Papers

 

In order to cite the Culgi software in your work you can use:

The Chemistry Unified Language Interface (Culgi), version 11, Culgi B.V., The Netherlands, 2004-2017.

 

List of papers:

 

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, Mix and Match: Coassembly of Amphiphilic Dendrimers and Phospholipids Creates Robust, Modular, and Controllable Interfaces, ACS Appl. Mater. Interfaces, 2017, 9, pp. 1029–1035.

Augustinus J. M. Sweere and Johannes G. E. M. Fraaije, Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC, J. Chem. Theory Comput., 2017, 13, pp .1911–1923.

Hon Vai Yee, Jan van Male, Jan-Willem Handgraaf, Ivy Chai Ching Hsia, and Noor 'Aliaa Amira M. Fauzi, Microemulsion Modeling for Surfactant Optimal Salinity Prediction in Chemical EOR Design, International Petroleum Technology Conference, 14-16 November, Bangkok, Thailand.

Augustinus J. M. Sweere, Ruben Serral Gracia, and Johannes G. E. M. Fraaije, Extensive Accuracy Test of the Force-Field-Based Quasichemical Method PAC–MAC, J. Chem. Eng. Data 2016, 61, pp. 3989–3997.

Johannes G. E. M. Fraaije, Jan van Male, Paul Becherer, and Rubèn Serral Gracià, Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases, J. Chem. Inf. Model. 2016, 56, pp. 2361–2377.

Nitish Nair, Michelle Park, Jan-Willem Handgraaf, and Flavia M. Cassiola, Coarse-Grained Simulations of Polymer-Grafted Nanoparticles: Structural Stability and Interfacial Behavior, J. Phys. Chem. B 2016, 120, pp. 9523–9539.

Jielin Pan and Rafiqul A. Tarefder, Investigation of asphalt aging behaviour due to oxidation using molecular dynamics simulation, Molecular Simulation 2016,42, pp. 667-678.

Rafiqul A. Tarefder, Jielin Pan, and Mohammad I. Hossain, 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 Engineering, Chapter 13, Publisher: IGI Global (2015), Editor: Pijush Samui, pp. 334-362.

Augustinus J. M. Sweere and Johannes G. E. M. Fraaije, Force-Field Based Quasi-Chemical Method for Rapid Evaluation of Binary Phase Diagrams, J. Phys. Chem. B 2015, 119, pp 14200–14209.

Jan-Willem Handgraaf, Kunj Tandon, Shekhar Jain, Marten Buijse, and Johannes G.E.M. Fraaije, Application of Computer Simulations to Surfactant Chemical Enhanced Oil Recovery; In book: Analytical Methods in Petroleum Upstream Applications, Chapter: 13, Publisher: CRC (2015), Editors: Cesar Ovalles, Carl E. Rechsteiner Jr., pp. 259-274.

Marco Dallavalle, Matteo Calvaresi, Andrea Bottoni, Manuel Melle-Franco, and Francesco Zerbetto, Graphene Can Wreak Havoc with Cell Membranes, ACS Appl. Mater. Interfaces 2015, 7, pp 4406–4414.

Sergio Manzetti, Remediation technologies for oil-drilling activities in the Arctic: oil-spill containment and remediation in open waterEnvironmental Technology Reviews 20143, pp 1-12.

Marco Dallavalle, Marco Leonzio, Matteo Calvaresi and Francesco Zerbetto, Explaining Fullerene Dispersion by using Micellar SolutionsChemPhysChem 201415, 2998–3005.

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, Pitch variations of self-assembled cylindrical block copolymers in lithographically defined trenches, J. Micro/Nanolith. MEMS MOEMS. 201413, 033015.

Sander F. Wuister, Davide Ambesi, Tamara S. Druzhinina, Emiel Peeters, Jo Finders, Joanne Klein Wolterink and Johannes G. E. M. Fraaije, Fundamental study of placement errors in directed self-assembly, J. Micro/Nanolith. MEMS MOEMS. 201413, 033005.

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, Hierarchical Structuring in Block Copolymer Nanocomposites through Two Phase-Separation Processes Operating on Different Time ScalesAdvanced Functional Materials 201323, pp 4215-42263.

Marten Buijse, Kunj Tandon, Shekhar Jain, Amit Jain, Jan-Willem Handgraaf, and Johannes G.E.M. Fraaije, Accelerated Surfactant Selection for EOR Using Computational MethodsSPE Enhanced Oil Recovery Conference, 2-4 July 2013, Malaysia, 165268-MS.

G. J. A. Sevink, M. Charlaganov and J. G. E. M. Fraaije, Coarse-grained hybrid simulation of liposomesSoft Matter 20139, pp 2816-2831.

Johannes G.E.M. Fraaije, Kunj Tandon,  Shekhar Jain,  Jan-Willem Handgraaf and Marten Buise, Method of Moments for Computational Microemulsion Analysis and Prediction in Tertiary Oil Recovery, Langmuir 201329, pp 2136-2151.

Welchy Leite Cavalcanti, Andreas Brinkmann, Michael Noeske, Sascha Buchbach, Felix Straetmans and Marko Soltau, Dual-purpose defenders: Organic polymers protect metals in both thin layers and coatings, European Coatings Journal 2012, 10, pp. 1-4.

Karol M. Langner and G. J. A. Sevink, Mesoscale modeling of block copolymer nanocompositesSoft Matter 20128, pp. 5102-5118.

Klaas Remerie, Jan Groenewold, Morphology formation in polypropylene impact copolymers under static melt conditions: A simulation studyJournal of Applied Polymer Science 2012125, pp. 212-223.

Hary L. Razafindralambo, Aurore Richel, Michel Paquot, Laurence Lins, and Christophe Blecker, Liquid Crystalline Phases Induced by the Hydroxyl Group Stereochemistry of Amphiphilic Carbohydrate Bicatenary DerivativesJournal of Physical Chemistry B 2012116, pp 3998–4005.

Paola Posocco, Cristina Gentilini, Silvia Bidoggia, Alice Pace, Paola Franchi, Marco Lucarini, Maurizio Fermeglia, Sabrina Pricl, and Lucia Pasquato, Self-Organization of Mixtures of Fluorocarbon and Hydrocarbon Amphiphilic Thiolates on the Surface of Gold NanoparticlesACS Nano 20126, pp 7243–7253.

Leslie R. Farris, Melisenda J. McDonald,Computational analysis of non-covalent polymer–protein interactions governing antibody orientationAnalytical and Bioanalytical Chemistry 2012402, pp 1731-1736.

Marten Buijse, Kunj Tandon, Shekhar Jain, Jan-Willem Handgraaf, and Johannes G.E.M. Fraaije, Surfactant Optimization for EOR using Advanced Chemical Computational MethodsSPE Improved Oil Recovery Symposium, 14-18 April 2012, Tulsa, Oklahoma, USA, 154212-MS.

Francesca Lugli, Emiliano Brini and Francesco Zerbetto, Shape Governs the Motion of Chemically Propelled Janus SwimmersJournal of Physical Chemistry C 2012116, pp 592-598.

Siegfried Höfinger, Manuel Melle-Franco, Tommaso Gallo, Andrea Cantelli, Matteo Calvaresi, José A.N.F. Gomes and Francesco Zerbetto, A computational analysis of the insertion of carbon nanotubes into cellular membranesBiomaterials 201132, pp 7079-7085.

Rafiqul A. Tarefder and Iffat R. Arisa, Molecular Dynamic Simulations for Determining Change in Thermodynamic Properties of Asphaltene and Resin Because of AgingEnergy & Fuels 201125, pp 2211-2222.

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, A Multiscale Modeling Protocol To Generate Realistic Polymer SurfacesMacromolecules 201144, pp. 1053-1061.

Johannes G. E. M. Fraaije, Shyamal K. Nath, Klaas Remerie, and Jan Groenewold, Phase Evolution Theory for Polymer Blends with Extreme Chemical Dispersity: Parameterization of DDFT Simulations and Application to Poly(propylene) Impact CopolymersMacromolecular Theory and Simulations 201120, pp 133-145.

Jun-Bo Xu, Sheng-Fei Zhang , Hao Wu, Yue-Hong Zhao, and Hao Wen, Mesoscopic Simulation of Aggregate Structure and Stability of Heavy Crude Oil by GPU accelerated DPDEnergy Chemical Engineering Transactions 201124, pp. 1531-1536.

Hao Wu, Junbo Xu, Shengfei Zhang and Hao Wen, GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list UpdatingEIT Journal of Adaptive & Dynamic Computing 2011, pp. 26-32.

Sheng-Fei Zhang, Li-Li Sun, Jun-Bo Xu, Hao Wu, and Hao Wen, Aggregate Structure in Heavy Crude Oil: Using a Dissipative Particle Dynamics Based Mesoscale PlatformEnergy & Fuels 201024, pp 4312-4326.

Jan Groenewold and Klaas Remerie, Size-Dependent Interfacial Tension of Polymer Blends with Broad Composition PolydispersityMacromolecular Theory and Simulations 201019, pp 370-377.

Radovan Toth, Dirk-Jan Voorn, Jan-Willem Handgraaf, Johannes G.E.M. Fraaije, Maurizio Fermeglia, Sabrina Pricl, and Paola Posocco, Multiscale Computer Simulation Studies of Water-Based Montmorillonite/Poly(ethylene oxide) NanocompositesMacromolecules 200942, pp 8260-8270.

Matteo Calvaresi, Marco Dallavalle, and Francesco Zerbetto, Wrapping Nanotubes with Micelles, Hemimicelles, and Cylindrical MicellesSmall 20095, pp 2191 - 2198.

Giulio Scocchi, Paola Posocco, Jan-Willem Handgraaf, Johannes G.E.M. Fraaije, Maurizio Fermeglia, and Sabrina Pricl, A Complete Multiscale Modelling Approach for Polymer-Clay Nanocomposites, Chemistry, A European Journal 200915, pp 7586-7592.

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, Base Invaders. Coupling Experiments and Multiscale Modeling of Dendrimer-Based siRNA Delivery Agents, Advances in Science and Technology 200857, pp 154-159.

Andriy V. Kyrylyuk, Fiona H. Case, and Johannes G.E.M. Fraaije, Property Prediction and Hybrid Modeling for Combinatorial Materials, QSAR & Combinatorial Science 200524, pp 131-137.