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Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
The polarisation of cells and tissues is fundamental for tissue morphogenesis during biological development and regeneration. A deeper understanding of biological polarity pattern formation can be gained from the consideration of pattern…
In this work, we present a multiscale kinetic framework for consensus-based image segmentation. By interpreting an image as a system of interacting particles, each pixel is characterised by its spatial position and an internal feature…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
From tumour invasion to cell sorting and animal territoriality, many biological systems rely on nonlocal interactions that drive complex spatial organisation. Partial differential equations (PDEs) with nonlocal advection are increasingly…
Cellular patterns formed by self-organization of dislocations are a most conspicuous feature of dislocation microstructure evolution during plastic deformation. To elucidate the physical mechanisms underlying dislocation cell structure…
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…
Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on…
Pollen grains are known for their impressive variety of species-specific, microscale surface patterning. Despite having similar biological developmental steps, pollen grain surface features are remarkably geometrically varied. Previous work…
The Min proteins from Escherichia coli can self-organize into traveling waves on supported lipid bilayers. In Proc. Natl. Acad. Sci. USA 109, 15283 (2012) we showed that these waves are guided along the boundaries of membrane patches. We…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
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…
Point patterns are characterized by their density and correlation. While spatial variation of density is well-understood, analysis and synthesis of spatially-varying correlation is an open challenge. No tools are available to intuitively…
The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
The lateral diffusion and trapping of protein receptors within the postsynaptic membrane of a neuron plays a key role in determining the strength of synaptic connections and their regulation during learning and memory. In this paper we…