No Arabic abstract
It is shown that applying manifold learning techniques to Poincare sections of high-dimensional, chaotic dynamical systems can uncover their low-dimensional topological organization. Manifold learning provides a low-dimensional embedding and intrinsic coordinates for the parametrization of data on the Poincare section, facilitating the construction of return maps with well defined symbolic dynamics. The method is illustrated by numerical examples for the Rossler attractor and the Kuramoto-Sivashinsky equation. For the latter we present the reduction of the high-dimensional, continuous-time flow to dynamics on one- and two two-dimensional Poincare sections. We show that in the two-dimensional embedding case the attractor is organized by one-dimensional unstable manifolds of short periodic orbits. In that case, the dynamics can be approximated by a map on a tree which can in turn be reduced to a trimodal map of the unit interval. In order to test the limits of the one-dimensional map approximation we apply classical kneading theory in order to systematically detect all periodic orbits of the system up to any given topological length.
Transport and mixing of scalar quantities in fluid flows is ubiquitous in industry and Nature. Turbulent flows promote efficient transport and mixing by their inherent randomness. Laminar flows lack such a natural mixing mechanism and efficient transport is far more challenging. However, laminar flow is essential to many problems and insight into its transport characteristics of great importance. Laminar transport, arguably, is best described by the Lagrangian fluid motion (`advection) and the geometry, topology and coherence of fluid trajectories. Efficient laminar transport being equivalent to `chaotic advection is a key finding of this approach. The Lagrangian framework enables systematic analysis and design of laminar flows. However, the gap between scientific insights into Lagrangian transport and technological applications is formidable primarily for two reasons. First, many studies concern two-dimensional (2D) flows yet the real world is three dimensional (3D). Second, Lagrangian transport is typically investigated for idealised flows yet practical relevance requires studies on realistic 3D flows. The present review aims to stimulate further development and utilisation of know-how on 3D Lagrangian transport and its dissemination to practice. To this end 3D practical flows are categorised into canonical problems. First, to expose the diversity of Lagrangian transport and create awareness of its broad relevance. Second, to enable knowledge transfer both within and between scientific disciplines. Third, to reconcile practical flows with fundamentals on Lagrangian transport and chaotic advection. This may be a first incentive to structurally integrate the `Lagrangian mindset into the analysis and design of 3D practical flows.
The long-term average response of observables of chaotic systems to dynamical perturbations can often be predicted using linear response theory, but not all chaotic systems possess a linear response. Macroscopic observables of complex dissipative chaotic systems, however, are widely assumed to have a linear response even if the microscopic variables do not, but the mechanism for this is not well-understood. We present a comprehensive picture for the linear response of macroscopic observables in high-dimensional coupled deterministic dynamical systems, where the coupling is via a mean field and the microscopic subsystems may or may not obey linear response theory. We derive stochastic reductions of the dynamics of these observables from statistics of the microscopic system, and provide conditions for linear response theory to hold in finite dimensional systems and in the thermodynamic limit. In particular, we show that for large systems of finite size, linear response is induced via self-generated noise. We present examples in the thermodynamic limit where the macroscopic observable satisfies LRT, although the microscopic subsystems individually violate LRT, as well a converse example where the macroscopic observable does not satisfy LRT despite all microscopic subsystems satisfying LRT when uncoupled. This latter, maybe surprising, example is associated with emergent non-trivial dynamics of the macroscopic observable. We provide numerical evidence for our results on linear response as well as some analytical intuition.
The 2.5-MDa 26S proteasome maintains proteostasis and regulates myriad cellular processes. How polyubiquitylated substrate interactions regulate proteasome activity is not understood. Here we introduce a deep manifold learning framework, named AlphaCryo4D, which enables atomic-level cryogenic electron microscopy (cryo-EM) reconstructions of nonequilibrium conformational continuum and reconstitutes hidden dynamics of proteasome autoregulation in the act of substrate degradation. AlphaCryo4D integrates 3D deep residual learning with manifold embedding of free-energy landscapes, which directs 3D clustering via an energy-based particle-voting algorithm. In blind assessments using simulated heterogeneous cryo-EM datasets, AlphaCryo4D achieved 3D classification accuracy three times that of conventional method and reconstructed continuous conformational changes of a 130-kDa protein at sub-3-angstrom resolution. By using AlphaCryo4D to analyze a single experimental cryo-EM dataset, we identified 64 conformers of the substrate-bound human 26S proteasome, revealing conformational entanglement of two regulatory particles in the doubly capped holoenzymes and their energetic differences with singly capped ones. Novel ubiquitin-binding sites are discovered on the RPN2, RPN10 and Alpha5 subunits to remodel polyubiquitin chains for deubiquitylation and recycle. Importantly, AlphaCryo4D choreographs single-nucleotide-exchange dynamics of proteasomal AAA-ATPase motor during translocation initiation, which upregulates proteolytic activity by allosterically promoting nucleophilic attack. Our systemic analysis illuminates a grand hierarchical allostery for proteasome autoregulation.
Normalizing flows are invertible neural networks with tractable change-of-volume terms, which allows optimization of their parameters to be efficiently performed via maximum likelihood. However, data of interest is typically assumed to live in some (often unknown) low-dimensional manifold embedded in high-dimensional ambient space. The result is a modelling mismatch since -- by construction -- the invertibility requirement implies high-dimensional support of the learned distribution. Injective flows, mapping from low- to high-dimensional space, aim to fix this discrepancy by learning distributions on manifolds, but the resulting volume-change term becomes more challenging to evaluate. Current approaches either avoid computing this term entirely using various heuristics, or assume the manifold is known beforehand and therefore are not widely applicable. Instead, we propose two methods to tractably calculate the gradient of this term with respect to the parameters of the model, relying on careful use of automatic differentiation and techniques from numerical linear algebra. Both approaches perform end-to-end nonlinear manifold learning and density estimation for data projected onto this manifold. We study the trade-offs between our proposed methods, empirically verify that we outperform approaches ignoring the volume-change term by more accurately learning manifolds and the corresponding distributions on them, and show promising results on out-of-distribution detection.
Symmetry reduction by the method of slices quotients the continuous symmetries of chaotic flows by replacing the original state space by a set of charts, each covering a neighborhood of a dynamically important class of solutions, qualitatively captured by a `template. Together these charts provide an atlas of the symmetry-reduced `slice of state space, charting the regions of the manifold explored by the trajectories of interest. Within the slice, relative equilibria reduce to equilibria and relative periodic orbits reduce to periodic orbits. Visualizations of these solutions and their unstable manifolds reveal their interrelations and the role they play in organizing turbulence/chaos.