Recovery of free energy branches in single molecule experiments

Roles of local nonequilibrium free energy in the description of biomolecules

When a system is in equilibrium, external perturbations yield a time series of nonequilibrium distributions, and recent experimental techniques give access to the nonequilibrium data that may contain critical information. Jinwoo and Tanaka [Sci. Rep. 5, 7832 (2015)2045-232210.1038/srep07832] have provided mathematical proof that such a process's nonequilibrium 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 the ATPase motor allocates the hydrolysis energy between individual substates until the end of the process. It turns out that the efficiency of RNA translocation is 48%-60% for most molecules, but 12% of molecules achieve 80%-100% efficiency, which is consistent with the literature. This theory would be a valuable tool for extracting quantitative information about molecular nonequilibrium behavior from experimental observations.

Measurement of the specific and non-specific binding energies of Mg2+ to RNA

Determining the non-specific and specific electrostatic contributions of magnesium binding to RNA is a challenging problem. We introduce a single-molecule method based on measuring the folding energy of a native RNA in magnesium and at its equivalent sodium concentration. The latter is defined so that the folding energy in sodium equals the non-specific electrostatic contribution in magnesium. The sodium equivalent can be estimated according to the empirical 100/1 rule (1 M NaCl is equivalent to 10 mM MgCl2), which is a good approximation for most RNAs. The method is applied to an RNA three-way junction (3WJ) that contains specific Mg2+ binding sites and misfolds into a double hairpin structure without binding sites. We mechanically pull the RNA with optical tweezers and use fluctuation theorems to determine the folding energies of the native and misfolded structures in magnesium (10 mM MgCl2) and at the equivalent sodium condition (1 M NaCl). While the free energies of the misfolded structure are equal in magnesium and sodium, they are not for the native structure, the difference being due to the specific binding energy of magnesium to the 3WJ, which equals ΔG≃ 10 kcal/mol. Besides stabilizing the 3WJ, Mg2+ also kinetically rescues it from the misfolded structure over timescales of tens of seconds in a force-dependent manner. The method should generally be applicable to determine the specific binding energies of divalent cations to other tertiary RNAs.

Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments

Force-spectroscopy techniques have led to significant progress in studying the physicochemical properties of biomolecules that are not accessible in bulk assays. The application of piconewton forces with laser optical tweezers to single nucleic acids has permitted the characterization of molecular thermodynamics and kinetics with unprecedented accuracy. Some examples are the hybridization reaction between complementary strands in DNA and the folding of secondary, tertiary, and other heterogeneous structures, such as intermediate and misfolded states in RNA. Here we review the results obtained in our lab on deriving the nearest-neighbor free energy parameters in DNA and RNA duplexes from mechanical unzipping experiments. Remarkable nonequilibrium effects are also observed, such as the large irreversibility of RNA unzipping and the formation of non-specific secondary structures in single-stranded DNA. These features originate from forming stem-loop structures along the single strands of the nucleic acid. The recently introduced barrier energy landscape model quantifies kinetic trapping effects due to stem-loops being applicable to both RNA and DNA. The barrier energy landscape model contains the essential features to explain the many behaviors observed in heterogeneous nucleic-acid folding.

Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems

Nonequilibrium work relations and fluctuation theorems permit us to extract equilibrium information from nonequilibrium measurements. They find application in single-molecule pulling experiments where molecular free energies can be determined from irreversible work measurements by using unidirectional (e.g., Jarzynski’s equality) and bidirectional (e.g., Crooks fluctuation theorem and Bennet’s acceptance ratio (BAR)) methods. However, irreversibility and the finite number of pulls limit their applicability: the higher the dissipation, the larger the number of pulls necessary to estimate ΔG within a few kBT. Here, we revisit pulling experiments on an RNA three-way junction (3WJ) that exhibits significant dissipation and work-distribution long tails upon mechanical unfolding. While bidirectional methods are more predictive, unidirectional methods are strongly biased. We also consider a cyclic protocol that combines the forward and reverse work values to increase the statistics of the measurements. For a fixed total experimental time, faster pulling rates permit us to efficiently sample rare events and reduce the bias, compensating for the increased dissipation. This analysis provides a more stringent test of the fluctuation theorem in the large irreversibility regime.

