生物物理
The response of cell populations to external stimuli plays a central role in biological mechanical processes such as epithelial wound healing and developmental morphogenesis. Wave-like propagation of a signal of ERK MAP kinase has been…
The functional computation of the human brain arises from the collective behaviour of the underlying neural network. The emerging technology enables the recording of population activity in neurons, and the theory of neural networks is…
We use a three-dimensional formulation of the cell vertex model to describe the mechanical properties of a confluent planar monolayer of prismatic cells. Treating cell height as a degree of freedom, we reduce the model to a two-dimensional…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
Organisms use specialized sensors to measure their environments, but the fundamental principles that determine their accuracy remain largely unknown. In Escherichia coli chemotaxis, we previously found that gradient-climbing speed is…
Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
The structure of grey matter has long been a key focus in neuroscience, as cell morphology varies by type and can be affected by neurological conditions. Understanding these variations is essential for studying brain function and disease.…
Among living organisms, there are species that change their patterns on their body surface during their growth process and those that maintain their patterns. Theoretically, it has been shown that large-scale species do not form distinct…
Solid-state nanopores have received substantial attention in the past years owing to their simplicity and potential applications expected in genomics, sensing, archival information storage, and computing. The underlying sensing technique of…
Understanding how biomechanical reorganization governs key biological processes, such as morphogenesis and development, requires predictive insights into stress distributions and cellular behavior. While traditional approaches focused on…
The modulator pocket is a cryptic site discovered in the TREK1 K2P channel that accommodates agonists capable of increasing the channel's activity. Since its discovery, equivalent sites in other K2P channels have been shown to bind various…
Emperor penguins are the only penguin species that winter in Antarctica. As is known, during cold weather, birds huddle together to share body heat. We developed a microscopic model in which penguins interact with each other through an…
There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of biological images. Turning these data…
A short (<150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as…
Small-scale structures on biological surfaces can profoundly impact how animals move, appear, and interact with their environments. Such textures may be especially important for limbless reptiles, such as snakes and legless lizards, because…
In the field of complex systems, self-organization magnifies the compounding effects of element interactions by propagating, modifying, and enhancing functionality, ultimately leading to emergent system properties. The intricacies of…
We present a novel nonlinear state transition model for inositol 1,4,5-trisphosphate receptors (IP$_3$Rs) that incorporates a pre-activated state, as suggested by electron microscopy observations. Our model provides a theoretical framework…
Particle-based simulations are an essential tool for the study of biochemical systems for scales between molecular/Brownian dynamics and the reaction-diffusion master equation. These simulations utilise proximity-based reaction conditions…
Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized,…
Characterizing the morpho-mechanical properties of red blood cells (RBCs) is crucial for understanding microvascular transport mechanisms and cellular pathophysiological processes, yet current computational models are constrained by…