Related papers: Multi-Layer Free Energy Perturbation
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…
In this paper, we develop an iterative scheme to construct multiscale basis functions within the framework of the Constraint Energy Minimizing Generalized Multiscale Finite Element Method (CEM-GMsFEM) for the mixed formulation. The…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
Energy recovering an electron beam after it has participated in a free-electron laser (FEL) interaction can be quite challenging because of the substantial FEL-induced energy spread and the energy anti-damping that occurs during…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
Beam energy compression via chicane magnets has been proved to be an effective method to reduce the slice energy spread of electron beams generated by laser wakefield accelerators (LWFAs). This technique has been widely adopted by leading…
Accurate free energy representations are crucial for understanding phase dynamics in materials. We employ a scale-bridging approach to incorporate atomistic information into our free energy model by training a neural network on DFT-informed…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
Standard attention stores keys/values losslessly but reads them via a per-head convex average, blocking channel-wise selection. We propose the Free Energy Mixer (FEM): a free-energy (log-sum-exp) read that applies a value-driven,…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
We examine the sensitiveness of the free-energy landscape of a directed polymer in random media with respect to various kinds of infinitesimally weak perturbation including the intriguing case of temperature-chaos. To this end, we combine…
We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics.…
Potential Energy Surfaces (PESs) are an indispensable tool to investigate, characterise and understand chemical and biological systems in the gas and condensed phases. Advances in Machine Learning (ML) methodologies have led to the…
We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap…
Ensembling is now recognized as an effective approach for increasing the predictive performance and calibration of deep networks. We introduce a new approach, Parameter Ensembling by Perturbation (PEP), that constructs an ensemble of…
Free energy principle (FEP) is a burgeoning theory in theoretical neuroscience that provides a universal law for modelling living systems of any scale. Expecting a digital twin mind from this first principle, we propose a macro-level…
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…
Estimating the effort of software systems is an essential topic in software engineering, carrying out an estimation process reliably and accurately for a software forms a vital part of the software development phases. Many researchers have…