Related papers: Metadynamics with adaptive Gaussians
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
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…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Adaptive or dynamic signal sampling in sensing systems can adapt subsequent sampling strategies based on acquired signals, thereby potentially improving image quality and speed. This paper proposes a Bayesian method for adaptive sampling…
Within the past two decades, Gaussian process regression has been increasingly used for modeling dynamical systems due to some beneficial properties such as the bias variance trade-off and the strong connection to Bayesian mathematics. As…
In conventional well-known derivation methods for the adaptive Thouless-Anderson-Palmer (TAP) free energy, special assumptions that are difficult to mathematically justify except in some mean-field models, must be made. Here, we present a…
While 3D Gaussian Splatting (3DGS) excels in static scene modeling, its extension to dynamic scenes introduces significant challenges. Existing dynamic 3DGS methods suffer from either over-smoothing due to low-rank decomposition or feature…
Ab initio thermodynamics is a widespread, computationally efficient approach to predict the stable configuration of a surface in contact with a surrounding (gas or liquid) environment. In a prevalent realization of this approach, this…
A simple, efficient, and accurate method is proposed to map multi-dimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [Maragliano & Vanden-Eijnden, Chem. Phys. Lett. 426,…
We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to…
We develop a novel data-driven approach to the inverse problem of classical statistical mechanics: given experimental data on the collective motion of a classical many-body system, how does one characterise the free energy landscape of that…
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…
We investigate the consequences of fluid flowing on a continuous surface upon the geometric and statistical distribution of the flow. We find that the ability of a surface to collect water by its mere geometrical shape is proportional to…
The potential flow of two-dimensional ideal incompressible fluid with a free surface is studied. Using the theory of conformal mappings and Hamiltonian formalism allows us to derive exact equations of surface evolution. Simple form of the…
We consider estimating the parameters of a Gaussian mixture density with a given number of components best representing a given set of weighted samples. We adopt a density interpretation of the samples by viewing them as a discrete Dirac…
Understanding the impact of extractant functionalization in solvent extraction is essential to guide the development of better separations processes. Traditionally, computational extractant design uses electronic structure calculations to…
A gaussian distribution of binding energies, but conditioned to exploit generally available information on packing in liquids, provides a statistical-thermodynamic theory of liquid water that is structurally non-committal, molecularly…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
This paper introduces variational design methods that are novel to Geophysics, and discusses their benefits and limitations in the context of geophysical applications and more established design methods. Variational methods rely on…