arXiv subjects

Lee Jinwoo

Publications and source records attributed to Lee Jinwoo.

5 recordsLinked to original sources

arXiv2022

Roles of Local Non-equilibrium Free Energy in the Description of Biomolecules

When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and Tanaka (L. Jinwoo and H. Tanaka, Sci. Rep. 2015, 5, 7832) have provided mathematical proof that such a process's non-equilibrium free energy profile over a system's substates has Jarzynski's work as content, which spontaneously dissipates while molecules perform their tasks. Here we numerically verify this fact and give a practical example where we analyze a computer simulation of RNA translocation by a ring-shaped ATPase motor. By interpreting the cyclic process of substrate translocation as a series of quenching, relaxation, and second quenching, the theory gives how much individual sub-states of the ATPase motor have been energized until the end of the process. It turns out that the efficiency of RNA translocation is $48\sim 60\%$ for most molecules, but $12\%$ of molecules achieve $80\sim 100\%$ efficiency, which is consistent with the literature. This theory would be a valuable tool for extracting quantitative information about molecular non-equilibrium behavior from experimental observations.

cond-mat.stat-mech↗

arXiv2019

Complementary aspects of non-equilibrium thermodynamics

Bio-molecules are active agents in that they consume energy to perform tasks. The standard theoretical description, however, considers only a system-external work agent. Fluctuation theorems, for example, do not allow work-exchange between fluctuating molecules. This tradition leaves `action through work', an essential characteristic of an active agent, out of proper thermodynamic consideration. Here, we investigate thermodynamics that considers internal-work. We find a complementary set of relations that capture the production of free energy in molecular interactions while obeying the second law of thermodynamics. This thermodynamic description is in stark contrast to the traditional one. A choice of an axiom whether one treats a portion of Hamiltonian as `internal-work' or `internal-energy' decides which of the two complementary descriptions manifests among the dual. We illustrate, by examining an allosteric transition and a single-molecule fluorescence-resonance-energy-transfer measurement of proteins, that the complementary set is useful in identifying work content by experimental and numerical observation.

cond-mat.stat-mech↗

arXiv2019

Fluctuation Theorem of Information Exchange within an Ensemble of Paths Conditioned on Correlated-Microstates

Fluctuation theorems are a class of equalities that express universal properties of the probability distribution of a fluctuating path functional such as heat, work or entropy production over an ensemble of trajectories during a non-equilibrium process with a well-defined initial distribution. Jinwoo and Tanaka (Jinwoo, L.; Tanaka, H. Sci. Rep. 2015, 5, 7832) have shown that work fluctuation theorems hold even within an ensemble of paths to each state, making it clear that entropy and free energy of each microstate encode heat and work, respectively, within the conditioned set. Here we show that information that is characterized by the point-wise mutual information for each correlated state between two subsystems in a heat bath encodes the entropy production of the subsystems and heat bath during a coupling process. To this end, we extend the fluctuation theorem of information exchange (Sagawa, T.; Ueda, M. Phys. Rev. Lett. 2012, 109, 180602) by showing that the fluctuation theorem holds even within an ensemble of paths that reach a correlated state during dynamic co-evolution of two subsystems.

cond-mat.stat-mech↗

arXiv2019

Fluctuation Theorem of Information Exchange between Subsystems that Co-Evolve in Time

Sagawa and Ueda established a fluctuation theorem of information exchange by revealing the role of correlations in stochastic thermodynamics and unified the non-equilibrium thermodynamics of measurement and feedback control [T. Sagawa and M. Ueda, Phys. Rev. Lett. 109, 180602 (2012)]. They considered a process where a non-equilibrium system exchanges information with other degrees of freedom such as an observer or a feedback controller. They proved the fluctuation theorem of information exchange under the assumption that the state of the other degrees of freedom that exchange information with the system does not change over time while the states of the system evolve in time. Here we relax this constraint and prove that the same form of the fluctuation theorem holds even if both subsystems co-evolve during information exchange processes. This result may extend the applicability of the fluctuation theorem of information exchange to a broader class of non-equilibrium processes, such as a dynamic coupling in biological systems, where subsystems that exchange information interact with each other.

cond-mat.stat-mech↗

arXiv2015

Local non-equilibrium thermodynamics

Local Shannon entropy lies at the heart of modern thermodynamics, with much discussion of trajectory-dependent entropy production. When taken at both boundaries of a process in phase space, it reproduces the second law of thermodynamics over a finite time interval for small scale systems. However, given that entropy is an ensemble property, it has never been clear how one can assign such a quantity locally. Given such a fundamental omission in our knowledge, we construct a new ensemble composed of trajectories reaching an individual microstate, and show that locally defined entropy, information, and free energy are properties of the ensemble, or trajectory-independent true thermodynamic potentials. We find that the Boltzmann-Gibbs distribution and Landauer's principle can be generalized naturally as properties of the ensemble, and that trajectory-free state functions of the ensemble govern the exact mechanism of non-equilibrium relaxation.

cond-mat.stat-mech↗