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Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
Nanoparticle surface structural dynamics is believed to play a significant role in regulating functionalities such as diffusion, reactivity, and catalysis but the atomic-level processes are not well understood. Atomic resolution…
We presented a new 3D refinement method for Cryo-EM single particle analysis which can improve the resolution of final electron density map in this paper. We proposed to enforce both sparsity and smoothness to improve the regularity of…
We target the problem of estimating the center of mass of noisy 2-D images. We assume that the noise dominates the image, and thus many standard approaches are vulnerable to estimation errors. Our approach uses a surrogate function to the…
Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of bio-molecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle…
Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying…
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated by the knowledge of their structures, thermodynamics and dynamics. All this information can be provided in an effective manner in terms of…
The focus of this viewpoint is to identify, in the era of atomistic resolution cryo-electron microscopy data, the areas in which computational modelling and molecular simulations will bring valuable contributions to structural biologists…
Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and…
Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Cryogenic electron microscopy (cryo-EM) provides images from different copies of the same biomolecule in arbitrary orientations. Here, we present an end-to-end unsupervised approach that learns individual particle orientations from cryo-EM…
The goal of cryo-electron microscopy (EM) is to reconstruct the 3-dimensional structure of a molecule from a collection of its 2-dimensional projected images. In this article, we show that the basic premise of cryo-EM --- patching together…
Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
Understanding the causal effects of organ-specific features from medical imaging on clinical outcomes is essential for biomedical research and patient care. We propose a novel Functional Linear Structural Equation Model (FLSEM) to capture…
Knowledge of the molecular structure is key to understanding the function of participating molecules in photo-induced chemical reactions. Visualizing the nuclear dynamics of a photochemical reaction requires an ultrafast measurement…
Single molecule X-ray scattering experiments with free electron lasers have opened a new route to the structure determination of biomolecules. Because typically only very few photons per scattering image are recorded and thus the…
Cryo-electron microscopy (cryo-EM) is an indispensable technique for determining the 3D structures of dynamic biomolecular complexes. While typically applied to image a single molecular species, cryo-EM has the potential for structure…
Neutron reflectometry is a critical tool for investigating the structure of thin films and interfaces. However, the misapplication of the Born approximation to reflection geometry leads some to assume that the minimum thickness that may be…