Publications

  1. Baker, S. L., Munasinghe, A., Kaupbayeva, B., Kang, N. R., Certiat, M., Murata, H., Matyjaszewski, K., Lin, P., Colina, C. M., Russell, A. J., “Transforming protein-polymer conjugate purification by tuning protein solubility” Nat. Commun., 2019, 10, 4718. [doi]
  2. Tang, D., Kupgan, G., Colina, C. M., Sholl, D. S., “Rapid Prediction of Adsorption Isotherms of a Diverse Range of Molecules in Hyper-Crosslinked Polymers” J. Phys. Chem. C, 2019, 123(29), 17884-17893. [doi]
  3. Rukmani, S. J., Lin, P., Andrew, J. S., Colina, C. M., “Molecular Modeling of Complex Cross-Linked Networks of PEGDA Nanogels” J. Phys. Chem. B, 2019, 132(18), 4129-4138. [doi]
  4. Lin, P., Colina, C. M., “Molecular simulation of protein-polymer conjugates” Current opinion in Chemical Engineering, 2019. 23, 44-50. [doi]
  5. Munasinghe, A., Mathavan, A., Mathavan, A., Lin, P., Colina, C. M., “Molecular insight into the protein-polymer interactions in N-terminal PEGylated Bovine Serum Albumin” J. Phys. Chem. B, 2019[doi]
  6. Rukmani, S. J., Kupgan, G., Anstine, D. M., Colina, C. M., “A molecular dynamics study of water-soluble polymers: analysis of force fields from atomistic simulations” Molecular Simulation2018[doi]
  7. Ramezanghorbani, F., Lin, P., Colina, C. M., “Optimizing Protein-Polymer Interactions in a Poly(ethylene glycol) Coarse-Grained Model.” J. Phys. Chem. B2018, 122(33), 7997-8005. [doi]
  8. Baker, S., Munasinghe, A., Murata, H., Lin, P., Matyjaszewski, K., Colina, C. M., Russel, A. J., “Intramolecular interactions of conjugated polymers mimic molecular chaperones to stabilize protein-polymer conjugates” Biomacromolecules, 2018, 19(9), 3798-3813. [doi]
  9. Kupgan, G., Demidov, A. G., Colina, C. M., “Plasticization Behavior in Polymers of Intrinsic Microporosity (PIM-1): a Simulation Study from Combined Monte Carlo and Molecular Dynamics” J. Membrane Sci., 2018, 565, 95-103.[doi]
  10. Mathavan, A., Mathavan, A., Fortunato, M. E. and C. M. Colina, “An All-Atomistic Molecular Dynamics Study to Determine the Structural Importance of Disulfide Bonds in Immunoglobulin G and Bovine Serum Albumin,” American Journal of Undergraduate Research, 2018, in press.
  11. Russel, A. J., Baker, S., Colina, C. M., Figg, C. A., Kaar, J. L., Matyjaszewski, K. Simakova, A., Summerlin, B. S., “Next generation protein-polymer conjugates” AIChE Journal, 2018, 64(9), 3230-3245.[doi]
  12. Alzate-Vargas, L., Fortunato, M. E., Haley, B. P., Li, C., Colina, C. M., Strachan, A., “Uncertainties on predictions of thermo-physical properties of thermoplastic polymers via molecular dynamics” Modelling Simul. Mater. Sci. Eng., 2018, 26, 065007.[doi]
  13. Ruckmani, S. J., Liyana-Arachchi, T. P., Hart, K. E., Colina, C. M., “Ionic-Functionalized Polymers of Intrinsic Microporosity for Gas Separation Applications” Langmuir, 2018, 34(13), 3949-3960.[doi]
  14. Kupgan, G., Abbott, L. J., Hart, K. E., Colina, C. M., “Modeling Amorphous Microporous Polymers for CO2 Capture and Separations,” Chem. Rev., 2018, 118(11), 5488-5538.[doi]
  15. Bezzu, C. G., Carta, M., Ferrari, M.-C., Jansen, J. C., Monteleone, M., Esposito, E., Fuoco, A., Hart, K., Liyana-Arachchi, T. P., Colina, C. M., McKeown, N. B., “The synthesis, chain-packing simulation and long-term gas permeability of highly selective spirobifluorene-based polymers of intrinsic microporosity.”, J. Mater. Chem. A, 2018, 6, 10507-10514.[doi]
  16. Demidov, A. G., Fortunato, M. E., Colina, C. M., “Update 0.2 to ‘pysimm: A Python package for simulation of molecular systems’.”, SoftwareX, 2018, 7, 70-73. [doi]
  17. Goethe, E. V., Colina, C. M., “Taking Advantage of Diversity within the Classroom”, J. Chem. Educ. 2018, 95(2), 189-192.[doi]
  18. Fortunato, M. E., Mattson, J., Taylor, D., Larentzos, J.P., Brennan, J.K., “Pre- and Post-Processing Tools to Create and Characterize Particle-Based Composite Model Structures”, ARL Technical Report, ARL-TR-8213, 2017
