Ionic Coulomb blockade and anomalous mole fraction effect in NaChBac bacterial ion channels

We report an experimental study of the influences of the fixed charge and bulk ionic concentrations on the conduction of biological ion channels, and we consider the results within the framework of the ionic Coulomb blockade model of permeation and selectivity. Voltage clamp recordings were used to investigate the Na$^+$/Ca$^{2+}$ anomalous mole fraction effect (AMFE) exhibited by the bacterial sodium channel NaChBac and its mutants. Site-directed mutagenesis was used to study the effect of either increasing or decreasing the fixed charge in their selectivity filters for comparison with the predictions of the Coulomb blockade model. The model was found to describe well some aspects of the experimental (divalent blockade and AMFE) and simulated (discrete multi-ion conduction and occupancy band) phenomena, including a concentration-dependent shift of the Coulomb staircase. These results substantially extend the understanding of ion channel selectivity and may also be applicable to biomimetic nanopores with charged walls

Ionic Coulomb blockade and anomalous mole fraction effect in the NaChBac bacterial ion channel and its charge-varied mutants

Abstract Background. The selectivity of biological cation channels is defined by a short, narrow selectivity filter, having a negative net fixed charge Qf. Voltage gated bacterial channels (NaChBac and some others) are frequently used in biophysics as simplified models of mammalian calcium and sodium channels. We report an experimental, analytic and numerical study of the effects of Qf and bulk ionic concentrations of Ca2+ and Na+ on conduction and selectivity of NaChBac channels, wild type and Qf-varied mutants. Methods. Site-directed mutagenesis and voltage clamp recordings were used to investigate the Na+/Ca2+ selectivity, divalent blockade and anomalous mole fraction effect (AMFE) for different NaChBac wild type/mutants channels and the properties dependence on Qf. Experimental results were compared with Brownian dynamics simulations and with analytic predictions of the ionic Coulomb blockade (ICB) model, which was extended to encompass bulk concentration effects. Results. It was shown that changing of Qf from –4e (for LESWAS wild type) to –8e (for LEDWAS mutant) leads to strong divalent blockade of the Na+ current by micromolar amounts of Ca2+ ions, similar to the effects seen in mammalian calcium channels. The BD simulations revealed a concentration-related logarithmic shift of the conduction bands. These results were shown to be consistent with ICB model predictions. Conclusions. The extended ICB model explains the experimental (divalent blockade and AMFE) and simulated (multi-ion bands and their concentration-related shifts) selectivity phenomena of NaChBac channel and its charge-varied mutants. These results extend the understanding of ion channel selectivity and may also be applicable to biomimetic nanopores with charged walls

Semiconductor seeded fibre amplified sources of ultra short pulses

This thesis reports upon an experimental investigation of passively mode-locked optically pumped vertical-external-cavity surface-emitting semiconductor lasers (VECSEL). Mode-locked VECSELs are a compact source of ultra-short pulses at GHz repetition rates, with pulse lengths as short as 190 fs being generated directly from the laser. The VECSEL is a power scalable device offering spectral versatility through band gap engineering of semiconductor gain material.Here, for the first time the technique of frequency resolved optical gating (FROG) has been used to record a second harmonic spectrogram of the VECSEL pulse train, from which the phase information of non-transform limited sub-picosecond pulses has been retrieved. I also report the characterisation of a single stage VECSEL seeded ytterbium-doped fibre amplifier, capable of increasing the average power of a VECSEL from 20 mW to over 1.5 W while maintaining the sub-picosecond duration of the pulse train. The amplifier is capable of operating at any repetition rate obtainable with a VECSEL, amplification is demonstrated here with 1 GHz and 6 GHz seeds.Finally, the nonlinear evolution of VECSEL pulses inside a single stage fibre amplifier has been investigated. Computer modelling of the linear gain and nonlinear pulse propagation within a single fibre has been used to design an amplifier capable of producing pulses with a parabolic profile. The modelling reveals that a parabolic amplifier would produce spectrally broader linearly chirped pulses which could be compressed to below 100 fs, with average powers > 3 W. An experimental realisation of the parabolic amplifier will require a seed with average power greater than 100 mW, this could be achieved with a re-growth of an existing sample, QT1544

