Related papers: The macroscopic effects of microscopic heterogenei…
Simplified representations of macromolecules help in rationalising and understanding the outcome of atomistic simulations, and serve to the construction of effective, coarse-grained models. The number and distribution of coarse-grained…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
Many complex systems are representable as macroscopic set of elements which interact by simple rules. The complex macroscopically relevant phenomena are then the result of the generic emergence of a space-time multi-scale dynamics. Critical…
This article concerns a systemic manifestation of small scale interfacial heterogeneities in large scale quantities of interest to a variety of diverse applications spanning the earth, biological and ecological sciences. Beginning with…
The typical temporal resolution used in modern simulations significantly exceeds characteristic time scales at which the system is driven. This is especially so when systems are simulated over time-scales that are much longer than the…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
Because of the potentially large number of important applications of nonlinear optics, researchers have expended a great deal of effort to optimize the second-order molecular nonlinear-optical response, called the hyperpolarizability. The…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to…
We discuss a simple model of particles hopping in one dimension with attractive interactions. Taking a hydrodynamic limit in which the interaction strength increases with the system size, we observe the formation of multiple clusters of…
We discuss the far-field spatio-temporal cross-correlations of waves multiple-scattered in a turbid medium in which is embedded a hidden heterogeneous region (inclusion) characterized by a distinct scatterer dynamics (as compared to the…
Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has…
We study the influence of cell-level mechanical heterogeneity in epithelial tissues using a vertex-based model. Heterogeneity in single cell stiffness is introduced as a quenched random variable in the preferred shape index($p_0$) for each…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
We develop a mesoscopic modeling framework for diffusion in a crowded environment, particularly targeting applications in the modeling of living cells. Through homogenization techniques we effectively coarse-grain a detailed microscopic…
The collective motion of interacting self-driven particles describes many types of coordinated dynamics and self-organisation. Prominent examples are alignment or lane formation which can be observed alongside other ordered structures and…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…