4,170 results on '"Pearson, John"'
Search Results
2. Automatic Differentiation for All-at-once Systems Arising in Certain PDE-Constrained Optimization Problems
- Author
-
Leveque, Santolo, Maddison, James R., and Pearson, John W.
- Subjects
Mathematics - Numerical Analysis - Abstract
An automated framework is presented for the numerical solution of optimal control problems with PDEs as constraints, in both the stationary and instationary settings. The associated code can solve both linear and non-linear problems, and examples for incompressible flow equations are considered. The software, which is based on a Python interface to the Firedrake system, allows for a compact definition of the problem considered by providing a few lines of code in a high-level language. The software is provided with efficient iterative linear solvers for optimal control problems with PDEs as constraints. The use of advanced preconditioning techniques results in a significant speed-up of the solution process for large-scale problems. We present numerical examples of the applicability of the software on classical control problems with PDEs as constraints.
- Published
- 2024
3. Fast numerical solvers for parameter identification problems in mathematical biology
- Author
-
Benková, Karolína, Pearson, John W., and Ptashnyk, Mariya
- Subjects
Mathematics - Numerical Analysis ,Mathematics - Optimization and Control ,49M41, 92C15, 65M22, 65M60, 65F08, 65F10 - Abstract
In this paper, we consider effective discretization strategies and iterative solvers for nonlinear PDE-constrained optimization models for pattern evolution within biological processes. Upon a Sequential Quadratic Programming linearization of the optimization problem, we devise appropriate time-stepping schemes and discrete approximations of the cost functionals such that the discretization and optimization operations are commutative, a highly desirable property of a discretization of such problems. We formulate the large-scale, coupled linear systems in such a way that efficient preconditioned iterative methods can be applied within a Krylov subspace solver. Numerical experiments demonstrate the viability and efficiency of our approach., Comment: 33 pages, 3 figures, 7 tables
- Published
- 2024
4. Inflationary Flows: Calibrated Bayesian Inference with Diffusion-Based Models
- Author
-
de Albuquerque, Daniela and Pearson, John
- Subjects
Computer Science - Machine Learning ,Statistics - Machine Learning ,68T99 (Primary) 62M45 (Secondary) ,G.3 ,I.6.5 ,I.2 - Abstract
Beyond estimating parameters of interest from data, one of the key goals of statistical inference is to properly quantify uncertainty in these estimates. In Bayesian inference, this uncertainty is provided by the posterior distribution, the computation of which typically involves an intractable high-dimensional integral. Among available approximation methods, sampling-based approaches come with strong theoretical guarantees but scale poorly to large problems, while variational approaches scale well but offer few theoretical guarantees. In particular, variational methods are known to produce overconfident estimates of posterior uncertainty and are typically non-identifiable, with many latent variable configurations generating equivalent predictions. Here, we address these challenges by showing how diffusion-based models (DBMs), which have recently produced state-of-the-art performance in generative modeling tasks, can be repurposed for performing calibrated, identifiable Bayesian inference. By exploiting a previously established connection between the stochastic and probability flow ordinary differential equations (pfODEs) underlying DBMs, we derive a class of models, inflationary flows, that uniquely and deterministically map high-dimensional data to a lower-dimensional Gaussian distribution via ODE integration. This map is both invertible and neighborhood-preserving, with controllable numerical error, with the result that uncertainties in the data are correctly propagated to the latent space. We demonstrate how such maps can be learned via standard DBM training using a novel noise schedule and are effective at both preserving and reducing intrinsic data dimensionality. The result is a class of highly expressive generative models, uniquely defined on a low-dimensional latent space, that afford principled Bayesian inference., Comment: 10 pages, 6 figures
- Published
- 2024
5. Efficient nonlocal linear image denoising: Bilevel optimization with Nonequispaced Fast Fourier Transform and matrix-free preconditioning
- Author
-
Miniguano-Trujillo, Andrés, Pearson, John W., and Goddard, Benjamin D.
- Subjects
Mathematics - Numerical Analysis ,Mathematics - Optimization and Control - Abstract
We present a new approach for nonlocal image denoising, based around the application of an unnormalized extended Gaussian ANOVA kernel within a bilevel optimization algorithm. A critical bottleneck when solving such problems for finely-resolved images is the solution of huge-scale, dense linear systems arising from the minimization of an energy term. We tackle this using a Krylov subspace approach, with a Nonequispaced Fast Fourier Transform utilized to approximate matrix-vector products in a matrix-free manner. We accelerate the algorithm using a novel change of basis approach to account for the (known) smallest eigenvalue-eigenvector pair of the matrices involved, coupled with a simple but frequently very effective diagonal preconditioning approach. We present a number of theoretical results concerning the eigenvalues and predicted convergence behavior, and a range of numerical experiments which validate our solvers and use them to tackle parameter learning problems. These demonstrate that very large problems may be effectively and rapidly denoised with very low storage requirements on a computer., Comment: 30 pages, 8 figures, 3 tables
- Published
- 2024
6. Diagonalization-Based Parallel-in-Time Preconditioners for Instationary Fluid Flow Control Problems
- Author
-
Heinzelreiter, Bernhard and Pearson, John W.
- Subjects
Mathematics - Numerical Analysis - Abstract
We derive a new parallel-in-time approach for solving large-scale optimization problems constrained by time-dependent partial differential equations arising from fluid dynamics. The solver involves the use of a block circulant approximation of the original matrices, enabling parallelization-in-time via the use of fast Fourier transforms, and we devise bespoke matrix approximations which may be applied within this framework. These make use of permutations, saddle-point approximations, commutator arguments, as well as inner solvers such as the Uzawa method, Chebyshev semi-iteration, and multigrid. Theoretical results underpin our strategy of applying a block circulant strategy, and numerical experiments demonstrate the effectiveness and robustness of our approach on Stokes and Oseen problems. Noteably, satisfying results for the strong and weak scaling of our methods are provided within a fully parallel architecture., Comment: 24 pages
- Published
- 2024
7. Spectral analysis of block preconditioners for double saddle-point linear systems with application to PDE-constrained optimization
- Author
-
Bergamaschi, Luca, Martinez, Angeles, Pearson, John, and Potschka, Andreas
- Subjects
Mathematics - Numerical Analysis - Abstract
In this paper, we describe and analyze the spectral properties of a symmetric positive definite inexact block preconditioner for a class of symmetric, double saddle-point linear systems. We develop a spectral analysis of the preconditioned matrix, showing that its eigenvalues can be described in terms of the roots of a cubic polynomial with real coefficients. We illustrate the efficiency of the proposed preconditioners, and verify the theoretical bounds, in solving large-scale PDE-constrained optimization problems.