Stem-loop formation drives RNA folding in mechanical unzipping experiments

Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong irreversible effects with hysteresis and several intermediates, precluding the extraction of the NNBP energies with currently available methods. The combination of a suitable RNA synthesis with a tailored pulling protocol allowed us to obtain the fully reversible FDCs necessary to derive the NNBP energies. We demonstrate the equivalence of sodium and magnesium free-energy salt corrections at the level of individual NNBP. To characterize the irreversibility of the unzipping-rezipping process, we introduce a barrier energy landscape of the stem-loop structures forming along the complementary strands, which compete against the formation of the native hairpin. This landscape correlates with the hysteresis observed along the FDCs. RNA sequence analysis shows that base stacking and base pairing stabilize the stem-loops that kinetically trap the long-lived intermediates observed in the FDC. Stem-loops formation appears as a general mechanism to explain a wide range of behaviors observed in RNA folding.

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.

The Measurement of Information and Free Energy in Mechanical-Force-Driven Coil-Globule Transitions

We study the role of information (the relative entropy) for polymers undergoing coil-globule transitions driven by a time-dependent force. Pulling experiments at various speeds are performed by Brownian dynamics simulations. We obtain the work distributions for the forward and time-reversed backward processes and information stored at the end of the nonequilibrium pulling processes. We present the systematic method to measure the information from the pulling experiments and extract the information by analyzing slowly relaxing modes. When the information is incorporated, the work distributions modified by the information allow access to the proper free energy via the formulation of the generalized fluctuation theorems even if the initial states of the forward and time-reversed backward processes are out of equilibrium. This demonstrates that the work-information conversion works well for a single-molecule system with many degrees of freedom.

Free energy measurements by the generalized fluctuation theorems: Theory and numerical study of a model filament

We measure the free energy of a model filament, which undergoes deformations and structural transitions, as a function of its extension, in silico. We perform Brownian Dynamics (BD) simulations of pulling experiments at various speeds, following a protocol close to experimental ones. The results from the fluctuation theorems are compared with the estimates from Monte Carlo (MC) simulation, where the rugged free energy landscape is produced by the density of states method. The fluctuation theorems (FT) give accurate estimates of the free energy up to moderate pulling speeds. At higher pulling speeds, the work distributions do not efficiently sample the domain of small work and FT slightly overestimates free energy. In order to comprehend the differences, we analyze the work distributions from the BD simulations in the framework of trajectory thermodynamics and propose the generalized fluctuation theorems that take into account the information (relative entropy) evaluated in the expanded phase space. The measured work - free energy relation is consistent with the results obtained from the generalized fluctuation theorems. We discuss operational methods to improve the estimates at high pulling speed.

Path-integral approach to the calculation of the characteristic function of work

Work statistics characterizes important features of a nonequilibrium thermodynamic process, but the calculation of the work statistics in an arbitrary nonequilibrium process is usually a cumbersome task. In this work, we study the work statistics in quantum systems by employing Feynman's path-integral approach. We derive the analytical work distributions of two prototype quantum systems. The results are proved to be equivalent to the results obtained based on Schrödinger's formalism. We also calculate the work distributions in their classical counterparts by employing the path-integral approach. Our study demonstrates the effectiveness of the path-integral approach for the calculation of work statistics in both quantum and classical thermodynamics, and brings important insights to the understanding of the trajectory work in quantum systems.

Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states

The problem of recovering the free energy difference between two electronic states has been investigated by Frezzato [Chem. Phys. Lett. 533, 106 (2012)], exploring the equivalence between light-absorption spectra and work distribution, hence opening to the application of a spectroscopic version of the Jarzynski equality (JE) [Phys. Rev. Lett. 78, 2690 (1997)]. Here, assuming the validity of the time-dependent perturbation theory, we demonstrate that such equivalence does not lead to the known form of the JE. This is ascribed to the fact that light-absorption processes cannot be described as stochastic processes. To emphasize such an aspect, we devise a stochastic model for the UV-vis (ultraviolet and visible) absorption, suitable for determining the free energy difference between two generic quantum manifolds in a JE-like fashion. However, the model would require explicit knowledge of the transition dipole moments, which are in general not available. Nonetheless, we derive a spectroscopic version of the JE that allows us to recover the free energy difference between the ground and an excited electronic state when the latter state is the only one observed in the spectrum.

The life of proteins under mechanical force

Although much of our understanding of protein folding comes from studies of isolated protein domains in bulk, in the cellular environment the intervention of external molecular machines is essential during the protein life cycle. During the past decade single molecule force spectroscopy techniques have been extremely useful to deepen our understanding of these interventional molecular processes, as they allow for monitoring and manipulating mechanochemical events in individual protein molecules. Here, we review some of the critical steps in the protein life cycle, starting with the biosynthesis of the nascent polypeptide chain in the ribosome, continuing with the folding supported by chaperones and the translocation into different cell compartments, and ending with proteolysis in the proteasome. Along these steps, proteins experience molecular forces often combined with chemical transformations, affecting their folding and structure, which are measured or mimicked in the laboratory by the application of force with a single molecule apparatus. These mechanochemical reactions can potentially be used as targets for fighting against diseases. Inspired by these insightful experiments, we devise an outlook on the emerging field of mechanopharmacology, which reflects an alternative paradigm for drug design.

Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems

Thermodynamic bulk measurements of binding reactions rely on the validity of the law of mass action and the assumption of a dilute solution. Yet, important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, or misfolded molecules may not follow these assumptions and may require a particular reaction model. Here we introduce a fluctuation theorem for ligand binding and an experimental approach using single-molecule force spectroscopy to determine binding energies, selectivity, and allostery of nucleic acids and peptides in a model-independent fashion. A similar approach could be used for proteins. This work extends the use of fluctuation theorems beyond unimolecular folding reactions, bridging the thermodynamics of small systems and the basic laws of chemical equilibrium.

Direct measurement of weakly nonequilibrium system entropy is consistent with Gibbs-Shannon form

Stochastic thermodynamics extends classical thermodynamics to small systems in contact with one or more heat baths. It can account for the effects of thermal fluctuations and describe systems far from thermodynamic equilibrium. A basic assumption is that the expression for Shannon entropy is the appropriate description for the entropy of a nonequilibrium system in such a setting. Here we measure experimentally this function in a system that is in local but not global equilibrium. Our system is a micron-scale colloidal particle in water, in a virtual double-well potential created by a feedback trap. We measure the work to erase a fraction of a bit of information and show that it is bounded by the Shannon entropy for a two-state system. Further, by measuring directly the reversibility of slow protocols, we can distinguish unambiguously between protocols that can and cannot reach the expected thermodynamic bounds.

Nonequilibrium interactions between ideal polymers and a repulsive surface

We use Newtonian and overdamped Langevin dynamics to study long flexible polymers dragged by an external force at a constant velocity v. The work W performed by that force depends on the initial state of the polymer and the details of the process. The Jarzynski equality can be used to relate the nonequilibrium work distribution P(W) obtained from repeated experiments to the equilibrium free energy difference ΔF between the initial and final states. We use the power law dependence of the geometrical and dynamical characteristics of the polymer on the number of monomers N to suggest the existence of a critical velocity v_{c}(N), such that for v<v_{c} the reconstruction of ΔF is an easy task, while for v significantly exceeding v_{c} it becomes practically impossible. We demonstrate the existence of such v_{c} analytically for an ideal polymer in free space and numerically for a polymer which is being dragged away from a repulsive wall. Our results suggest that the distribution of the dissipated work W_{d}=W-ΔF in properly scaled variables approaches a limiting shape for large N.

