Embedding classical dynamics in a quantum computer

We develop a framework for simulating measure-preserving, ergodic dynamical systems on a quantum computer. Our approach provides a new operator-theoretic representation of classical dynamics by combining ergodic theory with quantum information science. The resulting quantum embedding of classical dynamics (QECD) enables efficient simulation of spaces of classical observables with exponentially large dimension using a quadratic number of quantum gates. The QECD framework is based on a quantum feature map for representing classical states by density operators on a reproducing kernel Hilbert space, $\mathcal H$, and an embedding of classical observables into self-adjoint operators on $\mathcal H$. In this scheme, quantum states and observables evolve unitarily under the lifted action of Koopman evolution operators of the classical system. Moreover, by virtue of the reproducing property of $\mathcal H$, the quantum system is pointwise-consistent with the underlying classical dynamics. To achieve an exponential quantum computational advantage, we project the state of the quantum system to a density matrix on a $2^n$-dimensional tensor product Hilbert space associated with $n$ qubits. By employing discrete Fourier-Walsh transforms, the evolution operator of the finite-dimensional quantum system is factorized into tensor product form, enabling implementation through a quantum circuit of size $O(n)$. Furthermore, the circuit features a state preparation stage, also of size $O(n)$, and a quantum Fourier transform stage of size $O(n^2)$, which makes predictions of observables possible by measurement in the standard computational basis. We prove theoretical convergence results for these predictions as $n\to\infty$. We present simulated quantum circuit experiments in Qiskit Aer, as well as actual experiments on the IBM Quantum System One.Comment: 42 pages, 9 figure

Data Assimilation in Operator Algebras

We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a non-abelian operator algebra, which provides a representation of observables by multiplication operators and probability densities by density operators (quantum states). In the algebraic approach, the forecast step of data assimilation is represented by a quantum operation induced by the Koopman operator of the dynamical system. Moreover, the analysis step is described by a quantum effect, which generalizes the Bayesian observational update rule. Projecting this formulation to finite-dimensional matrix algebras leads to new computational data assimilation schemes that are (i) automatically positivity-preserving; and (ii) amenable to consistent data-driven approximation using kernel methods for machine learning. Moreover, these methods are natural candidates for implementation on quantum computers. Applications to data assimilation of the Lorenz 96 multiscale system and the El Nino Southern Oscillation in a climate model show promising results in terms of forecast skill and uncertainty quantification.Comment: 46 pages, 4 figure

Bayesian algorithms for recovering structure from single-particle diffraction snapshots of unknown orientation: a comparison

The advent of X-ray Free Electron Lasers promises the possibility to determine the structure of individual particles such as microcrystallites, viruses and biomolecules from single-shot diffraction snapshots obtained before the particle is destroyed by the intense femtosecond pulse. This program requires the ability to determine the orientation of the particle giving rise to each snapshot at signal levels as low as ~10-2 photons/pixel. Two apparently different approaches have recently demonstrated this capability. Here we show they represent different implementations of the same fundamental approach, and identify the primary factors limiting their performance.Comment: 10 pages, 2 figure

Retrieving functional pathways of biomolecules from single-particle snapshots

A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.11Ysciescopu