- Published
- 2024
8. The Computer: Liberator or Jailer of the Creative Spirit
- Author
-
Pearson, John
- Published
- 2017
9. Optimal decision-making under task uncertainty: a computational basis for cognitive stability versus flexibility
- Author
-
Madlon-Kay, Seth, Pearson, John, and Egner, Tobias
- Subjects
Cognitive Neuroscience ,Attention ,Decision making ,Computational Modeling - Abstract
Cognitive control is thought to regulate the conflict between stability---maintaining the current task in the face of distraction---and flexibility---switching to a new task of greater priority. However, evidence conflicts regarding when and to what extent stability and flexibility trade-off. A normative theory of flexibility and stability may help clarify when and why we should expect such trade-offs to occur. Towards such a theory, we model task-switching as a problem of decision-making under uncertainty, in which the decision-maker must simultaneously infer both the identity of a stimulus and the task governing the correct response to that stimulus. We find that optimal behavior is either extremely stable or extremely flexible, but not both, indicating a normative basis for a trade-off between the two. However, we also show that a sub-optimal but more realistic decision-maker exhibits behavior between these two extremes, and more closely resembles experimental data.
- Published
- 2024
10. A Preconditioned Interior Point Method for Support Vector Machines Using an ANOVA-Decomposition and NFFT-Based Matrix-Vector Products
- Author
-
Wagner, Theresa, Pearson, John W., and Stoll, Martin
- Subjects
Mathematics - Numerical Analysis ,Computer Science - Machine Learning ,Mathematics - Optimization and Control ,05C50, 65F08, 65F10, 65T50, 90C20 - Abstract
In this paper we consider the numerical solution to the soft-margin support vector machine optimization problem. This problem is typically solved using the SMO algorithm, given the high computational complexity of traditional optimization algorithms when dealing with large-scale kernel matrices. In this work, we propose employing an NFFT-accelerated matrix-vector product using an ANOVA decomposition for the feature space that is used within an interior point method for the overall optimization problem. As this method requires the solution of a linear system of saddle point form we suggest a preconditioning approach that is based on low-rank approximations of the kernel matrix together with a Krylov subspace solver. We compare the accuracy of the ANOVA-based kernel with the default LIBSVM implementation. We investigate the performance of the different preconditioners as well as the accuracy of the ANOVA kernel on several large-scale datasets., Comment: Official Code https://github.com/wagnertheresa/NFFTSVMipm
- Published
- 2023
11. A Numerical Optimisation Framework for Parameter Identification of the SIRD Model
- Author
-
Miniguano-Trujillo, Andrés, Pearson, John W., and Goddard, Benjamin D.
- Subjects
Mathematics - Optimization and Control - Abstract
We consider a numerical framework tailored to identifying optimal parameters in the context of modelling disease propagation. Our focus is on understanding the behaviour of optimisation algorithms for such problems, where the dynamics are described by a system of ordinary differential equations associated with the epidemiological SIRD model. We examine properties of the solution operator and determine existence of optimal parameters for the problem considered. Further, first-order optimality conditions are derived, the solution of which provides a certificate of goodness of fit, which is not always guaranteed with parameter tuning techniques. We then propose strategies for the numerical solution of such problems, based on projected gradient descent, Fast Iterative Shrinkage-Thresholding Algorithm (FISTA), and limited memory BFGS trust region approaches. We carry out a thorough computational study for a range of problems of interest, determining the relative performance of these numerical methods. Our results provide insights into the efficacy of these strategies, contributing to ongoing research into optimising parameters for accurate and reliable disease spread modelling. Moreover, our approach paves the way for calibration of more intricate compartmental models., Comment: 26 pages, 7 figures, 3 tables
- Published
- 2023
12. Design and Performance of Parallel-channel Nanocryotrons in Magnetic Fields
- Author
-
Draher, Timothy, Polakovic, Tomas, Li, Yi, Pearson, John, Dibos, Alan, Meziani, Zein-Eddine, Xiao, Zhili, and Novosad, Valentine
- Subjects
Condensed Matter - Superconductivity ,Physics - Applied Physics - Abstract
We introduce a design modification to conventional geometry of the cryogenic three-terminal switch, the nanocryotron (nTron). The conventional geometry of nTrons is modified by including parallel current-carrying channels, an approach aimed at enhancing the device's performance in magnetic field environments. The common challenge in nTron technology is to maintain efficient operation under varying magnetic field conditions. Here we show that the adaptation of parallel channel configurations leads to an enhanced gate signal sensitivity, an increase in operational gain, and a reduction in the impact of superconducting vortices on nTron operation within magnetic fields up to 1 Tesla. Contrary to traditional designs that are constrained by their effective channel width, the parallel nanowire channels permits larger nTron cross sections, further bolstering the device's magnetic field resilience while improving electro-thermal recovery times due to reduced local inductance. This advancement in nTron design not only augments its functionality in magnetic fields but also broadens its applicability in technological environments, offering a simple design alternative to existing nTron devices., Comment: 6 pages, 5 figures. Accepted by Applied Physics Letters. Supplemental information includes additional supporting figures and tables
- Published
- 2023
- Full Text
- View/download PDF
13. Programmable Real-Time Magnon Interference in Two Remotely Coupled Magnonic Resonators
- Author
-
Song, Moojune, Polakovic, Tomas, Lim, Jinho, Cecil, Thomas W., Pearson, John, Divan, Ralu, Kwok, Wai-Kwong, Welp, Ulrich, Hoffmann, Axel, Kim, Kab-Jin, Novosad, Valentine, and Li, Yi
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Magnon interference is a signature of coherent magnon interactions for coherent information processing. In this work, we demonstrate programmable real-time magnon interference, with examples of nearly perfect constructive and destructive interference, between two remotely coupled yttrium iron garnet spheres mediated by a coplanar superconducting resonator. Exciting one of the coupled resonators by injecting single- and double-microwave pulse leads to the coherent energy exchange between the remote magnonic resonators and allows us to realize a programmable magnon interference that can define an arbitrary state of coupled magnon oscillation. The demonstration of time-domain coherent control of remotely coupled magnon dynamics offers new avenues for advancing coherent information processing with circuit-integrated hybrid magnonic networks.
- Published
- 2023
14. A15 Phase Ta3Sb Thin Films: Direct Synthesis and Giant Spin-Orbit Effects
- Author
-
Jiang, J. S., Du, Qianheng, Welp, Ulrich, Chapai, Ramakanta, Arava, Hanu, Liu, Yuzi, Li, Yue, Pearson, John, Bhattacharya, Anand, and Park, Hyowon
- Subjects
Condensed Matter - Materials Science - Abstract
We use co-sputtering to directly synthesize thin films of the A15 phase intermetallic compound Ta3Sb, which has been predicted to have a giant spin Hall conductivity. We identify a large window of Ta:Sb flux ratio that stabilizes single-phase A15 Ta3Sb. Composition analyses of these films show a Ta:Sb atomic ratio of 4:1, which is consistent with the known Ta-Sb phase diagram. The spin Hall conductivity of thin film Ta3Sb is -3400+/-400 (hbar/2e) S/cm and the spin-orbit torque efficiency is -0.6+/-0.1 at 20 K, as determined from harmonic Hall measurements of Ta3Sb/permalloy bilayer structures. These giant values make Ta3Sb a promising material for efficient charge-to-spin conversion in spintronic applications. Large field-like spin-orbit effective fields that are independent of the ferromagnetic layer thickness have also been measured in the Ta3Sb/permalloy bilayers. We attribute the field-like spin-orbit effective field to the Rashba effect at the interface.
- Published
- 2023
15. Tunable Magnon-Photon Coupling by Magnon Band Gap in a Layered Hybrid Perovskite Antiferromagnet
- Author
-
Li, Yi, Draher, Timothy, Comstock, Andrew H., Xiong, Yuzan, Haque, Md Azimul, Easy, Elham, Qian, Jiang-Chao, Polakovic, Tomas, Pearson, John E., Divan, Ralu, Zuo, Jian-Min, Zhang, Xian, Welp, Ulrich, Kwok, Wai-Kwong, Hoffmann, Axel, Luther, Joseph M., Beard, Matthew C., Sun, Dali, Zhang, Wei, and Novosad, Valentine
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Tunability of coherent coupling between fundamental excitations is an important prerequisite for expanding their functionality in hybrid quantum systems. In hybrid magnonics, the dipolar interaction between magnon and photon usually persists and cannot be switched off. Here, we demonstrate this capability by coupling a superconducting resonator to a layered hybrid perovskite antiferromagnet, which exhibits a magnon band gap due to its intrinsic Dzyaloshinskii-Moriya interaction. The pronounced temperature sensitivity of the magnon band gap location allows us to set the photon mode within the gap and to disable magnon-photon hybridization. When the resonator mode falls into the magnon band gap, the resonator damping rate increases due to the nonzero coupling to the detuned magnon mode. This phenomena can be used to quantify the magnon band gap using an analytical model. Our work brings new opportunities in controlling coherent information processing with quantum properties in complex magnetic materials., Comment: 8 pages, 4 figures
- Published
- 2023
16. No attributable effects of PRP on greater trochanteric pain syndrome
- Author
-
Thompson, Grant and Pearson, John F.
- Published
- 2019
17. Place and avoiding the race to the bottom of the fractured well
- Author
-
Pearson, John
- Published
- 2024
- Full Text
- View/download PDF
18. Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy
- Author
-
Brosda, Sandra, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lonie, James M., Belle, Clemence J., Newell, Felicity, Koufariotis, Lambros T., Addala, Venkateswar, Naeini, Marjan M., Pearson, John V., Krause, Lutz, Waddell, Nicola, and Barbour, Andrew P.
- Published
- 2024
- Full Text
- View/download PDF
19. Association of natriuretic peptides and receptor activity with cardio-metabolic health at middle age
- Author
-
Prickett, Timothy C. R., Espiner, Eric A., and Pearson, John F.
- Published
- 2024
- Full Text
- View/download PDF
20. The incidence of early onset colorectal cancer in Aotearoa New Zealand: 2000–2020
- Author
-
Waddell, Oliver, Pearson, John, McCombie, Andrew, Marshall, Harriet, Purcell, Rachel, Keenan, Jacqueline, Glyn, Tamara, and Frizelle, Frank
- Published
- 2024
- Full Text
- View/download PDF
21. Computational immunogenomic approaches to predict response to cancer immunotherapies
- Author
-
Addala, Venkateswar, Newell, Felicity, Pearson, John V., Redwood, Alec, Robinson, Bruce W., Creaney, Jenette, and Waddell, Nicola
- Published
- 2024
- Full Text
- View/download PDF
22. Parallel-in-Time Solver for the All-at-Once Runge--Kutta Discretization
- Author
-
Leveque, Santolo, Bergamaschi, Luca, Martínez, Ángeles, and Pearson, John W.
- Subjects
Mathematics - Numerical Analysis - Abstract
In this article, we derive fast and robust parallel-in-time preconditioned iterative methods for the all-at-once linear systems arising upon discretization of time-dependent PDEs. The discretization we employ is based on a Runge--Kutta method in time, for which the development of parallel solvers is an emerging research area in the literature of numerical methods for time-dependent PDEs. By making use of classical theory of block matrices, one is able to derive a preconditioner for the systems considered. The block structure of the preconditioner allows for parallelism in the time variable, as long as one is able to provide an optimal solver for the system of the stages of the method. We thus propose a preconditioner for the latter system based on a singular value decomposition (SVD) of the (real) Runge--Kutta matrix $A_{\mathrm{RK}} = U \Sigma V^\top$. Supposing $A_{\mathrm{RK}}$ is invertible, we prove that the spectrum of the system for the stages preconditioned by our SVD-based preconditioner is contained within the right-half of the unit circle, under suitable assumptions on the matrix $U^\top V$ (the assumptions are well posed due to the polar decomposition of $A_{\mathrm{RK}}$). We show the numerical efficiency of our SVD-based preconditioner by solving the system of the stages arising from the discretization of the heat equation and the Stokes equations, with sequential time-stepping. Finally, we provide numerical results of the all-at-once approach for both problems, showing the speed-up achieved on a parallel architecture.
- Published
- 2023
23. Unidirectional Microwave Transduction with Chirality Selected Short-Wavelength Magnon Excitations
- Author
-
Li, Yi, Lo, Tzu-Hsiang, Lim, Jinho, Pearson, John E., Divan, Ralu, Zhang, Wei, Welp, Ulrich, Kwok, Wai-Kwong, Hoffmann, Axel, and Novosad, Valentine
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Applied Physics - Abstract
Nonreciprocal magnon propagation has recently become a highly potential approach of developing chip-embedded microwave isolators for advanced information processing. However, it is challenging to achieve large nonreciprocity in miniaturized magnetic thin-film devices because of the difficulty of distinguishing propagating surface spin waves along the opposite directions when the film thickness is small. In this work, we experimentally realize unidirectional microwave transduction with sub-micron-wavelength propagating magnons in a yttrium iron garnet (YIG) thin film delay line. We achieve a non-decaying isolation of 30 dB with a broad field-tunable band-pass frequency range up to 14 GHz. The large isolation is due to the selection of chiral magnetostatic surface spin waves with the Oersted field generated from the coplanar waveguide antenna. Increasing the geometry ratio between the antenna width and YIG thickness drastically reduces the nonreciprocity and introduces additional magnon transmission bands. Our results pave the way for on-chip microwave isolation and tunable delay line with short-wavelength magnonic excitations., Comment: 6 pages, 4 figures
- Published
- 2023
- Full Text
- View/download PDF
24. Repetition and Subversion in Henry James's The Turn of the Screw
- Author
-
Pearson, John H.
