In this paper we propose a new formalism to map history-dependent metadynamics in a Markovian process. We apply this formalism to a model Langevin dynamics and determine the equilibrium distribution of a collection of simulations. We demonstrate that the reconstructed free energy is an unbiased estimate of the underlying free energy and analytically derive an expression for the error. The present results can be applied to other history-dependent stochastic processes such as Wang-Landau sampling.
Inspired by thermodynamic integration, we propose a method for the calculation of time-independent free energy profiles from history-dependent biased simulations via Mean Force Integration (MFI). MFI circumvents the need for computing the ensemble average of the bias acting on the system c(t) and can be applied to different variants of metadynamics. Moreover, MFI naturally extends to aggregate information obtained from independent metadynamics simulations, allowing to converge free energy surfaces without the need to sample recrossing events in a single continuous trajectory. We validate MFI a…
Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process as well as correctly calculating the relative free energies of different polymorphs. Here we demonstrate, for the prototypical case of urea nucleation from melt, how one can learn such a 1-dimensional reaction coordinate as a function of pre-specified order parameters, and use it to perform efficient biased all-atom molecular dynamics simulations. The r…
Adaptive tensor train metadynamics for high-dimensional free energy exploration
James Franck Institute, University of Chicago（詹姆斯·弗兰克研究所，芝加哥大学）；Department of Statistics, University of Chicago（统计学系，芝加哥大学）；Department of Chemistry, University of Chicago（化学系，芝加哥大学）
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we propose a replica exchange method. In each replica two copies of the same system with halved potential strengths interact via inelastic springs. The strength of the spring is varied in the different replicas so as to bridge the gap between the infinitely strong spring, that corresponds to the Boltzmann replica and the less tight ones. We enhance the spring leng…
We introduce an approach for the accurate calculation of thermal properties of classical nanoclusters. Based on a recently developed enhanced sampling technique, replica exchange metadynamics, the method yields the true free energy of each relevant cluster structure, directly sampling its basin and measuring its occupancy in full equilibrium. All entropy sources, whether vibrational, rotational anharmonic and especially configurational -- the latter often forgotten in many cluster studies -- are automatically included. For the present demonstration we choose the water nonamer (H2O)9, an extrem…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecu…
We discuss that the thermodynamics of composite systems with non-additive entropies and additive energies can be equivalently derived considering additive entropies and non-additive energies. The general discussion is illustrated by a particular example.
According to the Jarzynski theorem, equilibrium free energy differences can be calculated from the statistics of work carried out during non-equilibrium transformations. Although exact, this approach can be plagued by large statistical errors, particularly for systems driven strongly away from equilibrium. Recently, several approaches have been suggested to reduce these errors. In this paper we study the efficiency of these methods using two models for which analytical solutions exist.
A recent result, relating the (irreversible) work performed on a system during a non-quasistatic process, to the Helmholtz free energy difference between two equilibrium states of the system, is discussed. A proof of this result is given for the special case when the evolution of the system in question is modelled by a Langevin equation in configuration space.
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 th…
Cold atoms in dissipative optical lattices have long been known to exhibit anomalous kinetics due to an effective nonlinear friction force. Here we show that confining the spatial motion of the atoms will lead to an anomalous non-Boltzmann-Gibbs equilibrium state, with a power law tail at large energies. Only in the limit of deep optical lattices, do we regain the Boltzmann-Gibbs state. For strong confinement relative to the damping, we find an explicit expression for the equilibrium phase-space distribution, which generally differs from the canonical Boltzmann-Gibbs state at all energies. Bot…
We consider in this paper, a few important issues in non-equilibrium work fluctuations and their relations to equilibrium free energies. First we show that Jarzynski identity can be viewed as a cumulant expansion of work. For a switching process which is nearly quasistatic the work distribution is sharply peaked and Gaussian. We show analytically that dissipation given by average work minus reversible work $W_R$, decreases when the process becomes more and more quasistatic. Eventually, in the quasistatic reversible limit, the dissipation vanishes. However estimate of $p$ - the probability of v…
Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free energy differences that are in principle exact. Numerical simulations show that Newton's equation can be discretized to low order over very large time steps (limit…
We implement a general numerical calculation that allows for a direct comparison between nonlinear Hamiltonian dynamics and the Boltzmann-Gibbs canonical distribution in Gibbs $Γ$-space. Using paradigmatic first-neighbor models, namely, the inertial XY ferromagnet and the Fermi-Pasta-Ulam $β$-model, we show that at intermediate energies the Boltzmann-Gibbs equilibrium distribution is a consequence of Newton second law (${\mathbf F}=m{\mathbf a}$). At higher energies we discuss partial agreement between time and ensemble averages.
