Related papers: Lambda-ABF: Simplified, Portable, Accurate and Cos…
We present an Augmented Lagrangian formulation and its real-space implementation for non-periodic orbital-free Density Functional Theory (OF-DFT) calculations. In particular, we rewrite the constrained minimization problem of OF-DFT as a…
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…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear…
Nonstationary time series data exist in various scientific disciplines, including environmental science, biology, signal processing, econometrics, among others. Many Bayesian models have been developed to handle nonstationary time series.…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
We propose to relax geometries throughout chemical compound space (CCS) using alchemical perturbation density functional theory (APDFT). APDFT refers to perturbation theory involving changes in nuclear charges within approximate solutions…
Many modern computer vision and machine learning applications rely on solving difficult optimization problems that involve non-differentiable objective functions and constraints. The alternating direction method of multipliers (ADMM) is a…
Diffusion models have demonstrated strong generative capabilities across domains ranging from image synthesis to complex reasoning tasks. However, most inference-time scaling methods rely on fixed denoising schedules, limiting their ability…
Exploring the free-energy landscape along reaction coordinates or system parameters $\lambda$ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses. In simulations this usually…
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid…
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
In this paper, we present two multiple scalar auxiliary variable (MSAV)-based, finite element numerical schemes for the Abels-Garcke-Gr{\"u}n (AGG) model, which is a thermodynamically consistent phase field model of two-phase incompressible…
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…
Robotic trajectory planning in dynamic and cluttered environments remains a critical challenge, particularly when striving for both time efficiency and motion smoothness under actuation constraints. Traditional path planner, such as…
Nonadiabatic molecular dynamics is a key technique for investigating a broad range of photochemical and photophysical processes. Among the established approaches, surface hopping schemes are widely used and can be easily integrated with…
A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
Searching for potential active compounds in large databases is a necessary step to reduce time and costs in modern drug discovery pipelines. Such virtual screening methods seek to provide predictions that allow the search space to be…
Reactive, semi-permeable interfaces play important roles in key biological processes such as targeted drug delivery, lipid metabolism, and signal transduction. These systems involve coupled surface reactions, transmembrane transport, and…
The primary computational challenge when simulating nonadiabatic ab initio molecular dynamics is the unfavorable compute costs of electronic structure calculations with molecular size. Simple electronic structure theories, like…