Related papers: ATP binding to a multisubunit enzyme: statistical …
Chemical theories involving thermodynamical equilibrium states invariably utilize statistical mechanical equilibrium density distributions. Here, a definition of heat-work transformation termed thermo mechanical coherence is first made, and…
The framework of bipartite stochastic thermodynamics is a powerful tool to analyze a composite system's internal thermodynamics. It has been used to study the components of different molecular machines such as ATP synthase. However, this…
It is argued that a typical many body energy eigenstate has a well defined thermodynamic entropy and that individual eigenstates possess thermodynamic characteristics analogous to those of generic isolated systems. We examine large systems…
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…
Multi-molecular excited states accompanied by an intra- and inter-molecular geometric relaxation are commonly encountered in optical and electrooptical studies and applications of organic semiconductors as, for example excimers or charge…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
We demonstrate asymmetric enzyme kinetics of a biomolecular motor F1-ATPase between synthesis and hydrolysis of adenosine triphosphate (ATP). Our experiments show that ATP hydrolysis follows Michaelis-Menten kinetics, but ATP synthesis,…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The polymerization of actin filaments is coupled to the hydrolysis of adenosine triphosphate (ATP), which involves both the cleavage of ATP and the release of inorganic phosphate. We describe hydrolysis by a reduced two-state model with a…
The cytoskeletal component actomyosin is a canonical example of active matter since the powerstroke cycle locally converts chemical energy in the form of adenoside triphosphate (ATP) into mechanical work for remodelling. Observing myosin II…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis, with a focus on the coupling between chemical reactions and mechanical dynamics. Extending the classical Toner-Tu framework,…
Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex…
We study the stochastic dynamics of growth and shrinkage of single actin filaments taking into account insertion, removal, and ATP hydrolysis of subunits either according to the vectorial mechanism or to the random mechanism. In a previous…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
The equilibration of enzyme and complex concentrations in deterministic Michaelis-Menten reaction networks underlies the hyperbolic dependence between the input (substrates) and output (products). This relationship was first obtained by…
Muscle contraction is a prototypical multiscale chemomechanical process in which ATP hydrolysis at the molecular level drives force generation and mechanical work at larger scales. A long-standing challenge is to connect microscopic…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…