Publications
Below you can find a list of scientific publications in which the CULGI software was used. If you would like to know more about a publication, follow the link to the full article.
Highlights of (bio-)chemical tools and visualization software for computational science
David Dubbeldam, Jocelyne Vreede, Thijs J.H. Vlugt, and Sofia Calero; Current Opinion in Chemical Engineering 2019, 23, pp 1-13
Effectively parameterizing dissipative particle dynamics using COSMO-SAC: A partition coefficient study
Jonathan Saathoff; The Journal of Chemical Physics 2018, 148, pp 154102
Functionalization Pattern of Graphene Oxide Sheets Controls Entry or Produces Lipid Turmoil in Phospholipid Membranes
Marco Dallavalle, Andrea Bottoni, Matteo Calvaresi, and Francesco Zerbetto; ACS Applied Materials & Interfaces 2018, 10, pp 15487–15493
SCISSION FREE ENERGIES FOR WORMLIKE SURFACTANT MICELLES: DEVELOPMENT OF A SIMULATION PROTOCOL, APPLICATION, AND VALIDATION FOR PERSONAL CARE FORMULATIONS
Huan Wang, Xueming Tang, David M. Eike, Ronald G. Larson, and Peter H. Koenig; Langmuir 2018, 34, pp 1564–1573
CALCULATION OF DIFFUSION COEFFICIENTS THROUGH COARSE-GRAINED SIMULATIONS USING THE AUTOMATED-FRAGMENTATION-PARAMETRIZATION METHOD AND THE RECOVERY OF WILKE–CHANG STATISTICAL CORRELATION
Johannes G. E. M. Fraaije, Jan van Male, Paul Becherer, Rubèn Serral Gracià; J. Chem. Theory Comput. 2018, 14, pp. 479–485
Biomimetic PDMS-hydroxyurethane terminated with catecholic moieties for chemical grafting on transition metal oxide-based surfaces
Kelen R. de Aguiara, Klaus Rischka, Linda Gätjen, Paul-Ludwig Michael Noeske, Welchy Leite Cavalcanti, Ubirajara P. Rodrigues-Filho; Applied Surface Science 2018, 427, part B, pp. 166–175
Multiscale Molecular Modeling of Clay–Polymer Nanocomposites
Erik Laurini, Paola Posocco, Maurizio Fermeglia, Sabrina Pricl, In Clay-Polymer Composites, Chapter 3, Pages 83-112, New York, NY, 2007.
Temperature and Moisture Impacts on Asphalt before and after Oxidative Aging Using Molecular Dynamics Simulations
Jielin Pan, Mohammad I. Hossain, Rafiqul A. Tarefder; Journal of Nanomechanics and Micromechanics 2017, 7, pp. 1-10
Mix and Match: Coassembly of Amphiphilic Dendrimers and Phospholipids Creates Robust, Modular, and Controllable Interfaces
Samuel S. Hinman, Charles J. Ruiz, Yu Cao, Meghann C. Ma, Jingjie Tang, Erik Laurini, Paola Posocco, Suzanne Giorgio, Sabrina Pricl, Ling Peng, and Quan Cheng; ACS Appl. Mater. Interfaces 2017 9, pp. 1029–1035
Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC
Augustinus J. M. Sweere and Johannes G. E. M. Fraaije; J. Chem. Theory Comput. 2017, 13, pp.1911–1923.
Micro emulsion Modeling for Surfactant Optimal Salinity Prediction in Chemical EOR Design
Hon Vai Yee, Jan van Male, Jan-Willem Handgraaf, Ivy Chai Ching Hsia, and Noor ‘Aliaa Amira M. Fauzi; International Petroleum Technology Conference, 14-16 November, Bangkok, Thailand.
