arXiv subjects

Ilya Kuprov

Publications and source records attributed to Ilya Kuprov.

36 records · Page 2Linked to original sources

arXiv2016

Fokker-Planck formalism in magnetic resonance simulations

This paper presents an overview of the Fokker-Planck formalism for non-biological magnetic resonance simulations, describes its existing applications and proposes some novel ones. The most attractive feature of Fokker-Planck theory compared to the commonly used Liouville - von Neumann equation is that, for all relevant types of spatial dynamics (spinning, diffusion, flow, etc.), the corresponding Fokker-Planck Hamiltonian is time-independent. Many difficult NMR, EPR and MRI simulation problems (multiple rotation NMR, ultrafast NMR, gradient-based zero-quantum filters, diffusion and flow NMR, off-resonance soft microwave pulses in EPR, spin-spin coupling effects in MRI, etc.) are simplified significantly in Fokker-Planck space. The paper also summarises the author's experiences with writing and using the corresponding modules of the Spinach library - the methods described below have enabled a large variety of simulations previously considered too complicated for routine practical use.

quant-ph↗

arXiv2016

Modified Newton-Raphson GRAPE methods for optimal control of spin systems

Quadratic convergence throughout the active space is achieved for the gradient ascent pulse engineering (GRAPE) family of quantum optimal control algorithms. We demonstrate in this communication that the Hessian of the GRAPE fidelity functional is unusually cheap, having the same asymptotic complexity scaling as the functional itself. This leads to the possibility of using very efficient numerical optimization techniques. In particular, the Newton-Raphson method with a rational function optimization (RFO) regularized Hessian is shown in this work to require fewer system trajectory evaluations than any other algorithm in the GRAPE family. This communication describes algebraic and numerical implementation aspects (matrix exponential recycling, Hessian regularization, etc.) for the RFO Newton-Raphson version of GRAPE and reports benchmarks for common spin state control problems in magnetic resonance spectroscopy.

quant-ph↗

arXiv2015

Training Schrödinger's cat: quantum optimal control

It is control that turns scientific knowledge into useful technology: in physics and engineering it provides a systematic way for driving a system from a given initial state into a desired target state with minimized expenditure of energy and resources -- as famously applied in the Apollo programme. As one of the cornerstones for enabling quantum technologies, optimal quantum control keeps evolving and expanding into areas as diverse as quantum-enhanced sensing, manipulation of single spins, photons, or atoms, optical spectroscopy, photochemistry, magnetic resonance (spectroscopy as well as medical imaging), quantum information processing and quantum simulation. --- Here state-of-the-art quantum control techniques are reviewed and put into perspective by a consortium uniting expertise in optimal control theory and applications to spectroscopy, imaging, quantum dynamics of closed and open systems. We address key challenges and sketch a roadmap to future developments.

quant-ph↗

arXiv2015

Auxiliary matrix formalism for interaction representation transformations, optimal control and spin relaxation theories

Auxiliary matrix exponential method is used to derive simple and numerically efficient general expressions for the following, historically rather cumbersome and hard to compute, theoretical methods: (1) average Hamiltonian theory following interaction representation transformations; (2) Bloch-Redfield-Wangsness theory of nuclear and electron relaxation; (3) gradient ascent pulse engineering version of quantum optimal control theory. In the context of spin dynamics, the auxiliary matrix exponential method is more efficient than methods based on matrix factorizations and also exhibits more favourable complexity scaling with the dimension of the Hamiltonian matrix.

quant-ph↗

arXiv2014

A partial differential equation for pseudocontact shift

It is demonstrated that pseudocontact shift (PCS), viewed as a scalar or a tensor field in three dimensions, obeys an elliptic partial differential equation with a source term that depends on the Hessian of the unpaired electron probability density. The equation enables straightforward PCS prediction as well as analysis of experimental PCS data in systems with multiple and / or distributed unpaired electron centres.

