Explicit Green's Function of a Boundary Value Problem for a Sphere and Trapped Flux Analysis in Gravity Probe B Experiment

Magnetic flux trapped on the surface of superconducting rotors of the Gravity Probe B (GP-B) experiment produces some signal in the SQUID readout. For the needs of GP-B error analysis and simulation of data reduction, this signal is calculated and analyzed in the paper. We first solve a magnetostatic problem for a point source (fluxon) on the surface of a sphere, finding the closed form elementary expression for the corresponding Green's function. Second, we calculate the flux through the pick-up loop as a function of the fluxon position. Next, the time dependence of a fluxon position, caused by rotor motion according to a symmetric top model, and thus the time signature of the flux are determined, and the spectrum of the trapped flux signal is analyzed. Finally, a multi-purpose program of trapped flux signal generation based on the above results is described, various examples of the signal obtained by means of this program are given, and their features are discussed.Comment: 14 pages, including 7 figures. Submitted to: "Journal of Applied Physics

Gain control in molecular information processing: Lessons from neuroscience

Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain control. Here we argue that a certain simple mechanism of gain control, understood well in the context of systems neuroscience, also works for molecular signaling. The mechanism allows to transmit more than one bit (on or off) of information about the signal independently of the signal variance. It does not require additional molecular circuitry beyond that already present in many molecular systems, and, in particular, it does not depend on existence of feedback loops. The mechanism provides a potential explanation for abundance of ultrasensitive response curves in biological regulatory networks.Comment: 10 pages, 5 figure

Minimal subtraction and the Callan-Symanzik equation

The usual proof of renormalizability using the Callan-Symanzik equation makes explicit use of normalization conditions. It is shown that demanding that the renormalization group functions take the form required for minimal subtraction allows one to prove renormalizability using the Callan-Symanzik equation, without imposing normalization conditions. Scalar field theory and quantum electrodynamics are treated.Comment: 6 pages, plain Te

Modular Acquisition and Stimulation System for Timestamp-Driven Neuroscience Experiments

Dedicated systems are fundamental for neuroscience experimental protocols that require timing determinism and synchronous stimuli generation. We developed a data acquisition and stimuli generator system for neuroscience research, optimized for recording timestamps from up to 6 spiking neurons and entirely specified in a high-level Hardware Description Language (HDL). Despite the logic complexity penalty of synthesizing from such a language, it was possible to implement our design in a low-cost small reconfigurable device. Under a modular framework, we explored two different memory arbitration schemes for our system, evaluating both their logic element usage and resilience to input activity bursts. One of them was designed with a decoupled and latency insensitive approach, allowing for easier code reuse, while the other adopted a centralized scheme, constructed specifically for our application. The usage of a high-level HDL allowed straightforward and stepwise code modifications to transform one architecture into the other. The achieved modularity is very useful for rapidly prototyping novel electronic instrumentation systems tailored to scientific research.Comment: Preprint submitted to ARC 2015. Extended: 16 pages, 10 figures. The final publication is available at link.springer.co

On the detectability of quantum spacetime foam with gravitational-wave interferometers

We discuss a recent provocative suggestion by Amelino-Camelia and others that classical spacetime may break down into ``quantum foam'' on distance scales many orders of magnitude larger than the Planck length, leading to effects which could be detected using large gravitational wave interferometers. This suggestion is based on a quantum uncertainty limit obtained by Wigner using a quantum clock in a gedanken timing experiment. Wigner's limit, however, is based on two unrealistic and unneccessary assumptions: that the clock is free to move, and that it does not interact with the environment. Removing either of these assumptions makes the uncertainty limit invalid, and removes the basis for Amelino-Camelia's suggestion.Comment: Submitted to Phys. Lett.

Serially-regulated biological networks fully realize a constrained set of functions

We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends only on the direct path from the input to the target, even when there is a feedback loop allowing for multiple interaction pathways. Using a stochastic model for a set of small transcriptional regulatory networks that have been studied experimentally, we further find that all networks can achieve all functions permitted by this constraint under reasonable settings of biochemical parameters. This underscores the functional versatility of the networks.Comment: 9 pages, 3 figure

Statistical properties of multistep enzyme-mediated reactions

Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or "dose-response" curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.Comment: 8 pages, 3 figure