Related papers: Path collective variables without paths

In this article, we introduce the mean independent component analysis for multivariate time series to reduce the parameter space. In particular, we seek for a contemporaneous linear transformation that detects univariate mean independent…

Finding proper collective variables for complex systems and processes is one of the most challenging tasks in simulations, which limits the interpretation of experimental and simulated data and the application of enhanced sampling…

We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…

An accurate description of nonadiabatic dynamics of molecular species on metallic surfaces poses a serious computational challenge associated with a multitude of closely-spaced electronic states. We propose a mixed quantum-classical scheme…

Complex systems are often characterized by the interplay of multiple interconnected dynamical processes operating across a range of temporal scales. This phenomenon is widespread in both biological and artificial scenarios, making it…

We consider the Potts model on a two-dimensional periodic rectangular lattice with general coupling constants $J_{ij}>0$, where $i,j\in\{1,2,3\}$ are the possible spin values (or colors). The resulting energy landscape is thus significantly…

Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…

We establish an explicit data-driven criterion for identifying the solid-liquid transition of two-dimensional self-propelled colloidal particles in the far from equilibrium parameter regime, where the transition points predicted by…

We study the subradiant collective states of a periodic chain of two-level atoms with either transversal or longitudinal transition dipole moments with respect to the chain axis. We show that long-lived subradiant states can be obtained for…

We experimentally study the statistics of the transition path time taken by a submicron bead to successfully traverse an energy barrier created by two optical tweezers in two prototypical viscoelastic fluids, namely, aqueous polymer and…

We consider a class of parabolic semi-linear stochastic partial differential equations driven by space-time white noise on a compact space interval. Our aim is to obtain precise asymptotics of the transition times between metastable states.…

In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which acceleration occurs.…

The committor function is a central object for quantifying the transitions between metastable states of dynamical systems. Recently, a number of computational methods based on deep neural networks have been developed for computing the…

Strongly interacting, dynamically disordered and with no small parameter, liquids took a theoretical status between gases and solids. We review different approaches to liquids and propose that liquids do not need classifying in terms of…

We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…

A new empirical Bayes approach to variable selection in the context of generalized linear models is developed. The proposed algorithm scales to situations in which the number of putative explanatory variables is very large, possibly much…

Time scales associated with activated transitions between glassy metastable states of a free energy functional appropriate for a dense hard sphere system are calculated by using a new Monte Carlo method for the local density variables. We…

Pathway idea is a switching mechanism by which one can go from one functional form to another, and to yet another. It is shown that through a parameter $\alpha$, called the pathway parameter, one can connect generalized type-1 beta family…

The development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing long-time phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an…

We describe a novel procedure for deciding when a mass-action model is incompatible with observed steady-state data that does not require any parameter estimation. Thus, we avoid the difficulties of nonlinear optimization typically…