Related papers: Enhancing Cryo-EM Density Map Segmentation in Phen…
Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and graph neural networks…
High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta…
Differentiating signals from the background in micrographs is a critical initial step for cryogenic electron microscopy (cryo-EM), yet it remains laborious due to low signal-to-noise ratio (SNR), the presence of contaminants and densely…
Achieving optimal program performance requires deep insight into the interaction between hardware and software. For software developers without an in-depth background in computer architecture, understanding and fully utilizing modern…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic…
This study presents a novel approach for predicting wall thickness changes in tubes during the nosing process. Specifically, we first provide a thorough analysis of nosing processes and the influencing parameters. We further set-up a Finite…
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically…
Topologically interlocking architectures can generate tough ceramics with attractive thermo-mechanical properties. This concept can make the material design pathway a challenging task, since modeling the whole design space is neither…
Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the…
Process optimization in chemical engineering may be hindered by the limited availability of reliable thermodynamic data for fluid mixtures. Remarkable progress is being made in predicting thermodynamic mixture properties by machine learning…
Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional…
Atomic force microscopy (AFM) is a key tool for characterising nanoscale structures, with functionalised tips now offering detailed images of the atomic structure. In parallel, AFM simulations using the particle probe model provide a…
Electron Cryo-Tomography (ECT) enables 3D visualization of macromolecule structure inside single cells. Macromolecule classification approaches based on convolutional neural networks (CNN) were developed to separate millions of…
Scanning transmission electron microscopy (STEM) is now the primary tool for exploring functional materials on the atomic level. Often, features of interest are highly localized in specific regions in the material, such as ferroelectric…
Phase contrast transmission electron microscopy (TEM) is a powerful tool for imaging the local atomic structure of materials. TEM has been used heavily in studies of defect structures of 2D materials such as monolayer graphene due to its…
We introduce FENNIX (Force-Field-Enhanced Neural Network InteraXions), a hybrid approach between machine-learning and force-fields. We leverage state-of-the-art equivariant neural networks to predict local energy contributions and multiple…
Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep…
An accurate, physically-based, and differentiable model of soft robots can unlock downstream applications in optimal control. The Finite Element Method (FEM) is an expressive approach for modeling highly deformable structures such as…
Accurate prediction of crop states (e.g., phenology stages and cold hardiness) is essential for timely farm management decisions such as irrigation, fertilization, and canopy management to optimize crop yield and quality. While traditional…
The Finite Element Method (FEM) is a powerful modeling tool for predicting soft robots' behavior, but its computation time can limit practical applications. In this paper, a learning-based approach based on condensation of the FEM model is…