Stefan Engblom

Doghonay Arjmand, Stefan Engblom, Gunilla Kreiss

We consider a multiscale strategy addressing the disparate scales in the Landau-Lifschitz equations in micro-magnetism. At the microscopic scale, the dynamics of magnetic moments are driven by a high frequency field. On the macroscopic scale we are interested in simulating the dynamics of the magnetisation without fully resolving the microscopic scales. The method follows the framework of heterogeneous multiscale methods and it has two main ingredients: a micro- and a macroscale model. The microscopic model is assumed to be known exactly whereas the macro model is incomplete as it lacks effective quantities. The two models use different temporal and spatial scales and effective parameter values for the macro model are computed on the fly, allowing for improved efficiency over traditional one-scale schemes. For the analysis, we consider a single spin under a high frequency field and show that effective quantities can be obtained accurately with step-sizes much larger than the size of the microscopic scales required to resolve the microscopic features. Numerical results both for a single magnetic particle as well as a chain of interacting magnetic particles are given to validate the theory.

Fredrik Wrede, Robin Eriksson, Richard Jiang et al.

State-of-the-art neural network-based methods for learning summary statistics have delivered promising results for simulation-based likelihood-free parameter inference. Existing approaches require density estimation as a post-processing step building upon deterministic neural networks, and do not take network prediction uncertainty into account. This work proposes a robust integrated approach that learns summary statistics using Bayesian neural networks, and directly estimates the posterior density using categorical distributions. An adaptive sampling scheme selects simulation locations to efficiently and iteratively refine the predictive posterior of the network conditioned on observations. This allows for more efficient and robust convergence on comparatively large prior spaces. We demonstrate our approach on benchmark examples and compare against related methods.

Jing Liu, Stefan Engblom, Carl Nettelblad

Modern Flash X-ray diffraction Imaging (FXI) acquires diffraction signals from single biomolecules at a high repetition rate from X-ray Free Electron Lasers (XFELs), easily obtaining millions of 2D diffraction patterns from a single experiment. Due to the stochastic nature of FXI experiments and the massive volumes of data, retrieving 3D electron densities from raw 2D diffraction patterns is a challenging and time-consuming task. We propose a semi-automatic data analysis pipeline for FXI experiments, which includes four steps: hit finding and preliminary filtering, pattern classification, 3D Fourier reconstruction, and post analysis. We also include a recently developed bootstrap methodology in the post-analysis step for uncertainty analysis and quality control. To achieve the best possible resolution, we further suggest using background subtraction, signal windowing, and convex optimization techniques when retrieving the Fourier phases in the post-analysis step. As an application example, we quantified the 3D electron structure of the PR772 virus using the proposed data-analysis pipeline. The retrieved structure was above the detector-edge resolution and clearly showed the pseudo-icosahedral capsid of the PR772.

Stefan Engblom, Carl Nettelblad, Jing Liu

Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA. These two-dimensional diffraction patterns can be practically reconstructed and retrieved down to a resolution of a few \angstrom. In principle, a sufficiently large collection of diffraction patterns will contain the required information for a full three-dimensional reconstruction of the biomolecule. The computational methodology for this reconstruction task is still under development and highly resolved reconstructions have not yet been produced. We analyze the Expansion-Maximization-Compression scheme, the current state of the art approach for this very challenging application, by isolating different sources of uncertainty. Through numerical experiments on synthetic data we evaluate their respective impact. We reach conclusions of relevance for handling actual experimental data, as well as pointing out certain improvements to the underlying estimation algorithm. We also introduce a practically applicable computational methodology in the form of bootstrap procedures for assessing reconstruction uncertainty in the real data case. We evaluate the sharpness of this approach and argue that this type of procedure will be critical in the near future when handling the increasing amount of data.

Stefan Engblom

Mesoscopic models in the reaction-diffusion framework have gained recognition as a viable approach to describing chemical processes in cell biology. The resulting computational problem is a continuous-time Markov chain on a discrete and typically very large state space. Due to the many temporal and spatial scales involved many different types of computationally more effective multiscale models have been proposed, typically coupling different types of descriptions within the Markov chain framework. In this work we look at the strong convergence properties of the basic first order Strang, or Lie-Trotter, split-step method, which is formed by decoupling the dynamics in finite time-steps. Thanks to its simplicity and flexibility, this approach has been tried in many different combinations. We develop explicit sufficient conditions for path-wise well-posedness and convergence of the method, including error estimates, and we illustrate our findings with numerical examples. In doing so, we also suggest a certain partition of unity representation for the split-step method, which in turn implies a concrete simulation algorithm under which trajectories may be compared in a path-wise sense.

Tomas Ekeberg, Stefan Engblom, Jing Liu

The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a beam of streaming particles to be intercepted and hit by an ultrashort high energy X-ray beam. Through machine learning methods the data thus collected can be transformed into a three-dimensional volumetric intensity map of the particle itself. The computational complexity associated with this problem is very high such that clusters of data parallel accelerators are required. We have implemented a distributed and highly efficient algorithm for inversion of large collections of diffraction patterns targeting clusters of hundreds of GPUs. With the expected enormous amount of diffraction data to be produced in the foreseeable future, this is the required scale to approach real time processing of data at the beam site. Using both real and synthetic data we look at the scaling properties of the application and discuss the overall computational viability of this exciting and novel imaging technique.