Related papers: Geometric phase shifts in biological oscillators
We study the general-setting quantum geometric phase acquired by a particle in a vibrating cavity. Solving the two-level theory with the rotating-wave approximation and the SU(2) method, we obtain analytic formulae that give excellent…
Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…
A number of biological rhythms originate from networks comprised of multiple cellular oscillators. But analytical results are still lacking on the collective oscillation period of inter-coupled gene regulatory oscillators, which, as has…
Geometric phase has historically been defined using closed cycles of polarization states, often derived using differential geometry on the Poincare sphere. Using the recently-developed wave model of geometric phase, we show that it is…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
The importance of molecular-scale forces in sculpting biological form and function has been acknowledged for more than a century. Accounting for forces in biology is a problem that lies at the intersection of soft condensed matter physics,…
Superconducting circuits reveal themselves as promising physical devices with multiple uses. Within those uses, the fundamental concept of the geometric phase accumulated by the state of a system shows up recurrently, as, for example, in…
The temporal behaviour of segmentation clock oscillations show phase synchrony via mean field like coupling of delta protein restricting to nearest neighbours only, in a configuration of cells arranged in a regular three dimensional array.…
It is demonstrated by analyzing real examples that phase transitions in layered crystals occur like all other solid-state phase transitions by nucleation and crystal growth, but have a specific morphology. There the nucleation is epitaxial,…
Oscillator models are central to the study of system properties such as entrainment or synchronization. Due to their nonlinear nature, few system-theoretic tools exist to analyze those models. The paper develops a sensitivity analysis for…
A wave function picks up, in addition to the dynamic phase, the geometric (Berry) phase when traversing adiabatically a closed cycle in parameter space. We develop a general multidimensional theory of the geometric phase for (double) cycles…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
A relation between geometric phases and criticality of spin chains is established. As a result, we show how geometric phases can be exploited as a tool to detect regions of criticality without having to undergo a quantum phase transition.…
We calculate the geometric phase associated to the evolution of a system subjected to decoherence through a quantum-jump approach. The method is general and can be applied to many different physical systems. As examples, two main source of…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Distinct from the dynamical phase, in a cyclic evolution, a system's state may acquire an additional component, a.k.a. geometric phase. The latter is a manifestation of a closed path in state space. Geometric phases underlie various…
In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…
As an injury heals, an embryo develops, or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively, whereas variation of shape from cell-to-cell is dismissed most…
The dynamics of phase transitions plays a crucial r\^ole in the so-called interface between high energy particle physics and cosmology. Many of the interesting results generated during the last fifteen years or so rely on simplified…