399 citations · 921 across the 13 of their papers we have counts for
15 papers
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Advanced simulations with PLUMED: OPES and Machine Learning Collective Variables
Enrico Trizio, Andrea Rizzi, Pablo M. Piaggi +2
Many biological processes occur on time scales longer than those accessible to molecular dynamics simulations. Identifying collective variables (CVs) and introducing an external po…
Rigid Body Flows for Sampling Molecular Crystal Structures
Jonas Köhler, Michele Invernizzi, Pim de Haan +1
Normalizing flows (NF) are a class of powerful generative models that have gained popularity in recent years due to their ability to model complex distributions with high flexibili…
Skipping the Replica Exchange Ladder with Normalizing Flows
Michele Invernizzi, Andreas Krämer, Cecilia Clementi +1
We combine replica exchange (parallel tempering) with normalizing flows, a class of deep generative models. These two sampling strategies complement each other, resulting in an eff…
Rare Event Kinetics from Adaptive Bias Enhanced Sampling
Dhiman Ray, Narjes Ansari, Valerio Rizzi +2
We introduce a novel enhanced sampling approach named OPES flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived…
Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling
Michele Invernizzi, Michele Parrinello
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to drive transitions between metastable states. The bias potential is a function of a few collec…
OPES: On-the-fly Probability Enhanced Sampling Method
Michele Invernizzi
Molecular simulations are playing an ever increasing role, finding applications in fields as varied as physics, chemistry, biology and material science. However, many phenomena of…
Collective Variables for the Study of Crystallization
Tarak Karmakar, Michele Invernizzi, Valerio Rizzi +1
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious inform…
Attenuating the fermion sign problem in path integral Monte Carlo simulations using the Bogoliubov inequality and thermodynamic integration
Tobias Dornheim, Michele Invernizzi, Jan Vorberger +1
Accurate thermodynamic simulations of correlated fermions using path integral Monte Carlo (PIMC) methods are of paramount importance for many applications such as the description o…
A Unified Approach to Enhanced Sampling
Michele Invernizzi, Pablo Miguel Piaggi, Michele Parrinello
The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods…
Path Integral Molecular Dynamics for Fermions: Alleviating the Sign Problem with the Bogoliubov Inequality
Barak Hirshberg, Michele Invernizzi, Michele Parrinello
We present a method for performing path integral molecular dynamics (PIMD) simulations for fermions and address its sign problem. PIMD simulations are widely used for studying many…
Rethinking Metadynamics: from bias potentials to probability distributions
Michele Invernizzi, Michele Parrinello
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 variab…
Making the best of a bad situation: a multiscale approach to free energy calculation
Michele Invernizzi, Michele Parrinello
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in…
Enhanced sampling of transition states
Jayashrita Debnath, Michele Invernizzi, Michele Parrinello
The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes…
Superlubric-Pinned Transition in Sliding Incommensurate Colloidal Monolayers
Davide Mandelli, Andrea Vanossi, Michele Invernizzi +3
Two-dimensional (2D) crystalline colloidal monolayers sliding over a laser-induced optical lattice recently emerged as a new tool for the study of friction between ideal crystal su…