Related papers: ATP Synthase: A Moonlighting Enzyme with Unprecede…
Measurements of the analysing power for the p(pol)p --> ppeta reaction have been performed in the close-to-threshold energy region at beam momenta of p_{beam}=2.010 and 2.085 GeV/c, corresponding to excess energies of Q=10 and 36 MeV,…
A complete mathematical theory of nonequilibrium thermodynamics of stochastic systems in terms of master equations is presented. As generalizations of isothermal entropy and free energy, two functions of states play central roles: the Gibbs…
We introduce axiomatically a complete thermodynamic formalism for a single macromolecule, either with or without detailed balance, in an isothermal ambient fluid based on its stochastic dynamics. With detailed balance, the novel theory…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
The nanoscopic isothermal machines are not only energy but also information transducers. We show that the generalized fluctuation theorem with information creation and entropy reduction can be fulfilled for the enzymatic molecular machines…
The theory describing action of medicines explored in this paper is based on assumption that vital activity of the cell may be described in terms of the model of two states: resting state and excitation. According to available physiological…
We introduce machine-learned potentials for Ag-Pd to describe the energy of alloy configurations over a wide range of compositions. We compare two different approaches. Moment tensor potentials (MTP) are polynomial-like functions of…
The quasi-steady state assumption (QSSA) forms the basis for rigorous mathematical justification of the Michaelis-Menten formalism commonly used in modeling a broad range of intracellular phenomena. A critical supposition of QSSA-based…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
Maxwell defined a true or total current in a way not widely used today. He said "... true electric current ... is not the same thing as the current of conduction but that the time-variation of the electric displacement must be taken into…
In this study, through phenomenological comparison of the velocity-force data of processive motor proteins, including conventional kinesin, cytoplasmic dynein and myosin V, we found that, the ratio between motor velocities of two different…
We establish Extended Thermodynamics (ET) of rarefied polyatomic gases with six independent fields, i.e., the mass density, the velocity, the temperature and the dynamic pressure, without adopting the near-equilibrium approximation. The…
Photosystem 0 concerns a primitive mechanism for free energy gain as ATP from fluctuating light during early evolution. The PS0 reaction centers had no reducing power: charge transport was only temporary. Light induced within the reaction…
FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. Briefly, proton…
Free energy and entropy are examined in detail from the standpoint of classical thermodynamics. The approach is logically based on the fact that thermodynamic work is mediated by thermal energy through the tendency for nonthermal energy to…
Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by…
A mathematical model for chemical reactions in electrolytes is developed using an Energy variational method consistent with classical thermodynamics. Electrostatics and chemical reactions are included in properly defined energetic and…
Terpene synthases (TPS) are a key family of enzymes responsible for generating the diverse terpene scaffolds that underpin many natural products, including front-line anticancer drugs such as Taxol. However, de novo TPS design through…
Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing…