Publications
17 results found
Svoboda M, Jimenez MGS, Kowalski A, et al., 2021, Structural properties of cationic surfactant-fatty alcohol bilayers: insights from dissipative particle dynamics, SOFT MATTER, Vol: 17, Pages: 9967-9984, ISSN: 1744-683X
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- Citations: 5
Jimenez-Serratos G, Cardenas H, Muller E, 2019, Extension of the effective solid-fluid Steele potential for Mie force fields, Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, Vol: 117, Pages: 3840-3851, ISSN: 0026-8976
Molecular simulation of fluid systems in the presence of surfaces require computationally expen-sive calculations due to the large number of solid–fluid pair interactions involved. Representingthe explicit solid as a continuous wall with an effective potential can significantly reduce thecomputational time and allows exploring larger temporal and spatial scales. Different ana-lytical expressions can be found in the literature depending on the structural characteristicsof the solid and the approximations adopted in the derivation. The well-known (10-4-3) Steelepotential is one such analytic expression that faithfully represents the effective solid–fluid inter-actions for homonuclear crystalline solids with hexagonal lattice symmetry. However, this andmost of the effective potentials found in the literature have been developed for fluids and solidsinteracting exclusively through Lennard-Jones potentials. In this work, we extend the Steelemodel to obtain the effective wall–fluid potentials for Mie force fields. We perform moleculardynamics simulations of coarse-grained fluids modelled via the SAFT force field approach inthe presence of explicit and implicit surfaces to compare structural and dynamic properties inboth representations. Also, we study the adsorption of ethane into slit-like pores with explicitand implicit surfaces via grand canonical Monte Carlo simulations. We explore the validityand the improvement in the simulation performance as well as the limitations of the proposedexpression.
Muller E, Law J, Headen T, et al., 2019, A catalogue of plausible molecular models for the molecular dynamics of asphaltenes and resins obtained from quantitative molecular representation, Energy and Fuels, Vol: 33, Pages: 9779-9795, ISSN: 0887-0624
Computer simulation studies aimed at elucidating the phase behavior of crude oils inevitably require atomistically-detailed models of representative molecules. For the lighter fractions of crudes, such molecules are readily available, as the chemical composition can be resolved experimentally. Heavier fractions pose a challenge, on one hand due to their polydispersity and on the other due to poor description of the morphology of the molecules involved. The Quantitative Molecular Representation (QMR) approach is used here to generate a catalogue of 100 plausible asphaltene and resin structures based on elemental analysis and 1H – 13C NMR spectroscopy experimental data. The computer-generated models are compared in the context of a review of previously proposed literature structures and categorized by employing their molecular weights, double bond equivalents (DBE) and hydrogen to carbon (H/C) ratios. Sample atomistic molecular dynamics simulations were carried out for two of the proposed asphaltene structures with contrasting morphologies, one island-type and one archipelago-type, at 7 wt% in either toluene or heptane. Both asphaltene models, which shared many characteristics in terms of average molecular weight, chemical composition and solubility parameters showed marked differences in their aggregation behavior. The example showcases the importance of considering diversity and polydispersity when considering molecular models of heavy fractions.
Kaimaki D-M, Haire B, Ryan H, et al., 2019, Multiscale approach linking self-aggregation and surface interactions of synthesized foulants to fouling mitigation strategies, Energy & Fuels, Vol: 33, Pages: 7216-7224, ISSN: 0887-0624
Fouling of oil-exposed surfaces remains a crucial issue as a result of the continued importance of oil as the world’s primary energy source. The key perpetrators in crude oil fouling have been identified as asphaltenes, a poorly described mixture of diverse polyfunctional molecules that form part of the heaviest fractions of oil. Asphaltenes are responsible for a decrease in oil production and energy efficiency and an increase in the risk of environmental hazards. Hence, understanding and managing systems that are prone to fouling is of great value but constitutes a challenge as a result of their complexity. In an effort to reduce that complexity, a study of a synthesized foulant of archipelago structure is presented. A critical perspective on previously described solubility and aggregation mechanisms (e.g., critical nanoaggrerate concentration and critical clustering concentration) is offered because the characterized system favors a continuous distribution of n-mers instead. A battery of experimental and modeling techniques have been employed to link the bulk and interfacial behavior of a representative foulant monomer to effective fouling mitigation strategies. This systematic approach defines a new multiscale methodology in the investigation of fouling systems.
