiconductor lasers attract significant interest in many practical applications due to their advantages such as high-power pulse generation because to the high gain efficiency. In this work, the pulse shape of an electrically pumped QD-laser under high current is analyzed. We find that the slow rise time of the pulsed pump may significantly affect the high intensity output pulse. It results in sharp power dropouts and deformation of the pulse profile. We address the effect to dynamical change of the phase-amplitude coupling in the proximity of the excited state (ES) threshold. Under 30ns pulse pumping, the output pulse shape strongly depends on pumping amplitude. At lower currents, which correspond to lasing in the ground state (GS), the pulse shape mimics that of the pump pulse. However, at higher currents the pulse shape becomes progressively unstable. The instability is greatest when in proximity to the secondary threshold which corresponds to the beginning of the ES lasing. After the slow rise stage, the output power sharply drops out. It is followed by a long-time power-off stage and large-scale amplitude fluctuations. We explain these observations by the dynamical change of the alpha-factor in the QD-laser and reveal the role of the slowly rising pumping processes in the pulse shaping and power dropouts at higher currents. The modeling is in very good agreement with the experimental observations. © 2014 SPIE.

Ultra-long range distributed fibre sensing using virtually transparent propagation

Distributed fibre sensors provide unique capabilities for monitoring large infrastructures with high resolution. Practically, all these sensors are based on some kind of backscattering interaction. A pulsed activating signal is launched on one side of the sensing fibre and the backscattered signal is read as a function of the time of flight of the pulse along the fibre. A key limitation in the measurement range of all these sensors is introduced by fibre attenuation. As the pulse travels along the fibre, the losses in the fibre cause a drop of signal contrast and consequently a growth in the measurement uncertainty. In typical single-mode fibres, attenuation imposes a range limit of less than 30km, for resolutions in the order of 1-2 meters. An interesting improvement in this performance can be considered by using distributed amplification along the fibre [1]. Distributed amplification allows having a more homogeneous signal power along the sensing fibre, which also enables reducing the signal power at the input and therefore avoiding nonlinearities. However, in long structures (≥ 50 km), plain distributed amplification does not perfectly compensate the losses and significant power variations along the fibre are to be expected, leading to inevitable limitations in the measurements. From this perspective, it is simple to understand intuitively that the best possible solution for distributed sensors would be offered by a virtually transparent fibre, i.e. a fibre exhibiting effectively zero attenuation in the spectral region of the pulse. In addition, it can be shown that lossless transmission is the working point that allows the minimization of the amplified spontaneous emission (ASE) noise build-up. © 2011 IEEE.

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

Motivation: In any macromolecular polyprotic system - for example protein, DNA or RNA - the isoelectric point - commonly referred to as the pI - can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge - and thus the electrophoretic mobility - of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information: Supplementary data are available at Bioinformatics online.

Exergoeconomic analysis of solar organic rankine cycle for geothermal air conditioned net zero energy buildings

This study is an attempt at achieving Net Zero Energy Building (NZEB) using a solar Organic Rankine Cycle (ORC) based on exergetic and economic measures. The working fluid, working conditions of the cycle, cycle configuration, and solar collector type are considered the optimization parameters for the solar ORC system. In the first section, a procedure is developed to compare ORC working fluids based on their molecular components, temperature-entropy diagram and fluid effects on the thermal efficiency, net power generated, vapor expansion ratio, and exergy efficiency of the Rankine cycle. Fluids with the best cycle performance are recognized in two different temperature levels within two different categories of fluids: refrigerants and non-refrigerants. Important factors that could lead to irreversibility reduction of the solar ORC are also investigated in this study. In the next section, the system requirements needed to maintain the electricity demand of a geothermal air-conditioned commercial building located in Pensacola of Florida is considered as the criteria to select the optimal components and optimal working condition of the system. The solar collector loop, building, and geothermal air conditioning system are modeled using TRNSYS. Available electricity bills of the building and the 3-week monitoring data on the performance of the geothermal system are employed to calibrate the simulation. The simulation is repeated for Miami and Houston in order to evaluate the effect of the different solar radiations on the system requirements. The final section discusses the exergoeconomic analysis of the ORC system with the optimum performance. Exergoeconomics rests on the philosophy that exergy is the only rational basis for assigning monetary costs to a system’s interactions with its surroundings and to the sources of thermodynamic inefficiencies within it. Exergoeconomic analysis of the optimal ORC system shows that the ratio Rex of the annual exergy loss to the capital cost can be considered a key parameter in optimizing a solar ORC system from the thermodynamic and economic point of view. It also shows that there is a systematic correlation between the exergy loss and capital cost for the investigated solar ORC system.

