Related papers: Design principles for biochemical oscillations wit…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic.…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
Biochemical oscillations, regulating the timing of life processes, need consume energy to achieve good performance on crucial functions, such as high accuracy of phase period and high sensitivity to external signals. However, it is a great…
Biochemical oscillations are prevalent in living organisms. Systems with a small number of constituents cannot sustain coherent oscillations for an indefinite time because of fluctuations in the period of oscillation. We show that the…
Living cells deploy many resources to sense their environments, including receptors, downstream signaling molecules, time and fuel. However, it is not known which resources fundamentally limit the precision of sensing, like weak links in a…
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
Energy efficiency is closely related to the evolution of biological systems and is important to their information processing. In this paper, we calculated the excitation probability of a simple model of a bistable biological unit in…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
Biochemical clocks are essential for virtually all living systems. A biochemical clock that is isolated from an external periodic signal and subjected to fluctuations can oscillate coherently only for a finite number of oscillations.…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Despite being optimized, the information processing of biological organisms exhibits significant variability in its complexity and capability. One potential source of this diversity is the limitation of resources required for information…
Both theoretical and experimental evidence are presented in this work in order to validate the existence of an Energy/Frequency Convexity Rule, which relates energy consumption and microprocessor frequency for nanometer-scale…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Circadian rhythms in living organisms are temporal orders emerging from biochemical circuits driven out of equilibrium. Here, considering the KaiABC system, a minimal model in the synthetic biology, we study how the oscillation emerges from…
Information processing machines at the nanoscales are unavoidably affected by thermal fluctuations. Efficient design requires understanding how nanomachines can operate at minimal energy dissipation. In this letter we focus on mechanical…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…