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The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…

Statistical Mechanics · Physics 2009-10-31 R. Bundschuh , T. Hwa

By controlling in real-time the variance of the radiation pressure exerted on an optically trapped microsphere, we engineer temperature protocols that shortcut thermal relaxation when transferring the microsphere from one thermal…

We propose an optimization strategy to control the dynamics of a stochastic system transferred from one thermal equilibrium to another and apply it experimentally to a Brownian particle in an optical trap under compression. Based on a…

We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are…

Statistical Mechanics · Physics 2016-11-04 David A. Sivak , Gavin E. Crooks

Single-molecule experiments have found near-perfect thermodynamic efficiency in the rotary motor F1-ATP synthase. To help elucidate the principles underlying nonequilibrium energetic efficiency in such stochastic machines, we investigate…

Statistical Mechanics · Physics 2019-09-05 Joseph N. E. Lucero , Aliakbar Mehdizadeh , David A. Sivak

We present a detailed analytical investigation of the optimal control of uniformly heated granular gases in the linear regime. The intensity of the stochastic driving is therefore assumed to be bounded between two values that are close,…

Statistical Mechanics · Physics 2022-01-19 Natalia Ruiz-Pino , Antonio Prados

We characterize finite-time thermodynamic processes of multidimensional quadratic overdamped systems. Analytic expressions are provided for heat, work, and dissipation for any evolution of the system covariance matrix. The Bures-Wasserstein…

Statistical Mechanics · Physics 2022-11-28 Paolo Abiuso , Viktor Holubec , Janet Anders , Zhuolin Ye , Federico Cerisola , Martí Perarnau-Llobet

Constructing optimal thermodynamic processes in quantum systems relies on managing the balance between the average excess work and its stochastic fluctuations. Recently it has been shown that two different quantum generalisations of…

Quantum Physics · Physics 2021-12-06 Mohammad Mehboudi , Harry J. D. Miller

We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…

Statistical Mechanics · Physics 2021-08-02 Marco Ancona , Alessandro Bentivoglio , Michele Caraglio , Giuseppe Gonnella , Alessandro Pelizzola

Optimization of cyclic stochastic heat engines, a topic spanning decades of research, commonly assumes fixed control or response parameters at discrete points in the cycle-a limitation that often leads to experimentally impractical…

Statistical Mechanics · Physics 2025-07-02 Monojit Chatterjee , Viktor Holubec , Rahul Marathe

Asking for the optimal protocol of an external control parameter that minimizes the mean work required to drive a nano-scale system from one equilibrium state to another in finite time, Schmiedl and Seifert ({\it Phys. Rev. Lett.} {\bf 98},…

Statistical Mechanics · Physics 2008-04-14 Holger Then , Andreas Engel

Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…

Statistical Mechanics · Physics 2018-11-26 Steven J. Large , Raphaël Chetrite , David A. Sivak

The energetic optimization problem, e.g., searching for the optimal switch- ing protocol of certain system parameters to minimize the input work, has been extensively studied by stochastic thermodynamics. In current work, we study this…

Statistical Mechanics · Physics 2010-01-07 Linchen Gong , Ming Li , Zhong-can Ou-yang

Optimal (reversible) processes in thermodynamics can be modelled as step-by-step processes, where the system is successively thermalized with respect to different Hamiltonians by an external thermal bath. However, in practice interactions…

The phase transitions for many-body systems have been understood using field theories. A few canonical physical model classes encapsulate the underlying physical properties of a large number of systems. The finite-time driving of such…

Statistical Mechanics · Physics 2024-06-24 Atul Tanaji Mohite

By combining different ideas, a general and efficient protocol to deal with discontinuous phase transitions at low temperatures is proposed. For small $T$'s, it is possible to derive a generic analytic expression for appropriate order…

Statistical Mechanics · Physics 2015-06-03 C. E. Fiore , M. G. E. da Luz

To achieve efficient and reliable control of microscopic systems one should look for driving protocols that mitigate both the average dissipation and stochastic fluctuations in work. This is especially important in fast driving regimes in…

Quantum Physics · Physics 2023-07-26 Alberto Rolandi , Martí Perarnau-Llobet , Harry J. D. Miller

The realization of efficient micro-machines built from active matter requires precise thermodynamic control far from equilibrium. Despite theoretical progress, the focus on single-parameter driving, coupled with strict theoretical…

Soft Condensed Matter · Physics 2026-03-18 Luke K. Davis

Generative models of complex systems often require post-hoc parameter adjustments to produce useful outputs. For example, energy-based models for protein design are sampled at an artificially low ''temperature'' to generate novel,…

Quantitative Methods · Quantitative Biology 2025-12-11 Peter W Fields , Vudtiwat Ngampruetikorn , David J Schwab , Stephanie E Palmer

For two canonical examples of driven mesoscopic systems - a harmonically-trapped Brownian particle and a quantum dot - we numerically determine the finite-time protocols that optimize the compromise between the standard deviation and the…

Statistical Mechanics · Physics 2018-05-09 Alexandre P. Solon , Jordan M. Horowitz