Related papers: Hierarchic Theory of Complex Systems (biosystems, …
Self-organization is ubiquitous in nature and mind. However, machine learning and theories of cognition still barely touch the subject. The hurdle is that general patterns are difficult to define in terms of dynamical equations and…
Classic approaches to General Systems Theory often adopt an individual perspective and a limited number of systemic classes. As a result, those classes include a wide number and variety of systems that result equivalent to each other. This…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Unravelling the physical mechanisms behind the organisation of lipid domains is a central goal in cell biology and membrane biophysics. Previous studies on cells and model lipid bilayers featuring phase-separated domains found an intricate…
We study the problem of how a ``living'' system complex in structure can respond perfectly to local changes in the environment. Such a system is assumed to consist of a distributed ``living'' medium and a hierarchical ``supplying'' network…
In this paper, we develop a multiscale hierarchy framework for objective molecular dynamics (OMD), a reduced order molecular dynamics with a certain symmetry, that connects it to the statistical kinetic equation, and the macroscopic…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…
Colloids are abundant in nature, science and technology, with examples ranging from milk to quantum dots and the "colloidal atom" paradigm. Similarly, liquid crystal ordering is important in contexts ranging from biological membranes to…
Battiston et al. (arXiv:2110.06023) provide a comprehensive overview of how investigations of complex systems should take into account interactions between more than two elements, which can be modelled by hypergraphs and studied via…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The question how complex systems become more organized and efficient with time is open. Examples are, the formation of elementary particles from pure energy, the formation of atoms from particles, the formation of stars and galaxies, the…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
Although it is now understood that chaos in complex classical systems is the foundation of thermodynamic behavior, the detailed relations between the microscopic properties of the chaotic dynamics and the macroscopic thermodynamic…
Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical…
Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically-driven nonequilibrium…
Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA.…
In this paper we explore the mathematical structure of hierarchical organization in smooth dynamical systems. We start by making precise what we mean by a level in a hierarchy, and how the higher le vels need to respect the dynamics on the…
We study a model of a lipid bilayer membrane described by two order parameters: the chemical composition described using the Gaussian model and the spatial configuration described with the elastic deformation model of a membrane with a…