相关论文: Harvesting chemical power from cyclic environments
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…
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…
The study of chemical reactions in aqueous media is very important for its implications in several fields of science, from biology to industrial processes. Modelling these reactions is however difficult when water directly participates in…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Quantifying the flow of energy within and through fluctuating nanoscale systems poses a significant challenge to understanding microscopic biological machines. A common approach involves coarse-graining, which allows a simplified…
We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three classes of random networks, including Erdoes-Renyi…
Cell reproduction involves replication of diverse molecule species, in contrast to simple replication system with fewer components. Here, we address why such diversity is sustained despite the efficiency of simple replication systems, using…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Plastics have become integral to our society due to their durability and water stability, which is achieved through strong intermolecular interactions. However, these properties also make them persistent disruptors of ecological cycles, in…
The impact of liquid drops onto solid surfaces leads to conversion of kinetic energy of directed drop motion into various forms of energy including surface energy, vibrational energy, heat, and under suitable conditions, electrical energy.…
Human-created engines and evolutionarily optimized molecular motors exhibit sophisticated design in order to harvest chemical or thermal energy for generating unidirectional motion. The complexity of these motors makes their random…
We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange…
Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
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…
The quantum-mechanical and thermodynamic properties of a 3-level molecular cooling cycle are derived. An inadequacy of earlier models is rectified in accounting for the spontaneous emission and absorption associated with the coupling to the…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
In a pioneering study experimental evidence was sought of thermosynthesis, a theoretical biological mechanism for free energy gain from thermal cycling that has been invoked as energy source for the origin of life. A PCR machine applied…