arXiv subjects

Robert S. Maier

Publications and source records attributed to Robert S. Maier.

At least 37 records · Page 2Linked to original sources

arXiv2007

Parametrized Stochastic Grammars for RNA Secondary Structure Prediction

We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a posteriori estimation of the secondary structure of any new sequence in the family. The proposed SCFG architecture models RNA subsequences comprising paired bases as stochastically weighted Dyck-language words, i.e., as weighted balanced-parenthesis expressions. The length of each run of unpaired bases, forming a loop or a bulge, is taken to have a phase-type distribution: that of the hitting time in a finite-state Markov chain. Without loss of generality, each such Markov chain can be taken to have a bounded complexity. The scheme yields an overall family SCFG with a manageable number of parameters.

q-bio.BM↗

arXiv2006

Algebraic Hypergeometric Transformations of Modular Origin

It is shown that Ramanujan's cubic transformation of the Gauss hypergeometric function ${}_2F_1$ arises from a relation between modular curves, namely the covering of $X_0(3)$ by $X_0(9)$. In general, when $2\le N\le 7$ the N-fold cover of $X_0(N)$ by $X_0(N^2)$ gives rise to an algebraic hypergeometric transformation. The N=2,3,4 transformations are arithmetic-geometric mean iterations, but the N=5,6,7 transformations are new. In the final two the change of variables is not parametrized by rational functions, since $X_0(6),X_0(7)$ are of genus 1. Since their quotients $X_0^+(6),X_0^+(7)$ under the Fricke involution (an Atkin-Lehner involution) are of genus 0, the parametrization is by two-valued algebraic functions. The resulting hypergeometric transformations are closely related to the two-valued modular equations of Fricke and H. Cohn.

math.NT↗

arXiv2006

A Generalization of Euler's Hypergeometric Transformation

Euler's transformation formula for the Gauss hypergeometric function 2F1 is extended to hypergeometric functions of higher order. Unusually, the generalized transformation constrains the hypergeometric function parameters algebraically but not linearly. Its consequences for hypergeometric summation are explored. It has as corollary a summation formula of Slater. From this formula new one-term evaluations of 2F1(-1) and 3F2(1) are derived, by applying transformations in the Thomae group. Their parameters are also constrained nonlinearly. Several new one-term evaluations of 2F1(-1) with linearly constrained parameters are derived as well.

math.CA↗

arXiv2006

The 192 Solutions of the Heun Equation

A machine-generated list of 192 local solutions of the Heun equation is given. They are analogous to Kummer's 24 solutions of the Gauss hypergeometric equation, since the two equations are canonical Fuchsian differential equations on the Riemann sphere with four and three singular points, respectively. Tabulation is facilitated by the identification of the automorphism group of the equation with n singular points as the Coxeter group D_n. Each of the 192 expressions is labeled by an element of D_4. Of the 192, 24 are equivalent expressions for the local Heun function Hl, and it is shown that the resulting order-24 group of transformations of Hl is isomorphic to the symmetric group S_4. The isomorphism encodes each transformation as a permutation of an abstract four-element set, not identical to the set of singular points.

math.CA↗

arXiv2004

On reducing the Heun equation to the hypergeometric equation

The reductions of the Heun equation to the hypergeometric equation by polynomial transformations of its independent variable are enumerated and classified. Heun-to-hypergeometric reductions are similar to classical hypergeometric identities, but the conditions for the existence of a reduction involve features of the Heun equation that the hypergeometric equation does not possess; namely, its cross-ratio and accessory parameters. The reductions include quadratic and cubic transformations, which may be performed only if the singular points of the Heun equation form a harmonic or an equianharmonic quadruple, respectively; and several higher-degree transformations. This result corrects and extends a theorem in a previous paper, which found only the quadratic transformations. [See K. Kuiken, "Heun's equation and the hypergeometric equation", SIAM Journal on Mathematical Analysis 10:3 (1979), 655-657.]

math.CA↗

arXiv2004

Lamé polynomials, hyperelliptic reductions and Lamé band structure

The band structure of the Lamé equation, viewed as a one-dimensional Schrödinger equation with a periodic potential, is studied. At integer values of the degree parameter l, the dispersion relation is reduced to the l=1 dispersion relation, and a previously published l=2 dispersion relation is shown to be partially incorrect. The Hermite-Krichever Ansatz, which expresses Lamé equation solutions in terms of l=1 solutions, is the chief tool. It is based on a projection from a genus-l hyperelliptic curve, which parametrizes solutions, to an elliptic curve. A general formula for this covering is derived, and is used to reduce certain hyperelliptic integrals to elliptic ones. Degeneracies between band edges, which can occur if the Lamé equation parameters take complex values, are investigated. If the Lamé equation is viewed as a differential equation on an elliptic curve, a formula is conjectured for the number of points in elliptic moduli space (elliptic curve parameter space) at which degeneracies occur. Tables of spectral polynomials and Lamé polynomials, i.e., band edge solutions, are given. A table in the older literature is corrected.