physics.chem-ph↗

arXiv2014

Exact NMR simulation of protein-size spin systems using tensor train formalism

We introduce a new method, based on alternating optimization, for compact representation of spin Hamiltonians and solution of linear systems of algebraic equations in the tensor train format. We demonstrate the method's utility by simulating, without approximations, a 15N NMR spectrum of ubiquitin --- a protein containing several hundred interacting nuclear spins. Existing simulation algorithms for the spin system and the NMR experiment in question either require significant approximations or scale exponentially with the spin system size. We compare the proposed method to the Spinach package that uses heuristic restricted state space techniques to achieve polynomial complexity scaling. When the spin system topology is close to a linear chain (e.g. for the backbone of a protein), the tensor train representation is more compact and can be computed faster than the sparse representation using restricted state spaces.

quant-ph↗

arXiv2014

A quantum mechanical NMR simulation algorithm for protein-scale spin systems

Nuclear magnetic resonance spectroscopy is one of the few remaining areas of physical chemistry for which polynomially scaling simulation methods have not so far been available. Here, we report such a method and illustrate its performance by simulating common 2D and 3D liquid state NMR experiments (including accurate description of spin relaxation processes) on isotopically enriched human ubiquitin - a protein containing over a thousand nuclear spins forming an irregular polycyclic three-dimensional coupling lattice. The algorithm uses careful tailoring of the density operator space to only include nuclear spin states that are populated to a significant extent. The reduced state space is generated by analyzing spin connectivity and decoherence properties: rapidly relaxing states as well as correlations between topologically remote spins are dropped from the basis set. In the examples provided, the resulting reduction in the quantum mechanical simulation time is by many orders of magnitude.

physics.chem-ph↗

arXiv2013

A standard format and a graphical user interface for spin system specification

We introduce a simple and general XML format for spin system description that is the result of extensive consultations within Magnetic Resonance community and unifies under one roof all major existing spin interaction specification conventions. The format is human-readable, easy to edit and easy to parse using standard XML libraries. We also describe a graphical user interface that was designed to facilitate construction and visualization of complicated spin systems. The interface is capable of generating input files for several popular spin dynamics simulation packages.

quant-ph↗

arXiv2013

Grid-free powder averages: on the applications of the Fokker-Planck equation to solid state NMR

We demonstrate that Fokker-Planck equations in which spatial coordinates are treated on the same conceptual level as spin coordinates yield a convenient formalism for treating magic angle spinning NMR experiments. In particular, time dependence disappears from the background Hamiltonian (sample spinning is treated as an interaction), spherical quadrature grids are avoided completely (coordinate distributions are a part of the formalism) and relaxation theory with any linear diffusion operator is easily adopted from the Stochastic Liouville Equation theory. The proposed formalism contains Floquet theory as a special case. The elimination of the spherical averaging grid comes at the cost of increased matrix dimensions, but we show that this can be mitigated by the use of state space restriction and tensor train techniques. It is also demonstrated that low correlation order basis sets apparently give accurate answers in powder-averaged MAS simulations, meaning that polynomially scaling simulation algorithms do exist for a large class of solid state NMR experiments.

physics.chem-ph↗

arXiv2012

Spin system trajectory analysis under optimal control pulses

Several methods are proposed for the analysis, visualization and interpretation of high-dimensional spin system trajectories produced by quantum mechanical simulations. It is noted that expectation values of specific observables in large spin systems often feature fast, complicated and hard-to-interpret time dynamics and suggested that populations of carefully selected subspaces of states are much easier to analyze and interpret. As an illustration of the utility of the proposed methods, it is demonstrated that the apparent "noisy" appearance of many optimal control pulses in NMR and EPR spectroscopy is an illusion - the underlying spin dynamics is shown to be smooth, orderly and very tightly controlled.

quant-ph↗

arXiv2011

Molecular structure refinement by direct fitting of atomic coordinates to experimental ESR spectra

An attempt is made to bypass spectral analysis and fit internal coordinates of radicals directly to experimental liquid- and solid-state electron spin resonance (ESR) spectra. We take advantage of the recently introduced large-scale spin dynamics simulation algorithms and of the fact that the accuracy of quantum mechanical calculations of ESR parameters has improved to the point of quantitative correctness. Partial solutions are offered to the local minimum problem in spectral fitting and to the problem of spin interaction parameters (hyperfine couplings, chemical shifts, etc.) being very sensitive to distortions in molecular geometry.