Scaling Law for Irreversible Entropy Production in Critical Systems

We examine the Jarzynski equality for a quenching process across the critical point of second-order phase transitions, where absolute irreversibility and the effect of finite-sampling of the initial equilibrium distribution arise in a single setup with equal significance. We consider the Ising model as a prototypical example for spontaneous symmetry breaking and take into account the finite sampling issue by introducing a tolerance parameter. The initially ordered spins become disordered by quenching the ferromagnetic coupling constant. For a sudden quench, the deviation from the Jarzynski equality evaluated from the ideal ensemble average could, in principle, depend on the reduced coupling constant ε₀ of the initial state and the system size L. We find that, instead of depending on ε₀ and L separately, this deviation exhibits a scaling behavior through a universal combination of ε₀ and L for a given tolerance parameter, inherited from the critical scaling laws of second-order phase transitions. A similar scaling law can be obtained for the finite-speed quench as well within the Kibble-Zurek mechanism.

Jarzynski matrix equality: Calculating the free-energy difference by nonequilibrium simulations with an arbitrary initial distribution

The Jarzynski equality (JE) method, which relates the work of a nonequilibrium process to the free-energy difference between its initial and final states, provides an efficient way to calculate free energies of thermodynamic systems in simulations or experiments. However, more extensive applications of the JE are hindered by the requirement that the initial state must be in equilibrium. In this work we extend the JE method to be the Jarzynski matrix equality (JME) method, which relates the work of trajectories connecting metastable conformational regions to their local free energies, and thus we can estimate the free energy from the nonequilibrium trajectories starting from an almost arbitrary initial distribution. We then apply the JME to toy models, Lennard-Jones fluids, and polymer chain models, demonstrating its efficiency in free-energy calculations with satisfactory accuracy. The JME extends the applicability of the nonequilibrium methods to complex systems whose initial equilibrium states are difficult to reach.

Jarzynski equality, Crooks fluctuation theorem, and the fluctuation theorems of heat for arbitrary initial states

By taking full advantage of the dynamic property imposed by the detailed balance condition, we derive a new refined unified fluctuation theorem (FT) for general stochastic thermodynamic systems. This FT involves the joint probability distribution functions of the final phase-space point and a thermodynamic variable. Jarzynski equality, Crooks fluctuation theorem, and the FTs of heat as well as the trajectory entropy production can be regarded as special cases of this refined unified FT, and all of them are generalized to arbitrary initial distributions. We also find that the refined unified FT can easily reproduce the FTs for processes with the feedback control, due to its unconventional structure that separates the thermodynamic variable from the choices of initial distributions. Our result is heuristic for further understanding of the relations and distinctions between all kinds of FTs and might be valuable for studying thermodynamic processes with information exchange.

Multifractality of random eigenfunctions and generalization of Jarzynski equality

Systems driven out of equilibrium experience large fluctuations of the dissipated work. The same is true for wavefunction amplitudes in disordered systems close to the Anderson localization transition. In both cases, the probability distribution function is given by the large-deviation ansatz. Here we exploit the analogy between the statistics of work dissipated in a driven single-electron box and that of random multifractal wavefunction amplitudes, and uncover new relations that generalize the Jarzynski equality. We checked the new relations theoretically using the rate equations for sequential tunnelling of electrons and experimentally by measuring the dissipated work in a driven single-electron box and found a remarkable correspondence. The results represent an important universal feature of the work statistics in systems out of equilibrium and help to understand the nature of the symmetry of multifractal exponents in the theory of Anderson localization.

The work fluctuations of systems driven out of equilibrium are governed by the same large-deviation theory as wavefunction amplitudes close to the Anderson localization transition. Exploiting this analogy, the authors generalize the Jarzynski equality, verifying their relation on a single-electron box.