The Jarzynski equality (JE), which relates works of non-equilibrium trajectories to the free energy difference of the initial and final states of the non-equilibrium process, provides an efficient way to calculate free energies of systems in simulations and experiments. However, wider applications of the JE are limited by the requirement that the initial distribution of non-equilibrium trajectories must be equilibrium. Here we extend the JE to a matrix form, the Jarzynski matrix equality (JME), which transforms the free energies of metastable conformational regions in the initial system to tha…
The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to non-equilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics of proteins and nucleic acids. The effects of experimental error and instrument noise have not previously been considered. Here, we present a Bayesian formalism for estimating free-energy changes from non-equilibrium work measurements that compensates for instrument noise and combines data from multiple driving protocols. We reanalyze a recent set of experi…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-alpha. Second…
Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead that is weakly bound to a cell and then removed by an optical tweezer. The external driving force arises from the combined optical tweezer and substrate potentials, and thermal fluctuations are taken into account by a Brownian force. The Jarzynski equality and Crooks' fluctuation theorem are applied to obtain the equilibrium free energy difference between t…
In recent years it has been found that quantum systems can posses entanglement in equilibrium thermal states provided temperature is low enough. In the present work we explore a possibility of having entanglement in nonequilibrium stationary states. We show analytically that, in a simple one-dimensional spin chain, there is entanglement even at highest attainable energies; that is, starting from an equilibrium state at infinite temperature, a sufficiently strong driving can induce entanglement, even in the thermodynamic limit. We also show that dissipative dephasing, on the other hand, destroy…
We perform extensive simulations of a binary mixture Lennard-Jones system subjected to a temperature jump in order to study the time evolution of fluctuations during aging. Analyzing data from 1500 different aging realizations, we calculate distributions of inherent structure energies for different aging times and contrast them with equilibrium. We find that the distributions initially become narrower and then widen as the system equilibrates. For deep quenches, fluctuations in the glassy system differ significantly from those observed in equilibrium. Simulation results are partially captured …
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the WHAM technique applied to al…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is considered, wherein the system is prepared and released from a nonequilibrium state, and no external work is involved during its observation. For such ``clamp-and-release'' processes, a simple strategy for the estimation of equilibrium free energies is offered. The method is illustrated with numerical simulations, and analyzed in the context of tethered sin…
The distributions of work for strongly non-equilibrium processes are studied using a very general form of a large-deviation approach, which allows one to study distributions of almost arbitrary quantities of interest for equilibrium, non-equilibrium stationary and even non-stationary processes. The method is applied to varying quickly the external field in a wide range B=3 <-> 0 for critical (T=2.269) two-dimensional Ising system of size LxL=128x128. To obtain free energy differences from the work distributions, they must be studied in ranges where the probabilities are as small as 10^{-240}, …
The Hamiltonian Mean-Field model (HMF), an inertial XY ferromagnet with infinite-range interactions, has been extensively studied in the last few years, especially due to its long-lived meta-equilibrium states, which exhibit a series of anomalies, such as, breakdown of ergodicity, anomalous diffusion, aging, and non-Maxwell velocity distributions. The most widely investigated meta-equilibrium states of the HMF arise from special (fully magnetized) initial conditions that evolve to a spatially homogeneous state with well defined macroscopic characteristics and whose lifetime increases with the …
