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A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
Ultracold quantum gases offer unique possibilities to study interacting many-body quantum systems. Probing and manipulating such systems with ever increasing degree of control requires novel experimental techniques. Scanning electron…
A general framework for solving image inverse problems is introduced in this paper. The approach is based on Gaussian mixture models, estimated via a computationally efficient MAP-EM algorithm. A dual mathematical interpretation of the…
We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…
Non-Gaussian and multimodal distributions are an important part of many recent robust sensor fusion algorithms. In difference to robust cost functions, they are probabilistically founded and have good convergence properties. Since their…
Resonant Energy Transfer (RET) from an optically excited donor molecule (D) to a non-excited acceptor molecule (A) residing nearby is widely used to detect molecular interactions in living cells. Stoichiometric information, such as the…
We propose a new technique for the detection of single atoms in ultracold quantum gases. The technique is based on scanning electron microscopy and employs the electron impact ionization of trapped atoms with a focussed electron probe.…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
In this paper, we study the problem of learning multi-dimensional Gaussian Mixture Models (GMMs), with a specific focus on model order selection and efficient mixing distribution estimation. We first establish an information-theoretic lower…
Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope. Although reconstruction algorithms typically model the 3D volume as…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
We consider a framework for determining and estimating the conditional pairwise relationships of variables when the observed samples are contaminated with measurement error in high dimensional settings. Assuming the true underlying…
An image or volume of interest in positron emission tomography (PET) is reconstructed from pairs of gamma rays emitted from a radioactive substance. Many image reconstruction methods are based on estimation of pixels or voxels on some…
Current deep learning based segmentation models often generalize poorly between domains due to insufficient training data. In real-world clinical applications, cross-domain image analysis tools are in high demand since medical images from…
We demonstrated a biosensing approach which, for the first time, combines the high-sensitivity of whispering gallery modes (WGM) with a metallic nanoparticle based assay. We provided a computational model based on generalized Mie theory to…
Cryo-electron tomography enables 3D visualization of cells in a near native state at molecular resolution. The produced cellular tomograms contain detailed information about all macromolecular complexes, their structures, their abundances…
We revisit the topic of common lines between projection images in single particle cryo-electron microscopy (cryo-EM). We derive a novel low-rank constraint on a certain $2n \times n$ matrix storing properly-scaled basis vectors for the…
Electron cryotomography (CryoET) is currently the only method capable of visualizing cells in 3D at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information,…
The nonlinear energy response of cryogenic microcalorimeters is usually corrected through an empirical calibration. X-ray or gamma-ray emission lines of known shape and energy anchor a smooth function that generalizes the calibration data…
We implement a full nonlinear optimization method to fit continuum states with complex Gaussians. The application to a set of regular scattering Coulomb functions allows us to validate the numerical feasibility, to explore the range of…