math-ph↗

arXiv2004

A Theory of Magnetization Reversal in Nanowires

Magnetization reversal in a ferromagnetic nanowire which is much narrower than the exchange length is believed to be accomplished through the thermally activated growth of a spatially localized nucleus, which initially occupies a small fraction of the total volume. To date, the most detailed theoretical treatments of reversal as a field-induced but noise-activated process have focused on the case of a very long ferromagnetic nanowire, i.e., a highly elongated cylindrical particle, and have yielded a reversal rate per unit length, due to an underlying assumption that the nucleus may form anywhere along the wire. But in a bounded-length (though long) cylindrical particle with flat ends, it is energetically favored for nucleation to begin at either end. We indicate how to compute analytically the energy of the critical nucleus associated with either end, i.e., the activation barrier to magnetization reversal, which governs the reversal rate in the low-temperature (Kramers) limit. Our treatment employs elliptic functions, and is partly analytic rather than numerical. We also comment on the Kramers prefactor, which for this reversal pathway does not scale linearly as the particle length increases, and tends to a constant in the low-temperature limit.

cond-mat.stat-mech↗

arXiv2003

The Effects of Weak Spatiotemporal Noise on a Bistable One-Dimensional System

We treat analytically a model that captures several features of the phenomenon of spatially inhomogeneous reversal of an order parameter. The model is a classical Ginzburg-Landau field theory restricted to a bounded one-dimensional spatial domain, perturbed by weak spatiotemporal noise having a flat power spectrum in time and space. Our analysis extends the Kramers theory of noise-induced transitions to the case when the system acted on by the noise has nonzero spatial extent, and the noise itself is spatially dependent. By extending the Langer-Coleman theory of the noise-induced decay of a metastable state, we determine the dependence of the activation barrier and the Kramers reversal rate prefactor on the size of the spatial domain. As this is increased from zero and passes through a certain critical value, a transition between activation regimes occurs, at which the rate prefactor diverges. Beyond the transition, reversal preferentially takes place in a spatially inhomogeneous rather than in a homogeneous way. Transitions of this sort were not discovered by Langer or Coleman, since they treated only the infinite-volume limit. Our analysis uses higher transcendental functions to handle the case of finite volume. Similar transitions between activation regimes should occur in other models of metastable systems with nonzero spatial extent, perturbed by weak noise, as the size of the spatial domain is varied.

cond-mat.stat-mech↗

arXiv2002

On Crossing Event Formulas in Critical Two-Dimensional Percolation

Several formulas for crossing functions arising in the continuum limit of critical two-dimensional percolation models are studied. These include Watts's formula for the horizontal-vertical crossing probability and Cardy's new formula for the expected number of crossing clusters. It is shown that under the assumption of conformal invariance, they simplify when the spatial domain is taken to be the interior of an equilateral triangle. The two crossing functions can be expressed in terms of an equianharmonic elliptic function with a triangular rotational symmetry. This suggests that rigorous proofs of Watts's formula and Cardy's new formula will be easiest to construct if the underlying lattice is triangular. The simplification in a triangular domain of Schramm's `bulk Cardy's formula' is also studied.

math-ph↗

arXiv2002

Algebraic Solutions of the Lamé Equation, Revisited

A minor error in the necessary conditions for the algebraic form of the Lamé equation to have a finite projective monodromy group, and hence for it to have only algebraic solutions, is pointed out. [See F. Baldassarri, "On algebraic solutions of Lamé's differential equation", J. Differential Equations 41 (1981), 44-58.] It is shown that if the group is the octahedral group S_4, then the degree parameter of the equation may differ by +1/6 or -1/6 from an integer; this possibility was missed. The omission affects a recent result on the monodromy of the Weierstrass form of the Lamé equation. [See R. C. Churchill, "Two-generator subgroups of SL(2,C) and the hypergeometric, Riemann, and Lamé equations", J. Symbolic Computation 28 (1999), 521-545.] The Weierstrass form, which is a differential equation on an elliptic curve, may have, after all, an octahedral projective monodromy group.

math.CA↗

arXiv2001

Droplet Nucleation and Domain Wall Motion in a Bounded Interval

We study a spatially extended model of noise-induced magnetization reversal: a classical Ginzburg-Landau theory, restricted to a bounded interval and perturbed by weak spatiotemporal noise. We compute the activation barrier and Kramers prefactor. As the interval length increases, a transition between activation regimes occurs, at which the prefactor diverges. We relate this to transitions that occur in low-temperature quantum field theory.

cond-mat.stat-mech↗

arXiv2000

Noise-Activated Escape from a Sloshing Potential Well

We treat the noise-activated escape from a one-dimensional potential well of an overdamped particle, to which a periodic force of fixed frequency is applied. We determine the boundary layer behavior, and the physically relevant length scales, near the oscillating well top. We show how stochastic behavior near the well top generalizes the behavior first determined by Kramers, in the case without forcing. Both the case when the forcing dies away in the weak noise limit, and the case when it does not, are examined. We also discuss the relevance of various scaling regimes to recent optical trap experiments.

