Related papers: Molecular-scale, nonlinear actomyosin binding dyna…
The actin cortex is a thin layer of actin, myosin, and actin binding proteins that underlies the membrane of most animal cells. It is highly dynamic and can undergo remodelling on time-scales of tens of seconds thanks to protein turnover…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Myosin II is the muscle molecular motor that works in two bipolar arrays in each thick filament of the striated (skeletal and cardiac) muscle, converting the chemical energy into steady force and shortening by cyclic ATP--driven…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
We present a model of active particles interacting through a dynamic, heterogeneous environment, leading to emergent collective behaviors without direct agent-to-agent communication. Expanding the resource-dependent framework introduced in…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
Feedback loops between population dynamics of individuals and their ecological environment are ubiquitously found in nature, and have shown profound effects on the resulting eco-evolutionary dynamics. Incorporating linear environmental…
The cytoskeleton -- a composite network of biopolymers, molecular motors, and associated binding proteins -- is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous…
Active force generation by actin-myosin cortex coupled to the cell membrane allows the cell to deform, respond to the environment, and mediate cell motility and division. Several membrane-bound activator proteins move along it and couple to…
We show that autocatalytic networks of epsilon-machines and their population dynamics differ substantially between spatial (geographically distributed) and nonspatial (panmixia) populations. Generally, regions of spacetime-invariant…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
We study the evolutionary dynamics of a phenotypically structured population in a changing environment , where the environmental conditions vary with a linear trend but in an oscillatory manner. Such phenomena can be described by parabolic…
On large scales a nonlinear transformation of matter density field can be viewed as a biased tracer of the density field itself. A nonlinear transformation also modifies the redshift space distortions in the same limit, giving rise to a…
Material renewability in active living systems, such as in cells and tissues, can drive the large-scale patterning of forces, with distinctive phenotypic consequences. This is especially significant in the cell cytoskeleton, where multiple…
We classify and predict the asymptotic dynamics of a class of swarming models. The model consists of a conservation equation in one dimension describing the movement of a population density field. The velocity is found by convolving the…
The runtime of evolutionary algorithms (EAs) depends critically on their parameter settings, which are often problem-specific. Automated schemes for parameter tuning have been developed to alleviate the high costs of manual parameter…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
Highly nonlinear behavior of a system of discrete sites on a lattice is observed when a specific feedback loop is introduced into models employing coupled map lattices, quantum cellular automata, or the real-valued analogues of the latter.…
A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the…