No Arabic abstract
The computation of free energies is a common issue in statistical physics. A natural technique to compute such high dimensional integrals is to resort to Monte Carlo simulations. However these techniques generally suffer from a high variance in the low temperature regime, because the expectation is often dominated by high values corresponding to rare system trajectories. A standard way to reduce the variance of the estimator is to modify the drift of the dynamics with a control enhancing the probability of rare event, leading to so-called importance sampling estimators. In theory, the optimal control leads to a zero-variance estimator; it is however defined implicitly and computing it is of the same difficulty as the original problem. We propose here a general strategy to build approximate optimal controls in the small temperature limit for diffusion processes, with the first goal to reduce the variance of free energy Monte Carlo estimators. Our construction builds upon low noise asymptotics by expanding the optimal control around the instanton, which is the path describing most likely fluctuations at low temperature. This technique not only helps reducing variance, but it is also interesting as a theoretical tool since it differs from usual small temperature expansions (WKB ansatz). As a complementary consequence of our expansion, we provide a perturbative formula for computing the free energy in the small temperature regime, which refines the now standard Freidlin--Wentzell asymptotics. We compute this expansion explicitly for lower orders, and explain how our strategy can be extended to an arbitrary order of accuracy. We support our findings with illustrative numerical examples.
We derive the optimal proposal density for Approximate Bayesian Computation (ABC) using Sequential Monte Carlo (SMC) (or Population Monte Carlo, PMC). The criterion for optimality is that the SMC/PMC-ABC sampler maximise the effective number of samples per parameter proposal. The optimal proposal density represents the optimal trade-off between favoring high acceptance rate and reducing the variance of the importance weights of accepted samples. We discuss two convenient approximations of this proposal and show that the optimal proposal density gives a significant boost in the expected sampling efficiency compared to standard kernels that are in common use in the ABC literature, especially as the number of parameters increases.
In a spatially periodic temperature profile, directed transport of an overdamped Brownian particle can be induced along a periodic potential. With a load force applied to the particle, this setup can perform as a heat engine. For a given load, the optimal potential maximizes the current and thus the power output of the heat engine. We calculate the optimal potential for different temperature profiles and show that in the limit of a periodic piecewise constant temperature profile alternating between two temperatures, the optimal potential leads to a divergent current. This divergence, being an effect of both the overdamped limit and the infinite temperature gradient at the interface, would be cut off in any real experiment.
Freidlin-Wentzell theory of large deviations can be used to compute the likelihood of extreme or rare events in stochastic dynamical systems via the solution of an optimization problem. The approach gives exponential estimates that often need to be refined via calculation of a prefactor. Here it is shown how to perform these computations in practice. Specifically, sharp asymptotic estimates are derived for expectations, probabilities, and mean first passage times in a form that is geared towards numerical purposes: they require solving well-posed matrix Riccati equations involving the minimizer of the Freidlin-Wentzell action as input, either forward or backward in time with appropriate initial or final conditions tailored to the estimate at hand. The usefulness of our approach is illustrated on several examples. In particular, invariant measure probabilities and mean first passage times are calculated in models involving stochastic partial differential equations of reaction-advection-diffusion type.
Alchemical binding free energy (BFE) calculations offer an efficient and thermodynamically rigorous approach to in silico binding affinity predictions. As a result of decades of methodological improvements and recent advances in computer technology, alchemical BFE calculations are now widely used in drug discovery research. They help guide the prioritization of candidate drug molecules by predicting their binding affinities for a biomolecular target of interest (and potentially selectivity against undesirable anti-targets). Statistical variance associated with such calculations, however, may undermine the reliability of their predictions, introducing uncertainty both in ranking candidate molecules and in benchmarking their predictive accuracy. Here, we present a computational method that substantially improves the statistical precision in BFE calculations for a set of ligands binding to a common receptor by dynamically allocating computational resources to different BFE calculations according to an optimality objective established in a previous work from our group and extended in this work. Our method, termed Network Binding Free Energy (NetBFE), performs adaptive binding free energy calculations in iterations, re-optimizing the allocations in each iteration based on the statistical variances estimated from previous iterations. Using examples of NetBFE calculations for protein-binding of congeneric ligand series, we demonstrate that NetBFE approaches the optimal allocation in a small number (<= 5) of iterations and that NetBFE reduces the statistical variance in the binding free energy estimates by approximately a factor of two when compared to a previously published and widely used allocation method at the same total computational cost.
We study Nash equilibria for a sequence of symmetric $N$-player stochastic games of finite-fuel capacity expansion with singular controls and their mean-field game (MFG) counterpart. We construct a solution of the MFG via a simple iterative scheme that produces an optimal control in terms of a Skorokhod reflection at a (state-dependent) surface that splits the state space into action and inaction regions. We then show that a solution of the MFG of capacity expansion induces approximate Nash equilibria for the $N$-player games with approximation error $varepsilon$ going to zero as $N$ tends to infinity. Our analysis relies entirely on probabilistic methods and extends the well-known connection between singular stochastic control and optimal stopping to a mean-field framework.