arXiv subjects

James A. Yorke

Publications and source records attributed to James A. Yorke.

At least 37 records · Page 2Linked to original sources

arXiv2018

Quasiperiodic orbits in Siegel disks/balls and the Babylonian problem

We investigate numerically complex dynamical systems where a fixed point is surrounded by a disk or ball of quasiperiodic orbits, where there is a change of variables (or conjugacy) that converts the system into a linear map. We compute this "linearization" (or conjugacy) from knowledge of a single quasiperiodic trajectory. In our computations of rotation rates of the almost periodic orbits and Fourier coefficients of the conjugacy, we only use knowledge of a trajectory, and we do not assume knowledge of the explicit form of a dynamical system. This problem is called the Babylonian Problem: determining the characteristics of a quasiperiodic set from a trajectory. Our computation of rotation rates and Fourier coefficients depends on the very high speed of our computational method "the weighted Birkhoff average".

math.DS↗

arXiv2018

Low-dimensional paradigms for high-dimensional hetero-chaos

The dynamics on a chaotic attractor can be quite heterogeneous, being much more unstable in some regions than others. Some regions of a chaotic attractor can be expanding in more dimensions than other regions. Imagine a situation where two such regions and each contains trajectories that stay in the region for all time while typical trajectories wander throughout the attractor. Such an attractor is "hetero-chaotic" (i.e. it has heterogeneous chaos) if furthermore arbitrarily close to each point of the attractor there are points on periodic orbits that have different unstable dimensions. This is hard to picture but we believe that most physical systems possessing a high-dimensional attractor are of this type. We have created simplified models with that behavior to give insight to real high-dimensional phenomena.

nlin.CD↗

arXiv2018

The continuous route to multi-chaos

For low-dimensional chaotic attractors there is usually a single number of unstable dimensions for all of its periodic orbits and we can say such attractors exhibit "mono-chaos". In high-dimensional chaotic attractors, trajectories are prone to travel through quite different regions of phase space, some far more unstable than others. This heterogeneity makes predictability even more difficult than in low-dimensional homogeneous chaotic attractors. A chaotic attractor is "multi-chaotic" if every point of the attractor is arbitrarily close to periodic points with different numbers of unstable dimensions. We believe that most physical systems possessing a high-dimensional attractor are of this type. We make three conjectures about multi-chaos which we explore using three two-dimensional paradigmatic examples of multi-chaotic attractors. They can be thought of as small-scale examples that give insight for real high-dimensional phenomena. We find a single route from mono-chaos to multi-chaos if an attractor changes continuously as a parameter is varied. This multi-chaos bifurcation (MCB) is a periodic orbit bifurcation; one branch of periodic orbits is created with a number of unstable dimensions that is different from the mono-chaos.

nlin.CD↗

arXiv2017

Super convergence of ergodic averages for quasiperiodic orbits

By definition, a map quasiperiodic on a set $X$ if the map is conjugate to a pure rotation. Suppose we have a trajectory $(x_n)$ that we suspect is quasiperiodic. How do we determine if it is? In this paper we show how to compute the conjugacy map using only knowledge of $(x_n)$. Our main tool is a variant of Birkhoff averages. The Birkhoff Ergodic Theorem asserts that time averages of a function evaluated along a trajectory of length $N$ converge to the space average, the integral of $f$, as $N\to\infty$, for ergodic dynamical systems. But that convergence can be slow. Instead of uniform averages that assign equal weights to points along the trajectory, we use an average with a non-uniform distribution of weights, weighing the early and late points of the trajectory much less than those near the midpoint $N/2$. We show that in quasiperiodic dynamical systems, our weighted averages converge far faster provided $f$ is sufficiently differentiable. This result can be applied to obtain efficient numerical computation of rotation numbers, invariant densities and conjugacies of quasiperiodic systems.

math.DS↗

arXiv2016

Partially controlling transient chaos in the Lorenz equations

Transient chaos is a characteristic behavior in nonlinear dynamics where trajectories in a certain region of phase space behave chaotically for a while, before escaping to an external attractor. In some situations the escapes are highly undesirable, so that it would be necessary to avoid such a situation. In this paper we apply a control method known as partial control that allows one to prevent the escapes of the trajectories to the external attractors, keeping the trajectories in the chaotic region forever. To illustrate how the method works, we have chosen the Lorenz system for a choice of parameters where transient chaos appears, as a paradigmatic example in nonlinear dynamics. We analyze three quite different ways to implement the method. First, we apply this method by building a 1D map using the successive maxima of one of the variables. Next, we implement it by building a 2D map through a Poincaré section. Finally, we built a 3D map, which has the advantage of using a fixed time interval between application of the control, which can be useful for practical applications.

