Random Boolean Network Models and the Yeast Transcriptional Network

The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.Comment: 23 pages, 5 figure

The Importance of Broad Emission-Line Widths in Single Epoch Black Hole Mass Estimates

Estimates of the mass of super-massive black holes (BHs) in distant active galactic nuclei (AGNs) can be obtained efficiently only through single-epoch spectra, using a combination of their broad emission-line widths and continuum luminosities. Yet the reliability and accuracy of the method, and the resulting mass estimates, M_BH, remain uncertain. A recent study by Croom using a sample of SDSS, 2QZ and 2SLAQ quasars suggests that line widths contribute little information about the BH mass in these single-epoch estimates and can be replaced by a constant value without significant loss of accuracy. In this Letter, we use a sample of nearby reverberation-mapped AGNs to show that this conclusion is not universally applicable. We use the bulge luminosity (L_Bulge) of these local objects to test how well the known M_BH - L_Bulge correlation is recovered when using randomly assigned line widths instead of the measured ones to estimate M_BH. We find that line widths provide significant information about M_BH, and that for this sample, the line width information is just as significant as that provided by the continuum luminosities. We discuss the effects of observational biases upon the analysis of Croom and suggest that the results can probably be explained as a bias of flux-limited, shallow quasar samples.Comment: 10 text pages + 4 Figures + 1 Table. Accepted for publication in ApJ Letter

Practical quantum key distribution over a 48-km optical fiber network

The secure distribution of the secret random bit sequences known as "key" material, is an essential precursor to their use for the encryption and decryption of confidential communications. Quantum cryptography is a new technique for secure key distribution with single-photon transmissions: Heisenberg's uncertainty principle ensures that an adversary can neither successfully tap the key transmissions, nor evade detection (eavesdropping raises the key error rate above a threshold value). We have developed experimental quantum cryptography systems based on the transmission of non-orthogonal photon states to generate shared key material over multi-kilometer optical fiber paths and over line-of-sight links. In both cases, key material is built up using the transmission of a single-photon per bit of an initial secret random sequence. A quantum-mechanically random subset of this sequence is identified, becoming the key material after a data reconciliation stage with the sender. Here we report the most recent results of our optical fiber experiment in which we have performed quantum key distribution over a 48-km optical fiber network at Los Alamos using photon interference states with the B92 and BB84 quantum key distribution protocols.Comment: 13 pages, 7 figures, .pdf format submitted to Journal of Modern Optic

Allosteric Activation of the Par-6 PDZ Via a Partial Unfolding Transition

Proteins exist in a delicate balance between the native and unfolded states, where thermodynamic stability may be sacrificed to attain the flexibility required for efficient catalysis, binding, or allosteric control. Partition-defective 6 (Par-6) regulates the Par polarity complex by transmitting a GTPase signal through the Cdc42/Rac interaction binding PSD-95/Dlg/ZO-1 (CRIB-PDZ) module that alters PDZ ligand binding. Allosteric activation of the PDZ is achieved by local rearrangement of the L164 and K165 side chains to stabilize the interdomain CRIB:PDZ interface and reposition a conserved element of the ligand binding pocket. However, microsecond to millisecond dynamics measurements revealed that L164/K165 exchange requires a larger rearrangement than expected. The margin of thermodynamic stability for the PDZ domain is modest (∼3 kcal/mol) and further reduced by transient interactions with the disordered CRIB domain. Measurements of local structural stability revealed that tertiary contacts within the PDZ are disrupted by a partial unfolding transition that enables interconversion of the L/K switch. The unexpected participation of partial PDZ unfolding in the allosteric mechanism of Par-6 suggests that native-state unfolding may be essential for the function of other marginally stable proteins

A Variational Approach for Minimizing Lennard-Jones Energies

A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and consists in the iterative solution of a set of deterministic equations with annealing in temperature. The singular short-distance behaviour of the Lennard-Jones potential is adiabatically switched on in order to obtain stable convergence. As testbeds for the approach two distinct ensembles of molecules are used, characterized by a roughly dense-packed ore a more elongated ground state. For the latter, problems are generated from natural frequencies of occurrence of amino acids and phenomenologically determined potential parameters; they seem to represent less disorder than was previously assumed in synthetic protein studies. For the dense-packed problems in particular, the variational algorithm clearly outperforms a gradient descent method in terms of minimal energies. Although it cannot compete with a careful simulating annealing algorithm, the variational approach requires only a tiny fraction of the computer time. Issues and results when applying the method to polyelectrolytes at a finite temperature are also briefly discussed.Comment: 14 pages, uuencoded compressed postscript fil

First Steps Toward Change in Teacher Preparation for Elementary Science

Unless introductory undergraduate science classes for prospective elementary teachers actively incorporate the philosophy of inquiry-based learning called for in K-l2 science education refom little will change in elementary science education. Thus, at James Madison University, we have developed a new integrated science core curriculum called Understanding our World [1]. This course sequence was not only designed to fulfill general education science requirements. but also to focus on content areas our students will need to know as teachers. The objectives of these courses are based on the National Science Education Standards and Virginia’s Science Standards of Learning, including earth and space science, chemistry, physics, life sciences, and environmental science [2,3]. As an integrated package, this course sequence addresses basic science content, calculation skills, the philosophy and history of science, the process of how science is done, the role of science in society, and applications of computers and technology in science. Keeping in mind that students tend to teach in the same way they were taught, Understanding our World core classes embrace the concepts associated with reform in elementary math and science

Evaluation of bistable systems versus matched filters in detecting bipolar pulse signals

This paper presents a thorough evaluation of a bistable system versus a matched filter in detecting bipolar pulse signals. The detectability of the bistable system can be optimized by adding noise, i.e. the stochastic resonance (SR) phenomenon. This SR effect is also demonstrated by approximate statistical detection theory of the bistable system and corresponding numerical simulations. Furthermore, the performance comparison results between the bistable system and the matched filter show that (a) the bistable system is more robust than the matched filter in detecting signals with disturbed pulse rates, and (b) the bistable system approaches the performance of the matched filter in detecting unknown arrival times of received signals, with an especially better computational efficiency. These significant results verify the potential applicability of the bistable system in signal detection field.Comment: 15 pages, 9 figures, MikTex v2.