Probing molecular free energy landscapes by periodic loading

Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a challenge, in particular, for the unstable barrier regions. We propose a new method for obtaining the full profile by introducing a periodic ramp and using Jarzynski's relation for obtaining equilibrium quantities from nonequilibrium data. Our simulated experiments show that this method delivers significant more accurate data than previous methods, under the constraint of equal experimental effort.     

平衡和非平衡方法计算相对结合自由能的精度和效率比较

Estimation of protein-ligand binding affinity within chemical accuracy is one of the grand challenges in structure-based rational drug design. With the efforts over three decades, free energy methods based on equilibrium molecular dynamics (MD) simulations have become mature and are nowadays routinely applied in the community of computational chemistry. On the contrary, nonequilibrium MD simulation methods have attracted less attention, despite their underlying rigor in mathematics and potential advantage in efficiency. In this work, the equilibrium and nonequilibrium simulation methods are compared in terms of accuracy and convergence rate in the calculations of relative binding free energies. The proteins studied are T4-lysozyme mutant L99A and COX-2. For each protein, two ligands are studied. The results show that the nonequilibrium simulation method can be competitively as accurate as the equilibrium method, and the former is more efficient than the latter by considering the convergence rate with respect to the cost of wall clock time. In addition, Bennett acceptance ratio, which is a bidirectional post-processing method, converges faster than the unidirectional Jarzynski equality for the nonequilibrium simulations.     

Reconstructing Free Energy Profiles from Nonequilibrium Relaxation Trajectories

Reconstructing free energy profiles is an important problem in bimolecular reactions, protein folding or allosteric conformational changes. Nonequilibrium trajectories are readily measured experimentally, but their statistical significance and relation to equilibrium system properties still call for rigorous methods of assessment and interpretation. Here we introduce methods to compute the equilibrium free energy profile of a given variable from a set of short nonequilibrium trajectories, obtained by externally driving a system out of equilibrium and subsequently observing its relaxation. This protocol is not suitable for the Jarzynski equality since the irreversible work on the system is instantaneous. Assuming that the variable of interest satisfies an overdamped Langevin equation, which is frequently used for modeling biomolecular processes, we show that the trajectories sample a nonequilibrium stationary distribution that can be calculated in closed form. This allows for the estimation of the free energy via an inversion procedure that is analogous to that used in equilibrium and bypasses more complicated path integral methods, which we derive for comparison. We generalize the inversion procedure to systems with a diffusion constant that depends on the reaction coordinate, as is the case in protein folding, as well as to protocols in which the trajectories are initiated at random points. Using only a statistical pool of tens of synthetic trajectories, we demonstrate the versatility of these methods by reconstructing double and multi-well potentials, as well as a proposed profile for the hydrophobic collapse of a protein.     

Work and power production in non-equilibrium systems

We study work production in a Markov system obeying discrete stochastic dynamics. As our main result, we establish a new equality concerning the work produced during a spontaneous transformation in an isothermal, non-equilibrium system. Then we consider the overall evolution of a non-equilibrium system driven by an external parameter and generalize Jarzynski's equality for systems maintained out of equilibrium. That equality is recovered if the initial and final state distributions are equilibriums.     

非平衡功与自由能差的关系

以一个受迫谐振子为对象证明了Jarzynski等式,即两平衡态的自由能差可以用它们之间非平衡功的指数平均来表示,这里两个态的转换是在有限时间完成的.当外部驱动力是一个周期信号时,发现外界对系统所做的广义功存在一个共振现象.     

Length of time's arrow

An unresolved problem in physics is how the thermodynamic arrow of time arises from an underlying time reversible dynamics. We contribute to this issue by developing a measure of time-symmetry breaking, and by using the work fluctuation relations, we determine the time asymmetry of recent single molecule RNA unfolding experiments. We define time asymmetry as the Jensen-Shannon divergence between trajectory probability distributions of an experiment and its time-reversed conjugate. Among other interesting properties, the length of time's arrow bounds the average dissipation and determines the difficulty of accurately estimating free energy differences in nonequilibrium experiments.     

Employing trapped cold ions to verify the quantum Jarzynski equality

We propose a scheme to investigate the nonequilibrium work distribution of a quantum particle under well controlled transformations of the external potential, exploiting the versatility of a single ion in a segmented linear Paul trap. We describe in detail how the motional quantum state of a single ion can be prepared, manipulated, and finally readout to fully determine the free energy difference in both harmonic and anharmonic potentials. Uniquely to our system, we show how an ion may be immersed in an engineered laser-field reservoir. Trapped ions therefore represent an ideal tool for investigating the Jarzynski equality in open and closed quantum systems.     

Effect of quantum collapse on the distribution of work in driven single molecules

Two sources of quantum deviations from Jarzynski's celebrated classical relation between the free energy change and the distribution of work are analyzed using an exactly solvable harmonic model: Quantum dynamics retains the Gaussian profile of the distribution and merely gives rise to analytic corrections in variant Planck's over 2pi, whereas quantum measurements (wave function collapse) induce extended power-law tails which fundamentally alter the distribution. These results may be observed in quantum information processing and in experiments involving mechanically or optically driven single quantum objects.     