We discuss different free energies for materials in static electric and magnetic fields. We explain what the corresponding Hamiltonians are, and describe which choice gives rise to which result for the free energy change, dF, in the thermodynamic identity. We also discuss which Hamiltonian is the most appropriate for calculations using statistical mechanics, as well as the relationship between the various free energies and the "Landau function", which has to be minimized to determine the equilibrium polarization or magnetization, and is central to Landau's theory of second order phase transiti…
In small systems where relevant energies are comparable to thermal agitation, fluctuations are of the order of average values. In systems in thermodynamical equilibrium, the variance of these fluctuations can be related to the dissipation constant in the system, exploiting the Fluctuation-Dissipation Theorem (FDT). In non-equilibrium steady systems, Fluctuations Theorems (FT) additionally describe symmetry properties of the probability density functions (PDFs) of the fluctuations of injected and dissipated energies. We experimentally probe a model system: an electrical dipole driven out of equ…
Configurational states that are to be associated, according to Goldstein, with the basins in the potential energy landscape cannot be characterized by any particular basin identifier such as the basin minima, the lowest barrier, the most probable energy barrier, etc. since the basin free energy turns out to be independent of the energies of these identifiers. Thus, our analysis utilizes basin free energies to characterize configurational states. When the basin identifier energies are monotonic, we can express the equilibrium basin free energy as a function of an equilibrium basin identifier en…
The theory of dynamical quantum phase transitions represents an attempt to extend the concept of phase transitions to the far from equilibrium regime. While there are many formal analogies to conventional transitions, it is a major question to which extent it is possible to formulate a nonequilibrium counterpart to a Landau-Ginzburg theory. In this work we take a first step in this direction by constructing an effective free energy for continuous dynamical quantum phase transitions appearing after quantum quenches in the transverse-field Ising chain. Due to unitarity of quantum time evolution …
Fluctuation relations allow for the computation of equilibrium properties, like free energy, from an ensemble of non-equilibrium dynamics simulations. Computing them for quantum systems, however, can be difficult, as performing dynamic simulations of such systems is exponentially hard on classical computers. Quantum computers can alleviate this hurdle, as they can efficiently simulate quantum systems. Here, we present an algorithm utilizing a fluctuation relation known as the Jarzynski equality to approximate free energy differences of quantum systems on a quantum computer. We discuss under wh…
The equilibrium crystal shape (ECS) of oxygen-covered tungsten micricrystal is studied as a function of temperature. The specially designed ultrafast crystal quenching setup with the cooling rate of 6000 K/s allows to draw conclusions about ECS at high temperatures. The edge-rounding transition is shown to occur between 1300 K and 1430 K. The ratio of surface free energies $γ(111)/γ(211)$ is determined as a function of temperature.
There is experimental and theoretical evidence that the broad rapidity distribution of net proton yield in central heavy-ion collisions at SPS energies could be a signal of non-equilibrium properties of the system. We show that the broad rapidity shape can be well reproduced in the framework of a non-linear relativistic Fokker-Planck dynamics which incorporates non-extensive statistics and anomalous diffusion.
In two recent papers, Maroney and Turgut separately and independently show generalisations of Landauer's erasure principle to indeterministic logical operations, as well as to logical states with variable energies and entropies. Here we show that, although Turgut's generalisation seems more powerful, in that it implies but is not implied by Maroney's and that it does not rely upon initial probability distributions over logical states, it does not hold for non-equilibrium states, while Maroney's generalisation holds even in non-equilibrium. While a generalisation of Turgut's inequality to non-e…
We develop a functional renormalization group approach to obtain the time evolution of the momentum distribution function of interacting bosons out of equilibrium. Using an external out-scattering rate as flow parameter, we derive formally exact renormalization group flow equations for the non-equilibrium self-energies in the Keldysh basis. A simple perturbative truncation of these flow equations leads to an approximate solution of the quantum Boltzmann equation which does not suffer from secular terms and gives accurate results even for long times. We demonstrate this explicitly within a simp…
