A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

A method to lower the detection limit for optical beat signals from a frequency-dithered stabilized laser

A narrow absorption feature in an atomic or molecular gas (such as iodine or methane) is used as the frequency reference in many stabilized lasers. As part of the stabilization scheme an optical frequency dither is applied to the laser. In optical heterodyne experiments, this dither is transferred to the RF beat signal, reducing the spectral power density and hence the signal to noise ratio over that in the absence of dither. We removed the dither by mixing the raw beat signal with a dithered local oscillator signal. When the dither waveform is matched to that of the reference laser the output signal from the mixer is rendered dither free. Application of this method to a Winters iodine-stabilized helium-neon laser reduced the bandwidth of the beat signal from 6 MHz to 390 kHz, thereby lowering the detection threshold from 5 pW of laser power to 3 pW. In addition, a simple signal detection model is developed which predicts similar threshold reductions.

Quantum noise in optical fibers. I. Stochastic equations

We analyze the quantum dynamics of radiation propagating in a single-mode optical fiber with dispersion, nonlinearity, and Raman coupling to thermal phonons. We start from a fundamental Hamiltonian that includes the principal known nonlinear effects and quantum-noise sources, including linear gain and loss. Both Markovian and frequency-dependent, non-Markovian reservoirs are treated. This treatment allows quantum Langevin equations, which have a classical form except for additional quantum-noise terms, to be calculated. In practical calculations, it is more useful to transform to Wigner or 1P quasi-probability operator representations. These transformations result in stochastic equations that can be analyzed by use of perturbation theory or exact numerical techniques. The results have applications to fiber-optics communications, networking, and sensor technology.

Experimental study of the quantum driven pendulum and its classical analog in atom optics

We present experimental results for the dynamics of cold atoms in a far detuned amplitude-modulated optical standing wave. Phase-space resonances constitute distinct peaks in the atomic momentum distribution containing up to 65% of all atoms resulting from a mixed quantum chaotic phase space. We characterize the atomic behavior in classical and quantum regimes and we present the applicable quantum and classical theory, which we have developed and refined. We show experimental proof that the size and the position of the resonances in phase space can be controlled by varying several parameters, such as the modulation frequency, the scaled well depth, the modulation amplitude, and the scaled Planck’s constant of the system. We have found a surprising stability against amplitude noise. We present methods to accurately control the momentum of an ensemble of atoms using these phase-space resonances which could be used for efficient phase-space state preparation.

Entanglement in a simple quantum phase transition

What entanglement is present in naturally occurring physical systems at thermal equilibrium? Most such systems are intractable and it is desirable to study simple but realistic systems that can be solved. An example of such a system is the one-dimensional infinite-lattice anisotropic XY model. This model is exactly solvable using the Jordan-Wigner transform, and it is possible to calculate the two-site reduced density matrix for all pairs of sites. Using the two-site density matrix, the entanglement of formation between any two sites is calculated for all parameter values and temperatures. We also study the entanglement in the transverse Ising model, a special case of the XY model, which exhibits a quantum phase transition. It is found that the next-nearest-neighbor entanglement (though not the nearest-neighbor entanglement) is a maximum at the critical point. Furthermore, we show that the critical point in the transverse Ising model corresponds to a transition in the behavior of the entanglement between a single site and the remainder of the lattice.

Optical study of a light diaphragm rupture process in an expansion tube

Rupture of a light cellophane diaphragm in an expansion tube has been studied by an optical method. The influence of the light diaphragm on test flow generation has long been recognised, however the diaphragm rupture mechanism is less well known. It has been previously postulated that the diaphragm ruptures around its periphery due to the dynamic pressure loading of the shock wave, with the diaphragm material at some stage being removed from the flow to allow the shock to accelerate to the measured speeds downstream. The images obtained in this series of experiments are the first to show the mechanism of diaphragm rupture and mass removal in an expansion tube. A light diaphragm was impulsively loaded via a shock wave and a series of images was recorded holographically throughout the rupture process, showing gradual destruction of the diaphragm. Features such as the diaphragm material, the interface between gases, and a reflected shock were clearly visualised. Both qualitative and quantitative aspects of the rupture dynamics were derived from the images and compared with existing one-dimensional theory.

Refractive index tomography of turbid media by bifocal optical coherence refractometry

We demonstrate tomographic imaging of the refractive index of turbid media using bifocal optical coherence refractometry (BOCR). The technique, which is a variant of optical coherence tomography, is based on the measurement of the optical pathlength difference between two foci simultaneously present in a medium of interest. We describe a new method to axially shift the bifocal optical pathlength that avoids the need to physically relocate the objective lens or the sample during an axial scan, and present an experimental realization based on an adaptive liquid-crystal lens. We present experimental results, including video clips, which demonstrate refractive index tomography of a range of turbid liquid phantoms, as well as of human skin in vivo.