Wand CR, Fayaz-Torshizi M, Jimenez-Serratos G, et al., 2019, Solubilities of pyrene in organic solvents: Comparison between chemical potential calculations using a cavity-based method and direct coexistence simulations, The Journal of Chemical Thermodynamics, Vol: 131, Pages: 620-629, ISSN: 0021-9614
In this paper, we benchmark a cavity-based simulation method for calculating the relative solubility of large molecules in explicit solvents. The essence of the procedure is the accounting of the Gibbs energy change associated with an alchemical thermodynamic cycle where, in sequence, a cavity is created in a solvent, a solute is inserted in the cavity and the cavity is annihilated. The Gibbs energy change is equated to the excess chemical potential allowing the comparison of solubilities in different solvents. The results obtained using the cavity-based method are compared to direct large-scale molecular dynamics simulations performed using coarse-grained models for calculating the partition coefficient of pyrene between heptane and toluene. We demonstrate the applicability of this cavity-based technique under high pressure/temperature conditions.
Jiménez-Serratos G, Totton TS, Jackson G, et al., 2019, Aggregation behavior of model asphaltenes revealed from large-scale coarse-grained molecular simulations, Journal of Physical Chemistry B, Vol: 123, Pages: 2380-2396, ISSN: 1520-5207
Fully atomistic simulations of models of asphaltenes in simple solvents have allowed the study of trends in aggregation phenomena and the understanding of the role that molecular structure plays therein. However, the detail included at this scale of molecular modeling is at odds with the required spatial and temporal resolution needed to fully understand the asphaltene aggregation. The computational cost required to explore the relevant scales can be reduced by employing coarse-grained (CG) models, which consist of lumping a few atoms into a single segment that is characterised by effective interac- tions. In this work CG force fields developed via the SAFT-γ [Müller, E.A., Jackson, G. (2014) Annu. Rev. Chem. Biomolec. Eng., 5, 405–427] equation of state (EoS) provide a reliable pathway to link the molecular description with macroscopic thermophysical data. A recent modification of the SAFT-VR EoS [Müller, E.A. and Mejía, A. (2017) Langmuir, 33, 11518–11529], that allows parametrizing homonuclear rings, is selected as the starting point to propose CG models for polycyclic aromatic hydrocarbons (PAHs). The new aromatic-core parameters, along with others published for simpler organic molecules, are adopted for the construction of asphaltene models by combining different chemical moieties in a group-contribution fashion. We apply the procedure to two previously reported asphaltene models and perform Molecular Dynamics simulations to validate the coarse-grained representation against benchmark systems of 27 asphaltenes in pure solvent (toluene or heptane) described in a fully atomistic fashion. An excellent match between both levels of description is observed for cluster size, radii of gyration, and relative-shape-anisotropy-factor distributions. We exploit the advantages of the CG representation by simulating systems containing up to 2000 asphaltene molecules in explicit solvent investigating the effect of asphaltene concentration, so
Shahruddin S, Jimenez-Serratos G, Britovsek G, et al., 2019, Fluid-solid phase transition of n-alkane mixtures: coarse-grained molecular dynamics simulations and diffusion-ordered spectroscopy nuclear magnetic resonance, Scientific Reports, Vol: 9, Pages: 1-9, ISSN: 2045-2322
Wax appearance temperature (WAT), defined as the temperature at which the first solid paraffin crystal appears in a crude oil, is one of the key flow assurance indicators in the oil industry. Although there are several commonly-used experimental techniques to determine WAT, none provides unambiguous molecular-level information to characterize the phase transition between the homogeneous fluid and the underlying solid phase. Molecular Dynamics (MD) simulations employing the statistical associating fluid theory (SAFT) force field are used to interrogate the incipient solidification states of models for long-chain alkanes cooled from a melt to an arrested state. We monitor the phase change of pure long chain n-alkanes: tetracosane (C24H50) and triacontane (C30H62), and an 8-component surrogate n-alkane mixture (C12-C33) built upon the compositional information of a waxy crude. Comparison to Diffusion Ordered Spectroscopy Nuclear Magnetic Resonance (DOSY NMR) results allows the assessment of the limitations of the coarse-grained models proposed. We show that upon approach to freezing, the heavier components restrict their motion first while the lighter ones retain their mobility and help fluidize the mixture. We further demonstrate that upon sub-cooling of long n-alkane fluids and mixtures, a discontinuity arises in the slope of the self-diffusion coefficient with decreasing temperature, which can be employed as a marker for the appearance of an arrested state commensurate with conventional WAT measurements.
