Presentation materials
The nucleation and growth theory, described by the Avrami equation (also called Johnson–Mehl–Avrami–Kolmogorov equation), and usually used to describe crystallization and nucleation processes in condensed matter physics, was applied to cancer physics as Avrami-Dobrzyński Model. This approach assumes the transforming system as a DNA chain including many oncogenic mutations. Finally, the...
The Thermodynamic Uncertainty Relation (TUR) establishes a fundamental trade-off between the cost of driving a system and the precision of its output. While TUR has been proven for discrete systems and overdamped Brownian motion, TUR violations for more general dynamics have been recently demonstrated using elaborate models based on underdamped dynamics. In our study, we present simple models...
Surfactant molecules, above a critical concentration in solution, are able to spontaneously self-assemble to form aggregates. One of these aggregates are micelles, which are used in many field of sciences and industry. In an aqueous environment, due to the amphiphilic nature of the surfactants, the micelles in the core have a hydrophobic part. Micelles comes into contact with the aqueous...
Correlation matrix estimation from functional magnetic resonance (fMRI) data presents a major challenge for a multitude of reasons, including non-stationarity of the signal and low temporal resolution, resulting in the number of variables (locations from which the signal is sampled) exceeding the number of time points. The Pearson correlation matrix is most commonly used, but likely...
Almost universally, individual agents in collectives of active particles require time to examine their surroundings and form an appropriate response. Examples of when perception and actuation delays significantly affect system dynamics can be found in living organisms, robotic collectives, communication networks, and cellular processes like biopolymer assembly and migration. Still,...
We consider an open (Brownian) classical harmonic oscillator in contact with a non-Markovian thermal bath and described by a generalized Langevin equation. When the bath's spectrum has a finite upper cutoff frequency, the oscillator may have ergodic and nonergodic configurations. In ergodic configurations (when exist, they correspond to lower oscillator frequencies) the oscillator...
According to the well-known biophysical Single Hit Target Model, DNA chain damage, caused for instance by ionizing radiation, is purely random in nature. This presentation demonstrates that such radiation-induced DNA damage is associated with an increase in system entropy, which is characteristic of purely stochastic processes. However, it turns out that not all changes in the DNA region...
We present a new set of Turing patterns based on the superposition of multiple waves. Turing patterns are well known solutions to a set of reaction-diffusion equations. Such patterns have been studied in the context of embryo development, chemical reactions, nonlinear optics, ecology and random walks, to name a few. The main feature of systems giving rise to Turing patterns is that a stable...
Escape kinetics of a stochastic process can be influenced by imposing stochastic resetting, a protocol of starting anew. We study the escape kinetics from a finite interval restricted by two absorbing boundaries in the presence of heavy-tailed, Lévy type, $\alpha$-stable noise. We find that the width of the domain where resetting is beneficial depends on the value of the stability index...
The phase of tissue and its transitions are critical phenomena during development. The Active Vertex Model is a well-known approach for studying tissue mechanical properties. In this model, the tissue is represented as a collection of polygonal cells, with forces applied to the vertices, leading to cell dynamics and rearrangement. This model includes passive forces representing the competition...
We studied equilibrium systems composed of wedge-shaped monodisperse molecules using hard-particle Monte Carlo simulations. Each model molecule was made up of six colinear tangent spheres with linearly decreasing diameters. Thus, the shape was unequivocally described by a single parameter $d$: the ratio of the smallest and largest diameters of the spheres. The phases of the systems were...
