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We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic (slow) dynamics of some low-dimensional set of reaction coordinates. The algorithm enhances exploration of the state space in the presence of metastability by allowing larger proposal moves at the macroscopic level, on which a conditional accept-reject procedure is applied. Only when the macroscopic proposal is accepted, the full microscopic state is reconstructed from the newly sampled reaction coordinate value and is subjected to a second accept/reject procedure. The computational gain stems from the fact that most proposals are rejected at the macroscopic level, at low computational cost, while microscopic states, once reconstructed, are almost always accepted. We analytically show convergence and discuss the rate of convergence of the proposed algorithm, and numerically illustrate its efficiency on two standard molecular test cases.

Finding saddle points of dynamical systems is an important problem in practical applications, such as the study of rare events of molecular systems. Gentlest ascent dynamics (GAD) (10.1088/0951-7715/24/6/008) is one of a number of algorithms in existence that attempt to find saddle points. It works by deriving a new dynamical system in which saddle points of the original system become stable equilibria. GAD has been recently generalized to the study of dynamical systems on manifolds (differential algebraic equations) described by equality constraints (10.1007/s10915-022-01838-3) and given in an extrinsic formulation. In this paper, we present an extension of GAD to manifolds defined by point-clouds, formulated by using an intrinsic viewpoint. These point-clouds are adaptively sampled during an iterative process that drives the system from the initial conformation (typically in the neighborhood of a stable equilibrium) to a saddle point. Our method requires the reactant (initial conformation), does not require the explicit constraint equations to be specified, and is purely data-driven.

We analyse the convergence and stability of a micro-macro acceleration algorithm for Monte Carlo simulations of stiff stochastic differential equations with a time-scale separation between the fast evolution of the individual stochastic realizations and some slow macroscopic state variables of the process. The micro-macro acceleration method performs a short simulation of a large ensemble of individual fast paths, before extrapolating the macroscopic state variables of interest over a larger time step. After extrapolation, the method constructs a new probability distribution that is consistent with the extrapolated macroscopic state variables, while minimizing Kullback-Leibler divergence with respect to the distribution available at the end of the Monte Carlo simulation. In the current work, we study the convergence and stability of this method on linear stochastic differential equations with additive noise, when only extrapolating the mean of the slow component. For this case, we prove convergence to the microscopic dynamics when the initial distribution is Gaussian and present a stability result for non-Gaussian initial laws.