Investigation of generation -recombination noise and related processes in aluminum gallium arsenide TEGFETs and Hall structures with quantum wells

Experimental and theoretical studies regarding noise processes in various kinds of AlGaAs/GaAs heterostructures with a quantum well are reported. The measurement processes, involving a Fast Fourier Transform and analog wave analyzer in the frequency range from 10 Hz to 1 MHz, a computerized data storage and processing system, and cryostat in the temperature range from 78 K to 300 K are described in detail. The current noise spectra are obtained with the “three-point method”, using a Quan-Tech and avalanche noise source for calibration. ^ The properties of both GaAs and AlGaAs materials and field effect transistors, based on the two-dimensional electron gas in the interface quantum well, are discussed. Extensive measurements are performed in three types of heterostructures, viz., Hall structures with a large spacer layer, modulation-doped non-gated FETs, and more standard gated FETs; all structures are grown by MBE techniques. ^ The Hall structures show Lorentzian generation-recombination noise spectra with near temperature independent relaxation times. This noise is attributed to g-r processes in the 2D electron gas. For the TEGFET structures, we observe several Lorentzian g-r noise components which have strongly temperature dependent relaxation times. This noise is attributed to trapping processes in the doped AlGaAs layer. The trap level energies are determined from an Arrhenius plot of log (τT2) versus 1/T as well as from the plateau values. The theory to interpret these measurements and to extract the defect level data is reviewed and further developed. Good agreement with the data is found for all reported devices. ^

Integrated System Technologies for Modular Trapped Ion Quantum Information Processing

Although trapped ion technology is well-suited for quantum information science, scalability of the system remains one of the main challenges. One of the challenges associated with scaling the ion trap quantum computer is the ability to individually manipulate the increasing number of qubits. Using micro-mirrors fabricated with micro-electromechanical systems (MEMS) technology, laser beams are focused on individual ions in a linear chain and steer the focal point in two dimensions. Multiple single qubit gates are demonstrated on trapped 171Yb+ qubits and the gate performance is characterized using quantum state tomography. The system features negligible crosstalk to neighboring ions (< 3e-4), and switching speeds comparable to typical single qubit gate times (< 2 us). In a separate experiment, photons scattered from the 171Yb+ ion are coupled into an optical fiber with 63% efficiency using a high numerical aperture lens (0.6 NA). The coupled photons are directed to superconducting nanowire single photon detectors (SNSPD), which provide a higher detector efficiency (69%) compared to traditional photomultiplier tubes (35%). The total system photon collection efficiency is increased from 2.2% to 3.4%, which allows for fast state detection of the qubit. For a detection beam intensity of 11 mW/cm2, the average detection time is 23.7 us with 99.885(7)% detection fidelity. The technologies demonstrated in this thesis can be integrated to form a single quantum register with all of the necessary resources to perform local gates as well as high fidelity readout and provide a photon link to other systems.