- Published
- 2010
- Full Text
- View/download PDF
25. Ion-beam Assisted Sputtering of Titanium Nitride Thin Films
- Author
-
Draher, Timothy, Polakovic, Tomas, Li, Juliang, Li, Yi, Welp, Ulrich, Jiang, Jidong Samuel, Pearson, John, Armstrong, Whitney, Meziani, Zein-Eddine, Chang, Clarence, Kwok, Wai-Kwong, Xiao, Zhili, and Novosad, Valentine
- Subjects
Condensed Matter - Superconductivity ,Condensed Matter - Materials Science - Abstract
Titanium nitride is a material of interest for many superconducting devices such as nanowire microwave resonators and photon detectors. Thus, controlling the growth of TiN thin films with desirable properties is of high importance. In previous work on niobium nitride, ion beam-assisted sputtering (IBAS) reduced nitrogen sensitivity during deposition in tandem with an increase in nominal critical temperature. We have deposited thin films of titanium nitride by both, the conventional method of DC reactive magnetron sputtering and the IBAS method and compare their superconducting critical temperatures Tc as functions of thickness, sheet resistance, and nitrogen flow rate. We perform electrical and structural characterizations by electric transport and X-ray diffraction measurements. Compared to the conventional method of reactive sputtering, the IBAS technique has demonstrated a 10% increase in nominal critical temperature and 33% reduced sensitivity to nitrogen flow, without noticeable variation in the lattice structure. Additionally, we explore the behavior of superconducting Tc in ultra-thin films. Trends in films grown at high nitrogen concentrations follow predictions of mean-field theory in disordered films and show suppression of superconducting Tc due to geometric effects, while nitride films grown at low nitrogen concentrations strongly deviate from the theoretical models.
- Published
- 2022
- Full Text
- View/download PDF
26. MultiShape: A Spectral Element Method, with Applications to Dynamic Density Functional Theory and PDE-Constrained Optimization
- Author
-
Roden, Jonna C., Mills-Williams, Rory D., Pearson, John W., and Goddard, Benjamin D.
- Subjects
Mathematics - Numerical Analysis ,35Q70, 35Q93, 65M70, 82C22, 82M22 - Abstract
A numerical framework is developed to solve various types of PDEs on complicated domains, including steady and time-dependent, non-linear and non-local PDEs, with different boundary conditions that can also include non-linear and non-local terms. This numerical framework, called MultiShape, is a class in Matlab, and the software is open source. We demonstrate that MultiShape is compatible with other numerical methods, such as differential--algebraic equation solvers and optimization algorithms. The numerical implementation is designed to be user-friendly, with most of the set-up and computations done automatically by MultiShape and with intuitive operator definition, notation, and user-interface. Validation tests are presented, before we introduce three examples motivated by applications in Dynamic Density Functional Theory and PDE-constrained optimization, illustrating the versatility of the method.
- Published
- 2022
27. Gene expression profiling of mucinous ovarian tumors and comparison with upper and lower gastrointestinal tumors identifies markers associated with adverse outcomes.
- Author
-
Meagher, Nicola S, Gorringe, Kylie L, Wakefield, Matthew, Bolithon, Adelyn, Pang, Chi Nam Ignatius, Chiu, Derek S, Anglesio, Michael S, Mallitt, Kylie-Ann, Doherty, Jennifer A, Harris, Holly R, Schildkraut, Joellen M, Berchuck, Andrew, Cushing-Haugen, Kara L, Chezar, Ksenia, Chou, Angela, Tan, Adeline, Alsop, Jennifer, Barlow, Ellen, Beckmann, Matthias W, Boros, Jessica, Bowtell, David DL, Group, for the AOCS, Brand, Alison H, Brenton, James D, Campbell, Ian, Cheasley, Dane, Cohen, Joshua, Cybulski, Cezary, Elishaev, Esther, Erber, Ramona, Farrell, Rhonda, Fischer, Anna, Fu, Zhuxuan, Gilks, Blake, Gill, Anthony J, Initiative, for the Australian Pancreatic Genome, Gourley, Charlie, Grube, Marcel, Harnett, Paul R, Hartmann, Arndt, Hettiaratchi, Anusha, Høgdall, Claus K, Huzarski, Tomasz, Jakubowska, Anna, Jimenez-Linan, Mercedes, Kennedy, Catherine J, Kim, Byoung-Gie, Kim, Jae-Weon, Kim, Jae-Hoon, Klett, Kayla, Koziak, Jennifer M, Lai, Tiffany, Laslavic, Angela, Lester, Jenny, Leung, Yee, Li, Na, Liauw, Winston, Lim, Belle WX, Linder, Anna, Lubiński, Jan, Mahale, Sakshi, Mateoiu, Constantina, McInerny, Simone, Menkiszak, Janusz, Minoo, Parham, Mittelstadt, Suzana, Morris, David, Orsulic, Sandra, Park, Sang-Yoon, Pearce, Celeste Leigh, Pearson, John V, Pike, Malcolm C, Quinn, Carmel M, Mohan, Ganendra Raj, Rao, Jianyu, Riggan, Marjorie J, Ruebner, Matthias, Salfinger, Stuart, Scott, Clare L, Shah, Mitul, Steed, Helen, Stewart, Colin JR, Subramanian, Deepak, Sung, Soseul, Tang, Katrina, Timpson, Paul, Ward, Robyn L, Wiedenhoefer, Rebekka, Thorne, Heather, Investigators, for the kConFab, Cohen, Paul A, Crowe, Philip, Fasching, Peter A, Gronwald, Jacek, Hawkins, Nicholas J, Høgdall, Estrid, Huntsman, David G, James, Paul A, Karlan, Beth Y, and Kelemen, Linda E
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Ovarian Cancer ,Rare Diseases ,Cancer ,Digestive Diseases ,Genetics ,4.1 Discovery and preclinical testing of markers and technologies ,Detection ,screening and diagnosis ,Female ,Humans ,Neoplasm Staging ,Ovarian Neoplasms ,Carcinoma ,Ovarian Epithelial ,Adenocarcinoma ,Mucinous ,Prognosis ,Gastrointestinal Neoplasms ,AOCS Group ,Australian Pancreatic Genome Initiative ,kConFab Investigators ,Oncology & Carcinogenesis ,Clinical sciences ,Oncology and carcinogenesis - Abstract