Extensive Accuracy Test of the Force-Field-Based Quasichemical Method PAC–MAC
Augustinus J. M. Sweere, Ruben Serral Gracia, and Johannes G. E. M. Fraaije; Chem. Eng. Data 2016, 61, pp. 3989–3997
Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases
Johannes G. E. M. Fraaije, Jan van Male, Paul Becherer, and Rubèn Serral Gracià; J. Chem. Inf. Model. 2016, 56, pp. 2361–2377
Coarse-Grained Simulations of Polymer-Grafted Nanoparticles: Structural Stability and Interfacial Behavior
Nitish Nair, Michelle Park, Jan-Willem Handgraaf, and Flavia M. Cassiola; J. Phys. Chem. B 2016, 120, pp. 9523–9539
Investigation of asphalt aging behaviour due to oxidation using molecular dynamics simulation
Jielin Pan and Rafiqul A. Tarefder; Molecular Simulation 2016, 42, pp. 667-678
Molecular Dynamics Simulation of Asphaltic Material: Molecular Dynamics Simulations of Oxidative Aging of Asphalt Molecules under Stress and Moisture
In book: Handbook of Research on Advanced Computational Techniques for Simulation-Based EngineeringRafiqul A. Tarefder, Jielin Pan, and Mohammad I. Hossain; Chapter 13, Publisher: IGI Global, 2015, Editor: Pijush Samui, pp. 334-362
Force-Field Based Quasi-Chemical Method for Rapid Evaluation of Binary Phase Diagrams
Augustinus J. M. Sweere and Johannes G. E. M. Fraaije; J. Phys. Chem. B 2015, 119, pp 14200–14209
Application of Computer Simulations to Surfactant Chemical Enhanced Oil Recovery
In book: Analytical Methods in Petroleum Upstream Applications, Jan-Willem Handgraaf, Kunj Tandon, Shekhar Jain, Marten Buijse, and Johannes G.E.M. Fraaije; Chapter: 13, Publisher: CRC (2015), Editors: Cesar Ovalles, Carl E. Rechsteiner Jr., pp. 259-274
Graphene Can Wreak Havoc with Cell Membranes
Marco Dallavalle, Matteo Calvaresi, Andrea Bottoni, Manuel Melle-Franco, and Francesco Zerbetto; ACS Appl. Mater. Interfaces 2015, 7, pp 4406–4414
Remediation technologies for oil-drilling activities in the Arctic: oil-spill containment and remediation in open water
Sergio Manzetti; Environmental Technology Reviews 2014, 3, pp 1-12
Explaining Fullerene Dispersion by using Micellar Solutions
Marco Dallavalle, Marco Leonzio, Matteo Calvaresi and Francesco Zerbetto; ChemPhysChem 2014, 15, 2998–3005
Pitch variations of self-assembled cylindrical block copolymers in lithographically defined trenches
Henk Boots, Jessica M. de Ruiter, Thanh Trung Nguyen, Aurelie Brizard, Emiel Peeters, Sander F. Wuister, Tamara S. Druzhinina, Joanne Klein Wolterink and Johannes G. E. M. Fraaije; J. Micro/Nanolith. MEMS MOEMS. 2014, 13, 033015
Fundamental study of placement errors in directed self-assembly
Sander F. Wuister, Davide Ambesi, Tamara S. Druzhinina, Emiel Peeters, Jo Finders, Joanne Klein Wolterink and Johannes G. E. M. Fraaije; J. Micro/Nanolith. MEMS MOEMS. 2014, 13, 033005
Hierarchical Structuring in Block Copolymer Nanocomposites through Two Phase-Separation Processes Operating on Different Time Scales
Elina Ploshnik, Karol M. Langner, Amit Halevi, Meirav Ben-Lulu, Axel H. E. Müller, Johannes G. E. M. Fraaije, G. J. Agur Sevink, and Roy Shenhar; Advanced Functional Materials 2013, 23, pp 4215-42263
Accelerated Surfactant Selection for EOR Using Computational Methods
Marten Buijse, Kunj Tandon, Shekhar Jain, Amit Jain, Jan-Willem Handgraaf, and Johannes G.E.M. Fraaije; SPE Enhanced Oil Recovery Conference, 2-4 July 2013, Malaysia, 165268-MS
Coarse-grained hybrid simulation of liposomes
G. J. A. Sevink, M. Charlaganov and J. G. E. M. Fraaije; Soft Matter 2013, 9, pp 2816-2831
Method of Moments for Computational Microemulsion Analysis and Prediction in Tertiary Oil Recovery
Johannes G.E.M. Fraaije, Kunj Tandon, Shekhar Jain, Jan-Willem Handgraaf and Marten Buise; Langmuir 2013, 29, pp 2136-2151
Dual-purpose defenders: Organic polymers protect metals in both thin layers and coatings
Welchy Leite Cavalcanti, Andreas Brinkmann, Michael Noeske, Sascha Buchbach, Felix Straetmans and Marko Soltau; European Coatings Journal 2012, 10, pp. 1-4
Mesoscale modeling of block copolymer nanocomposites
Karol M. Langner and G. J. A. Sevink; Soft Matter 2012, 8, pp. 5102-5118
Morphology formation in polypropylene impact copolymers under static melt conditions: A simulation study
Klaas Remerie, Jan Groenewold; Journal of Applied Polymer Science 2012, 125, pp. 212-223
