Related papers: Relaxing the aquaporin crystal structure in a memb…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
Recent advances in materials discovery have been driven by structure-based models, particularly those using crystal graphs. While effective for computational datasets, these models are impractical for real-world applications where atomic…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
Biological membranes are self-assembled complex fluid interfaces that host proteins, molecular motors and other macromolecules essential for cellular function. These membranes have a distinct in-plane fluid response with a surface viscosity…
Molecular and polymeric crystals show a wide range of functional properties that arise from the interplay between the atomic-scale structure of their constituent molecules and the organization of these molecules within the crystal lattice…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
Machine learning can reveal new insights into X-ray spectroscopy of liquids when the local atomistic environment is presented to the model in a suitable way. Many unique structural descriptor families have been developed for this purpose.…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Vibrational spectroscopy is key for probing the interplay between the structure and dynamics of aqueous systems. In order to map different regions of experimental spectra to the microscopic structure of a system, it is important to combine…
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…
Glass forming liquids exhibit structural relaxation behaviors, reflecting underlying atomic rearrangements on a wide range of timescales. These behaviors play a crucial role in determining many material properties. However, the relaxation…
Proteins are central to biological systems, participating as building blocks across all forms of life. Despite advancements in understanding protein functions through protein sequence analysis, there remains potential for further…
The strong spatial confinement of a nanocavity plasmonic field has made it possible to visualize the inner structure of a single molecule and even to distinguish its vibrational modes in real space. With such ever-improved spatial…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
Vibrational properties of molecular crystals are constantly used as structural fingerprints, in order to identify both the chemical nature and the structural arrangement of molecules. The simulation of these properties is typically very…
Generative AI models, such as score-based diffusion models, have recently advanced the field of computational materials science by enabling the generation of new materials with desired properties. In addition, these models could also be…
Our current understanding of the structure and dynamics of aqueous interfaces at the molecular level has grown substantially in the last few decades due to the continuous development of surface-specific spectroscopies, such as vibrational…
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are…
Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…