Related papers: Self-organization principles of intracellular patt…
Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction…
Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…
We study a class of branching processes in which the offspring distribution is not specified directly but is induced by a cycle of internal colony growth, catastrophic reduction and structured dispersal. The parameters governing growth,…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described…
We have studied experimentally transport properties in a slowly driven granular system which recently was shown to display self-organized criticality [Frette {\em et al., Nature} {\bf 379}, 49 (1996)]. Tracer particles were added to a pile…
In this work we approach cell migration under a large-scale assumption, so that the system reduces to a particle in motion. Unlike classical particle models, the cell displacement results from its internal activity: the cell velocity is a…
A thermodynamically motivated neural network model is described that self-organizes to transport charge associated with internal and external potentials while in contact with a thermal reservoir. The model integrates techniques for rapid,…
Diffusion plays an important role in a wide variety of phenomena, from bacterial quorum sensing to the dynamics of traffic flow. While it generally tends to level out gradients and inhomogeneities, diffusion has nonetheless been shown to…
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…
In recent years, numerous studies have focused on the mathematical modeling of social dynamics, with self-organization, i.e., the autonomous pattern formation, as the main driving concept. Usually, first or second order models are employed…
In this chapter of the e-book "Self-Organized Criticality Systems" we summarize some theoretical approaches to self-organized criticality (SOC) phenomena that involve percolation as an essential key ingredient. Scaling arguments, random…
Living systems are thermodynamically open but closed in their organization. In other words, even though their material components turn over constantly, a material-independent property persists, which we call organization. Moreover,…
The origin of cellular life can be described in terms of the transition from inorganic matter: solids, liquids and gases, to the emergence of cooperative assemblies of organic matter, DNA and proteins,capable of replication and metabolism.…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
The open nonlinear electrodynamic system - nonlinear transverse non-homogeneous dielectric layer, is an example of inorganic system having the properties of self-organization, peculiar to biological systems. The necessary precondition of…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
Packing of particles in confined environments is a common problem in multiple fields. Here, based on the two-dimensional Hertzian particle model, we study the packing of deformable spherical particles under compression, and reveal the…
Measures of complexity and entropy have not converged to a single quantitative description of levels of organization of complex systems. The need for such a measure is increasingly necessary in all disciplines studying complex systems. To…
This paper is concerned with mathematical modeling of intelligent systems, such as human crowds and animal groups. In particular, the focus is on the emergence of different self-organized patterns from non-locality and anisotropy of the…