PREDBALB/c: a system for the prediction of peptide binding to H2(d) molecules, a haplotype of the BALB/c mouse

PREDBALB/c is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I ( H2-K-d, H2-L-d and H2-D-d) and class II (I-E-d and I-A(d)) molecules. The prediction system utilizes quantitative matrices, which were rigorously validated using experimentally determined binders and non-binders and also by in vivo studies using viral proteins. The prediction performance of PREDBALB/c is of very high accuracy. To our knowledge, this is the first online server for the prediction of peptides binding to a complete set of major histocompatibility complex molecules in a model organism (H2(d) haplotype). PREDBALB/c is available at http://antigen.i2r.a-star.edu.sg/predBalbc/.

Molecular orbital calculations of two-electron states for P-donor solid-state spin qubits

We theoretically study the Hilbert space structure of two neighboring P-donor electrons in silicon-based quantum computer architectures. To use electron spins as qubits, a crucial condition is the isolation of the electron spins from their environment, including the electronic orbital degrees of freedom. We provide detailed electronic structure calculations of both the single donor electron wave function and the two-electron pair wave function. We adopted a molecular orbital method for the two-electron problem, forming a basis with the calculated single donor electron orbitals. Our two-electron basis contains many singlet and triplet orbital excited states, in addition to the two simple ground state singlet and triplet orbitals usually used in the Heitler-London approximation to describe the two-electron donor pair wave function. We determined the excitation spectrum of the two-donor system, and study its dependence on strain, lattice position, and interdonor separation. This allows us to determine how isolated the ground state singlet and triplet orbitals are from the rest of the excited state Hilbert space. In addition to calculating the energy spectrum, we are also able to evaluate the exchange coupling between the two donor electrons, and the double occupancy probability that both electrons will reside on the same P donor. These two quantities are very important for logical operations in solid-state quantum computing devices, as a large exchange coupling achieves faster gating times, while the magnitude of the double occupancy probability can affect the error rate.

Optimal estimation of one-parameter quantum channels

We explore the task of optimal quantum channel identification and in particular, the estimation of a general one-parameter quantum process. We derive new characterizations of optimality and apply the results to several examples including the qubit depolarizing channel and the harmonic oscillator damping channel. We also discuss the geometry of the problem and illustrate the usefulness of using entanglement in process estimation.

Macroscopic test of quantum mechanics versus stochastic electrodynamics

We identify a test of quantum mechanics versus macroscopic local realism in the form of stochastic electrodynamics. The test uses the steady-state triple quadrature correlations of a parametric oscillator below threshold.

A low-temperature insulating phase at v=1.5 for 2D holes in high-mobility SiSi1-xGex heterostructures with Landau level degeneracy

Magneto-transport measurements of the 2D hole system (2DHS) in p-type Si-Si1-xGex heterostructures identify the integer quantum Hall effect (IQHE) at dominantly odd-integer filling factors v and two low-temperature insulating phases (IPs) at v = 1.5 and v less than or similar to 0.5, with re-entrance to the quantum Hall effect at v = 1. The temperature dependence, current-voltage characteristics, and tilted field and illumination responses of the IP at v = 1.5 indicate that the important physics is associated with an energy degeneracy of adjacent Landau levels of opposite spin, which provides a basis for consideration of an intrinsic, many-body origin.

Satellite observation and climate system model simulation of the St. Lawrence Island polynya

