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An accurate and efficient characterization of the polyelectrolyte properties for cytoskeleton filaments are key to the molecular understanding of electrical signal propagation, bundle and network formation, as well as other relevant…
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling near-atomic-level visualization of biomolecular assemblies. However, the exponential growth in cryo-EM data throughput and complexity, coupled with diverse…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Improvements in experimental and computational technologies have led to significant increases in data available for analysis. Topological data analysis (TDA) is an emerging area of mathematical research that can identify structures in these…
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…
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…
Cryo-electron microscopy (cryo-EM) is an emerging experimental method to characterize the structure of large biomolecular assemblies. Single particle cryo-EM records 2D images (so-called micrographs) of projections of the three-dimensional…
Cell shape changes, essential for processes such as motility or division, are controlled by the actomyosin cortex that actively remodels biological membranes. Their mechanisms can be deciphered in___vitro using biomimetic reconstituted…
Accurate segmentation of critical anatomical structures is at the core of medical image analysis. The main bottleneck lies in gathering the requisite expert-labeled image annotations in a scalable manner. Methods that permit to produce…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
The growth of actin filament networks is a fundamental biological process that drives a variety of cellular and intracellular motions. During motility, eukaryotic cells and intracellular pathogens are propelled by actin networks organized…
The three-dimensional shape and conformation of small-molecule ligands are critical for biomolecular recognition, yet encoding 3D geometry has not improved ligand-based virtual screening approaches. We describe an end-to-end deep learning…
Cryogenic electron microscopy (Cryo-EM) has become an essential tool for capturing high-resolution biological structures. Despite its advantage in visualizations, the large storage size of Cryo-EM data file poses significant challenges for…
The actin and microtubule cytoskeletons are vital structures for cell growth and development across all species. While individual molecular mechanisms underpinning actin and microtubule dynamics have been intensively studied, principles…
We examine the mechanism of bundling of cytoskeletal actin filaments by two representative bundling proteins, fascin and espin. Small-angle X-ray studies show that increased binding from linkers drives a systematic \textit{overtwist} of…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
Semantic segmentation is a crucial task in biomedical image processing, which recent breakthroughs in deep learning have allowed to improve. However, deep learning methods in general are not yet widely used in practice since they require…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
Subcellular protein complexes and organelles exhibit diverse dynamic behaviors that reflect the mechanical constraints and organization of the intracellular environment. Although some structures follow classical Brownian motion, many…
The cytoskeleton is a model active matter system that controls diverse cellular processes from division to motility. While both active actomyosin dynamics and actin-microtubule interactions are key to the cytoskeleton's versatility and…