Galindo A, Rahman S, Lobanova O, et al., 2018, SAFT‑γ force field for the simulation of molecular fluids. 5. Hetero Group coarse-grained models of linear alkanes and the importance of intramolecular interactions, Journal of Physical Chemistry B, Vol: 122, Pages: 9161-9177, ISSN: 1520-5207
The SAFT-γ Mie group-contribution equation of state [Papaioannou J. Chem. Phys. 2014, 140, 054107] is used to develop a transferable coarse-grained (CG) force-field suitable for the molecular simulation of linear alkanes. A heterogroup model is fashioned at the resolution of three carbon atoms per bead in which different Mie (generalized Lennard-Jones) interactions are used to characterize the terminal (CH3–CH2–CH2−) and middle (−CH2–CH2–CH2−) beads. The force field is developed by combining the SAFT-γ CG top-down approach [Avendaño J. Phys. Chem. B 2011, 115, 11154], using experimental phase-equilibrium data for n-alkanes ranging from n-nonane to n-pentadecane to parametrize the intermolecular (nonbonded) bead–bead interactions, with a bottom-up approach relying on simulations based on the higher resolution TraPPE united-atom (UA) model [Martin; , Siepmann J. Phys. Chem. B 1998, 102, 2569] to establish the intramolecular (bonded) interactions. The transferability of the SAFT-γ CG model is assessed from a detailed examination of the properties of linear alkanes ranging from n-hexane (n-C6H14) to n-octadecane (n-C18H38), including an additional evaluation of the reliability of the description for longer chains such as n-hexacontane (n-C60H122) and a prototypical linear polyethylene of moderate molecular weight (n-C900H1802). A variety of structural, thermodynamic, and transport properties are examined, including the pair distribution functions, vapor–liquid equilibria, interfacial tension, viscosity, and diffusivity. Particular focus is placed on the impact of incorporating intramolecular interactions on the accuracy, transferability, and representability of the CG model. The novel SAFT-γ CG force field is shown to provide a reliable description of the thermophysical properties of the n-alkanes, in most cases at a level comparable to the that obtained with higher resolution models.
Jimenez-serratos M, Herdes C, Haslam A, et al., 2017, Group contribution coarse-grained molecular simulations of polystyrene melts and polystyrene solutions in alkanes using the SAFT-γ force field, Macromolecules, Vol: 50, Pages: 4840-4853, ISSN: 0024-9297
A coarse-grained (CG) model for atactic polystyrene is presented and studied with classical molecular-dynamics simulations. The interactions between the CG segments are described by Mie potentials, with parameters obtained from a top-down approach using the SAFT-γ methodology. The model is developed by taking a CG model for linear-chain-like backbones with parameters corresponding to those of an alkane and decorating it with side branches with parameters from a force field of toluene, which incorporate an “aromatic-like” nature. The model is validated by comparison with the properties of monodisperse melts, including the effect of temperature and pressure on density, as well as structural properties (the radius of gyration and end-to-end distance as functions of chain length). The model is employed within large-scale simulations that describe the temperature–composition fluid-phase behavior of binary mixtures of polystyrene in n-hexane and n-heptane. A single temperature-independent unlike interaction energy parameter is employed for each solvent to reproduce experimental solubility behavior; this is sufficient for the quantitative prediction of both upper and lower critical solution points and the transition to the characteristic “hourglass” phase behavior for these systems.
