Related papers: Metabolic scaling in small life forms
Microbial communities display extreme diversity. A variety of strains or species coexist even when limited by a single resource. It has been argued that metabolite secretion creates new niches and facilitates such diversity. Nonetheless, it…
We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
This study examines how patterns on mammal body surfaces change as they transition from juveniles to adults and with seasonal variations. Our previous research suggests that patterns formed in infancy may fade due to the growing domain…
A biophysical issue how the nuclear size dynamically scales with the cellular size remains mysterious. We develop a theoretical framework in which the interactions between polydisperse biomolecules and the mechanical elasticity of the cell…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
Most organisms grow according to simple laws, which in principle can be derived from energy conservation and scaling arguments, critically dependent on the relation between the metabolic rate B of energy flow and the organism mass m.…
The metabolic process in a cell is modeled with the use of the Fourier transformation. The histograms of the invariant measures of chaotic attractors are constructed. In particular, a scenario of adaptation of the metabolic process under a…
A number of biological processes, such as embryo development, cancer metastasis or wound healing, rely on cells moving in concert. The mechanisms leading to the emergence of coordinated motion remain however largely unexplored. Although…
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do…
A finite size scaling theory, originally developed only for transitions to absorbing states [Phys. Rev. E {\bf 92}, 062126 (2015)], is extended to distinct sorts of discontinuous nonequilibrium phase transitions. Expressions for quantities…
Recent progress has clarified many features of the global architecture of biological metabolic networks, which have highly organized and optimized tolerances and tradeoffs (HOT) for functional requirements of flexibility, efficiency,…
Nucleation, commonly associated with discontinuous transformations between metastable and stable phases, is crucial in fields as diverse as atmospheric science and nanoscale electronics. Traditionally, it is considered a microscopic process…
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…
The managed-metabolism hypothesis suggests that a cooperation barrier must be overcome if self-producing chemical organizations are to transition from non-life to life. This barrier prevents un-managed, self-organizing, autocatalytic…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
The energy dissipation rate in a nonequilibirum reaction system can be determined by the reaction rates in the underlying reaction network. By developing a coarse-graining process in state space and a corresponding renormalization procedure…