  19. Munasinghe, A., Lin, P., Colina, C. M., “Unraveling Binding Interactions between Human RANKL and Its Decoy Receptor Osteoprotegerin.” J. Phys. Chem. B, 2017, 121(39), 9141-9148.[doi]
  20. Kupgan, G., Liyana-Arachchi, T. P., Colina, C. M., “NLDFT Pore Size Distribution in Amorphous Microporous Material.” Langmuir, 2017, 33(42), 11138-11145.[doi]
  21. Rose, I., Bezzu, C. G., Carta, M., Comesaña-Gándara, B., Lasseuguette, E., Ferrari, M. C., Clarizia, G., Fuoco, A., Jansen, J. C., Hart, K. E., Liyana-Arachchi, T. P., Colina, C. M., McKeown, N. B., “Polymer ultrapermeability from the inefficient packing of 2D chains” Nature Materials, 2017, 16. 932-937.[doi]
  22. Hart, K.E., Colina, C. M., “Correction to “Ionomers of Intrinsic Microporosity: In Silico Development of Ionic-Functionalized Gas-Separation Membranes”” Langmuir, 2017, 33(24), 6203-6203.[doi]
  23. Zbyšek, P., Svoboda, M., Lísal, M., Colina, C. M., “Flow and aggregation of rod-like proteins in slit and cylindrical pores coated with polymer brushes: an insight from dissipative particle dynamics” Soft Matter, 2017,13 ,1634-1645.[doi]
  24. Fortunato, M.E., Colina, C. M., “pysimm: A python package for simulation of molecular systems,” SoftwareX, 2017, 6, 7-12. [doi]
  25. Liyana-Arachchi, T. P., Sturnfield, J. F., Colina, C. M., “Ultrathin Molecular-Layer-by-Layer Polyamide Membranes: Insights from Atomistic Molecular Simulations,” J. Phys. Chem. B, 2016,120 (35), 9484–9494. [doi]
  26. Kupgan, G., Liyana-Arachchi, T. P., Colina, C. M., “Pore size tuning of poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) hypercrosslinked polymers: Insights from molecular simulations,” Polymer, 2016, 99, 173-184. [doi]
  27. Moreno, N., Perilla, J. E., Colina, C. M., M Lisal, “Mucin Aggregation from a Rod-like Meso-scale Model,” Mol Phys2015, 113 (9-10), 898-909. [doi]
  28. Frentrup, H., Hart, K. E., Colina, C. M., Muller, E. A., “In Silico Determination of Gas Permeabilities by Non-Equilibrium Molecular Dynamics: CO2 and He through PIM-1.” Membranes2015, 5(1), 99-119. [doi]
  29. Zhou, X., Huang, J., Barr, K. W., Lin, Z., Maya, F., Abbott, L.J., Colina C. M., Svec, F., S. R. Turner, “Nanoporous Hypercrosslinked Polymers Containing Tg Enhancing Comonomer.” Polymer2015, 59, 42-48. [doi]
  30. Moustafa, I. M., Korboukh, V. K., Arnold, J. J., Smidansky, E. D., Marcotte, L. L., Gohara, D. W., Yang, X., Sanchez-Farran, M. A., Filman, D., Maranas, J. K., Boehr, D. D., Hogle, J. M., Colina, C. M., C. E. Cameron, “Structural Dynamics as a Contributor to Error-prone Replication by a RNA-dependent RNA Polymerase.” JBC2014, 289, 36229-36248. [doi]
  31. Hart, K. E.; Abbott, L. J.; Lisal, M.; Colina, C. M. “Morphology and Molecular Bridging in Comb- and Star-shaped Diblock Copolymers.” J. Chem. Phys2014, 141, 204902. [doi]
  32. Hart, K. E.; Colina, C. M. “Ionomers of Intrinsic Microporosity: In Silico Development of Ionic-Functionalized Gas-Separation Membranes.” Langmuir2014, 30 (40), 12039–12048. [doi]
  33. Abbott, L. J.; Colina, C. M. “Formation of Microporosity in Hyper-Cross-Linked Polymers.” Macromolecules2014, 47 (15), 5409-5415. [doi]
  34. Fortunato, M. E.; Colina, C. M. “Effects of Galactosylation in Immunoglobulin G from All-Atom Molecular Dynamics Simulations.” J. Phys. Chem. B2014, 118 (33), 9844–9851. [doi]
  35. Abbott, L. J.; Colina, C. M. “Porosity and Ring Formation in Conjugated Microporous Polymers.” J. Chem. Eng. Data2014, in press. Special Issue: Modeling and Simulation of Real Systems. [doi]
  36. Hart, K. E.; Colina, C. M. “Estimating gas permeability and permselectivity of microporous polymers.” J. Membr. Sci.2014, 468, 259-268. [doi]
  37. Perkins, S. L.; Painter, P.; Colina, C. M. “Experimental and Computational Studies of Choline Chloride-Based Deep Eutectic Solvents.” J. Chem. Eng. Data2014, 59 (11), 3652–3662. [doi]
