Related papers: Complex versus Complicated Systems Biology, Univer…
This article focuses on the optimization of a complex system which is composed of several subsystems. On the one hand, these subsystems are subject to multiple objectives, local constraints as well as local variables, and they are…
In the study of the basic properties observed in the immune system and, in a broader view, in biological systems, several concepts have already been mathematically formulated or treated in an analytical perspective, such as degeneracy,…
Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
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…
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…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
To better understand the structure and function of complex systems, researchers often represent direct interactions between components in complex systems with networks, assuming that indirect influence between distant components can be…
Complexity remains one of the central challenges in science and technology. Although several approaches at defining and/or quantifying complexity have been proposed, at some point each of them seems to run into intrinsic limitations or…
Building software-driven systems that are easily understood becomes a challenge, with their ever-increasing complexity and autonomy. Accordingly, recent research efforts strive to aid in designing explainable systems. Nevertheless, a common…
I investigate some properties of proposed definitions for subsystem/mixed state complexity and uncomplexity. A very strong dependence arises on the density matrix's degeneracy which gives a large separation in the scaling of maximum…
The human mind is known to be sensitive to complexity. For instance, the visual system reconstructs hidden parts of objects following a principle of maximum simplicity. We suggest here that higher cognitive processes, such as the selection…
The gradual accumulation of damage and dysregulation during the aging of living organisms can be quantified. Even so, the aging process is complex and has multiple interacting physiological scales -- from the molecular to cellular to whole…
It is not obvious what fraction of all the potential information residing in the molecules and structures of living systems is significant or meaningful to the system. Sets of random sequences or identically repeated sequences, for example,…
Biological engineering, the convergence between engineering and biology, is at the forefront of significant advances in healthcare, agriculture, and environmental sustainability, making it highly relevant to current scientific and societal…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…