相关论文: On morphological and functional complexity of prot…

One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear…

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…

Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational…

We use numerical simulations to study the crystallization of monodisperse systems of hard aspherical particles. We find that particle shape and crystallizability can be easily related to each other when particles are characterized in terms…

Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…

This work presents the implementation of a fragment-based, quantum-centric supercomputing workflow for computing molecular electronic structure using quantum hardware. The workflow is applied to predict the relative energies of two…

This is a summary of mathematical tools we used in research of analyzing the structure of proteins with amyloid form \cite{xi2024Top}. We defined several geometry indicators on the discrete curve namely the hop distance, the discrete…

The problem of inferring proteins from complex peptide cocktails (digestion products of biological samples) in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing…

AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are…

This paper examines the modulation of proteinoid spiking frequency in response to light. Proteinoids are proteins formed through thermal condensation of amino acids and have been found to exhibit spiking behaviour in response to various…

Layered "mosaic" metal-halide perovskite materials display a wide-variety of microstructures that span the order-disorder spectrum and can be tuned via the composition of their constituent B-site octahedral species. Such materials are…

Particulate composites underpin many solid-state chemical and electrochemical systems, where microstructural features such as multiphase boundaries and inter-particle connections strongly influence system performance. Advances in X-ray…

Kinematics of mechanisms is intricately coupled to their geometry and their utility often arises out of the ability to perform reproducible motion with fewer actuating degrees of freedom. In this article, we explore the assembly of…

Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have…

Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…

Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires…

Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…

Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…

We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…

Microscopy and particle-based simulations are both powerful techniques to study aggregated particulate matter such as colloidal gels. The data provided by these techniques often contains information on a wide array of length scales, but…