Iterative improvement of free energy landscape reconstructions with optimal protocols derived from differentiable simulations
Fuente:
arXiv
Saved in:
| Main Authors: | Cheng, Oliver, Adamska, Zosia, Brenner, Michael P., Engel, Megan C. |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Static vs dynamic rough energy landscapes: Where is diffusion faster?
by: Makarov, Dmitrii E., et al.
Published: (2025)
by: Makarov, Dmitrii E., et al.
Published: (2025)
Nonadiabatic force matching for alchemical free-energy estimation
by: Rosa-Raíces, Jorge L., et al.
Published: (2025)
by: Rosa-Raíces, Jorge L., et al.
Published: (2025)
Fluctuating landscapes and heavy tails in animal behavior
by: Costa, Antonio Carlos, et al.
Published: (2023)
by: Costa, Antonio Carlos, et al.
Published: (2023)
Universal bounds on optimization of free energy harvesting
by: Piñero, Jordi, et al.
Published: (2023)
by: Piñero, Jordi, et al.
Published: (2023)
Multiparameter optimal control of F1-ATPase
by: Wareham, W. Callum, et al.
Published: (2024)
by: Wareham, W. Callum, et al.
Published: (2024)
Trade-offs and thermodynamics of energy-relay proofreading
by: Berx, Jonas, et al.
Published: (2024)
by: Berx, Jonas, et al.
Published: (2024)
Information-to-energy trade-offs and the optimal alphabet of polymer replication
by: Hernández, Damián G.
Published: (2026)
by: Hernández, Damián G.
Published: (2026)
Decoding cell signaling via optimal transport and information theory
by: Nandi, Mintu, et al.
Published: (2026)
by: Nandi, Mintu, et al.
Published: (2026)
Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off
by: Tabanera-Bravo, Jorge, et al.
Published: (2024)
by: Tabanera-Bravo, Jorge, et al.
Published: (2024)
Tuning transduction from hidden observables to optimize information harvesting
by: Nicoletti, Giorgio, et al.
Published: (2024)
by: Nicoletti, Giorgio, et al.
Published: (2024)
An altruistic resource-sharing mechanism for synchronization: The energy-speed-accuracy tradeoff
by: Zhang, Dongliang, et al.
Published: (2025)
by: Zhang, Dongliang, et al.
Published: (2025)
Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations
by: Oliveira, A. S. F., et al.
Published: (2023)
by: Oliveira, A. S. F., et al.
Published: (2023)
In-vivo entropy production of A. subaru
by: Fu, Yu, et al.
Published: (2026)
by: Fu, Yu, et al.
Published: (2026)
Will a Large Complex System be a Maxwell Demon?
by: Leighton, Matthew P
Published: (2026)
by: Leighton, Matthew P
Published: (2026)
Flow of Energy and Information in Molecular Machines
by: Leighton, Matthew P., et al.
Published: (2024)
by: Leighton, Matthew P., et al.
Published: (2024)
Decomposing Non-Markovian History Dependence
by: Leighton, Matthew P., et al.
Published: (2025)
by: Leighton, Matthew P., et al.
Published: (2025)
Computing macroscopic reaction rates in reaction-diffusion systems using Monte Carlo simulations
by: Swailem, Mohamed, et al.
Published: (2024)
by: Swailem, Mohamed, et al.
Published: (2024)
Dissimilarity measures for generalized Lotka-Volterra systems on networks
by: Márquez, Nicolás A., et al.
Published: (2025)
by: Márquez, Nicolás A., et al.
Published: (2025)
Information thermodynamics of cellular ion pumps
by: Jiménez-Paz, Julian D., et al.
Published: (2025)
by: Jiménez-Paz, Julian D., et al.
Published: (2025)
Hierarchical Reconstruction of Time-arrow from Multi-time Correlations
by: Cheng, Yijia, et al.
Published: (2026)
by: Cheng, Yijia, et al.
Published: (2026)
Hunting for Maxwell's Demon in the Wild
by: Buisson, Johan du, et al.
Published: (2025)
by: Buisson, Johan du, et al.