physics.chem-ph↗

arXiv2011

Parallel density matrix propagation in spin dynamics simulations

Several methods for density matrix propagation in distributed computing environments, such as clusters and graphics processing units, are proposed and evaluated. It is demonstrated that the large communication overhead associated with each propagation step (two-sided multiplication of the density matrix by an exponential propagator and its conjugate) may be avoided and the simulation recast in a form that requires virtually no inter-thread communication. Good scaling is demonstrated on a 128-core (16 nodes, 8 cores each) cluster.

physics.chem-ph↗

arXiv2011

On the accuracy of the state space restriction approximation for spin dynamics simulations

We present an algebraic foundation for the state space restriction approximation in spin dynamics simulations and derive applicability criteria as well as minimal basis set requirements for practically encountered simulation tasks. The results are illustrated with NMR, ESR, DNP and Spin Chemistry simulations. It is demonstrated that state space restriction yields accurate results in systems where the time scale of spin relaxation processes approximately matches the time scale of the experiment. Rigorous error bounds and basis set requirements are derived.

quant-ph↗

arXiv2011

Second order gradient ascent pulse engineering

We report some improvements to the gradient ascent pulse engineering (GRAPE) algorithm for optimal control of quantum systems. These include more accurate gradients, convergence acceleration using the BFGS quasi-Newton algorithm as well as faster control derivative calculation algorithms. In all test systems, the wall clock time and the convergence rates show a considerable improvement over the approximate gradient ascent.

quant-ph↗

arXiv2011

Chemically Induced Dynamic Nuclear Polarization of 19F Nuclei

This study explores, both theoretically and experimentally, the photochemically induced dynamic nuclear polarization (photo-CIDNP) of 19F nuclei, the associated spin relaxation, cross-relaxation and cross-correlation effects, as well as potential applications of 19F CIDNP to protein structure and folding problems. Keywords: CIDNP, relaxation, fluorine, NMR, NOE, TR-CIDNP, tc5b, Trp-cage, GFP

physics.chem-ph↗

arXiv2010

Diagonalization-free implementation of spin relaxation theory for large spin systems

The Liouville space spin relaxation theory equations are reformulated in such a way as to avoid the computationally expensive Hamiltonian diagonalization step, replacing it by numerical evaluation of the integrals in the generalized cumulant expansion. The resulting algorithm is particularly useful in the cases where the static part of the Ha-miltonian is dominated by interactions other than Zeeman (e.g. in quadrupolar reson-ance, low-field EPR and Spin Chemistry). When used together with state space re-striction tools, the algorithm reported is capable of computing full relaxation supero-perators for NMR systems with more than 15 spins.

physics.chem-ph↗

arXiv2009

Derivatives of spin dynamics simulations

We report analytical equations for the derivatives of spin dynamics simulations with respect to pulse sequence and spin system parameters. The methods described are significantly faster, more accurate and more reliable than the finite difference approximations typically employed. The resulting derivatives may be used in fitting, optimization, performance evaluation and stability analysis of spin dynamics simulations and experiments. Keywords: NMR, EPR, simulation, analytical derivatives, optimal control, spin chemistry, radical pair.

physics.chem-ph↗

arXiv2007

Polynomially scaling spin dynamics simulation algorithm based on adaptive state space restriction

The conventional spin dynamics simulations are performed in direct products of state spaces of individual spins. In a general system of n spins, the total number of elements in the state basis is >4^n. A system propagation step requires an action by an operator on the state vector and thus requires >4^2n multiplications. It is obvious that with current computers there is no way beyond about ten spins, and the calculation complexity scales exponentially with the spin system size. We demonstrate that a polynomially scaling algorithm can be obtained if the state space is reduced by neglecting unimportant or unpopulated spin states. The class of such states is surprisingly wide. In particular, there are indications that very high multi-spin orders can be dropped completely, as can all the orders linking the spins that are remote on the interaction graph. The computational cost of the propagation step for a ktuples-restricted densely connected n-spin system with k<<n is O(n^2k). In cases of favourable interaction topologies (narrow graphs, e.g. in protein NMR) the asymptotic scaling is linear.

physics.comp-ph↗