PurposeAdvanced-stage mucinous ovarian carcinoma (MOC) has poor chemotherapy response and prognosis and lacks biomarkers to aid stage I adjuvant treatment. Differentiating primary MOC from gastrointestinal (GI) metastases to the ovary is also challenging due to phenotypic similarities. Clinicopathologic and gene-expression data were analyzed to identify prognostic and diagnostic features.Experimental designDiscovery analyses selected 19 genes with prognostic/diagnostic potential. Validation was performed through the Ovarian Tumor Tissue Analysis consortium and GI cancer biobanks comprising 604 patients with MOC (n = 333), mucinous borderline ovarian tumors (MBOT, n = 151), and upper GI (n = 65) and lower GI tumors (n = 55).ResultsInfiltrative pattern of invasion was associated with decreased overall survival (OS) within 2 years from diagnosis, compared with expansile pattern in stage I MOC [hazard ratio (HR), 2.77; 95% confidence interval (CI), 1.04-7.41, P = 0.042]. Increased expression of THBS2 and TAGLN was associated with shorter OS in MOC patients (HR, 1.25; 95% CI, 1.04-1.51, P = 0.016) and (HR, 1.21; 95% CI, 1.01-1.45, P = 0.043), respectively. ERBB2 (HER2) amplification or high mRNA expression was evident in 64 of 243 (26%) of MOCs, but only 8 of 243 (3%) were also infiltrative (4/39, 10%) or stage III/IV (4/31, 13%).ConclusionsAn infiltrative growth pattern infers poor prognosis within 2 years from diagnosis and may help select stage I patients for adjuvant therapy. High expression of THBS2 and TAGLN in MOC confers an adverse prognosis and is upregulated in the infiltrative subtype, which warrants further investigation. Anti-HER2 therapy should be investigated in a subset of patients. MOC samples clustered with upper GI, yet markers to differentiate these entities remain elusive, suggesting similar underlying biology and shared treatment strategies.
- Published
- 2022
28. Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers
- Author
-
Hakkaart, Christopher, Pearson, John F, Marquart, Louise, Dennis, Joe, Wiggins, George AR, Barnes, Daniel R, Robinson, Bridget A, Mace, Peter D, Aittomäki, Kristiina, Andrulis, Irene L, Arun, Banu K, Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B, Belhadj, Sami, Berger, Lieke, Blok, Marinus J, Boonen, Susanne E, Borde, Julika, Bradbury, Angela R, Brunet, Joan, Buys, Saundra S, Caligo, Maria A, Campbell, Ian, Chung, Wendy K, Claes, Kathleen BM, Collonge-Rame, Marie-Agnès, Cook, Jackie, Cosgrove, Casey, Couch, Fergus J, Daly, Mary B, Dandiker, Sita, Davidson, Rosemarie, de la Hoya, Miguel, de Putter, Robin, Delnatte, Capucine, Dhawan, Mallika, Diez, Orland, Ding, Yuan Chun, Domchek, Susan M, Donaldson, Alan, Eason, Jacqueline, Easton, Douglas F, Ehrencrona, Hans, Engel, Christoph, Evans, D Gareth, Faust, Ulrike, Feliubadaló, Lidia, Fostira, Florentia, Friedman, Eitan, Frone, Megan, Frost, Debra, Garber, Judy, Gayther, Simon A, Gehrig, Andrea, Gesta, Paul, Godwin, Andrew K, Goldgar, David E, Greene, Mark H, Hahnen, Eric, Hake, Christopher R, Hamann, Ute, Hansen, Thomas VO, Hauke, Jan, Hentschel, Julia, Herold, Natalie, Honisch, Ellen, Hulick, Peter J, Imyanitov, Evgeny N, Isaacs, Claudine, Izatt, Louise, Izquierdo, Angel, Jakubowska, Anna, James, Paul A, Janavicius, Ramunas, John, Esther M, Joseph, Vijai, Karlan, Beth Y, Kemp, Zoe, Kirk, Judy, Konstantopoulou, Irene, Koudijs, Marco, Kwong, Ava, Laitman, Yael, Lalloo, Fiona, Lasset, Christine, Lautrup, Charlotte, Lazaro, Conxi, Legrand, Clémentine, Leslie, Goska, Lesueur, Fabienne, Mai, Phuong L, Manoukian, Siranoush, Mari, Véronique, Martens, John WM, McGuffog, Lesley, Mebirouk, Noura, Meindl, Alfons, Miller, Austin, and Montagna, Marco
- Subjects
Human Genome ,Prevention ,Breast Cancer ,Cancer ,Genetics ,Aetiology ,2.1 Biological and endogenous factors ,BRCA1 Protein ,BRCA2 Protein ,Breast Neoplasms ,DNA Copy Number Variations ,Female ,Genetic Predisposition to Disease ,Heterozygote ,Humans ,RNA ,Messenger ,GEMO Study Collaborators ,EMBRACE Collaborators ,SWE-BRCA Investigators ,kConFab Investigators ,HEBON Investigators - Abstract
The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09-1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.
- Published
- 2022
29. Tunable superconductivity at the oxide-insulator/KTaO$_3$ interface and its origin
- Author
-
Liu, Changjiang, Zhou, Xianjing, Hong, Deshun, Fisher, Brandon, Zheng, Hong, Pearson, John, Jin, Dafei, Norman, Michael R, and Bhattacharya, Anand
- Subjects
Condensed Matter - Superconductivity - Abstract
Superconductivity forms out of the condensation of Cooper pairs of electrons. The mechanism by which Cooper pairs are created in non-conventional superconductors is often elusive because experimental signatures that connect a specific pairing mechanism to the properties of superconducting state are rare. The recently discovered superconducting oxide-insulator/KTaO$_3$ interface may offer clues about its origins. Here we observe distinct dependences of the superconducting transition temperature Tc on carrier density n$_{2D}$ for electron gases formed at KTaO$_3$ (111), (001) and (110) interfaces. For the KTaO$_3$ (111) interface, a remarkable linear dependence of Tc on n$_{2D}$ is observed over a range of nearly one order of magnitude. Further, our study of the dependence of superconductivity on gate electric fields reveals the role of the interface in mediating superconductivity, which also allows for a reversible electric switching of superconductivity at T = 2 K. We found that the extreme sensitivity of superconductivity to crystallographic orientation can be explained by Cooper pairing via inter-orbital interactions induced by the inversion-breaking transverse optical (TO1) phonons and quantum confinement. This mechanism is also consistent with the dependence of Tc on n$_{2D}$ at the KTaO$_3$ (111) interface. Our study may shed light on the pairing mechanism in other superconducting quantum-paraelectrics.
