Related papers: Determination of the chemical potential using ener…
The estimation of rare event probabilities plays a pivotal role in diverse fields. Our aim is to determine the probability of a hazard or system failure occurring when a quantity of interest exceeds a critical value. In our approach, the…
The so-called 'energy test' is a frequentist technique used in experimental particle physics to decide whether two samples are drawn from the same distribution. Its usage requires a good understanding of the distribution of the test…
The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…
Free energy of crystal phases is commonly evaluated by thermodynamic integration (TDI) along a reversible path that involves an external potential. A persistent problem in this method is that a significant hysteresis is observed due to…
Training on class-imbalanced data usually results in biased models that tend to predict samples into the majority classes, which is a common and notorious problem. From the perspective of energy-based model, we demonstrate that the free…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
Energy-based models (EBMs) are powerful probabilistic models, but suffer from intractable sampling and density evaluation due to the partition function. As a result, inference in EBMs relies on approximate sampling algorithms, leading to a…
Free energy calculations based on atomistic Hamiltonians provide microscopic insight into the thermodynamic driving forces of biophysical or condensed matter systems. Many approaches use intermediate Hamiltonians interpolating between the…
Based on an analysis of the short range chemical environment of each atom in a system, standard machine learning based approaches to the construction of interatomic potentials aim at determining directly the central quantity which is the…
Bias in causal comparisons has a direct correspondence with distributional imbalance of covariates between treatment groups. Weighting strategies such as inverse propensity score weighting attempt to mitigate bias by either modeling the…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling [Skilling J. (2004) In AIP Conference Proceedings, vol. 735, p. 395.; Skilling…
An ensemble of atoms in steady-state, whether in thermal equilibrium or not, has a well defined energy distribution. Since the energy of single atoms within the ensemble cannot be individually measured, energy distributions are typically…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
The numerical computation of chemical potential in dense, non-homogeneous fluids is a key problem in the study of confined fluids thermodynamics. To this day several methods have been proposed, however there is still need for a robust…
When studying high-dimensional dynamical systems such as macromolecules, quantum systems and polymers, a prime concern is the identification of the most probable states and their stationary probabilities or free energies. Often, these…
We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of…
Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly construction of a bias potential that is function of a selected number of collective variables. We propose here a change in perspective that shifts the…