Related papers: ATP Synthase: A Moonlighting Enzyme with Unprecede…
Isolated sarcoplasmic reticulum vesicles in the presence of Mg(2+) and absence of Ca(2+) retain significant ATP hydrolytic activity that can be attributed to the Ca(2+)-ATPase protein. At neutral pH and the presence of 5 mM Mg(2+), the…
In the framework of irreversible thermodynamics, we study autonomous systems of reaction-diffusion equations to show how the entropy and free energy of an open and irreversible reactor depend on concentrations. To do this, we find a…
ATP synthases utilize a proton motive force to synthesize ATP. In reverse, these membrane-embedded enzymes can also hydrolyze ATP to pump protons over the membrane. To prevent wasteful ATP hydrolysis, distinct control mechanisms exist for…
In models with flavour symmetries added to the gauge group of the Standard Model the CP-violating asymmetry necessary for leptogenesis may be related with low-energy parameters. A particular case of interest is when the flavour symmetry…
F$_{1}$-ATPase is a rotary molecular motor that \emph{in vivo} is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy…
Taking advantage from a recent analog realization of certain automata via spectral encodings as permutation machines, we reach at an improved version of the previously introduced remotely acting Maxwellian demon in arXiv:1408.3797. A number…
The asymptotic convergence of probability density function (pdf) and convergence of differential entropy are examined for the non-stationary processes that follow the maximum entropy principle (MaxEnt) and maximum entropy production…
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in…
We revisit here the mathematical model for ATP production in mitochondria introduced recently by Bertram, Pedersen, Luciani, and Sherman (BPLS) as a simplification of the more complete but intricate Magnus and Keizer's model. We identify…
Maxwell's demon explores the role of information in physical processes. Employing information about microscopic degrees of freedom, this "intelligent observer" is capable of compensating entropy production (or extracting work), apparently…
To synthesize proteins in a cell, an mRNA has to work with a finite pool of ribosomes. When this constraint is included in the modeling by a totally asymmetric simple exclusion process (TASEP), non-trivial consequences emerge. Here, we…
Identifying dissipation is essential for understanding the physical mechanisms underlying nonequilibrium processes. {In living systems, for example, the dissipation is directly related to the hydrolysis of fuel molecules such as adenosine…
F$_1$-ATPase (F$_1$) is central to cellular energy transduction. Forcibly rotated by another motor F$_\mathrm{o}$, F$_1$ catalyzes ATP synthesis by converting mechanical work into chemical free energy stored in the molecule ATP. The details…
Maxwell's demon (MD) has proven an instructive vehicle by which to explore the relationship between information theory and thermodynamics, fueling the possibility of information driven machines. A long standing debate has been the concern…
A discrete-state model of the F1-ATPase molecular motor is developed which describes not only the dependences of the rotation and ATP consumption rates on the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on…
In mathematical physical analyses of Szilard's engine and Maxwell's demon, a general assumption (explicit or implicit) is that one can neglect the energy needed for relocating the piston in Szilard's engine and for driving the trap door in…
We experimentally showed that biological molecular motor F$_1$-ATPase (F$_1$) implements an optimal rectification mechanism. F$_1$ hardly suppresses adenosine triphosphate (ATP) synthesis, which is the F$_1$'s physiological role while…
The diffusion of a molecular motor in the presence of a constant external force is considered on the basis of a simple theoretical model. The motor is represented by a Brownian particle moving in a series of parabolic potentials placed…
The construction of the potential energy surface (PES) of even a medium-sized molecule employing correlated theory, such as CCSD(T), is an arduous task due to the high computational cost. In this Letter, we report the possibility of…
Multiscale thermodynamics is a theory of relations among levels of description. Energy and entropy are its two main ingredients. Their roles in the time evolution describing approach of a level (starting level) to another level involving…