- Published
- 2022
- Full Text
- View/download PDF
30. Coherent coupling of two remote magnonic resonators mediated by superconducting circuits
- Author
-
Li, Yi, Yefremenko, Volodymyr G., Lisovenko, Marharyta, Trevillian, Cody, Polakovic, Tomas, Cecil, Thomas W., Barry, Pete S., Pearson, John, Divan, Ralu, Tyberkevych, Vasyl, Chang, Clarence L., Welp, Ulrich, Kwok, Wai-Kwong, and Novosad, Valentine
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
We demonstrate microwave-mediated distant magnon-magnon coupling on a superconducting circuit platform, incorporating chip-mounted single-crystal Y$_3$Fe$_5$O$_{12}$ (YIG) spheres. Coherent level repulsion and dissipative level attraction between the magnon modes of the two YIG spheres are demonstrated. The former is mediated by cavity photons of a superconducting resonator, and the latter is mediated by propagating photons of a coplanar waveguide. Our results open new avenues towards exploring integrated hybrid magnonic networks for coherent information processing on a quantum-compatible superconducting platform., Comment: 6 pages, 4 figures, Accepted in Phys. Rev. Lett
- Published
- 2022
- Full Text
- View/download PDF
31. Reproducible, incremental representation learning with Rosetta VAE
- Author
-
Martinez, Miles and Pearson, John
- Subjects
Computer Science - Machine Learning - Abstract
Variational autoencoders are among the most popular methods for distilling low-dimensional structure from high-dimensional data, making them increasingly valuable as tools for data exploration and scientific discovery. However, unlike typical machine learning problems in which a single model is trained once on a single large dataset, scientific workflows privilege learned features that are reproducible, portable across labs, and capable of incrementally adding new data. Ideally, methods used by different research groups should produce comparable results, even without sharing fully trained models or entire data sets. Here, we address this challenge by introducing the Rosetta VAE (R-VAE), a method of distilling previously learned representations and retraining new models to reproduce and build on prior results. The R-VAE uses post hoc clustering over the latent space of a fully-trained model to identify a small number of Rosetta Points (input, latent pairs) to serve as anchors for training future models. An adjustable hyperparameter, $\rho$, balances fidelity to the previously learned latent space against accommodation of new data. We demonstrate that the R-VAE reconstructs data as well as the VAE and $\beta$-VAE, outperforms both methods in recovery of a target latent space in a sequential training setting, and dramatically increases consistency of the learned representation across training runs., Comment: 16 pages, 7 figures, Bayesian Deep Learning Workshop at Neurips 2021
- Published
- 2022
32. Vocalization modulates the mouse auditory cortex even in the absence of hearing
- Author
-
Harmon, Thomas C., Madlon-Kay, Seth, Pearson, John, and Mooney, Richard
- Published
- 2024
- Full Text
- View/download PDF
33. Whole Genome Sequencing in Advanced Lung Cancer can be Performed Using Diff-Quik Cytology Smears Derived from Endobronchial Ultrasound, Transbronchial Needle Aspiration (EBUS TBNA)
- Author
-
Fielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Fairbairn, David, Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Hodgson, Alan, Pearson, John V., Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Nones, Katia, and Simpson, Peter T.
- Published
- 2023
- Full Text
- View/download PDF
34. Double Saddle-Point Preconditioning for Krylov Methods in the Inexact Sequential Homotopy Method
- Author
-
Pearson, John W. and Potschka, Andreas
- Subjects
Mathematics - Optimization and Control ,Mathematics - Numerical Analysis ,49M37, 65F08, 65F10, 65K05, 90C30, 93C20 - Abstract
We derive an extension of the sequential homotopy method that allows for the application of inexact Krylov methods for the linear (double) saddle-point systems arising in the local semismooth Newton method for the homotopy subproblems. For the class of problems that exhibit (after suitable partitioning of the variables) a zero in the off-diagonal blocks of the Hessian of the Lagrangian, we propose and analyze an efficient, parallelizable, symmetric positive definite preconditioner based on a double Schur complement approach. For discretized optimal control problems with PDE constraints, this structure is often present with the canonical partitioning of the variables in states and controls. We conclude with numerical results for a badly conditioned and highly nonlinear benchmark optimization problem with elliptic partial differential equations and control bounds. The resulting method is faster than using direct linear algebra for the 2D benchmark and allows for the parallel solution of large 3D problems., Comment: 25 pages
- Published
- 2021
35. Large Exotic Spin Torques in Antiferromagnetic Iron Rhodium
- Author
-
Gibbons, Jonathan, Dohi, Takaaki, Amin, Vivek P., Xue, Fei, Ren, Haowen, Xu, Jun-Wen, Arava, Hanu, Shim, Soho, Saglam, Hilal, Liu, Yuzi, Pearson, John E., Mason, Nadya, Petford-Long, Amanda K., Haney, Paul M., Stiles, Mark D., Fullerton, Eric E., Kent, Andrew D., Fukami, Shunsuke, and Hoffmann, Axel
- Subjects
Condensed Matter - Materials Science - Abstract
Spin torque is a promising tool for driving magnetization dynamics for novel computing technologies. These torques can be easily produced by spin-orbit effects, but for most conventional spin source materials, a high degree of crystal symmetry limits the geometry of the spin torques produced. Magnetic ordering is one way to reduce the symmetry of a material and allow exotic torques, and antiferromagnets are particularly promising because they are robust against external fields. We present spin torque ferromagnetic resonance measurements and second harmonic Hall measurements characterizing the spin torques in antiferromagnetic iron rhodium alloy. We report extremely large, strongly temperature-dependent exotic spin torques with a geometry apparently defined by the magnetic ordering direction. We find the spin torque efficiency of iron rhodium to be (330$\pm$150) % at 170 K and (91$\pm$32) % at room temperature. We support our conclusions with theoretical calculations showing how the antiferromagnetic ordering in iron rhodium gives rise to such exotic torques., Comment: 21 pages, 6 figures
- Published
- 2021
36. Bubblewrap: Online tiling and real-time flow prediction on neural manifolds
- Author
-
Draelos, Anne, Gupta, Pranjal, Jun, Na Young, Sriworarat, Chaichontat, and Pearson, John
- Subjects
Computer Science - Machine Learning ,Quantitative Biology - Neurons and Cognition ,Statistics - Machine Learning - Abstract
While most classic studies of function in experimental neuroscience have focused on the coding properties of individual neurons, recent developments in recording technologies have resulted in an increasing emphasis on the dynamics of neural populations. This has given rise to a wide variety of models for analyzing population activity in relation to experimental variables, but direct testing of many neural population hypotheses requires intervening in the system based on current neural state, necessitating models capable of inferring neural state online. Existing approaches, primarily based on dynamical systems, require strong parametric assumptions that are easily violated in the noise-dominated regime and do not scale well to the thousands of data channels in modern experiments. To address this problem, we propose a method that combines fast, stable dimensionality reduction with a soft tiling of the resulting neural manifold, allowing dynamics to be approximated as a probability flow between tiles. This method can be fit efficiently using online expectation maximization, scales to tens of thousands of tiles, and outperforms existing methods when dynamics are noise-dominated or feature multi-modal transition probabilities. The resulting model can be trained at kiloHertz data rates, produces accurate approximations of neural dynamics within minutes, and generates predictions on submillisecond time scales. It retains predictive performance throughout many time steps into the future and is fast enough to serve as a component of closed-loop causal experiments., Comment: Version of the work appearing in NeurIPS 2021
- Published
- 2021
37. Parameter-Robust Preconditioning for Oseen Iteration Applied to Stationary and Instationary Navier--Stokes Control
- Author
-
Leveque, Santolo and Pearson, John W.
