Related papers: Multi-Layer Free Energy Perturbation
Exact free energy minimization is a convex optimization problem that is usually approximated with stochastic sampling methods. Deterministic approximations have been less successful because many desirable properties have been difficult to…
The combination of Finite Element Method (FEM) simulation and experimental photo-elasticity provides both qualitative and quantitative information about the stress field in a polymer composite and particularly along the fibre-matrix…
The $hp$-adaptive finite element method (FEM) - where one independently chooses the mesh size ($h$) and polynomial degree ($p$) to be used on each cell - has long been known to have better theoretical convergence properties than either $h$-…
Data association, the reasoning over correspondence between targets and measurements, is a problem of fundamental importance in target tracking. Recently, belief propagation (BP) has emerged as a promising method for estimating the marginal…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…
Electron energy loss spectroscopy is consolidating as a powerful tool to explore electronic (as well as vibrational) excitations of matter, including molecules. Performed in a scanning transmission electron microscope, this technique is…
Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the…
Advances in manufacturing and characterization of complex molecular systems have created a need for new methods for design at molecular length scales. Emerging approaches are increasingly relying on the use of Artificial Intelligence (AI),…
The goal of these lecture notes is to review the problem of free energy minimization as a unified framework underlying the definition of maximum entropy modelling, generalized Bayesian inference, learning with latent variables, statistical…
Turbulent space and astrophysical plasmas exhibit a complex dynamics, which involves nonlinear coupling across different temporal and spatial scales. There is growing evidence that impulsive events, such as magnetic reconnection…
In this paper, we present a finite element method (FEM) framework enhanced by an operator-adapted wavelet decomposition algorithm designed for the efficient analysis of multiscale electromagnetic problems. Usual adaptive FEM approaches,…
Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with…
The energy landscape dictates pathways and outcomes in supramolecular selfassembly, yet harnessing it from the nano to the macro scales remains a major challenge. Here, we demonstrate liquid liquid phase separation (LLPS) as a powerful tool…
We derive the optimal energy error estimate for multiscale finite element method with oversampling technique applying to elliptic system with rapidly oscillating periodic coefficients under the assumption that the coefficients are bounded…
In a recent technical critique of the free energy principle (FEP) due to Aguilera-Millidge-Tschantz-Buckley, it is argued that there are a number of instances where the FEP$\unicode{x2014}$as conventionally written, in terms of densities…
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
In large-scale problems, standard reinforcement learning algorithms suffer from slow learning speed. In this paper, we follow the framework of using subspaces to tackle this problem. We propose a free-energy minimization framework for…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…