Reconstruction and identification of DNA sequence landscapes from unzipping experiments at equilibrium

Two methods for reconstructing the free-energy landscape of a DNA molecule from the knowledge of the equilibrium unzipping force versus extension signal are introduced: a simple and fast procedure, based on a parametric representation of the experimental force signal, and a maximum-likelihood inference of coarse-grained free-energy parameters. In addition, we propose a force alignment procedure to correct for the drift in the experimental measure of the opening position, a major source of error. For unzipping data obtained by Huguet et al., the reconstructed basepair (bp) free energies agree with the running average of the true free energies on a 20-50 bp scale, depending on the region in the sequence. Features of the landscape at a smaller scale (5-10 bp) could be recovered in favorable regions at the beginning of the molecule. Based on the analysis of synthetic data corresponding to the 16S rDNA gene of bacteria, we show that our approach could be used to identify specific DNA sequences among thousands of homologous sequences in a database.

Modulated two-level system: exact work statistics

We consider an open two-level system driven by a piecewise constant periodic field and described by a rate equation with Fermi, Bose, and Arrhenius rates, respectively. We derive an analytical expression for the generating function and large deviation function of the work performed by the field and show that a work fluctuation theorem holds.

Fluctuation theorems for quantum processes

We present fluctuation theorems and moment generating function equalities for generalized thermodynamic observables and quantum dynamics described by completely positive trace preserving maps, with and without feedback control. Our results include the quantum Jarzynski equality and Crooks fluctuation theorem, and clarify the special role played by the thermodynamic work and thermal equilibrium states in previous studies. We show that for a specific class of generalized measurements, which include projective measurements, unitality replaces microreversibility as the condition for the physicality of the reverse process in our fluctuation theorems. We present an experimental application of our theory to the problem of extracting the system-bath coupling magnitude, which we do for a system of pairs of coupled superconducting flux qubits undergoing quantum annealing.

Sawtooth patterns in force-extension curves of biomolecules: an equilibrium-statistical-mechanics theory

We analyze the force-extension curve for a general class of systems, which are described at the mesoscopic level by a free energy depending on the extension of its components. Similarly to what is done in real experiments, the total length of the system is the controlled parameter. This imposes a global constraint in the minimization procedure leading to the equilibrium values of the extensions. As a consequence, the force-extension curve has multiple branches in a certain range of forces. The stability of these branches is governed by the free energy: there are a series of first-order phase transitions at certain values of the total length, in which the free energy itself is continuous but its first derivative, the force, has a finite jump. This behavior is completely similar to that observed in real experiments with biomolecules like proteins and with other complex systems.

Probing small-scale intermittency with a fluctuation theorem

We characterize statistical properties of the flow field in developed turbulence using concepts from stochastic thermodynamics. On the basis of data from a free air-jet experiment, we demonstrate how the dynamic fluctuations induced by small-scale intermittency generate analogs of entropy-consuming trajectories with sufficient weight to make fluctuation theorems observable at the macroscopic scale. We propose an integral fluctuation theorem for the entropy production associated with the stochastic evolution of velocity increments along the eddy hierarchy and demonstrate its extreme sensitivity to the accurate description of the tails of the velocity distributions.

Work relations for time-dependent states

For time-dependent states generated by an external operation, a generalized free energy may be introduced by the relative entropy with respect to an equilibrium state realized after sufficient relaxation from the time-dependent states. Recently, by studying overdamped systems, Sivak and Crooks presented a formula that relates the generalized free energy with measurable thermodynamic works. We rederive this relation with emphasizing a connection to an extended Clausius relation proposed in the framework of steady state thermodynamics. As a natural consequence, we generalize this relation to be valid for systems with momentum degrees of freedom, where the Shannon entropy in the generalized free energy is replaced by a symmetric one.

Stochastic thermodynamics, fluctuation theorems and molecular machines

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation-dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.

Test of the Jarzynski and Crooks fluctuation relations in an electronic system

Recent progress on micro- and nanometer-scale manipulation has opened the possibility to probe systems small enough that thermal fluctuations of energy and coordinate variables can be significant compared with their mean behavior. We present an experimental study of nonequilibrium thermodynamics in a classical two-state system, namely, a metallic single-electron box. We have measured with high statistical accuracy the distribution of dissipated energy as single electrons are transferred between the box electrodes. The obtained distributions obey Jarzynski and Crooks fluctuation relations. A comprehensive microscopic theory exists for the system, enabling the experimental distributions to be reproduced without fitting parameters.