nlin.CD↗

arXiv2016

Measuring quasiperiodicity

The Birkhoff Ergodic Theorem asserts under mild conditions that Birkhoff averages (i.e. time averages computed along a trajectory) converge to the space average. For sufficiently smooth systems, our small modification of numerical Birkhoff averages significantly speeds the convergence rate for quasiperiodic trajectories -- by a factor of $10^{25}$ for 30-digit precision arithmetic, making it a useful computational tool for autonomous dynamical systems. Many dynamical systems and especially Hamiltonian systems are a complex mix of chaotic and quasiperiodic behaviors, and chaotic trajectories near quasiperiodic points can have long near-quasiperiodic transients. Our method can help determine which initial points are in a quasiperiodic set and which are chaotic. We use our {\bf weighted Birkhoff average} to study quasiperiodic systems, to distinguishing between chaos and quasiperiodicity, and for computing rotation numbers for self-intersecting curves in the plane. Furthermore we introduce the Embedding Continuation Method which is a significantly simpler, general method for computing rotation numbers.

math-ph↗

arXiv2015

Quantitative Quasiperiodicity

The Birkhoff Ergodic Theorem concludes that time averages, that is, Birkhoff averages, $Σ_{n=1}^N f(x_n)/N$ of a function $f$ along an ergodic trajectory $(x_n)$ of a function $T$ converges to the space average $\int f dμ$, where $μ$ is the unique invariant probability measure. Convergence of the time average to the space average is slow. We introduce a modified average of $f(x_n)$ by giving very small weights to the "end" terms when $n$ is near $0$ or $N$. When $(x_n)$ is a trajectory on a quasiperiodic torus and $f$ and $T$ are $C^\infty$, we show that our weighted Birkhoff averages converge "super" fast to $\int f dμ$, {\em i.e.} with error smaller than every polynomial of $1/N$. Our goal is to show that our weighted Birkhoff average is a powerful computational tool, and this paper illustrates its use for several examples where the quasiperiodic set is one or two dimensional. In particular, we compute rotation numbers and conjugacies (i.e. changes of variables) and their Fourier series, often with 30-digit precision.

math.DS↗

arXiv2014

The Scaling of Chaos vs Periodicity: How Certain is it that an Attractor is Chaotic?

The character of the time-asymptotic evolution of physical systems can have complex, singular behavior with variation of a system parameter, particularly when chaos is involved. A perturbation of the parameter by a small amount $ε$ can convert an attractor from chaotic to non-chaotic or vice-versa. We call a parameter value where this can happen $ε$-uncertain. The probability that a random choice of the parameter is $ε$-uncertain commonly scales like a power law in $ε$. Surprisingly, two seemingly similar ways of defining this scaling, both of physical interest, yield different numerical values for the scaling exponent. We show why this happens and present a quantitative analysis of this phenomenon.

nlin.CD↗

arXiv2013

QuorUM: an error corrector for Illumina reads

Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction procedure aims at producing a set of error-corrected reads (1) minimizing the number of distinct false k-mers, i.e. that are not present in the genome, in the set of reads and (2) maximizing the number that are true, i.e. that are present in the genome. Because coverage of a genome by Illumina reads varies greatly from point to point, we cannot simply eliminate k-mers that occur rarely. Results: Our software, called QuorUM, provides reasonably accurate correction and is suitable for large data sets (1 billion bases checked and corrected per day per core). Availability: QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at http://www.genome.umd.edu. Contact: gmarcais@umd.edu

q-bio.GN↗

arXiv2013

A hierarchical network heuristic for solving the orientation problem in genome assembly

In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves building ordered and oriented linear collections of contigs (continuous overlapping sequence reads) called scaffolds and relies on the use of mate pair data. A mate pair is a set of two reads that are sequenced from the ends of a single fragment of DNA, and therefore have opposite mutual orientations. When two reads of a mate-pair are placed into two different contigs, one can infer the mutual orientation of these contigs. While several orientation algorithms exist as part of assembly programs, all encounter challenges while solving the orientation problem due to errors from mis-assemblies in contigs or errors in read placements. In this paper we present an algorithm based on hierarchical clustering that independently solves the orientation problem and is robust to errors. We show that our algorithm can correctly solve the orientation problem for both faux (generated) assembly data and real assembly data for {\em R. sphaeroides bacteria}. We demonstrate that our algorithm is stable to both changes in the initial orientations as well as noise in the data, making it advantageous compared to traditional approaches.

q-bio.GN↗

arXiv2010

Connecting period-doubling cascades to chaos

The appearance of infinitely-many period-doubling cascades is one of the most prominent features observed in the study of maps depending on a parameter. They are associated with chaotic behavior, since bifurcation diagrams of a map with a parameter often reveal a complicated intermingling of period-doubling cascades and chaos. Period doubling can be studied at three levels of complexity. The first is an individual period-doubling bifurcation. The second is an infinite collection of period doublings that are connected together by periodic orbits in a pattern called a cascade. It was first described by Myrberg and later in more detail by Feigenbaum. The third involves infinitely many cascades and a parameter value $μ_2$ of the map at which there is chaos. We show that often virtually all (i.e., all but finitely many) ``regular'' periodic orbits at $μ_2$ are each connected to exactly one cascade by a path of regular periodic orbits; and virtually all cascades are either paired -- connected to exactly one other cascade, or solitary -- connected to exactly one regular periodic orbit at $μ_2$. The solitary cascades are robust to large perturbations. Hence the investigation of infinitely many cascades is essentially reduced to studying the regular periodic orbits of $F(μ_2, \cdot)$. Examples discussed include the forced-damped pendulum and the double-well Duffing equation.

