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An algorithm for determining crystal structures from diffraction data is described which does not rely on the usual Fourier-space formulations of atomicity. The new algorithm implements atomicity constraints in real-space, as well as…
Iterative phase retrieval algorithms typically employ projections onto constraint subspaces to recover the unknown phases in the Fourier transform of an image, or, in the case of x-ray crystallography, the electron density of a molecule.…
This paper explores an iterative coupling approach to solve linear thermo-poroelasticity problems, with its application as a high-fidelity discretization utilizing finite elements during the training of projection-based reduced order…
Achieving tight bounding boxes of a shape while guaranteeing complete boundness is an essential task for efficient geometric operations and unsupervised semantic part detection. But previous methods fail to achieve both full coverage and…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…
This paper presents a new algorithmic framework for computing sparse solutions to large-scale linear discrete ill-posed problems. The approach is motivated by recent perspectives on iteratively reweighted norm schemes, viewed through the…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free…
Phase retrieval aims to recover a signal from intensity-only measurements, a fundamental problem in many fields such as imaging, holography, optical computing, crystallography, and microscopy. Although there are several well-known phase…
This paper presents an efficient gradient projection-based method for structural topological optimization problems characterized by a nonlinear objective function which is minimized over a feasible region defined by bilateral bounds and a…
Tensor completion is the problem of estimating the missing values of high-order data from partially observed entries. Data corruption due to prevailing outliers poses major challenges to traditional tensor completion algorithms, which…
Time-evolving perforated domains arise in many engineering and geoscientific applications, including reactive transport, particle deposition, and structural degradation in porous media. Accurately capturing the macroscopic behavior of such…
Background. All-atom crystallographic refinement of proteins is a laborious manually driven procedure, as a result of which, alternative and multiconformer interpretations are not routinely investigated. Results. We describe efficient loop…
In this work, we develop a novel technique for reconstructing images from projection-based nano- and microtomography. Our contribution focuses on enhancing reconstruction quality, particularly for specimen composed of homogeneous material…
An adaptive refinement strategy, based on an equilibrated flux a posteriori error estimator, is proposed in the context of defeaturing problems. Defeaturing consists of removing features from complex domains to simplify mesh generation and…
In this paper we present a mixed projection- and density-based topology optimization approach. The aim is to combine the benefits of both parametrizations: the explicit geometric representation provides specific controls on certain design…
Accurate detection and segmentation of anatomical structures from ultrasound images are crucial for clinical diagnosis and biometric measurements. Although ultrasound imaging has been widely used with superiorities such as low cost and…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…