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Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
We present an efficient implementation of the Density Matrix Renormalization Group (DMRG) algorithm that includes an optimal ordering of the proton and neutron orbitals and an efficient expansion of the active space utilizing various…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
Comprehensive assessment of the various aspects of the brain's microstructure requires the use of complementary imaging techniques. This includes measuring the spatial distribution of cell bodies (cytoarchitecture) and nerve fibers…
Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, distribution, and efficacy of the vaccine. Previous work…
Magnetic resonance imaging (MRI) is a non-invasive medical imaging technique offering high-resolution 3D images and valuable insights into human tissue conditions. Even at present, the refinement of denoising methods for MRI remains a…
Despite the growing accessibility of skeletal motion data, integrating it for animating character meshes remains challenging due to diverse configurations of both skeletons and meshes. Specifically, the body scale and bone lengths of the…
Hyperspectral neutron tomography is an effective method for analyzing crystalline material samples with complex compositions in a non-destructive manner. Since the counts in the hyperspectral neutron radiographs directly depend on the…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
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…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good…
Vision foundation models (VFMs) are pre-trained on extensive image datasets to learn general representations for diverse types of data. These models can subsequently be fine-tuned for specific downstream tasks, significantly boosting…
The mRNA optimization is critical for therapeutic and biotechnological applications, since sequence features directly govern protein expression levels and efficacy. However, current methods face significant challenges in simultaneously…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
Extensively exploring protein conformational landscapes remains a major challenge in computational biology due to the high computational cost involved in dynamic physics-based simulations. In this work, we propose a novel pipeline, MoDyGAN,…
Atom probe tomography (APT) is a 3D analysis technique that offers unique chemical accuracy and sensitivity with sub-nanometer spatial resolution. Recently, there is an increasing interest in the application of APT to complex oxides…
Background and Objective: To assess the feasibility and accuracy of reconstructing time-resolved, three-dimensional, subject-specific aortic geometries from a limited number of standard cine 2D magnetic resonance imaging (MRI) acquisitions.…
Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum…