相关论文: How much regulation do we need from genomes to soc…

Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…

The growing need for affordable and accessible higher education is a major global challenge for the 21st century. Consequently, there is a need to develop a deeper understanding of the functionality and taxonomy of universities and colleges…

Developing and maintaining life requires a lot of computation. This is done by gene regulatory networks. But we have little understanding of how this computation is organized. I show that there is a direct correspondence between the…

Increased biological complexity is generally associated with the addition of new genetic information, which must be integrated into the existing regulatory network that operates within the cell. General arguments on network control, as well…

A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…

High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…

Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…

Function diversity, the range of tasks individuals perform, and specialization, the distribution of function abundances, are fundamental to complex adaptive systems. In the absence of overarching principles, these properties have appeared…

Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the…

Foundation models and generative artificial intelligence (AI) exacerbate a core regulatory challenge associated with AI: its heterogeneity. By their very nature, foundation models and generative AI can perform multiple functions for their…

With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…

Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…

Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…

Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…

The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…

The collective effort exceeds the sum of its parts when individuals coordinate and regulate their activities and behaviors. This holds true even in self-organizing systems with open, voluntary participation where coordination occurs…

In order to understand controlling a complex system, an estimation of the required effort needed to achieve control is vital. Previous works have addressed this issue by studying the scaling laws of energy cost in a general way with…

Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…

Understanding how size influences the internal characteristics of a system is a crucial concern across various fields. Concepts like scale invariance, universalities, and fractals are fundamental to this inquiry and find application in…

In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…