Optics-Based Quantum Information and Sensing Platforms Utilizing the Nitrogen-Vacancy Center in Diamond

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

Licenciamento zero: da mudança legal à mudança organizacional

A Administração Pública Portuguesa tem sentido necessidade de se modernizar e, na procura desse objetivo, têm sido criados diversos programas de simplificação administrativa em Portugal. No âmbito de um desses programas – o Simplex, surgiu o programa Licenciamento Zero que visa reduzir os procedimentos necessários ao licenciamento de determinadas atividades económicas. O presente trabalho pretendeu demonstrar como se projetou legalmente a implementação do Licenciamento Zero e como se procedeu a implementação organizacional desta medida, procurando identificar as principais dificuldades da sua implementação. Pretendeu-se ainda conhecer os procedimentos de licenciamento antes do projeto Licenciamento Zero, e compará-los com a realidade posterior à sua implementação. Para isso, fez-se um foco na área da publicidade. Por fim, procurou-se compreender quais as vantagens desta desmaterialização, desburocratização e modernização administrativa para as empresas, bem como compreender quais as consequências positivas e negativas sentidas pelas entidades responsáveis pelo licenciamento, nomeadamente a Câmara Municipal de Vagos.

Memory effects and geometrical considerations in open quantum systems

This thesis discusses memory effects in open quantum systems with an emphasis on the Breuer, Laine, Piilo (BLP) measure of non-Markovianity. It is shown how the calculation of the measure can be simplifed and how quantum information protocols can bene t from memory e ects. The superdense coding protocol is used as an example of this. The quantum Zeno effect will also be studied from the point of view of memory e ects. Finally the geometric ideas used in simplifying the calculation of the BLP measure are applied in studying the amount of resources needed for detecting bipartite quantum correlations. It is shown that to decide without prior information if an unknown quantum state is entangled or not, an informationally complete measurement is required. The first part of the thesis contains an introduction to the theoretical ideas such as quantum states, closed and open quantum systems and necessary mathematical tools. The theory is then applied in the second part of the thesis as the results obtained in the original publications I-VI are presented and discussed.

Asymptotic scattering and duality in the one-dimensional three-state quantum Potts model on a lattice

We determine numerically the single-particle and the two-particle spectrum of the three-state quantum Potts model on a lattice by using the density matrix renormalization group method, and extract information on the asymptotic (small momentum) S-matrix of the quasiparticles. The low energy part of the finite size spectrum can be understood in terms of a simple effective model introduced in a previous work, and is consistent with an asymptotic S-matrix of an exchange form below a momentum scale p*. This scale appears to vanish faster than the Compton scale, mc, as one approaches the critical point, suggesting that a dangerously irrelevant operator may be responsible for the behaviour observed on the lattice.

Measurement of finite-frequency current statistics in a single-electron transistor

Electron transport in nanoscale structures is strongly influenced by the Coulomb interaction that gives rise to correlations in the stream of charges and leaves clear fingerprints in the fluctuations of the electrical current. A complete understanding of the underlying physical processes requires measurements of the electrical fluctuations on all time and frequency scales, but experiments have so far been restricted to fixed frequency ranges, as broadband detection of current fluctuations is an inherently difficult experimental procedure. Here we demonstrate that the electrical fluctuations in a single-electron transistor can be accurately measured on all relevant frequencies using a nearby quantum point contact for on-chip real-time detection of the current pulses in the single-electron device. We have directly measured the frequency-dependent current statistics and, hereby, fully characterized the fundamental tunnelling processes in the single-electron transistor. Our experiment paves the way for future investigations of interaction and coherence-induced correlation effects in quantum transport.

Strong quantum memory at resonant Fermi edges revealed by shot noise

Studies of non-equilibrium current fluctuations enable assessing correlations involved in quantum transport through nanoscale conductors. They provide additional information to the mean current on charge statistics and the presence of coherence, dissipation, disorder, or entanglement. Shot noise, being a temporal integral of the current autocorrelation function, reveals dynamical information. In particular, it detects presence of non-Markovian dynamics, i.e., memory, within open systems, which has been subject of many current theoretical studies. We report on low-temperature shot noise measurements of electronic transport through InAs quantum dots in the Fermi-edge singularity regime and show that it exhibits strong memory effects caused by quantum correlations between the dot and fermionic reservoirs. Our work, apart from addressing noise in archetypical strongly correlated system of prime interest, discloses generic quantum dynamical mechanism occurring at interacting resonant Fermi edges.