- Subjects
Mathematics - Numerical Analysis ,Mathematics - Optimization and Control - Abstract
We derive novel, fast, and parameter-robust preconditioned iterative methods for steady and time-dependent Navier--Stokes control problems. Our approach may be applied to time-dependent problems which are discretized using backward Euler or Crank--Nicolson, and is also a valuable candidate for Stokes control problems discretized using Crank--Nicolson. The key ingredients of the solver are a saddle-point type approximation for the linear systems, an inner iteration for the $(1,1)$-block accelerated by a preconditioner for convection--diffusion control, and an approximation to the Schur complement based on a potent commutator argument applied to an appropriate block matrix. A range of numerical experiments validate the effectiveness of our new approach.
- Published
- 2021
38. General-purpose preconditioning for regularized interior point methods
- Author
-
Gondzio, Jacek, Pougkakiotis, Spyridon, and Pearson, John W.
- Subjects
Mathematics - Optimization and Control ,Mathematics - Numerical Analysis - Abstract
In this paper we present general-purpose preconditioners for regularized augmented systems arising from optimization problems, and their corresponding normal equations. We discuss positive definite preconditioners, suitable for CG and MINRES. We consider "sparsifications" which avoid situations in which eigenvalues of the preconditioned matrix may become complex. Special attention is given to systems arising from the application of regularized interior point methods to linear or nonlinear convex programming problems.
- Published
- 2021
39. The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study
- Author
-
Davidson, Aimee L., Dressel, Uwe, Norris, Sarah, Canson, Daffodil M., Glubb, Dylan M., Fortuno, Cristina, Hollway, Georgina E., Parsons, Michael T., Vidgen, Miranda E., Holmes, Oliver, Koufariotis, Lambros T., Lakis, Vanessa, Leonard, Conrad, Wood, Scott, Xu, Qinying, McCart Reed, Amy E., Pickett, Hilda A., Al-Shinnag, Mohammad K., Austin, Rachel L., Burke, Jo, Cops, Elisa J., Nichols, Cassandra B., Goodwin, Annabel, Harris, Marion T., Higgins, Megan J., Ip, Emilia L., Kiraly-Borri, Catherine, Lau, Chiyan, Mansour, Julia L., Millward, Michael W., Monnik, Melissa J., Pachter, Nicholas S., Ragunathan, Abiramy, Susman, Rachel D., Townshend, Sharron L., Trainer, Alison H., Troth, Simon L., Tucker, Katherine M., Wallis, Mathew J., Walsh, Maie, Williams, Rachel A., Winship, Ingrid M., Newell, Felicity, Tudini, Emma, Pearson, John V., Poplawski, Nicola K., Mar Fan, Helen G., James, Paul A., Spurdle, Amanda B., Waddell, Nicola, and Ward, Robyn L.
- Published
- 2023
- Full Text
- View/download PDF
40. Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
- Author
-
Tran, Khoa A., Addala, Venkateswar, Johnston, Rebecca L., Lovell, David, Bradley, Andrew, Koufariotis, Lambros T., Wood, Scott, Wu, Sunny Z., Roden, Daniel, Al-Eryani, Ghamdan, Swarbrick, Alexander, Williams, Elizabeth D., Pearson, John V., Kondrashova, Olga, and Waddell, Nicola
- Published
- 2023
- Full Text
- View/download PDF
41. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy
- Author
-
M. Naeini, Marjan, Newell, Felicity, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lampe, Guy, Koufariotis, Lambros T., Lakis, Vanessa, Addala, Venkateswar, Kondrashova, Olga, Johnston, Rebecca L., Sharma, Sowmya, Brosda, Sandra, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Thomas, Janine, Walpole, Euan, Tao Mai, G., Ackland, Stephen P., Martin, Jarad, Burge, Matthew, Finch, Robert, Karapetis, Christos S., Shannon, Jenny, Nott, Louise, Bohmer, Robert, Wilson, Kate, Barnes, Elizabeth, Zalcberg, John R., Mark Smithers, B., Simes, John, Price, Timothy, Gebski, Val, Nones, Katia, Watson, David I., Pearson, John V., Barbour, Andrew P., and Waddell, Nicola
- Published
- 2023
- Full Text
- View/download PDF
42. Ion-beam assisted sputtering of titanium nitride thin films
- Author
-
Draher, Timothy, Polakovic, Tomas, Li, Juliang, Li, Yi, Welp, Ulrich, Jiang, Jidong Samuel, Pearson, John, Armstrong, Whitney, Meziani, Zein-Eddine, Chang, Clarence, Kwok, Wai-Kwong, Xiao, Zhili, and Novosad, Valentine
- Published
- 2023
- Full Text
- View/download PDF
43. Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology
- Author
-
MacDonald, Samual, Foley, Helena, Yap, Melvyn, Johnston, Rebecca L., Steven, Kaiah, Koufariotis, Lambros T., Sharma, Sowmya, Wood, Scott, Addala, Venkateswar, Pearson, John V., Roosta, Fred, Waddell, Nicola, Kondrashova, Olga, and Trzaskowski, Maciej
- Published
- 2023
- Full Text
- View/download PDF
44. Tunable superconductivity and its origin at KTaO3 interfaces
- Author
-
Liu, Changjiang, Zhou, Xianjing, Hong, Deshun, Fisher, Brandon, Zheng, Hong, Pearson, John, Jiang, Jidong Samuel, Jin, Dafei, Norman, Michael R., and Bhattacharya, Anand
- Published
- 2023
- Full Text
- View/download PDF
45. Measuring and Modeling Confidence in Human Causal Judgment
- Author
-
O’Neill, Kevin, Henne, Paul, Pearson, John, and DeBrigard, Felipe
- Subjects
Philosophy ,Psychology ,Causal reasoning ,Computational Modeling ,Quantitative Behavior - Abstract
The human capacity for causal judgment has long been thought to depend on an ability to consider counterfactual alternatives: the lightning strike caused the forest fire because had it not struck, the forest fire would not have ensued. To accommodate psychological effects on causal judgment, a range of recent accounts of causal judgment have proposed that people probabilistically sample counterfactual alternatives from which they compute a graded index of causal strength. While such models have had success in describing the influence of probability on causal judgments, among other effects, we show that these models make further untested predictions: probability should also influence people's metacognitive confidence in their causal judgments. In a large (N=3020) sample of participants in a causal judgment task, we found evidence that normality indeed influences people's confidence in their causal judgments and that these influences were predicted by a counterfactual sampling model. We take this result as supporting evidence for existing Bayesian accounts of causal judgment.
