Related papers: Crowding induced entropy-enthalpy compensation in …
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here we introduce the crowded…
We have introduced excluded volume effect, which is an important factor to model a realistic pedestrian queue, into queueing theory. The probability distributions of pedestrian number and pedestrian waiting time in a queue have been…
In a recent series of papers, we proposed a mathematical model for the dynamics of a group of interacting pedestrians. The model is based on a non-Newtonian potential, that accounts for the need of pedestrians to keep both their interacting…
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…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
It is well known that equilibrium in a thermodynamic system results from a competition or balance between lowering the energy and increasing the entropy, or at least the product of the temperature and entropy. This is remarkably similar to…
Macromolecular crowding plays a crucial role in modulating protein dynamics in cellular and in vitro environments. Polymeric crowders such as dextran and Ficoll are known to induce entropic forces, including depletion interactions, that…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
The work presented in this paper essentially focuses at providing a scientific theory to explain the growth of information bearing molecules (size and information contents) without the need of any enzymatic system. It infers the footprints…
This chapter focuses on the mathematical modelling of active particles (or agents) in crowded environments. We discuss several microscopic models found in literature and the derivation of the respective macroscopic partial differential…
We present a strategy capable of describing basic features of the dynamics of crowds. The behaviour of the crowd is considered from a twofold perspective. We examine both the large scale behaviour of the crowd, and phenomena happening at…
{\alpha}-synuclein ({\alpha}-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
In intracellular transports, motor proteins transport macromolecules as cargos to desired locations by moving on biopolymers such as microtubules. Recent experiments suggest that cargos that can associate motor proteins during their…
Although the traits emerged in a mass gathering are often non-deliberative, the act of mass impulse may lead to irre- vocable crowd disasters. The two-fold increase of carnage in crowd since the past two decades has spurred significant…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…