相关论文: 3D pattern formation of a protein-membrane suspens…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
Throughout developmental biology and ecology, transport can be driven by nonlocal interactions. Examples include cells that migrate based on contact with pseudopodia extended from other cells, and animals that move based on their vision of…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…
Micropatterning techniques have become an important tool for the study of cell behavior in controlled microenvironments. As a consequence, several approaches for the creation of micropatterns have been developed in recent years. However,…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
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…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Dynamic patterning of specific proteins is essential for the spatiotemporal regulation of many important intracellular processes in procaryotes, eucaryotes, and multicellular organisms. The emergence of patterns generated by interactions of…
Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…
We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability that extends down to zero wavevector, connecting at…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
Proteins can form droplets via liquid-liquid phase separation (LLPS) in cells. Recent experiments demonstrate that LLPS is qualitatively different on two-dimensional (2d) surfaces compared to three-dimensional (3d) solutions. In this paper,…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
We introduce a three-dimensional stochastic reaction-diffusion model to describe MinD/MinE dynamical structures in Escherichia coli. This model spontaneously generates pole-to-pole oscillations of the membrane-associated MinD proteins, MinE…
Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently,…