Published: (2025)
EPR-Net: Constructing non-equilibrium potential landscape via a variational force projection formulation
by: Zhao, Yue, et al.
Published: (2023)
by: Zhao, Yue, et al.
Published: (2023)
Cellular Griffiths-like phase
by: Squillante, Lucas, et al.
Published: (2024)
by: Squillante, Lucas, et al.
Published: (2024)
Epidemic Forecast Follies
by: Krapivsky, P. L., et al.
Published: (2023)
by: Krapivsky, P. L., et al.
Published: (2023)
Work Distribution for Unzipping Processes
by: Werner, P., et al.
Published: (2024)
by: Werner, P., et al.
Published: (2024)
Overflow metabolism originates from growth optimization and cell heterogeneity
by: Wang, Xin
Published: (2023)
by: Wang, Xin
Published: (2023)
Entropy Production by Underdamped Langevin Dynamics
by: Lyu, Jinghao, et al.
Published: (2024)
by: Lyu, Jinghao, et al.
Published: (2024)
Manifold-based transformation of probability distributions: application to the inverse problem of reconstructing distributions from experimental data
by: Oroguchi, Tomotaka, et al.
Published: (2024)
by: Oroguchi, Tomotaka, et al.
Published: (2024)
Agent-Based simulation reveals localized isolation key to saving lives and resources
by: Karmakar, Mintu
Published: (2023)
by: Karmakar, Mintu
Published: (2023)
Network-based drug repurposing for MYH9-related nephritis
by: Ali, Muhammad, et al.
Published: (2026)
by: Ali, Muhammad, et al.
Published: (2026)
Thermodynamic inference in molecular motors: a Martingale approach
by: Nadal-Rosa, Adrián, et al.
Published: (2025)
by: Nadal-Rosa, Adrián, et al.
Published: (2025)
Nonequilibrium relaxation inequality on short timescales
by: Auconi, Andrea
Published: (2024)
by: Auconi, Andrea
Published: (2024)
Poissonian cellular Potts models reveal nonequilibrium kinetics of cell sorting
by: Belousov, Roman, et al.
Published: (2023)
by: Belousov, Roman, et al.
Published: (2023)
Repulsive particle interactions enable selective information processing at cellular interfaces
by: Elliott, Jenna, et al.
Published: (2025)
by: Elliott, Jenna, et al.
Published: (2025)
Nonequilibrium Theory for Molecular Machine Design
by: Yang, Ying-Jen, et al.
Published: (2026)
by: Yang, Ying-Jen, et al.
Published: (2026)
Fluctuation-Response Design Rules for Nonequilibrium Flows
by: Yang, Ying-Jen, et al.
Published: (2026)
by: Yang, Ying-Jen, et al.
Published: (2026)
A Formal Physical Framework for the Origin of Life: Dissipation-Driven Selection of Evolving Replicators
by: Segal, Shlomo
Published: (2026)
by: Segal, Shlomo
Published: (2026)
Diffusion with a broad class of stochastic diffusion coefficients
by: Uchida, Go, et al.
Published: (2023)
by: Uchida, Go, et al.
Published: (2023)
Single-molecule Automata: Harnessing Kinetic-Thermodynamic Discrepancy for Temporal Pattern Recognition
by: Zhang, Zhongmin, et al.
Published: (2024)
by: Zhang, Zhongmin, et al.
Published: (2024)
The origin of the Poisson distribution in stochastic dynamics of gene expression
by: Lee, Julian
Published: (2022)
by: Lee, Julian
Published: (2022)
Similar Items
-
Static vs dynamic rough energy landscapes: Where is diffusion faster?
by: Makarov, Dmitrii E., et al.
Published: (2025) -
Nonadiabatic force matching for alchemical free-energy estimation
by: Rosa-Raíces, Jorge L., et al.
Published: (2025) -
Fluctuating landscapes and heavy tails in animal behavior
by: Costa, Antonio Carlos, et al.
Published: (2023) -
Universal bounds on optimization of free energy harvesting
by: Piñero, Jordi, et al.
Published: (2023) -
Multiparameter optimal control of F1-ATPase
by: Wareham, W. Callum, et al.
Published: (2024)