A scheme for efficient quantum computation wtih linear optics

Quantum computers promise to increase greatly the efficiency of solving problems such as factoring large integers, combinatorial optimization and quantum physics simulation. One of the greatest challenges now is to implement the basic quantum-computational elements in a physical system and to demonstrate that they can be reliably and scalably controlled. One of the earliest proposals for quantum computation is based on implementing a quantum bit with two optical modes containing one photon. The proposal is appealing because of the ease with which photon interference can be observed. Until now, it suffered from the requirement for non-linear couplings between optical modes containing few photons. Here we show that efficient quantum computation is possible using only beam splitters, phase shifters, single photon sources and photo-detectors. Our methods exploit feedback from photo-detectors and are robust against errors from photon loss and detector inefficiency. The basic elements are accessible to experimental investigation with current technology.

Micromanipulation of chloroplasts using optical tweezers

This paper describes experiments using optical tweezers to probe chloroplast arrangement, shape and consistency in cells of living leaf tissue and in suspension. Dual optical tweezers provided two-point contact on a single chloroplast or two-point contact on two adhered chloroplasts for manipulation in suspension. Alternatively, a microstirrer consisting of a birefringent particle trapped in an elliptically polarized laser trap was used to induce motion and tumbling of a selected chloroplast suspended in a solution. We demonstrate that displacement of chloroplasts inside the cell is extremely difficult, presumably due to chloroplast adhesion to the cytoskeleton and connections between organelles. The study also confirms that the chloroplasts are very thin and extremely cup-shaped with a concave inner surface and a convex outer surface.

Hamiltonian mappings and circle packing phase spaces.

We introduce three area preserving maps with phase space structures which resemble circle packings. Each mapping is derived from a kicked Hamiltonian system with one of the three different phase space geometries (planar, hyperbolic or spherical) and exhibits an infinite number of coexisting stable periodic orbits which appear to ‘pack’ the phase space with circular resonances.

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Short-term spatial diffusion in sigma o+ o- optical molasses

We have measured the spatial diffusion of atoms in a three-dimensional sigma(+)-sigma(-) optical molasses over twenty milliseconds timescale, starting from the initial interaction of the atoms with the molasses. We find that the diffusion constants agree well with a linear model for these short time scales and also compare favourably to other studies of diffusion made over longer time scales. These measurements enable us to quantify the detection method known as freezing molasses. We discuss this method, for detecting and measuring the momentum distribution of cold atoms, which relies on the slow diffusion of atoms in optical molasses to produce a freeze-frame of the spatial distribution of the atoms. This method enables a longer interrogation interval, providing a greatly increased signal-to-noise ratio. (C) 1998 Elsevier Science B.V.

An atom-optical Maxwell demon

The separation, by an optical standing wave, of a beam of two-level atoms prepared in a thermal mixture of ground and excited states, is considered as an example of a Maxwell demon. By including the momentum exchanged with the cavity, it is shown how no violation of the second law is possible. A classical and quantum analysis is given which illustrates this principle in some detail.

Hysteresis and phase transitions in a single partially internally wetted catalyst pellet: Thermogravimetric studies

The hydrogenation of cyclohexene over palladium supported in a microporous gamma-alumina pellet is studied thermogravimetrically with a view to measuring the extent of partial internal wetting associated with the different steady state branches. As many as three steady state branches having significantly different degrees of internal wetting and reaction rates, with transitions between them, are confirmed from observations of catalyst weight change. It is seen that with reduction in catalyst activity the middle branch, obtained by condensation from a vapor filled pellet, is much more prominent without showing an evaporative transition for the range of hydrogen partial pressures used here. The catalyst activity is therefore an important parameter affecting the structure of the steady state branches. Hysteresis effects are found to occur, and the thermogravimetric results also confirm the importance of history in determining the catalyst state. The measured degree of wetting is in accordance with that estimated from a mathematical model incorporating capillary condensation effects in addition to reaction-diffusion phenomena. The same model also satisfactorily interprets the reaction rate variations and transitions seen in the present work.

p-cresol as a reversible acylium ion scavenger in solid-phase peptide synthesis

In this work we have defined the nature of the p-cresol and p-thiocresol adducts generated from acylium ions during HF cleavage, following contemporary Boc/benzyl solid-phase peptide synthesis. Contrary to the results in previous reports, we found that both p-cresol and p-thiocresol predominantly form. aryl esters under typical cleavage conditions. Initially we investigated a number of small peptides containing either a single glutamate residue or a C-terminal long-chain amino acid which allowed us to unambiguously characterize the scavenged side products. Whereas, the p-cresol esters are stable at 0 degrees C they rearrange irreversibly at higher temperatures (5-20 degrees C) to form aryl ketones. By contrast, p-thiocresol esters do not undergo a Fries rearrangement but readily undergo further additions of p-thiocresol to form ketenebisthioacetals and trithio ortho esters, even at low temperatures. Importantly, we found by LC/MS and FT-ICR MS analysis that peptides containing p-cresol esters at glutamyl side chains are susceptible to amidation and fragmentation reactions at these sites during standard mild base workup procedures. The significance of these side reactions was further demonstrated in the synthesis of neutrophil immobilization factor, a 26-residue peptide, containing four glutamic acid residues. The side reactions were largely avoided by mild hydrogen peroxide-catalyzed hydrolysis which converted the p-cresol adducts to the free carboxylic acids in near quantitative yield. The choice of p-cresol as a reversible acylium ion scavenger when coupled with the simple workup conditions described is broadly applicable to Boc/benzyl peptide synthesis and will significantly enhance the quality of peptides produced.