Related papers: Hierarchic Theory of Complex Systems (biosystems, …
In conflict with standard notions of thermodynamics, mesoscopically-sized inclusions (``clusters'') of a solute-rich liquid have been observed in equilibrated solutions of proteins and other molecules. According to a complexation scenario…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
Instead of the homogeneous ordered particle distributions characteristic to equilibrium systems a self-organizing polydomain structure is found to be stable at low temperatures in a square lattice-gas model with repulsive nearest neighbor…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
We investigate the self-organization of point-particles with short-range interactions modeled via simple 1D and 2D Hubbard-like models. We show how various properties emerge such as, boson-like ordering leading to topological structures in…
Understanding the behavior and evolution of a dynamical many-body system by analyzing patterns in their experimentally captured images is a promising method relevant for a variety of living and non-living self-assembled systems. The arrays…
Mesoscopic physics concerns itself with systems which are intermediate between a single atom and a bulk solid. Besides the many intrinsically interesting properties of mesoscopic systems, they can also provide physical insight into the…
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,…
A simple periodically driven system displaying rich behavior is introduced and studied. The system self-organizes into a mosaic of static ordered regions with three possible patterns, which are threaded by one-dimensional paths on which a…
Multiscale thermodynamics is a theory of relations among levels of investigation of complex systems. It includes the classical equilibrium thermodynamics as a special case but it is applicable to both static and time evolving processes in…
This paper presents findings from a study of the email network of a large scientific research organization, focusing on methods for visualizing and modeling organizational hierarchies within large, complex network datasets. In the first…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
Aim of this paper is to provide preliminary elements for discussion about the implications of the Hierarchy Theory of Evolution on the design and evolution of artificial systems and socio-technical organizations. In order to achieve this…
Organogenesis involves large deformations and complex shape changes that require elaborate mechanical regulation. Models of tissue biomechanics have been introduced to account for the coupling between mechanical response and biochemical…
A mathematical model of the metabolic process of formation of the hemostasis in a blood-carrying vessel is constructed. As distinct from the earlier developed model of the multienzyme prostacyclin-thromboxane system of blood, this model…
We study the homotopy theory of locally ordered spaces, that is manifolds with boundary whose charts are partially ordered in a compatible way. Their category is not particularly well-behaved with respect to colimits. However, this category…