Nonequilibrium Thermodynamics of Polymeric Liquids via Atomistic Simulation

The challenge of calculating nonequilibrium entropy in polymeric liquids undergoing flow was addressed from the perspective of extending equilibrium thermodynamics to include internal variables that quantify the internal microstructure of chain-like macromolecules and then applying these principles to nonequilibrium conditions under the presumption of an evolution of quasie equilibrium states in which the requisite internal variables relax on different time scales. The nonequilibrium entropy can be determined at various levels of coarse-graining of the polymer chains by statistical expressions involving nonequilibrium distribution functions that depend on the type of flow and the flow strength. Using nonequilibrium molecular dynamics simulations of a linear, monodisperse, entangled C₁₀₀₀H₂₀₀₂ polyethylene melt, nonequilibrium entropy was calculated directly from the nonequilibrium distribution functions, as well as from their second moments, and also using the radial distribution function at various levels of coarse-graining of the constituent macromolecular chains. Surprisingly, all these different methods of calculating the nonequilibrium entropy provide consistent values under both planar Couette and planar elongational flows. Combining the nonequilibrium entropy with the internal energy allows determination of the Helmholtz free energy, which is used as a generating function of flow dynamics in nonequilibrium thermodynamic theory.     

Ising-like model for protein mechanical unfolding

The mechanical unfolding of proteins is studied by extending the Wako-Sait?-Mu?oz-Eaton model. This model is generalized by including an external force, and its thermodynamics turns out to be exactly solvable. We consider two molecules, the 27th immunoglobulin domain of titin and protein PIN1. We determine equilibrium force-extension curves for the titin and study the mechanical unfolding of this molecule, finding good agreement with experiments. By using an extended form of the Jarzynski equality, we compute the free energy landscape of the PIN1 as a function of the molecule length.     

Reconstructing the free-energy landscape of a mechanically unfolded model protein

The equilibrium free-energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the "folding transition" we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.     

Near-equilibrium measurements of nonequilibrium free energy

A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a nonequilibrium ensemble is that it is larger than that of the same system at equilibrium. Herein, we derive a formally exact expression for the probability distribution of a driven system, which involves path ensemble averages of the work over trajectories of the time-reversed system. From this we find a simple near-equilibrium approximation for the free energy in terms of an excess mean time-reversed work, which can be experimentally measured on real systems. With analysis and computer simulation, we demonstrate the accuracy of our approximations for several simple models.     

Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis

Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.     

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.     

Equilibrium Sampling From Nonequilibrium Dynamics

We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a nonequilibrium random process to keep closer to equilibrium at each time, thanks to a selection mechanism based on the relative virtual work induced on the system. It is therefore an efficient improvement of usual nonequilibrium simulations, which can be used to compute canonical averages, free energy differences, and typical transitions paths. AMS: 65C05 65C35 80A10     

Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments

We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (P(fold)=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that P(fold) is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.     

Equality connecting energy dissipation with a violation of the fluctuation-response relation

In systems driven away from equilibrium, the velocity correlation function and the linear-response function to a small perturbation force do not satisfy the fluctuation-response relation (FRR) due to the lack of detailed balance in contrast to equilibrium systems. In this Letter, an equality between an extent of the FRR violation and the rate of energy dissipation is proved for Langevin systems under nonequilibrium conditions. This equality enables us to calculate the rate of energy dissipation by quantifying the extent of the FRR violation, which can be measured experimentally.     

Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism

It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is to minimize free energy consumption given a free energy drain corresponding to growth. The interpretation is distinct from conventional nonequilibrium thermodynamics, although it does satisfy a minimum entropy production principle. It can be used to motivate extensions of constraint-based modeling, for example, to microbial ecosystems.     

Methods of calculating the band structure and low-energy secondary electron spectroscopy of iridium

A theoretical interpretation is put forward for the fine structure of the secondary electron emission spectra of Ir normal to the (111) surface and the total current spectrum of an Ir polycrystal. The calculations took into account the energy dependence of the broadening of the energy band levels, the electron-electron and electron-plasmon contributions to the nonequilibrium electron distribution function, and the isotropic component of the current from the electrons scattered at the surface. It is shown that the fine structure of the secondary electron emission spectrum and the total current spectrum is mainly attributable to the electron structure of the final states into which the electrons enter or from which they are emitted so that the characteristics of the band configuration in the energy band structure can be reconstructed directly from the experimental data. This method can be used to separate bulk effects from surface effects in the secondary electron emission and total current spectra. It is confirmed that the fine structure of the secondary electron emission and total current spectra depends on the geometric structure and the degree of ordering of the crystals. A reduction in the intensity of the fine structure serves as a measure of the defect structure in the surface region of the sample which can be successfully used to monitor the surface state during treatment. Zh. Tekh. Fiz. 69, 94–96 (June 1999)     

Mean energy of semibounded solids at equilibrium and with hot electrons in a subsurface layer

A method that allowed the calculation of the total mean energy of semibounded crystals at equilibrium and in the nonequilibrium state associated with the presence of a thin subsurface layer of hot electrons is developed. Two-temperature systems in which the temperature of electrons remains for a certain period higher than that of the crystal were considered. The layer can consist of either Fermi or Boltzmann electrons. The densities and mean energies of electrons in a two-dimensional layer were calculated. The interaction of electrons with lattice vibrations was postulated to be of deformational character. The temperature dependences of bulk and surface Rayleigh waves in equilibrium and nonequilibrium states were determined. It was demonstrated that the nonequilibrium energy of Rayleigh waves is inversely proportional to the width of their energy spectrum. Thick samples and films with a thickness comparable with the lattice vibration wavelength were considered. The calculations were performed using the Keldysh diagram technique. This method, suitable for calculating the macroscopic characteristics of nonequilibrium unbounded systems, was extended to semibounded systems.