Related papers: Hierarchic Theory of Complex Systems (biosystems, …
Complex systems of systems (SoS) are characterized by multiple interconnected subsystems. Typically, each subsystem is designed and analyzed using methodologies and formalisms that are specific to the particular subsystem model of…
We formulate a hydrodynamic theory of confluent epithelia: i.e. monolayers of epithelial cells adhering to each other without gaps. Taking advantage of recent progresses toward establishing a general hydrodynamic theory of p-atic liquid…
Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…
Real-world knowledge is often organized as hierarchies such as product taxonomies, medical ontologies, and label trees, yet learning hierarchical representations is challenging due to asymmetric structure and noisy semantics. We introduce…
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh,…
We consider the number of configurations of a surface in two dimensions that has a prescribed length and encloses a prescribed perimeter with respect to a baseline. An approximate analytical treatment in a semi--continuum compares…
The authors study the method of scaling in the context of the study of automorphism groups of complex domains in multiple dimensions. Various types of scaling techniques are compared and contrasted. Applications are given in a number of…
Partitioning of (bio)materials in polymeric mixtures is a key phenomenon both in cellular environments, as well as in industrial applications. In cells, several macromolecules are suspended within different biomolecular phases. On the other…
Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting…
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
A key problem in the study and design of complex systems is the apparent disconnection between the microscopic and the macroscopic. It is not straightforward to identify the local interactions that give rise to an observed global…
In this chapter, I review the main methods and techniques of complex systems science. As a first step, I distinguish among the broad patterns which recur across complex systems, the topics complex systems science commonly studies, the tools…
The network concept is increasingly used for the description of complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of macromolecules, cells, organisms, and ecosystems. Listing…
We present a method of discrete modeling and analysis of multilevel dynamics of complex large-scale hierarchical dynamic systems subject to external dynamic control mechanism. Architectural model of information system supporting simulation…
We do not attempt to provide yet another definition of selforganization, but explore the conditions under which we can model a system as self-organizing. These involve the dynamics of entropy, and the purpose, aspects, and description level…
The conventional wisdom is that liquids are completely disordered and lack non-trivial structure beyond nearest-neighbor distances. Recent observations have upended this view and demonstrated that the microstructure in liquids is…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Effect of an oscillatory decay of the charge density in concentrated ionic solutions and ionic liquids on the double-layer capacitance is studied in a framework of a mesoscopic theory. Only Coulomb and steric forces between the ions that…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates…