Thermodynamic bounds on ultrasensitivity in covalent switching.

Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a covalent modification. To work as a switch, such covalent modification cycles must be held out of thermodynamic equilibrium by continuous expenditure of energy.

Allosteric conformational ensembles have unlimited capacity for integrating information.

Integration of binding information by macromolecular entities is fundamental to cellular functionality. Recent work has shown that such integration cannot be explained by pairwise cooperativities, in which binding is modulated by binding at another site. Higher-order cooperativities (HOCs), in which binding is collectively modulated by multiple other binding events, appear to be necessary but an appropriate mechanism has been lacking.

Reversal symmetries for cyclic paths away from thermodynamic equilibrium.

If a system is at thermodynamic equilibrium, an observer cannot tell whether a film of it is being played forward or in reverse: any transition will occur with the same frequency in the forward as in the reverse direction. However, if expenditure of energy changes the rate of even a single transition to yield a nonequilibrium steady state, such time-reversal symmetry undergoes a widespread breakdown, far beyond the point at which the energy is expended. An explosion of interdependency also arises, with steady-state probabilities of system states depending in a complicated manner on the rate of every transition in the system.

Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA.

The mode of interaction of transcription factors (TFs) on eukaryotic genomes remains a matter of debate. Single-molecule data in living cells for the TFs Sox2 and Oct4 were previously interpreted as evidence of ordered assembly on DNA. However, the quantity that was calculated does not determine binding order but, rather, energy expenditure away from thermodynamic equilibrium.

Model discrimination for Ca -dependent regulation of myosin light chain kinase in smooth muscle contraction.

Excitation-contraction coupling in smooth muscle is mediated by the Ca - and calmodulin-dependent regulation of myosin light chain kinase. The precise mechanism of this regulation remains controversial, and several mathematical models have been proposed for the interaction of the three species. These models have previously been analyzed at steady state primarily by numerical simulation of differential equations, for which parameter values must be estimated from data.

Two-structure thermodynamics for the TIP4P/2005 model of water covering supercooled and deeply stretched regions.

One of the most promising frameworks for understanding the anomalies of cold and supercooled water postulates the existence of two competing, interconvertible local structures. If the non-ideality in the Gibbs energy of mixing overcomes the ideal entropy of mixing of these two structures, a liquid-liquid phase transition, terminated at a liquid-liquid critical point, is predicted. Various versions of the "two-structure equation of state" (TSEOS) based on this concept have shown remarkable agreement with both experimental data for metastable, deeply supercooled water and simulations of molecular water models.

Two-state thermodynamics and the possibility of a liquid-liquid phase transition in supercooled TIP4P/2005 water.

Water shows intriguing thermodynamic and dynamic anomalies in the supercooled liquid state. One possible explanation of the origin of these anomalies lies in the existence of a metastable liquid-liquid phase transition (LLPT) between two (high and low density) forms of water. While the anomalies are observed in experiments on bulk and confined water and by computer simulation studies of different water-like models, the existence of a LLPT in water is still debated.

Behavior of supercooled aqueous solutions stemming from hidden liquid-liquid transition in water.

A popular hypothesis that explains the anomalies of supercooled water is the existence of a metastable liquid-liquid transition hidden below the line of homogeneous nucleation. If this transition exists and if it is terminated by a critical point, the addition of a solute should generate a line of liquid-liquid critical points emanating from the critical point of pure metastable water. We have analyzed thermodynamic consequences of this scenario.

Thermal conductivity of supercooled water.

The heat capacity of supercooled water, measured down to -37°C, shows an anomalous increase as temperature decreases. The thermal diffusivity, i.e.