Liquid Crystalline Phases Induced by the Hydroxyl Group Stereochemistry of Amphiphilic Carbohydrate Bicatenary Derivatives
Hary L. Razafindralambo, Aurore Richel, Michel Paquot, Laurence Lins, and Christophe Blecker; Journal of Physical Chemistry B 2012, 116, pp 3998–4005
Self-Organization of Mixtures of Fluorocarbon and Hydrocarbon Amphiphilic Thiolates on the Surface of Gold Nanoparticles
Paola Posocco, Cristina Gentilini, Silvia Bidoggia, Alice Pace, Paola Franchi, Marco Lucarini, Maurizio Fermeglia, Sabrina Pricl, and Lucia Pasquato; ACS Nano 2012, 6, pp 7243–7253
Computational analysis of non-covalent polymer–protein interactions governing antibody orientation
Leslie R. Farris, Melisenda J. McDonald; Analytical and Bioanalytical Chemistry 2012, 402, pp 1731-1736
Surfactant Optimization for EOR using Advanced Chemical Computational Methods
Marten Buijse, Kunj Tandon, Shekhar Jain, Jan-Willem Handgraaf, and Johannes G.E.M. Fraaije; SPE Improved Oil Recovery Symposium, 14-18 April 2012, Tulsa, Oklahoma, USA, 154212-MS
Shape Governs the Motion of Chemically Propelled Janus Swimmers
Francesca Lugli, Emiliano Brini and Francesco Zerbetto; Journal of Physical Chemistry C 2012, 116, pp 592-598
A computational analysis of the insertion of carbon nanotubes into cellular membranes
Siegfried Höfinger, Manuel Melle-Franco, Tommaso Gallo, Andrea Cantelli, Matteo Calvaresi, José A.N.F. Gomes and Francesco Zerbetto; Biomaterials 2011, 32, pp 7079-7085
Molecular Dynamic Simulations for Determining Change in Thermodynamic Properties of Asphaltene and Resin Because of Aging
Rafiqul A. Tarefder and Iffat R. Arisa; Energy & Fuels 2011, 25, pp 2211-2222
A Multiscale Modeling Protocol To Generate Realistic Polymer Surfaces
Jan-Willem Handgraaf, Ruben Serral Gracia, Shyamal K. Nath, Zhong Chen, Shih-Hung Chou, Richard B. Ross, Nate E. Schultz, and Johannes G. E. M. Fraaije; Macromolecules 2011, 44, pp. 1053-1061
Phase Evolution Theory for Polymer Blends with Extreme Chemical Dispersity: Parameterization of DDFT Simulations and Application to Poly(propylene) Impact Copolymers
Johannes G. E. M. Fraaije, Shyamal K. Nath, Klaas Remerie, and Jan Groenewold; Macromolecular Theory and Simulations 2011, 20, pp 133-145
Mesoscopic Simulation of Aggregate Structure and Stability of Heavy Crude Oil by GPU accelerated DPD
Jun-Bo Xu, Sheng-Fei Zhang , Hao Wu, Yue-Hong Zhao, and Hao Wen; Energy Chemical Engineering Transactions 2011, 24, pp. 1531-1536
GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list Updating
Hao Wu, Junbo Xu, Shengfei Zhang and Hao Wen; EIT Journal of Adaptive & Dynamic Computing 2011, pp. 26-32
Aggregate Structure in Heavy Crude Oil: Using a Dissipative Particle Dynamics Based Mesoscale Platform
Sheng-Fei Zhang, Li-Li Sun, Jun-Bo Xu, Hao Wu, and Hao Wen; Energy & Fuels 2010, 24, pp 4312-4326
Size-Dependent Interfacial Tension of Polymer Blends with Broad Composition Polydispersity
Jan Groenewold and Klaas Remerie; Macromolecular Theory and Simulations 2010, 19, pp 370-377
Multiscale Computer Simulation Studies of Water-Based Montmorillonite/ Poly(ethylene oxide) Nanocomposites
Radovan Toth, Dirk-Jan Voorn, Jan-Willem Handgraaf, Johannes G.E.M. Fraaije, Maurizio Fermeglia, Sabrina Pricl, and Paola Posocco; Macromolecules 2009, 42, pp 8260-8270
Wrapping Nanotubes with Micelles, Hemimicelles, and Cylindrical Micelles
Matteo Calvaresi, Marco Dallavalle, and Francesco Zerbetto; Small 2009, 5, pp 2191 – 2198
A Complete Multiscale Modelling Approach for Polymer-Clay Nanocomposites
Giulio Scocchi, Paola Posocco, Jan-Willem Handgraaf, Johannes G.E.M. Fraaije, Maurizio Fermeglia, and Sabrina Pricl; Chemistry, A European Journal 2009, 15, pp 7586-7592
Base Invaders. Coupling Experiments and Multiscale Modeling of Dendrimer-Based siRNA Delivery Agents
Paola Posocco, Giovanni Maria Pavan, Giulio Scocchi, Jan-Willem Handgraaf, Anastasia Malek, Marek Maly, Maurizio Fermeglia, Johannes G.E.M. Fraaije, Carlo V. Catapano, Andrea Danani, and Sabrina Pricl; Advances in Science and Technology 2008, 57, pp 154-159
Property Prediction and Hybrid Modeling for Combinatorial Materials
Andriy V. Kyrylyuk, Fiona H. Case, and Johannes G.E.M. Fraaije; QSAR & Combinatorial Science 2005, 24, pp 131-137
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