Browsing NTNU Open by Author "Riccardi, Enrico"
Now showing items 1-18 of 18
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Analyzing Complex Reaction Mechanisms Using Path Sampling
van Erp, Titus Sebastiaan; Moqadam, Mahmoud; Riccardi, Enrico; Lervik, Anders (Journal article; Peer reviewed, 2016)We introduce an approach to analyze collective variables regarding their predictive power for a reaction. The method is based on already available path sampling data produced by for instance transition interface sampling ... -
Asynchronous and Infinite Replica Exchange Transition Interface Sampling
Zhang, Daniel Tianhou (Doctoral theses at NTNU;2024:215, Doctoral thesis, 2024)A possible alternative to running chemical experiments in the laboratory could be to conduct them digitally instead, by running computer simulations. One prominent simulation technique is Molecular Dynamics (MD), which ... -
Coalescence in oil-in-water emulsions characterized using optical tweezers and rare event simulations
Aarøen, Ola (Doctoral theses at NTNU;2021:369, Doctoral thesis, 2021)Emulsions are thermodynamically unstable systems comprised of two immiscible liquid phases, with one dispersed into the other as small droplets of varying size. Coalescence is a separation mechanism for emulsion systems, ... -
Enhanced path sampling using subtrajectory Monte Carlo moves
Zhang, Daniel Tianhou; Riccardi, Enrico; van Erp, Titus Sebastiaan (Journal article, 2023)Path sampling allows the study of rare events, such as chemical reactions, nucleation, and protein folding, via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short ... -
Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions
Aarøen, Ola; Riccardi, Enrico; Sletmoen, Marit (Journal article; Peer reviewed, 2021) -
Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling
Riccardi, Enrico; Dahlen, Oda; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2017)Many relevant processes in chemistry, physics, and biology are rare events from a computational perspective as they take place beyond the accessible time scale of molecular dynamics (MD). Examples are chemical reactions, ... -
From data analysis to molecular understanding
Kiær, Henrik (Master thesis, 2020)Tolkning av resultater og data fra molekylære simuleringer kan være svært krevende. Simuleringene kan ofte produsere mange terabyte av data med mange dimensjoner av høyt korrelerte deskriptorer. For å bedre tolke og behandle ... -
Local initiation conditions for water autoionization
Moqadam, Mahmoud; Lervik, Anders; Riccardi, Enrico; Venkatraman, Vishwesh; Alsberg, Bjørn Kåre; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2018)The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. ... -
Multiscale modeling of mass transfer and adsorption in liquid-liquid dispersions. 1. Molecular dynamics simulations and interfacial tension prediction for a mixed monolayer of mono- and tetracarboxylic acids
Kovalchuk, Karina; Riccardi, Enrico; Grimes, Brian Arthur (Journal article; Peer reviewed, 2014)Phase space trajectories of protonated and deprotonated mono- and tetracarboxylic acid surfactants at an oil/water interface are obtained from molecular dynamics (MD) simulations and are employed to calculate the interfacial ... -
Multiscale modeling of mass transfer and adsorption in liquid-liquid dispersions. 2. application to calcium naphthenate precipitation in oils containing mono- and tetracarboxylic acids
Kovalchuk, Karina; Riccardi, Enrico; Grimes, Brian Arthur (Journal article; Peer reviewed, 2014)A dynamic multicomponent mass transport model is constructed and solved to determine the interfacial composition and bulk phase concentrations of surfactant mixtures containing a synthetic tetracarboxylic acid (BP10) and ... -
Multiscale partial charge estimation on graphene for neutral, doped and charged flakes
Maslechko, Anastasiia; Verstraelen, Toon; van Erp, Titus Sebastiaan; Riccardi, Enrico (Journal article; Peer reviewed, 2018)The minimal-basis iterative stockholder (MBIS) and restrained electrostatic potential (RESP) methods were applied to examine the effects of edges and of nitrogen and boron dopants on the atomic partial charges of neutral ... -
Permeation Rates of Oxygen through a Lipid Bilayer Using Replica Exchange Transition Interface Sampling
Riccardi, Enrico; Krämer, Andreas; van Erp, Titus Sebastiaan; Ghysels, An (Journal article, 2021)Several simulations strategies have emerged to predict the permeability of solutes across membranes, which is important for many biological or industrial processes such as drug design. The widespread inhomogeneous ... -
Predicting the mechanism and rate of H-NS binding to at-rich DNA
Riccardi, Enrico; Van Mastbergen, Eva C; Navarre, William Wiley; Vreede, Jocelyne (Journal article; Peer reviewed, 2019)Bacteria contain several nucleoid-associated proteins that organize their genomic DNA into the nucleoid by bending, wrapping or bridging DNA. The Histone-like Nucleoid Structuring protein H-NS found in many Gram-negative ... -
PyRETIS: A well-done, medium-sized python library for rare events
Lervik, Anders; Riccardi, Enrico; van Erp, Titus Sebastiaan (Journal article, 2017)Transition Path Sampling techniques are becoming common approaches in the study of rare events at the molecular scale. More efficient methods, such as transition interface sampling (TIS) and replica exchange transition ... -
Rare event simulations reveal subtle key steps in aqueous silicate condensation
Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat; Lervik, Anders; van Erp, Titus Sebastiaan (Journal article; Peer reviewed, 2017)A replica exchange transition interface sampling (RETIS) study combined with Born-Oppenheimer molecular dynamics (BOMD) is used to investigate the dynamics, thermodynamics and mechanism of the early stages of the silicate ... -
The role of pressure and defects in the wurtzite to rock salt transition in cadmium selenide
Lervik, Anders; Svenum, Ingeborg-Helene; Wang, Zhaohui; Cabriolu, Raffaela; Riccardi, Enrico; Andersson, Stefan; van Erp, Titus Sebastiaan (Peer reviewed; Journal article, 2022)Using molecular dynamics and path sampling techniques we investigated the effect of pressure and defects in the wurtzite to rock salt transition in cadmium selenide (CdSe). In the pressure range 2–10 GPa, rate constants ... -
Structure and Orientation of Tetracarboxylic Acids at Oil-Water Interfaces
Riccardi, Enrico; Kovalchuk, Karina; Mehandzhiyski, Aleksandar Yordanov; Grimes, Brian Arthur (Journal article; Peer reviewed, 2014)Fouling caused by tetracarboxylic acids in transport and separation process chains involving petroemulsions occurs when the interfacial concentration of tetraacids becomes large enough for calcium ions in the water phase ... -
Thin film breakage in oil–in–water emulsions, a multidisciplinary study
Aarøen, Ola; Riccardi, Enrico; van Erp, Titus Sebastiaan; Sletmoen, Marit (Peer reviewed; Journal article, 2022)Coalescence is a critical phenomenon in separation and transport processes. An improved understanding of coalescence can enhance current models predicting emulsion stability and separation. We here report a combined ...