skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


This content will become publicly available on August 1, 2026

Title: Energetic Variational Modeling of Active Nematics: Coupling the Toner–Tu Model with ATP Hydrolysis
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis. Extending the classical Toner–Tu framework, we introduce a chemo-mechanical coupling mechanism in which the self-advection and polarization dynamics are modulated by the ATP hydrolysis rate. The model is derived using an energetic variational approach that integrates both chemical free energy and mechanical energy into a unified energy dissipation law. The reaction rate equation explicitly incorporates mechanical feedback, revealing how active transport and alignment interactions influence chemical fluxes and vice versa. This formulation not only preserves consistency with non-equilibrium thermodynamics but also provides a transparent pathway for modeling energy transduction in active systems. We also present numerical simulations demonstrating the positive energy transduction under a specific choice of model parameters. The new modeling framework offers new insights into energy transduction and regulation mechanisms in biologically related active systems.  more » « less
Award ID(s):
2410740
PAR ID:
10626862
Author(s) / Creator(s):
Publisher / Repository:
MDPI
Date Published:
Journal Name:
Entropy
Volume:
27
Issue:
8
ISSN:
1099-4300
Page Range / eLocation ID:
801
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Beard, Daniel A (Ed.)
    Understanding muscle contraction mechanisms is a standing challenge, and one of the approaches has been to create models of the sarcomere–the basic contractile unit of striated muscle. While these models have been successful in elucidating many aspects of muscle contraction, they fall short in explaining the energetics of functional phenomena, such as rigor, and in particular, their dependence on the concentrations of the biomolecules involved in the cross-bridge cycle. Our hypothesis posits that the stochastic time delay between ATP adsorption and ADP/Pi release in the cross-bridge cycle necessitates a modeling approach where the rates of these two reaction steps are controlled by two independent parts of the total free energy change of the hydrolysis reaction. To test this hypothesis, we built a two-filament, stochastic-mechanical half-sarcomere model that separates the energetic roles of ATP and ADP/Pi in the cross-bridge cycle’s free energy landscape. Our results clearly demonstrate that there is a nontrivial dependence of the cross-bridge cycle’s kinetics on the independent concentrations of ATP, ADP, and Pi. The simplicity of the proposed model allows for analytical solutions of the more basic systems, which provide novel insight into the dominant mechanisms driving some of the experimentally observed contractile phenomena. 
    more » « less
  2. Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5′-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Here we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution. 
    more » « less
  3. Molecular motors, kinesin and myosin, are dimeric consisting of two linked identical monomeric globular proteins. Fueled by the free energy generated by ATP hydrolysis, they walk on polar tracks (microtubule or filamentous actin) processively, which means that only one head detaches and executes a mechanical step while the other stays bound to the track. One motor head must regulate the chemical state of the other, referred to as “gating”, a concept that is still not fully understood. Inspired by experiments, showing that only a fraction of the energy from ATP hydrolysis is used to advance the kinesin motors against load, we demonstrate that the rest of the energy is associated with chemical transitions in the two heads. The coordinated chemical transitions involve communication between the two heads - a feature that characterizes gating. We develop a general framework, based on information theory and stochastic thermodynamics, and establish that gating could be quantified in terms of information flow between the motor heads. Applications to kinesin-1 and Myosin V show that information flow, with positive cooperativity, at external resistive loads less than a critical value, F c . When force exceeds F c , effective information flow ceases. Interestingly, F c , which is independent of the input energy generated through ATP hydrolysis, coincides with the force at which the probability of backward steps starts to increase. Our findings suggest that transport efficiency is optimal only at forces less than F c , which implies that these motors must operate at low loads under in vivo conditions. 
    more » « less
  4. Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors. 
    more » « less
  5. In this paper, we summarize some recent advances related to the energetic variational approach (EnVarA), a general variational framework of building thermodynamically consistent models for complex fluids, by some examples. Particular focus will be placed on how to model systems involving chemo-mechanical couplings and non-isothermal effects. 
    more » « less