Crystallographic Analyses of Ion Channels: Lessons and Challenges

Membrane proteins fascinate at many levels, from their central functional roles in transport, energy transduction, and signal transduction processes to structural questions concerning how they fold and operate in the exotic environments of the membrane bilayer and the water-bilayer interface and to methodological issues associated with studying membrane proteins either in situ or extracted from the membrane. This interplay is beautifully exemplified by ion channels, a collection of integral membrane proteins that mediate the transmembrane passage of ions down their electrochemical potential gradient (for general reviews, see Refs. 1 and 2). Ion channels are key elements of signaling and sensing pathways, including nerve cell conduction, hormone response, and mechanosensation. The characteristic properties of ion channels reflect their conductance, ion selectivity, and gating. Ion channels are often specific for a particular type of ion (such as potassium or chloride) or a class of ions (such as anions) and are typically regulated by conformational switching of the protein structure between "open" and "closed" states. This conformational switching may be gated in response to changes in membrane potential, ligand binding, or application of mechanical forces. Detailed functional characterizations of channels and their gating mechanisms have been achieved, reflecting exquisite methodological advances such as patch clamp methods that can monitor the activities of individual channels (3). Until recently, corresponding information about the three-dimensional structures of channels was not available, reflecting difficulties in obtaining sufficient quantities of membrane proteins for crystallization trials. Happily, this situation has started to change with the structure determinations of the Streptomyces lividans K+ channel (KcsA (4)) and the Mycobacterium tuberculosis mechanosensitive channel (MscL (5)). A variety of reviews (6-12) have appeared recently that discuss functional implications of these channel structures. This review discusses these developments from a complementary perspective, by considering the implications of these structures from within the larger framework of membrane protein structure and function. Because of space restrictions, this review necessarily emphasizes membrane proteins that are composed primarily of alpha-helical bundles, such as KcsA and MscL, rather than beta-barrel proteins, such as porins, typically found in bacterial outer membranes

Photon molecules in atomic gases trapped near photonic crystal waveguides

Realizing systems that support robust, controlled interactions between individual photons is an exciting frontier of nonlinear optics. To this end, one approach that has emerged recently is to leverage atomic interactions to create strong and spatially non-local interactions between photons. In particular, effective interactions have been successfully created via interactions between atoms excited to Rydberg levels. Here, we investigate an alternative approach, in which atomic interactions arise via their common coupling to photonic crystal waveguides. This technique takes advantage of the ability to separately tailor the strength and range of interactions via the dispersion engineering of the structure itself, which can lead to qualitatively new types of phenomena. As an example, we discuss the formation of correlated transparency windows, in which photonic states of a certain number and shape selectively propagate through the system. Through this technique, we show in particular that one can create molecular-like potentials that lead to molecular bound states of photon pairs

Observation of emission from chaotic lasing modes in deformed microspheres: displacement by the stable orbit modes

By combining detailed imaging measurements at different tilt angles with simulations of ray emission from prolate deformed lasing micro-droplets, we conclude that the probability density for the lasing modes in a three-dimensional dielectric microcavity must reside in the chaotic region of the ray phase space. In particular, maximum emission from such chaotic lasing modes is not from tangent rays emerging from the highest curvature part of the rim. The laser emission is observed and calculated to be non-tangent and displaced from the highest curvature due to the presence of stable orbits. In this Letter we present the first experimental evidence for this phenomenon of ``dynamical eclipsing''.Comment: 4 figure

Directional emission from asymmetric resonant cavities

Asymmetric resonant cavities (ARCs) with highly non-circular but convex cross-sections are predicted theoretically to have high-Q whispering gallery modes with very anisotropic emission. We develop a ray dynamics model for the emission pattern and present numerical and experimental confirmation of the theory.Comment: 7 pages LaTeX, 3 postscript figure

