Related papers: Crowding-Regulated Binding of Divalent Biomolecule…
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…
Assembly and disassembly dynamics of microtubules (MTs) is tightly controlled by MT associated proteins. Here, we investigate how plus-end-directed depolymerases of the kinesin-8 family regulate MT depolymerization dynamics. Employing an…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
We report a new mechanism for nucleation in a monolayer of hexagonally packed monodisperse droplet arrays. Upon cooling, we observe solidified droplets to nucleate their supercooled neighbors giving rise to an autocatalytic-like mechanism…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
Swarms of large numbers of agents appear in many biological and engineering fields. Dynamic bi-stability of co-existing spatio-temporal patterns has been observed in many models of large population swarms. However, many reduced models for…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical…
The social organization of microorganisms has long been a fascinating and challenging subject in both biology and sociology. In these organisms, the role of the individual is far less dominant than that of the community, which functions as…
Multi-modal crowd counting involves estimating crowd density from both visual and thermal/depth images. This task is challenging due to the significant gap between these distinct modalities. In this paper, we propose a novel approach by…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Understanding the spatio-temporal evolution of epidemics with multiple pathogens requires not only new theoretical models but also careful analysis of their practical consequences. Building on the Multiplex Bi-Virus Reaction-Diffusion…
Ultra-dense crowds, in which physical contact between people cannot be avoided, pose major safety concerns. Nevertheless, the underlying dynamics driving their collective behaviours remain poorly understood. Existing dense crowd models,…
Controlling and understanding phenomena in coupled systems remains a significant challenge across diverse fields. This study investigates a simple globally coupled chemical system that exhibits a range of rich collective dynamics, from…
Unsupervised clustering has broad applications in data stratification, pattern investigation and new discovery beyond existing knowledge. In particular, clustering of bioactive molecules facilitates chemical space mapping,…
Biochemical reactions inside living cells often occur in the presence of crowders -- molecules that do not participate in the reactions but influence the reaction rates through excluded volume effects. However the standard approach to…
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular…
Experiments and theories have shown that when steric interactions between crowding particles and proteins are dominant, which give rise to Asakura-Oosawa depletion forces, then the stabilities of the proteins increase compared to the…