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Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron…
Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together…
Accurate segmentation of medical images is essential for diagnosis and treatment of diseases. These problems are solved by highly complex models, such as deep networks (DN), requiring a large amount of labeled data for training. Thereby,…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
High-fidelity electron microscopy simulations required for quantitative crystal structure refinements face a fundamental challenge: while physical interactions are well-described theoretically, real-world experimental effects are…
Electrospray ion beam deposition (ESIBD) is the intact, chemically selective deposition of molecular ions on surfaces in vacuum. Here, we present a general method and dedicated instrumentation for ESIBD-based cryoEM sample preparation of…
After AlphaFold won the Nobel Prize, protein prediction with deep learning once again became a hot topic. We comprehensively explore advanced deep learning methods applied to protein structure prediction and design. It begins by examining…
Electron microscopy (EM) imaging offers unparalleled resolution for analyzing neural tissues, crucial for uncovering the intricacies of synaptic connections and neural processes fundamental to understanding behavioral mechanisms. Recently,…
Different tasks in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM) require enhancing the quality of the highly noisy raw images. To this end, we develop an efficient algorithm for signal enhancement of…
Fourier Ptychographic Microscopy (FPM) is a computational imaging method that is able to super-resolve features beyond the diffraction-limit set by the objective lens of a traditional microscope. This is accomplished by using synthetic…
Atomic force microscopy (AFM) is one of the most promising methods for investigating the structure of materials at the micro and nanoscale levels, as well as their local physical-mechanical properties. The experimental data obtained with…
Cryo-electron microscopy (cryo-EM) is a widely used technique for recovering the 3-D structure of biological molecules from a large number of experimentally generated noisy 2-D tomographic projection images of the 3-D structure, taken from…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Cellular processes are governed by macromolecular complexes inside the cell. Study of the native structures of macromolecular complexes has been extremely difficult due to lack of data. With recent breakthroughs in Cellular electron cryo…
Automated fiber placement (AFP) is an advanced manufacturing technology that increases the rate of production of composite materials. At the same time, the need for adaptable and fast inline control methods of such parts raises. Existing…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Laser flash melting and revitrification experiments have recently improved the time resolution of cryo-electron microscopy (cryo-EM) to the microsecond timescale, making it fast enough to observe many of the protein motions that are…
Cryo-electron microscopy (cryoEM) is an increasingly popular method for protein structure determination. However, identifying a sufficient number of particles for analysis (often >100,000) can take months of manual effort. Current…
Host-guest interactions govern the chemistry of a broad range of functional materials. However, the weak bonding between host and guest prevents atomic-resolution studies of their structure and chemistry using transmission electron…