Bandwidth statistics from the eigenvalue moments for the Harper–Hofstadter problem

A method for studying the product of bandwidths for the Harper–Hofstader model is proposed, which requires knowledge of the moments of the midband energies. A general formula for these moments is conjectured, and the asymptotic representation for the product of bandwidths computed in the limit of a weak magnetic flux using Szeg¨o’s theorem for Hankel matrices. Then a first approximation for the edge of the butterfly spectrum is given and its connection with L´evy’s formula for Brownian motion discussed

Fusion rules for Quantum Transfer Matrices as a Dynamical System on Grassmann Manifolds

We show that the set of transfer matrices of an arbitrary fusion type for an integrable quantum model obey these bilinear functional relations, which are identified with an integrable dynamical system on a Grassmann manifold (higher Hirota equation). The bilinear relations were previously known for a particular class of transfer matrices corresponding to rectangular Young diagrams. We extend this result for general Young diagrams. A general solution of the bilinear equations is presented.Comment: LaTex (MPLA macros included) 10 pages, 1 figure, included in the tex

Quantum Integrable Systems and Elliptic Solutions of Classical Discrete Nonlinear Equations

Functional relation for commuting quantum transfer matrices of quantum integrable models is identified with classical Hirota's bilinear difference equation. This equation is equivalent to the completely discretized classical 2D Toda lattice with open boundaries. The standard objects of quantum integrable models are identified with elements of classical nonlinear integrable difference equation. In particular, elliptic solutions of Hirota's equation give complete set of eigenvalues of the quantum transfer matrices. Eigenvalues of Baxter's $Q$-operator are solutions to the auxiliary linear problems for classical Hirota's equation. The elliptic solutions relevant to Bethe ansatz are studied. The nested Bethe ansatz equations for $A_{k-1}$-type models appear as discrete time equations of motions for zeros of classical $\tau$-functions and Baker-Akhiezer functions. Determinant representations of the general solution to bilinear discrete Hirota's equation and a new determinant formula for eigenvalues of the quantum transfer matrices are obtained.Comment: 32 pages, LaTeX file, no figure

Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics

The use of oscillatory signals in the study of genetic networks

The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. It is found that there are important advantages in using oscillatory signals over step or impulse signals, and that the system may enter into a pure fluctuation resonance for a specific input frequency.Comment: 46 pages, 5 figures. Submitted to PNAS on May 27th 2004. The paper is under consideratio

Area versus Length Distribution for Closed Random Walks

Using a connection between the $q$-oscillator algebra and the coefficients of the high temperature expansion of the frustrated Gaussian spin model, we derive an exact formula for the number of closed random walks of given length and area, on a hypercubic lattice, in the limit of infinite number of dimensions. The formula is investigated in detail, and asymptotic behaviours are evaluated. The area distribution in the limit of long loops is computed. As a byproduct, we obtain also an infinite set of new, nontrivial identities.Comment: 17 page

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify “phenotypic signatures” by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains

Trade-offs and Noise Tolerance in Signal Detection by Genetic Circuits

Genetic circuits can implement elaborated tasks of amplitude or frequency signal detection. What type of constraints could circuits experience in the performance of these tasks, and how are they affected by molecular noise? Here, we consider a simple detection process–a signal acting on a two-component module–to analyze these issues. We show that the presence of a feedback interaction in the detection module imposes a trade-off on amplitude and frequency detection, whose intensity depends on feedback strength. A direct interaction between the signal and the output species, in a type of feed-forward loop architecture, greatly modifies these trade-offs. Indeed, we observe that coherent feed-forward loops can act simultaneously as good frequency and amplitude noise-tolerant detectors. Alternatively, incoherent feed-forward loop structures can work as high-pass filters improving high frequency detection, and reaching noise tolerance by means of noise filtering. Analysis of experimental data from several specific coherent and incoherent feed-forward loops shows that these properties can be realized in a natural context. Overall, our results emphasize the limits imposed by circuit structure on its characteristic stimulus response, the functional plasticity of coherent feed-forward loops, and the seemingly paradoxical advantage of improving signal detection with noisy circuit components

Simple molecular networks that respond optimally to time-periodic stimulation

<p>Abstract</p> <p>Background</p> <p>Bacteria or cells receive many signals from their environment and from other organisms. In order to process this large amount of information, Systems Biology shows that a central role is played by regulatory networks composed of genes and proteins. The objective of this paper is to present and to discuss simple regulatory network motifs having the property to maximize their responses under time-periodic stimulations. In elucidating the mechanisms underlying these responses through simple networks the goal is to pinpoint general principles which optimize the oscillatory responses of molecular networks.</p> <p>Results</p> <p>We took a look at basic network motifs studied in the literature such as the Incoherent Feedforward Loop (IFFL) or the interlerlocked negative feedback loop. The former is also generalized to a diamond pattern, with network components being either purely genetic or combining genetic and signaling pathways. Using standard mathematics and numerical simulations, we explain the types of responses exhibited by the IFFL with respect to a train of periodic pulses. We show that this system has a non-vanishing response only if the inter-pulse interval is above a threshold. A slight generalisation of the IFFL (the diamond) is shown to work as an ideal pass-band filter. We next show a mechanism by which average of oscillatory response can be maximized by bursting temporal patterns. Finally we study the interlerlocked negative feedback loop, i.e. a 2-gene motif forming a loop where the nodes respectively activate and repress each other, and show situations where this system possesses a resonance under periodic stimulation.</p> <p>Conclusion</p> <p>We present several simple motif designs of molecular networks producing optimal output in response to periodic stimulations of the system. The identified mechanisms are simple and based on known network motifs in the literature, so that that they could be embodied in existing organisms, or easily implementable by means of synthetic biology. Moreover we show that these designs can be studied in different contexts of molecular biology, as for example in genetic networks or in signaling pathways.</p