PC-CUBE: A Personal Computer Based Hypercube

PC-CUBE is an ensemble of IBM PCs or close compatibles connected in the hypercube topology with ordinary computer cables. Communication occurs at the rate of 115.2 K-band via the RS-232 serial links. Available for PC-CUBE is the Crystalline Operating System III (CrOS III), Mercury Operating System, CUBIX and PLOTIX which are parallel I/O and graphics libraries. A CrOS performance monitor was developed to facilitate the measurement of communication and computation time of a program and their effects on performance. Also available are CXLISP, a parallel version of the XLISP interpreter; GRAFIX, some graphics routines for the EGA and CGA; and a general execution profiler for determining execution time spent by program subroutines. PC-CUBE provides a programming environment similar to all hypercube systems running CrOS III, Mercury and CUBIX. In addition, every node (personal computer) has its own graphics display monitor and storage devices. These allow data to be displayed or stored at every processor, which has much instructional value and enables easier debugging of applications. Some application programs which are taken from the book Solving Problems on Concurrent Processors (Fox 88) were implemented with graphics enhancement on PC-CUBE. The applications range from solving the Mandelbrot set, Laplace equation, wave equation, long range force interaction, to WaTor, an ecological simulation

Quantum dynamics of propagating photons with strong interactions: a generalized input-output formalism

There has been rapid development of systems that yield strong interactions between freely propagating photons in one dimension via controlled coupling to quantum emitters. This raises interesting possibilities such as quantum information processing with photons or quantum many-body states of light, but treating such systems generally remains a difficult task theoretically. Here, we describe a novel technique in which the dynamics and correlations of a few photons can be exactly calculated, based upon knowledge of the initial photonic state and the solution of the reduced effective dynamics of the quantum emitters alone. We show that this generalized "input-output" formalism allows for a straightforward numerical implementation regardless of system details, such as emitter positions, external driving, and level structure. As a specific example, we apply our technique to show how atomic systems with infinite-range interactions and under conditions of electromagnetically induced transparency enable the selective transmission of correlated multi-photon states

Steady-state Ab Initio Laser Theory: Generalizations and Analytic Results

We improve the steady-state ab initio laser theory (SALT) of Tureci et al. by expressing its fundamental self-consistent equation in a basis set of threshold constant flux states that contains the exact threshold lasing mode. For cavities with non-uniform index and/or non-uniform gain, the new basis set allows the steady-state lasing properties to be computed with much greater efficiency. This formulation of the SALT can be solved in the single-pole approximation, which gives the intensities and thresholds, including the effects of nonlinear hole-burning interactions to all orders, with negligible computational effort. The approximation yields a number of analytic predictions, including a "gain-clamping" transition at which strong modal interactions suppress all higher modes. We show that the single-pole approximation agrees well with exact SALT calculations, particularly for high-Q cavities. Within this range of validity, it provides an extraordinarily efficient technique for modeling realistic and complex lasers.Comment: 17 pages, 11 figure

Quantum many-body models with cold atoms coupled to photonic crystals

Using cold atoms to simulate strongly interacting quantum systems represents an exciting frontier of physics. However, as atoms are nominally neutral point particles, this limits the types of interactions that can be produced. We propose to use the powerful new platform of cold atoms trapped near nanophotonic systems to extend these limits, enabling a novel quantum material in which atomic spin degrees of freedom, motion, and photons strongly couple over long distances. In this system, an atom trapped near a photonic crystal seeds a localized, tunable cavity mode around the atomic position. We find that this effective cavity facilitates interactions with other atoms within the cavity length, in a way that can be made robust against realistic imperfections. Finally, we show that such phenomena should be accessible using one-dimensional photonic crystal waveguides in which coupling to atoms has already been experimentally demonstrated

A digital ecosystem for ICT educators, ICT industry and ICT students

Worldwide ICT education (Information Communication Technology) is facing a major challenge of declining student enrolments; battling to keep its curriculum relevant and up-to-date while trying to meet the high demand of ICT skilled workers in domain, such as resources, health, government and commerce. This paper, documenting research in progress, discusses these issues and challenges in ICT education and proposes a solution in the form of a digital ecosystem in ICT education involving three main stakeholders: academics, students and the IT industry, and how they could come together to tackle the problems faced