Related papers: Geometry-controlled kinetics
Many chemical reactions can be formulated in terms of particle diffusion in a complex energy landscape. Transition path theory (TPT) is a theoretical framework for describing the direct (reaction) pathways from reactant to product states…
Intracellular protein patterns regulate a variety of vital cellular processes such as cell division and motility, which often involve dynamic changes of cell shape. These changes in cell shape may in turn affect the dynamics of…
In biochemical reaction networks, the first passage time (FPT) of a reaction quantifies the time it takes for the reaction to first occur, from the initial state. While the mean FPT historically served as a summary metric, a far more…
For two molecules to react they first have to meet. Yet, reaction times are rarely on par with the first-passage times that govern such molecular encounters. A prime reason for this discrepancy is stochastic transitions between reactive and…
We consider a random walk in confined geometry, starting from a site and eventually reaching a target site. We calculate analytically the distribution of the occupation time on a third site, before reaching the target site. The obtained…
Evolution and geometry generate complexity in similar ways. Evolution drives natural selection while geometry may capture the logic of this selection and express it visually, in terms of specific generic properties representing some kind of…
Time delays, modelling the process of intracellular gene expression, have been shown to have important impacts on the dynamics of pattern formation in reaction-diffusion systems. In particular, past work has shown that such time delays can…
We explore the influence of geometry in the critical behavior of sparse long-range spin models. We examine a model with interactions that can be continuously tuned to induce distinct changes in the metric, topology, and dimensionality of…
The notion that the geometry of our space-time is not only a static background but can be physically dynamic is well established in general relativity. Geometry can be described as shaped by the presence of matter, where such shaping…
First passage phenomena arise across physics, biology, and finance when stochastic processes first reach a threshold, triggering downstream events. Examples include the irreversible exit from a domain, a biochemical reaction, a financial…
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation and filtration processes.…
Complex networks are characterized by latent geometries induced by their topology or by the dynamics on the top of them. In the latter case, different network-driven processes induce distinct geometric features that can be captured by…
Geometry can fundamentally govern the propagation of light, independent of material constraints. Here, we demonstrate that a fractal phase space, endowed with a non-Euclidean, scale-dependent geometry, can intrinsically induce resonance…
In this work we consider a class of recursively-grown fractal networks $G_n(t)$, whose topology is controlled by two integer parameters $t$ and $n$. We first analyse the structural properties of $G_n(t)$ (including fractal dimension,…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
We analyze the diffusive transport of Brownian particles in narrow channels with periodically varying cross-section. The geometrical confinements lead to entropic barriers, the particle has to overcome in order to proceed in transport…
Polymer translocation across a corrugated channel is a paradigmatic stochastic process encountered in diverse systems. The instance of time when a polymer first arrives to some prescribed location defines an important characteristic time…
Quantum walks are accepted as a generic model for quantum transport. The character of the transport crucially depends on the properties of the walk like its geometry and the driving coin. We demonstrate that increasing transport distance…
While controlling particle diffusion in a confined geometry is a popular approach taken by both natural and artificial systems, it has not been widely adopted for controlling light transport in random media, where wave interference effects…
As phenomena that necessarily emerge from the collective behavior of interacting particles, phase transitions continue to be difficult to predict using statistical thermodynamics. A recent proposal called the topological hypothesis suggests…