Related papers: Randomness with constraints: constructing minimal …
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
One of the basic frameworks in science views behavioral products as a process within a dynamic system. The mechanism might be seen as a representation of many instances of centralized control in real time. Many real systems, however,…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow,…
We propose a new approach to model composition, based on reducing several models to the same level of complexity and subsequent combining them together. Firstly, we suggest a set of model reduction tools that can be systematically applied…
Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…
The universal concept of complexity by the dynamic redundance paradigm and the ensuing concept of extended dynamic fractality (physics/9806002) are applied here to higher levels of complexity corresponding to living systems. After recalling…
The dynamics of many-body systems can often be captured in terms of only a few relevant variables. Mathematical and numerical approaches exist to identify these variables by exploiting a separation of time scales between slow relevant and…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
A celebrated and controversial hypothesis conjectures that some biological systems --parts, aspects, or groups of them-- may extract important functional benefits from operating at the edge of instability, halfway between order and…
Empirical complex systems can be characterized not only by pairwise interactions, but also by higher-order (group) interactions influencing collective phenomena, from metabolic reactions to epidemics. Nevertheless, higher-order networks'…
Compartmental epidemic models have been widely used for predicting the course of epidemics, from estimating the basic reproduction number to guiding intervention policies. Studies commonly acknowledge these models' assumptions but less…
There has been a long-standing and at times fractious debate whether complex and large systems can be stable. In ecology, the so-called `diversity-stability debate' arose because mathematical analyses of ecosystem stability were either…
We study special systems with infinitely many degrees of freedom with regard to dynamical evolution and fulfillment of constraint conditions. Attention is focused on establishing a meaningful functional framework, and for that purpose,…
To construct models of large, multivariate complex systems, such as those in biology, one needs to constrain which variables are allowed to interact. This can be viewed as detecting "local" structures among the variables. In the context of…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Understanding the macroscopic characteristics of biological complexes demands precision and specificity in statistical ensemble modeling. One of the primary challenges in this domain lies in sampling from particular subsets of the…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…