Ervik A, Lysgaard MO, Herdes C, et al., 2016, A multiscale method for simulating fluid interfaces covered with large molecules such as asphaltenes, Journal of Computational Physics, Vol: 327, Pages: 576-611, ISSN: 0021-9991
The interface between two liquids is fully described by the interfacial tension only for very pure liquids. In most cases the system also contains surfactant molecules which modify the interfacial tension according to their concentration at the interface. This has been widely studied over the years, and interesting phenomena arise, e.g. the Marangoni effect. An even more complicated situation arises for complex fluids like crude oil, where large molecules such as asphaltenes migrate to the interface and give rise to further phenomena not seen in surfactant-contaminated systems. An example of this is the “crumpling drop” experiments, where the interface of a drop being deflated becomes non-smooth at some point. In this paper we report on the development of a multiscale method for simulating such complex liquid–liquid systems. We consider simulations where water drops covered with asphaltenes are deflated, and reproduce the crumpling observed in experiments. The method on the nanoscale is based on using coarse-grained molecular dynamics simulations of the interface, with an accurate model for the asphaltene molecules. This enables the calculation of interfacial properties. These properties are then used in the macroscale simulation, which is performed with a two-phase incompressible flow solver using a novel hybrid level-set/ghost-fluid/immersed-boundary method for taking the complex interface behaviour into account. We validate both the nano- and macroscale methods. Results are presented from nano- and macroscale simulations which showcase some of the interesting behaviour caused by asphaltenes affecting the interface. The molecular simulations presented here are the first in the literature to obtain the correct interfacial orientation of asphaltenes. Results from the macroscale simulations present a new physical explanation of the crumpled drop phenomenon, while highlighting shortcomings in previous hypotheses.
Ervik AS, Serratos GJ, Müller EA, 2016, raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT-γ Mie force field, Computer Physics Communications, Vol: 212, Pages: 161-179, ISSN: 0010-4655
We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT-γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid–liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.
Yang J, Serratos MGJ, Fari-Arole DS, et al., 2015, Crude Oil Fouling: Fluid Dynamics, Reactions and Phase Change, IUTAM SYMPOSIUM ON MULTIPHASE FLOWS WITH PHASE CHANGE: CHALLENGES AND OPPORTUNITIES, Vol: 15, Pages: 186-193, ISSN: 2210-9838
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- Citations: 10
Coletti F, Crittenden BD, Haslam AJ, et al., 2015, Modeling of Fouling from Molecular to Plant Scale, CRUDE OIL FOULING: DEPOSIT CHARACTERIZATION, MEASUREMENTS, AND MODELING, Editors: Coletti, Hewitt, Publisher: GULF PROFESSIONAL PUBL, Pages: 179-320, ISBN: 978-0-12-801256-7
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- Citations: 7
Jimenez-Serratos G, Gil-Villegas A, Vega C, et al., 2013, Monte Carlo simulation of flexible trimers: From square well chains to amphiphilic primitive models, JOURNAL OF CHEMICAL PHYSICS, Vol: 139, ISSN: 0021-9606
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- Citations: 8
Jimenez-Serratos G, Vega C, Gil-Villegas A, 2012, Evaluation of the pressure tensor and surface tension for molecular fluids with discontinuous potentials using the volume perturbation method, JOURNAL OF CHEMICAL PHYSICS, Vol: 137, ISSN: 0021-9606
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- Citations: 15
Jimenez-Serratos G, Avendano C, Gil-Villegas A, et al., 2011, Computer simulation of charged hard spherocylinders at low temperatures, MOLECULAR PHYSICS, Vol: 109, Pages: 27-36, ISSN: 0026-8976
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- Citations: 19
Jimenez G, Santillan S, Avendano C, et al., 2008, Molecular thermodynamics of adsorption using discrete-potential systems, OIL & GAS SCIENCE AND TECHNOLOGY-REVUE D IFP ENERGIES NOUVELLES, Vol: 63, Pages: 329-341, ISSN: 1294-4475
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- Citations: 31
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