nlin.CD↗

arXiv2009

The cascades route to chaos

The presence of a period-doubling cascade in dynamical systems that depend on a parameter is one of the basic routes to chaos. It is rarely mentioned that there are virtually always infinitely many cascades whenever there is one. We report that for one- and two-dimensional phase space, in the transition from no chaos to chaos -- as a parameter is varied -- there must be infinitely many cascades under some mild hypotheses. Our meaning of chaos includes the case of chaotic sets which are not attractors. Numerical studies indicate that this result applies to the forced-damped pendulum and the forced Duffing equations, viewing the solutions once each period of the forcing. We further show that in many cases cascades appear in pairs connected (in joint parameter-state space) by an unstable periodic orbit. Paired cascades can be destroyed or created by perturbations, whereas unpaired cascades are conserved under even significant perturbations.

nlin.CD↗

arXiv2009

Period-doubling cascades for large perturbations of Henon families

The Henon family has been shown to have period-doubling cascades. We show here that the same occurs for a much larger class: Large perturbations do not destroy cascades. Furthermore, we can classify the period of a cascade in terms of the set of orbits it contains, and count the number of cascades of each period. This class of families extends a general theory explaining why cascades occur.

math.DS↗

arXiv2009

Period-doubling cascades galore

The appearance of numerous period-doubling cascades is among the most prominent features of {\bf parametrized maps}, that is, smooth one-parameter families of maps $F:R \times {\mathfrak M} \to {\mathfrak M}$, where ${\mathfrak M}$ is a smooth locally compact manifold without boundary, typically $R^N$. Each cascade has infinitely many period-doubling bifurcations, and it is typical to observe -- such as in all the examples we investigate here -- that whenever there are any cascades, there are infinitely many cascades. We develop a general theory of cascades for generic $F$. We illustrate this theory with several examples. We show that there is a close connection between the transition through infinitely many cascades and the creation of a horseshoe.

math.DS↗

arXiv2003

A Local Ensemble Kalman Filter for Atmospheric Data Assimilation

In this paper, we introduce a new, local formulation of the ensemble Kalman Filter approach for atmospheric data assimilation. Our scheme is based on the hypothesis that, when the Earth's surface is divided up into local regions of moderate size, vectors of the forecast uncertainties in such regions tend to lie in a subspace of much lower dimension than that of the full atmospheric state vector of such a region. Ensemble Kalman Filters, in general, assume that the analysis resulting from the data assimilation lies in the same subspace as the expected forecast error. Under our hypothesis the dimension of this subspace is low. This implies that operations only on relatively low dimensional matrices are required. Thus, the data analysis is done locally in a manner allowing massively parallel computation to be exploited. The local analyses are then used to construct global states for advancement to the next forecast time. The method, its potential advantages, properties, and implementation requirements are illustrated by numerical experiments on the Lorenz-96 model. It is found that accurate analysis can be achieved at a cost which is very modest compared to that of a full global ensemble Kalman Filter.

physics.ao-ph↗

arXiv1999

Multiple Attractor Bifurcations: A Source of Unpredictability in Piecewise Smooth Systems

There exists a variety of physically interesting situations described by continuous maps that are nondifferentiable on some surface in phase space. Such systems exhibit novel types of bifurcations in which multiple coexisting attractors can be created simultaneously. The striking feature of these bifurcations is that they lead to fundamentally unpredictable behavior of orbits as a system parameter is varied slowly through its bifurcation value. This unpredictability gradually disappears as the speed of variation of the system parameter through the bifurcation is reduced to zero.

chao-dyn↗

arXiv1998

Robust Chaos

It has been proposed to make practical use of chaos in communication, in enhancing mixing in chemical processes and in spreading the spectrum of switch-mode power suppies to avoid electromagnetic interference. It is however known that for most smooth chaotic systems, there is a dense set of periodic windows for any range of parameter values. Therefore in practical systems working in chaotic mode, slight inadvertent fluctuation of a parameter may take the system out of chaos. We say a chaotic attractor is robust if, for its parameter values there exists a neighborhood in the parameter space with no periodic attractor and the chaotic attractor is unique in that neighborhood. In this paper we show that robust chaos can occur in piecewise smooth systems and obtain the conditions of its occurrence. We illustrate this phenomenon with a practical example from electrical engineering.

chao-dyn↗

arXiv1995

Bizarre topology is natural in dynamical systems

We describe an example of a $C^\infty$ diffeomorphism on a 7--manifold which has a compact invariant set such that uncountably many of its connected components are pseudocircles. (Any 7--manifold will suffice.) Furthermore, any diffeomorphism which is sufficiently close (in the $C^1$ metric) to the constructed map has a similar invariant set, and the dynamics of the map on the invariant set are chaotic.

math.DS↗