- Published
- 2022
46. On Symmetric Positive Definite Preconditioners for Multiple Saddle-Point Systems
- Author
-
Pearson, John W. and Potschka, Andreas
- Subjects
Mathematics - Numerical Analysis ,65F08, 65F10, 65N99, 49M41 - Abstract
We consider symmetric positive definite preconditioners for multiple saddle-point systems of block tridiagonal form, which can be applied within the MINRES algorithm. We describe such a preconditioner for which the preconditioned matrix has only two distinct eigenvalues, 1 and -1, when the preconditioner is applied exactly. We discuss the relative merits of such an approach compared to a more widely studied block diagonal preconditioner, specify the computational work associated with applying the new preconditioner inexactly, and survey a number of theoretical results for the block diagonal case. Numerical results validate our theoretical findings., Comment: 19 pages
- Published
- 2021
47. Phase-resolved electrical detection of coherently coupled magnonic devices
- Author
-
Li, Yi, Zhao, Chenbo, Amin, Vivek P., Zhang, Zhizhi, Vogel, Michael, Xiong, Yuzan, Sklenar, Joseph, Divan, Ralu, Pearson, John, Stiles, Mark D., Zhang, Wei, Hoffmann, 1 Axel, and Novosad, Valentyn
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
We demonstrate the electrical detection of magnon-magnon hybrid dynamics in yttrium iron garnet/permalloy (YIG/Py) thin film bilayer devices. Direct microwave current injection through the conductive Py layer excites the hybrid dynamics consisting of the uniform mode of Py and the first standing spin wave ($n=1$) mode of YIG, which are coupled via interfacial exchange. Both the two hybrid modes, with Py or YIG dominated excitations, can be detected via the spin rectification signals from the conductive Py layer, providing phase resolution of the coupled dynamics. The phase characterization is also applied to a nonlocally excited Py device, revealing the additional phase shift due to the perpendicular Oersted field. Our results provide a device platform for exploring hybrid magnonic dynamics and probing their phases, which are crucial for implementing coherent information processing with magnon excitations
- Published
- 2021
- Full Text
- View/download PDF
48. Saddle point preconditioners for weak-constraint 4D-Var
- Author
-
Tabeart, Jemima M. and Pearson, John W.
- Subjects
Mathematics - Numerical Analysis ,65F08, 65F10, 65N21 - Abstract
Data assimilation algorithms combine information from observations and prior model information to obtain the most likely state of a dynamical system. The linearised weak-constraint four-dimensional variational assimilation problem can be reformulated as a saddle point problem, which admits more scope for preconditioners than the primal form. In this paper we design new terms which can be used within existing preconditioners, such as block diagonal and constraint-type preconditioners. Our novel preconditioning approaches: (i) incorporate model information, and (ii) are designed to target correlated observation error covariance matrices. To our knowledge (i) has not previously been considered for data assimilation problems. We develop new theory demonstrating the effectiveness of the new preconditioners within Krylov subspace methods. Linear and non-linear numerical experiments reveal that our new approach leads to faster convergence than existing state-of-the-art preconditioners for a broader range of problems than indicated by the theory alone. We present a range of numerical experiments performed in serial., Comment: 22 pages, 2 figures
- Published
- 2021
49. Superconducting diode effect via conformal-mapped nanoholes
- Author
-
Lyu, Yang-Yang, Jiang, Ji, Wang, Yong-Lei, Xiao, Zhi-Li, Dong, Sining, Chen, Qing-Hu, Milošević, Milorad V., Wang, Huabing, Divan, Ralu, Pearson, John E., Wu, Peiheng, Peeters, Francois M., and Kwok, Wai-Kwong
- Subjects
Condensed Matter - Superconductivity ,Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Applied Physics - Abstract
A superconducting diode is an electronic device that conducts supercurrent and exhibits zero resistance primarily for one direction of applied current. Such a dissipationless diode is a desirable unit for constructing electronic circuits with ultralow power consumption. However, realizing a superconducting diode is fundamentally and technologically challenging, as it usually requires a material structure without a centre of inversion, which is scarce among superconducting materials. Here, we demonstrate a superconducting diode achieved in a conventional superconducting film patterned with a conformal array of nanoscale holes, which breaks the spatial inversion symmetry. We showcase the superconducting diode effect through switchable and reversible rectification signals, which can be three orders of magnitude larger than that from a flux-quantum diode. The introduction of conformal potential landscapes for creating a superconducting diode is thereby proven as a convenient, tunable, yet vastly advantageous tool for superconducting electronics. This could be readily applicable to any superconducting materials, including cuprates and iron-based superconductors that have higher transition temperatures and are desirable in device applications., Comment: 25 pages, 4 figures
- Published
- 2021
- Full Text
- View/download PDF
50. Optimizing Process Design of Flash Vessels
- Author
-
Prince, Joseph F., Pearson, John T., Verster, Roelof J., Robison, Jeffrey C., and Metallurgy and Materials Society of the Canadian Institute of Mining Metallurgy and Petroleum (CIM)
- Published
- 2023
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.