Related papers: Modal Geometry Governs Proteoform Dynamics
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Grain boundary (GB) migration governs microstructure evolution and can mediate plastic deformation through sliding or shear coupling. Numerous experimental and numerical studies have reported a wide range of behaviors associated with…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…
Since protein mutations are the main driving force of evolution at the molecular level, a proper analysis of them (and the factors controlling them) will enable us to find a response to several crucial queries in evolutionary biology. Among…
Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs.…
Locomotion is essential for living cells. It enables bacteria and algae to explore space for food, cancer to spread, and immune system to fight infections. Motile cells display trajectories of intriguing complexity, from regular (e.g.…
The interplay between the diffusion-controlled dynamics of a solidification front and the trajectory of a grain boundary groove at the solid-liquid interface is studied by means of thin-sample directional solidification experiments of a…
Recent experimental investigations into Hydra regeneration revealed a remarkable phenomenon: the morphological transformation of a tissue fragment from the incipient spherical configuration to a tube-like structure - the hallmark of a…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
Proteins are the most important biomolecules for living organisms. The understanding of protein structure, function, dynamics and transport is one of most challenging tasks in biological science. In the present work, persistent homology is,…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
Extending our previous work on 2D growth for the Laplace equation we study here {\it multidimensional} growth for {\it arbitrary elliptic} equations, describing inhomogeneous and anisotropic pattern formations processes. We find that these…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
A simple geometrical model is presented for the gravity-driven motion of a single particle on a rough inclined surface. Adopting a simple restitution law for the collisions between the particle and the surface, we arrive at a model in which…
Invasion fronts in ecology are well studied but very few mathematical results concern the case with variable motility (possibly due to mutations). Based on an apparently simple reaction-diffusion equation, we explain the observed phenomena…
Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single…
Plant morphogenesis relies on dynamic growth deformations at the cell and tissue scales driven by osmotic fluxes. A mechanistic understanding of this phenomenon demands a physical framework that integrates cell imbibition, tissue mechanics,…