Publications by Michele Parrinello

Accuracy of Molecular Simulation-Based Predictions of k(off) Values: A Metadynamics Study

Ursula Röthlisberger, Michele Parrinello, Paolo Carloni, Simone Meloni, Viacheslav Bolnykh

The k(off) values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-i ...

AMER CHEMICAL SOC2020

Atomistic Mechanism of the Nucleation of Methylammonium Lead Iodide Perovskite from Solution

Michael Graetzel, Ursula Röthlisberger, Michele Parrinello, Mohammad Ibrahim Dar, Paramvir Ahlawat

In the ongoing intense quest to increase the performance of perovskite solar cells, optimizing the morphology of perovskite material has become imperative to achieve high power conversion efficiencies. Despite the fact that nucleation plays a key role in c ...

ACS2019

Multithermal-Multibaric Molecular Simulations from a Variational Principle

Michele Parrinello, Pablo Miguel Piaggi

We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev. Lett. 113, 0906 ...

2019

Naphthalene crystal shape prediction from molecular dynamics simulations

Michele Parrinello, Pablo Miguel Piaggi

We used molecular dynamics simulations to predict the steady state crystal shape of naphthalene grown from ethanol solution. The simulations were performed at constant supersaturation by utilizing a recently proposed algorithm [Perego et al., J. Chem. Phys ...

2019

Predicting polymorphism in molecular crystals using orientational entropy

Michele Parrinello, Pablo Miguel Piaggi

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This id ...

National Academy of Sciences2018

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations

Michele Parrinello, Pablo Miguel Piaggi

Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is an interplay between enthalpy and entropy. B ...

American Physical Society2017

Entropy based fingerprint for local crystalline order

Michele Parrinello, Pablo Miguel Piaggi

We introduce a new fingerprint that allows distinguishing between liquid-like and solid-like atomic environments. This fingerprint is based on an approximate expression for the entropy projected on individual atoms. When combined with local enthalpy, this ...

Amer Inst Physics2017

A variational approach to nucleation simulation

Michele Parrinello, Pablo Miguel Piaggi

We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. T ...

Royal Soc Chemistry2016

Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

Michele Parrinello, Michele Ceriotti, Gareth Aneurin Tribello

This work examines the conformational ensemble involved in beta-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, an ...

2015

The Role of Quantum Effects on Structural and Electronic Fluctuations in Neat and Charged Water

Michele Parrinello, Michele Ceriotti, Federico Giberti

In this work, we revisit the role of nuclear quantum effects on the structural and electronic properties of the excess proton in bulk liquid water using advanced molecular dynamics techniques. The hydronium ion is known to be a weak acceptor of a hydrogen ...

Amer Chemical Soc2014

Evaluating functions of positive-definite matrices using colored-noise thermostats

Michele Parrinello, Michele Ceriotti

Many applications in computational science require computing the elements of a function of a large matrix. A commonly used approach is based on the the evaluation of the eigenvalue decomposition, a task that, in general, involves a computing time that scal ...

Amer Physical Soc2014

The allosteric communication pathways in KIX domain of CBP

Michele Parrinello, Alessandro Barducci

Allosteric regulation plays an important role in a myriad of bio-macromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the ...

National Academy of Sciences2013

Free-energy landscape of protein oligomerization from atomistic simulations

Michele Parrinello, Alessandro Barducci

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of ...

National Academy of Sciences2013