Related papers: Crowding-Regulated Binding of Divalent Biomolecule…
Diffusive transport of small molecules within the internal structures of biological and synthetic material systems is complex because the crowded environment presents chemical and physical barriers to mobility. We explored this mobility…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
Visual clutter affects our ability to see: objects that would be identifiable on their own, may become unrecognizable when presented close together ("crowding") -- but the psychophysical characteristics of crowding have resisted…
Macromolecules occupy between 34 and 44% of the cell cytoplasm, about half the maximum pack- ing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental…
We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random…
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…
Depletion-induced interactions between colloids in colloid-polymer mixtures depend in range and strength on size, shape, and concentration of depletants. Crowding by colloids in turn affects shapes of polymer coils, such as biopolymers in…
Using molecular dynamics simulations, we investigate the aggregation behavior of neutral stiff (rod-like) and flexible polymer chains mediated by attractive crowders. Attractive crowders serve as bridging agents, inducing aggregation…
Molecules with an excess number of hydrogen-bonding partners play a crucial role in fundamental chemical processes, ranging from the anomalous diffusion in supercooled water to the transport of aqueous proton defects and the ordering of…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
In this paper a new multiscale modeling technique is proposed. It relies on a recently introduced measure-theoretic approach, which allows to manage the microscopic and the macroscopic scale under a unique framework. In the resulting…
This paper is devoted to the important yet unexplored subject of crowding effects on market impact, that we call "co-impact". Our analysis is based on a large database of metaorders by institutional investors in the U.S. equity market. We…
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a…
As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as in…
Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor…
Social and economic networks are often multiplexed, meaning that people are connected by different types of relationships -- such as borrowing goods and giving advice. We make two contributions to the study of multiplexing and the…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or…
Crowdedness caused by overlapping among similar objects is a ubiquitous challenge in the field of 2D visual object detection. In this paper, we first underline two main effects of the crowdedness issue: 1) IoU-confidence correlation…
We study a two-species bidirectional exclusion process, and a single species variant, which is motivated by the motion of organelles and vesicles along microtubules. Specifically, we are interested in the clustering of the particles and…
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics…