Related papers: Processive and Distributive Non-Equilibrium Networ…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism which enables lower error at the cost of higher energy dissipation. Elucidating physicochemical constraints for…
Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($\mu$), speed ($\sigma$) and total entropy production rate ($P$)? Previous…
Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as "biological hardware." In this context, it is important to understand the…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available…
Non-equilibrium driving of biochemical reactions is believed to enable their robust functioning despite the presence of thermal fluctuations and other sources of disorder. Such robust functions include sensory adaptation, enhanced enyzmatic…
Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
Controlling the evolution of nonequilibrium systems to minimize dissipated heat or work is a key goal for designing nanodevices, both in nanotechnology and biology. Progress in computing optimal protocols has thus far been limited to either…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
In an equilibrium chemical reaction mixture, the number of molecules present obeys a Poisson distribution. We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain an essentially complete answer. In…
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step…
Diverse physical systems are characterized by their response to small perturbations. Near thermodynamic equilibrium, the fluctuation-dissipation theorem provides a powerful theoretical and experimental tool to determine the nature of…
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…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
There is a growing trend in molecular and synthetic biology of using mechanistic (non machine learning) models to design biomolecular networks. Once designed, these networks need to be validated by experimental results to ensure the…
We study the response of chemical reaction networks driven far from equilibrium to logarithmic perturbations of reaction rates. The response of the mean number of a chemical species is observed to be quantitively limited by number…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…