Related papers: ATP Synthase: A Moonlighting Enzyme with Unprecede…
We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
The process of deriving an interatomic potentials represents an attempt to integrate out the electronic degrees of freedom from the full quantum description of a condensed matter system. In practice it is the derivatives of the interatomic…
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor Fo-F1…
Adenosine-5'-triphosphate (ATP) plays a crucial role in many biocatalytic reactions and its regeneration can influence the performance of a related enzymatic reaction significantly. Here, we established an electrochemically coupled ATP…
The efficiency at maximum power (EMP) for tight-coupling molecular motors is investigated within the framework of irreversible thermodynamics. It is found that the EMP depends merely on the constitutive relation between the thermodynamic…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
We propose a concept of autonomous energy transducer at a molecular scale, where output is produced with small input energy, of the same order of the thermal energy, without restriction of magnitude or timing of input, and without any…
Two simple (rotator and one-particle) mechanistic models are suggested to describe simultaneously at a minimal level of sophistication two basic functions of F$_1$-ATPase: a motor regime driven by ATP hydrolysis and its inverted function as…
ATP-hydrolysis is the basic energy source of many physiological processes, but there is a lack of knowledge regarding its biological role other than energy transfer and thermogenesis. Not all the energy released by ATP-hydrolysis could be…
The molecular electrostatic potential (MEP) is a key quantity for describing and predicting intermolecular and ion-molecule interactions. Here, we assess the ability of machine-learning (ML) models to infer the MEP, based on the equivariant…
The excess work required to drive a stochastic system out of thermodynamic equilibrium through a time-dependent external perturbation is directly related to the amount of entropy produced during the driving process, allowing excess work and…
Molecular motors transduce chemical energy obtained from hydrolizing ATP into mechanical work exerted against an external force. We calculate their efficiency at maximum power output for two simple generic models and show that the…
We present a quantitative analysis of recent data on the kinetics of ATP hydrolysis, which has presented a puzzle regarding the load dependence of the Michaelis constant. Within the framework of coarse grained two-state ratchet models, our…
Kinesins move processively toward the plus end of microtubules by hydrolyzing ATP for each step. From an enzymatic perspective, the mechanism of mechanical motion coupled to the nucleotide chemistry is often well explained using a…
Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical…
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…
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,…
Active ion transport is very critical for living cells to maintain and regular internal and external environment. It is known that adenosine 5'-triphosphate (ATP) is a general energy source that applies bond energy for pumps to overcome ion…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…