The St. Lawrence Island polynya (SLIP) is a commonly occurring winter phenomenon in the Bering Sea, in which dense saline water produced during new ice formation is thought to flow northward through the Bering Strait to help maintain the Arctic Ocean halocline. Winter darkness and inclement weather conditions have made continuous in situ and remote observation of this polynya difficult. However, imagery acquired from the European Space Agency ERS-1 Synthetic Aperture Radar (SAR) has allowed observation of the St. Lawrence Island polynya using both the imagery and derived ice displacement products. With the development of ARCSyM, a high resolution regional model of the Arctic atmosphere/sea ice system, simulation of the SLIP in a climate model is now possible. Intercomparisons between remotely sensed products and simulations can lead to additional insight into the SLIP formation process. Low resolution SAR, SSM/I and AVHRR infrared imagery for the St. Lawrence Island region are compared with the results of a model simulation for the period of 24-27 February 1992. The imagery illustrates a polynya event (polynya opening). With the northerly winds strong and consistent over several days, the coupled model captures the SLIP event with moderate accuracy. However, the introduction of a stability dependent atmosphere-ice drag coefficient, which allows feedbacks between atmospheric stability, open water, and air-ice drag, produces a more accurate simulation of the SLIP in comparison to satellite imagery. Model experiments show that the polynya event is forced primarily by changes in atmospheric circulation followed by persistent favorable conditions: ocean surface currents are found to have a small but positive impact on the simulation which is enhanced when wind forcing is weak or variable.

Role of galectin-1 in the olfactory nervous system

The olfactory nervous system is responsible for the detection of odors. Primary sensory olfactory neurons are located in a neuroepithelial sheet lining the nasal cavity. The axons from these neurons converge on to discrete loci or glomeruli in the olfactory bulb. Each glomerulus consists of the termination of thousands of primary axons on the dendrites of second-order olfactory neurons. What are the molecular mechanisms which guide growing olfactory axons to select sites in the olfactory bulb? We have shown that subpopulations of these axons differentially express cell surface carbohydrates and that these different subpopulations target and terminate in particular regions of the olfactory bulb. Interestingly, the olfactory neurons and glial components in the olfactory pathway between the nose and brain express galectin-1. By using in vitro assays of neurite outgrowth we found that both galectin-1 and it's ligands were capable of specifically stimulating neurite elongation. Examination of the olfactory system in galectin-1 null mutants revealed that a subpopulation of axons failed to navigate to their target site in the olfactory bulb. This is the first phenotypic effect observed in galectin-1 null mutants and indicates that galectin-1 has a role in the growth and/or guidance of a subpopulation of axons in the olfactory system during development.

On the construction of integrable closed chains with quantum supersymmetry

We present a general prescription for the construction of integrable one-dimensional systems with closed boundary conditions and quantum supersymmetry.

Plasminogen activator system in osteoclasts

To determine which genes of the plasminogen activator (PA) system were expressed in osteoclasts, RNA extracted from microisolated mouse osteoclasts was used as template for reverse transcribed polymerase chain reaction (RT-PCR) with gene-specific primer pairs, Using this approach, the expression of RNAs for tissue-type plasminogen activator, urokinase-type plasminogen activator, plasminogen activator inhibitor-1, plasminogen activator inhibitor-2, protease nexin, and urokinase receptor isoform 1 (uPAR1) were detected in mouse osteoclasts. The expression of uPAR RNA in osteoclasts was confirmed by in situ hybridization with a uPAR1 probe, RNA encoding the uPAR isoform 2 was not detected in mouse osteoclasts, but a novel unspliced uPAR RNA variant was detected in these cells, The novel uPAR variant and uPAR1 RNA were also detected in mouse calvarial osteoblasts, kidney, muscle, and the mouse macrophage cell line J774A.1 by RT-PCR The presence of RNAs for most of the components of the PA system in osteoclasts suggests that it may have a functional role in this cell type.

Presence of novel N-CAM glycoforms in the rat olfactory system

The functional activity of the neural cell adhesion molecule N-CAM can be modulated by posttranslational modifications such as glycosylation. For instance, the long polysialic acid side chains of N-CAM alter the adhesion properties of the protein backbone. In the present study, we identified two novel carbohydrates present on N-CAM, NOC-3 and NOC-4. Both carbohydrates were detected on N-CAM glycoforms expressed by subpopulations of primary sensory olfactory neurons in the rat olfactory system. Based on the expression of NOC-3 and NOC-4 and the olfactory marker protein (OMP), four independent subpopulations of primary sensory olfactory neurons were characterized. These neurons expressed: both NOC-3 and NOC-4 but not OMP; both NOC-4 and OMP but not NOC-3; NOC-3, NOC-4, and OMP together; and OMP alone. The NOC-3- and NOC-4-expressing neurons were widely dispersed in the olfactory neuroepithelium lining the nasal cavity. The axons of NOC-4 expressing neurons innervated all glomeruli in the olfactory bulb, whereas the NOC-3 expressing axons terminated in a discrete subset of glomeruli scattered throughout the whole olfactory bulb. We propose that both NOC-3 and NOC-4 are part of a chemical code of olfactory neurons which is used in establishing the topography of connections between the olfactory neuroepithelium and the olfactory bulb. (C) 1997 John Wiley & Sons, Inc.

Quantum Lie algebras, their existence, uniqueness and q-antisymmetry

Quantum Lie algebras are generalizations of Lie algebras which have the quantum parameter h built into their structure. They have been defined concretely as certain submodules L-h(g) of the quantized enveloping algebras U-h(g). On them the quantum Lie product is given by the quantum adjoint action. Here we define for any finite-dimensional simple complex Lie algebra g an abstract quantum Lie algebra g(h) independent of any concrete realization. Its h-dependent structure constants are given in terms of inverse quantum Clebsch-Gordan coefficients. We then show that all concrete quantum Lie algebras L-h(g) are isomorphic to an abstract quantum Lie algebra g(h). In this way we prove two important properties of quantum Lie algebras: 1) all quantum Lie algebras L-h(g) associated to the same g are isomorphic, 2) the quantum Lie product of any Ch(B) is q-antisymmetric. We also describe a construction of L-h(g) which establishes their existence.

The formal representation of process system modelling assumptions and their implications

In order to analyse the effect of modelling assumptions in a formal, rigorous way, a syntax of modelling assumptions has been defined. The syntax of modelling assumptions enables us to represent modelling assumptions as transformations acting on the set of model equations. The notion of syntactical correctness and semantical consistency of sets of modelling assumptions is defined and methods for checking them are described. It is shown on a simple example how different modelling assumptions act on the model equations and their effect on the differential index of the resulted model is also indicated.

Classical and quantum signatures of competing chi((2)) nonlinearities

We report the observation of the quantum effects of competing chi((2)) nonlinearities. We also report classical signatures of competition, namely, clamping of the second-harmonic power and production of nondegenerate frequencies in the visible. Theory is presented that describes the observations as resulting from competition between various chi((2)) up-conversion and down-conversion processes. We show that competition imposes hitherto unsuspected limits to both power generation and squeezing. The observed signatures are expected to be significant effects in practical systems.

Quantum noise limits to terabaud communications

From a general model of fiber optics, we investigate the physical limits of soliton-based terabaud communication systems. In particular we consider Raman and initial quantum noise effects which are often neglected in fiber communications. Simulations of the position diffusion in dark and bright solitons show that these effects become increasingly important at short pulse durations, even over kilometer-scale distances. We also obtain an approximate analytic theory in agreement with numerical simulations, which shows that the Raman effects exceed the Gordon-Haus jitter for sub-picosecond pulses. (C) 1997 Elsevier Science B.V.

Twisted quantum affine superalgebra U-q[sl(2/2)((2))], U-q[osp(2/2)] invariant R-matrices and a new integrable electronic model

We describe the twisted affine superalgebra sl(2\2)((2)) and its quantized version U-q[sl(2\2)((2))]. We investigate the tensor product representation of the four-dimensional grade star representation for the fixed-point sub superalgebra U-q[osp(2\2)]. We work out the tensor product decomposition explicitly and find that the decomposition is not completely reducible. Associated with this four-dimensional grade star representation we derive two U-q[osp(2\2)] invariant R-matrices: one of them corresponds to U-q [sl(2\2)(2)] and the other to U-q [osp(2\2)((1))]. Using the R-matrix for U-q[sl(2\2)((2))], we construct a new U-q[osp(2\2)] invariant strongly correlated electronic model, which is integrable in one dimension. Interestingly this model reduces in the q = 1 limit, to the one proposed by Essler et al which has a larger sl(2\2) symmetry.