Semiconductor seeded fibre amplified sources of ultra short pulses

Semiconductor Seeded Fibre Amplified Sources of Ultra Short Pulses By Stephen Paul Elsmere This thesis reports upon an experimental investigation of passively mode-locked optically pumped vertical-external-cavity surface-emitting semiconductor lasers (VECSEL). Mode-locked VECSELs are a compact source of ultra-short pulses at GHz repetition rates, with pulse lengths as short as 190 fs being generated directly from the laser. The VECSEL is a power scalable device offering spectral versatility through band gap engineering of semiconductor gain material. Here, for the first time the technique of frequency resolved optical gating (FROG) has been used to record a second harmonic spectrogram of the VECSEL pulse train, from which the phase information of non-transform limited sub-picosecond pulses has been retrieved. I also report the characterisation of a single stage VECSEL seeded ytterbium-doped fibre amplifier, capable of increasing the average power of a VECSEL from 20 mW to over 1.5 W while maintaining the sub-picosecond duration of the pulse train. The amplifier is capable of operating at any repetition rate obtainable with a VECSEL, amplification is demonstrated here with 1 GHz and 6 GHz seeds. Finally, the nonlinear evolution of VECSEL pulses inside a single stage fibre amplifier has been investigated. Computer modelling of the linear gain and nonlinear pulse propagation within a single fibre has been used to design an amplifier capable of producing pulses with a parabolic profile. The modelling reveals that a parabolic amplifier would produce spectrally broader linearly chirped pulses which could be compressed to below 100 fs, with average powers > 3 W. An experimental realisation of the parabolic amplifier will require a seed with average power greater than 100 mW, this could be achieved with a re-growth of an existing sample, QT1544.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Spectrotemporal gain bandwidth measurement in an InGaAs/GaAsP quantum well vertical-external-cavity surface-emitting semiconductor laser

Analysis of spectral condensation in a VECSEL with a near-antiresonant gain structure incorporating InGaAs/GaAsP quantum wells emitting around 1030 nm shows the effective FWHM gain bandwidth of this laser to be 32 nm

Quantized Dehydration and the Determinants of Selectivity in the NaChBac Bacterial Sodium Channel

A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena measured in the bacterial NaChBac sodium channel and some of its mutants. Site-directed mutagenesis and the whole-cell patch-clamp technique were used to investigate how the value $Q_f$ of the fixed charge at the selectivity filter (SF) affected both valence and alike-charge selectivity. The new ICB/QD model predicts that increasing ${Q_f}$ should lead to a shift of selectivity sequences towards larger ion sizes and charges, a result that agrees with the present experiments and with earlier work. Comparison of the model with experimental data provides evidence for an {\it effective charge} $Q_f^*$ at the SF that is smaller in magnitude than the nominal $Q_f$ corresponding to the charge on the isolated protein residues. Furthermore, $Q_f^*$ was different for aspartate and glutamate charged rings and also depended on their position within the SF. It is suggested that protonation of the residues within the restricted space is an important factor in significantly reducing the effective charge of the EEEE ring. Values of $Q_f^*$ derived from experiments on the anomalous mole fraction effect (AMFE) agree well with expectations based on the ICB/QD model and have led to the first clear demonstration of the expected ICB oscillations in Ca$^{2+}$ conduction as a function of the fixed charge. Pilot studies of the dependence of Ca$^{2+}$ conduction on pH are consistent with the predictions of the model. \

Ultrafast optical Stark mode-locked semiconductor laser

We report on 260 fs transform-limited pulses generated directly by an optical Stark passively mode-locked semiconductor disk laser at a 1 GHz repetition rate. A surface recombination semiconductor saturable absorber mirror and a step-index gain structure are used. Numerical propagation modeling of the optical Stark effect confirms that this mechanism is able to form the pulses that we observe

First demonstration of an all-semiconductor room-temperature terahertz time-domain spectrometer

We report the first demonstration of an all-semiconductor, room temperature terahertz time-domain spectrometer using a femtosecond mode-locked Vertical-External-Cavity Surface-Emitting Laser at 1040 nm and photoconductive antennae.</p