cond-mat.stat-mech↗

arXiv2000

How an Anomalous Cusp Bifurcates

We study the pattern of activated trajectories in a double well system without detailed balance, in the weak noise limit. The pattern may contain cusps and other singular features, which are similar to the caustics of geometrical optics. Their presence is reflected in the quasipotential of the system, much as phase transitions are reflected in the free energy of a thermodynamic system. By tuning system parameters, a cusp may be made to coincide with the saddle point. Such an anomalous cusp is analogous to a nonclassical critical point. We derive a scaling law, and nonpolynomial `equations of state', that govern its bifurcation into conventional cusps.

cond-mat.stat-mech↗

arXiv1996

Oscillatory Behavior of the Rate of Escape through an Unstable Limit Cycle

Suppose a two-dimensional dynamical system has a stable attractor that is surrounded by an unstable limit cycle. If the system is additively perturbed by white noise, the rate of escape through the limit cycle will fall off exponentially as the noise strength tends to zero. By analysing the associated Fokker-Planck equation we show that in general, the weak-noise escape rate is non-Arrhenius: it includes a factor that is periodic in the logarithm of the noise strength. The presence of this slowly oscillating factor is due to the nonequilibrium potential of the system being nondifferentiable at the limit cycle. We point out the implications for the weak-noise limit of stochastic resonance models.

cond-mat↗

arXiv1995

A Scaling Theory of Bifurcations in the Symmetric Weak-Noise Escape Problem

We consider the overdamped limit of two-dimensional double well systems perturbed by weak noise. In the weak noise limit the most probable fluctuational path leading from either point attractor to the separatrix (the most probable escape path, or MPEP) must terminate on the saddle between the two wells. However, as the parameters of a symmetric double well system are varied, a unique MPEP may bifurcate into two equally likely MPEP's. At the bifurcation point in parameter space, the activation kinetics of the system become non-Arrhenius. In this paper we quantify the non-Arrhenius behavior of a system at the bifurcation point, by using the Maslov-WKB method to construct an approximation to the quasistationary probability distribution of the system that is valid in a boundary layer near the separatrix. The approximation is a formal asymptotic solution of the Smoluchowski equation. Our analysis relies on the development of a new scaling theory, which yields `critical exponents' describing weak-noise behavior near the saddle, at the bifurcation point.

cond-mat↗

arXiv1994

Asymptotic Exit Location Distributions in the Stochastic Exit Problem

Consider a two-dimensional continuous-time dynamical system, with an attracting fixed point $S$. If the deterministic dynamics are perturbed by white noise (random perturbations) of strength $ε$, the system state will eventually leave the domain of attraction $Ω$ of $S$. We analyse the case when, as $ε\to0$, the exit location on the boundary $\partialΩ$ is increasingly concentrated near a saddle point $H$ of the deterministic dynamics. We show that the asymptotic form of the exit location distribution on $\partialΩ$ is generically non-Gaussian and asymmetric, and classify the possible limiting distributions. A key role is played by a parameter $μ$, equal to the ratio $|λ_s(H)|/λ_u(H)$ of the stable and unstable eigenvalues of the linearized deterministic flow at $H$. If $μ<1$ then the exit location distribution is generically asymptotic as $ε\to0$ to a Weibull distribution with shape parameter $2/μ$, on the $O(ε^{μ/2})$ length scale near $H$. If $μ>1$ it is generically asymptotic to a distribution on the $O(ε^{1/2})$ length scale, whose moments we compute. The asymmetry of the asymptotic exit location distribution is attributable to the generic presence of a `classically forbidden' region: a wedge-shaped subset of $Ω$ with $H$ as vertex, which is reached from $S$, in the $ε\to0$ limit, only via `bent' (non-smooth) fluctuational paths that first pass through the vicinity of $H$. We deduce from the presence of this forbidden region that the classical Eyring formula for the small-$ε$ exponential asymptotics of the mean first exit time is generically inapplicable.

adap-org↗

arXiv1993

Large Fluctuations in Stochastically Perturbed Nonlinear Systems: Applications in Computing

This is the transcript of a talk given at the 1992 Complex Systems Summer School. The theory of large fluctuations of stochastically perturbed continuous-time dynamical systems is reviewed, and the large fluctuations of two stochastic models arising in computer science are analysed. One is a stochastic model of a communications network, resembling an Ethernet, which experiences traffic fluctuations. The other is a simple model of two dynamic data structures in the same memory space. In both models `large fluctuations' are unlikely, undesirable events. The mean time between occurrences of such events is estimated.

chao-dyn↗

arXiv1993

The Effect of Focusing and Caustics on Exit Phenomena in Systems Lacking Detailed Balance

We study the trajectories followed by a particle subjected to weak noise when escaping from the domain of attraction of a stable fixed point. If detailed balance is absent, a _focus_ may occur along the most probable exit path, leading to a breakdown of symmetry (if present). The exit trajectory bifurcates, and the exit location distribution may become `skewed' (non-Gaussian). The weak-noise asymptotics of the mean escape time are strongly affected. Our methods extend to the study of skewed exit location distributions in stochastic models without symmetry.

chao-dyn↗