Crooks relation in optical spectra: universality in work distributions for weak local quenches

We show that work distributions and nonequilibrium work fluctuation theorems can be measured in optical spectra for a wide class of quantum systems. We consider systems where the absorption or emission of a photon corresponds to the sudden switch on or off of a local perturbation. For the particular case of a weak local perturbation, the Crooks relation establishes a universal relation in absorption as well as in emission spectra. Because of a direct relation between the spectra and work distribution functions this is equivalent to universal relations in work distributions for weak local quenches. As two concrete examples we treat the x-ray edge problem and the Kondo exciton.

Measuring the folding landscape of a harmonically constrained biopolymer

Pioneering studies have shown that the probability distribution of opening length for a DNA hairpin, recorded under constant force using an optical trap, can be used to reconstruct the energy landscape of the transition. However, measurements made under constant force are subject to some limitations. Under constant force a system with a sufficiently high energy barrier spends most of its time in the closed or open conformation, with relatively few statistics collected in the transition state region. We describe a measurement scheme in which the system is driven progressively through the transition by an optical trap and an algorithm is used to extract the energy landscape of the transition from the fluctuations recorded during this process. We illustrate this technique in simulations and demonstrate its effectiveness in experiments on a DNA hairpin. We find that the combination of this technique with the use of short DNA handles facilitates a high-resolution measurement of the hairpin's folding landscape with a very short measurement time.

Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments

Recently discovered identities in statistical mechanics have enabled the calculation of equilibrium ensemble averages from realizations of driven nonequilibrium processes, including single-molecule pulling experiments and analogous computer simulations. Challenges in collecting large data sets motivate the pursuit of efficient statistical estimators that maximize use of available information. Along these lines, Hummer and Szabo developed an estimator that combines data from multiple time slices along a driven nonequilibrium process to compute the potential of mean force. Here, we generalize their approach, pooling information from multiple time slices to estimate arbitrary equilibrium expectations. Our expression may be combined with estimators of path-ensemble averages, including existing optimal estimators that use data collected by unidirectional and bidirectional protocols. We demonstrate the estimator by calculating free energies, moments of the polymer extension, the thermodynamic metric tensor, and the thermodynamic length in a model single-molecule pulling experiment. Compared to estimators that only use individual time slices, our multiple time-slice estimators yield substantially smoother estimates and achieve lower variance for higher-order moments.

Stochastic thermodynamics of single enzymes and molecular motors

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 of internal energy, intrinsic entropy and free energy for states follows from a microscopic description using one assumption on time scale separation. A first-law energy balance then allows the unique identification of the heat dissipated in one transition. Consistency with the second law on the ensemble level enforces both stochastic entropy as third contribution to the entropy change involved in one transition and the local detailed balance condition for the ratio between forward and backward rates for any transition. These results follow without assuming weak coupling between the enzyme and the solutes, ideal solution behavior or mass action law kinetics. The present approach highlights both the crucial role of the intrinsic entropy of each state and the physically questionable role of chemiostats for deriving the first law for molecular motors subject to an external force under realistic conditions.

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

Existing optimal estimators of nonequilibrium path-ensemble averages are shown to fall within the framework of extended bridge sampling. Using this framework, we derive a general minimal-variance estimator that can combine nonequilibrium trajectory data sampled from multiple path-ensembles to estimate arbitrary functions of nonequilibrium expectations. The framework is also applied to obtain asymptotic variance estimates, which are a useful measure of statistical uncertainty. In particular, we develop asymptotic variance estimates pertaining to Jarzynski's equality for free energies and the Hummer-Szabo expressions for the potential of mean force, calculated from uni- or bidirectional path samples. These estimators are demonstrated on a model single-molecule pulling experiment. In these simulations, the asymptotic variance expression is found to accurately characterize the confidence intervals around estimators when the bias is small. Hence, the confidence intervals are inaccurately described for unidirectional estimates with large bias, but for this model it largely reflects the true error in a bidirectional estimator derived by Minh and Adib.