Publications related to Water model

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Solvation Free Energies from Machine Learning Molecular Dynamics

Nicola Marzari, Nicéphore Arthur François Bonnet

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] to calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations of a hybrid solvation model. The approa ...

Amer Chemical Soc2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

Comparing transferability in neural network approaches and linear models for machine-learning interaction potentials

Kevin Rossi

Atomic simulations using machine learning interatomic potential (MLIP) have gained a lot of popularity owing to their accuracy in comparison to conventional empirical potentials. However, the transferability of MLIP to systems outside the training set pose ...

AMER PHYSICAL SOC2023

A recipe for cracking the quantum scaling limit with machine learned electron densities

Mario Geiger

A long-standing goal of science is to accurately simulate large molecular systems using quantum mechanics. The poor scaling of current quantum chemistry algorithms on classical computers, however, imposes an effective limit of about a few dozen atoms on tr ...

IOP Publishing Ltd2023

The Three-Phase Contact Potential Difference Modulates the Water Surface Charge

Aleksandra Radenovic, Andrei Kiselev, Vasily Artemov, Roman Doronin

The surface charge of an open water surface is crucialfor solvationphenomena and interfacial processes in aqueous systems. However, themagnitude of the charge is controversial, and the physical mechanismof charging remains incompletely understood. Here we ...

AMER CHEMICAL SOC2023

Impact of dipole-dipole interactions on motility-induced phase separation

Ignacio Pagonabarraga Mora, Elena Sesé Sansa

We present a hydrodynamic theory for systems of dipolar active Brownian particles which, in the regime of weak dipolar coupling, predicts the onset of motility-induced phase separation (MIPS), consistent with Brownian dynamics (BD) simulations. The hydrody ...

ROYAL SOC CHEMISTRY2022

Effects of surface wettability on (001)-WO3 and (100)-WSe2: A spin-polarized DFT-MD study

Kevin Sivula, Rangsiman Ketkaew

An extensive understanding of WO3 and WSe2 bulk crystalline structures and explicit solvent effects on (001)-WO3 and (100)-WSe2 facets are essential for design of efficient (photo) electrocatalysts. The atomistic level understanding of both WO(3 )and WSe2 ...

ELSEVIER2022

High-Throughput Nanopore Fabrication and Classification Using Xe-Ion Irradiation and Automated Pore-Edge Analysis

Aleksandra Radenovic, Andras Kis, Martina Lihter, Mukesh Kumar Tripathi, Mukeshchand Thakur, Sanjin Marion, Michal Daniel Macha

Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding ...

AMER CHEMICAL SOC2022

Estimating flexibility preferences to resolve temporal scheduling conflicts in activity-based modelling

Michel Bierlaire, Timothy Michael Hillel, Janody Pougala

This paper presents a novel activity-based demand model that combines an optimisation framework for continuous temporal scheduling decisions (i.e. activity timings and durations) with traditional discrete choice models for non-temporal choice dimensions (i ...

SPRINGER2022

Effects of surface rigidity and metallicity on dielectric properties and ion interactions at aqueous hydrophobic interfaces

Philip Robin Loche

Using classical molecular dynamics simulations, we investigate the dielectric properties at interfaces of water with graphene, graphite, hexane, and water vapor. For graphite, we compare metallic and nonmetallic versions. At the vapor-liquid water and hexa ...

AIP Publishing2022

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Rubén Laplaza Solanas, Anne-Clémence Corminboeuf, Frédéric Célerse, Veronika Juraskova

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry, and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environme ...

2022

Modeling non-covalent interactions in condensed phase

Veronika Juraskova

The modeling of non-covalent interactions, solvation effects, and chemical reactions in complex molecular environment is a challenging task. Current state-of-the-art approaches often rely on static computations using implicit solvent models and harmonic ap ...

EPFL2022

Microscopic field theory for structure formation in systems of self-propelled particles with generic torques

Ignacio Pagonabarraga Mora, Elena Sesé Sansa

We derive a dynamical field theory for self-propelled particles subjected to generic torques and forces by explicitly coarse-graining their microscopic dynamics, described by a many-body Fokker-Planck equation. The model includes both intrinsic torques ind ...

AIP Publishing2022

Transferable machine-learning models of complex materials: the case of GaAs

Giulio Imbalzano

Molecular simulations allow to investigate the behaviour of materials at the atomistic level, shedding light on phenomena that cannot be directly observed in experiments. Accurate results can be obtained with ab initio methods, while simulations of large-s ...

EPFL2021

Optimal radial basis for density-based atomic representations

Michele Ceriotti, Sergey Pozdnyakov, Jigyasa Nigam, Félix Benedito Clément Musil, Alexander Jan Goscinski

The input of almost every machine learning algorithm targeting the properties of matter at the atomic scale involves a transformation of the list of Cartesian atomic coordinates into a more symmetric representation. Many of the most popular representations ...

2021

Passenger-centric timetable rescheduling: A user equilibrium approach

Michel Bierlaire, Shadi Sharif Azadeh, Mohammad Yousef Maknoon, Stefan Yves Gabriel Binder

Unexpected disruptions commonly occur in the railway network, causing delays, and extra cost for operators and inconvenience for passengers by missing their connection and facing overcrowded trains. This paper presents a passenger-centric approach for time ...

PERGAMON-ELSEVIER SCIENCE LTD2021

Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy

Oleg Boyarkine, Andrei Zviagin, Viktoriia Aladinskaia

The native-like structures of protonated glycine and peptide Gly3H+ were elucidated using cold ion IR spectroscopy of these biomolecules hydrated by a controlled number of water molecules. The complexes were generated directly from an aqueous solution usin ...

2021

Rapid screening of nanopore candidates in nanoporous single-layer graphene for selective separations using molecular visualization and interatomic potentials

Luc Sébastien Bondaz, Rohit Karnik

Nanoporous single-layer graphene is promising as an ideal membrane because of its extreme thinness, chemical resistance, and mechanical strength, provided that selective nanopores are successfully incorporated. However, screening and understanding the tran ...

AIP Publishing2021

Simulating Solvation and Acidity in Complex Mixtures with First-Principles Accuracy: The Case of CH3SO3H and H2O2 in Phenol

Michele Ceriotti, Anne-Clémence Corminboeuf, Kevin Rossi, Veronika Juraskova

We present a generally applicable computational framework for the efficient and accurate characterization of molecular structural patterns and acid properties in an explicit solvent using H2O2 and CH3SO3H in phenol as an example. To address the challenges ...

AMER CHEMICAL SOC2020