  38. McDermott, A.; Budd, P. M.; McKeown, N. B.; Colina, C. M.; Runt J. “Physical aging of polymers of intrinsic microporosity: a SAXS/WAXS study.” J. Mater. Chem. A2014, 2 (30), 11742-11752. [doi]
  39. Larsen, G. S.; Hart, K. E.; Colina, C. M. “Predictive simulations of the structural and adsorptive properties for PIM-1 variations.” Mol. Simul.2014, 40 (7-9), 599-609. Special Issue: Recent Advances in the Molecular Simulation of Adsorption. [doi]
  40. Abbott, L. J.; Hughes, J. E.; Colina, C. M. “Virtual Synthesis of Thermally Cross-Linked Copolymers from a Novel Implementation of Polymatic.” J. Phys. Chem. B2014, 118 (7), 1916-1924. [doi]
  41. Castellanos, M. M.; Colina, C. M. “Molecular Dynamics Simulations of Human Serum Albumin and Role of Disulfide Bonds.” J. Phys. Chem. B2013, 117 (40), 11895-11905. [doi]
  42. Hart , K. E.; Springmeier, J. M.; McKeown, N. B.; Colina, C. M. “Simulated swelling during low-temperature N2 adsorption in polymers of intrinsic microporosity.” Phys. Chem. Chem. Phys.2013, 15 (46), 20161-20169. [doi]
  43. Abbott, L. J.; McKeown, N. B.; Colina, C. M. “Design Principles for Microporous Organic Solids From Predictive Computational Screening.” J. Mater. Chem. A2013, 1, 11950-11960. [doi]
  44. Perkins, S. L.; Painter, P.; Colina, C. M. “Molecular Dynamic Simulations and Vibrational Analysis of an Ionic Liquid Analogue.” J. Phys. Chem. B2013, 117 (35), 10250–10260. [doi]
  45. Zhou, X.; Li, Y.; Hart, K. E.; Abbott, L. J.; Lin, Z.; Svec, F.; Colina, C. M.; Turner, S. R. “Nanoporous Properties of Semi-Rigid Alternating Copolymers via Nitrogen Sorption and Molecular Simulation.” Macromolecules2013, 46 (15), 5968-5973. [doi]
  46. Hart, K. E.; Abbott, L. J.; McKeown, N. B.; Colina, C. M. “Toward Effective CO2/CH4 Separations by Sulfur-Containing PIMs via Predictive Molecular Simulations.” Macromolecules2013, 46 (13), 5371-5380. [doi]
  47. Abbott, L. J.; Hart, K. E.; Colina, C. M. “Polymatic: A Generalized Simulated Polymerization Algorithm for Amorphous Polymers.” Theor. Chem. Acc.2013, 132, 1334. [doi]
  48. Abbott, L. J.; McDermott, A. G.; Del Regno, A.; Taylor, R. G. D.; Bezzu, C. G.; Msayib, K. J.; McKeown, N. B.; Siperstein, F. R.; Runt, J.; Colina, C. M. “Characterizing the Structure of Organic Molecules of Intrinsic Microporosity by Molecular Simulations and X-ray Scattering.” J. Phys. Chem. B2013, 117, 355-364. [doi]
  49. Hart, K. E.; Abbott, L. J.; Colina, C. M. “Analysis of Force Fields and BET Theory for Polymers of Intrinsic Microporosity.” Mol. Simul.2013, 39 (5), 397-404. [doi] (Cover art)
  50. Shen, H.; Moustafa, I. M.; Cameron, C. E.; Colina, C. M. “Exploring the Dynamics of Four RNA-Dependent RNA Polymerases by a Coarse-Grained Model.” J. Phys. Chem. B2012, 116 (50), 14515-14524. [doi]
  51. Shen, H.; Hricko, P. J.; Colina, C. M.; Milner, S. T. “Chiral Elasticity of DNA.” Soft Matter2012, 8, 10090-10094. [doi]
  52. Kim, S.; Palomino, A. M.; Colina, C. M. “Responsive Polymer Conformation and Resulting Permeability of Clay-Polymer Nanocomposites.” Mol. Simul.2012, 38 (8-9), 723-734. Special Issue: New Developments in Molecular Simulation. [doi]
  53. Cataño-Barrera, A. M.; Figueira, F. L.; Olivera-Fuentes, C.; Colina, C. M. “Correlation and Prediction of Fluid-Fluid Equilibria of Carbon Dioxide-Aromatics and Carbon Dioxide-Dichlorobenzoates Binary Mixtures.” Fluid Phase Equilib.2011, 311, 45-53. [doi]
  54. Larsen, G. S.; Lin, P.; Hart, K. E.; Colina, C. M. “Molecular Simulations of PIM-1-like Polymers of Intrinsic Microporosity.” Macromolecules2011, 44 (17), 6944-6951. [doi]
  55. Moustafa, I. M.; Shen, H.; Morton, B.; Colina, C. M.; Cameron, C. E. “Molecular Dynamics Simulations of the Viral RNA Polymerases Link Conserved and Correlated Motions of Functional Elements to Fidelity.” J. Mol. Biol.2011, 410, 159-181. Cover article[doi]
  56. Van Niekerk, D.; Castro-Marcano, F.; Colina, C. M.; Mathews, J. P. “Solvent Swelling Extent of Permian-Aged Vitrinite- and Inertinite-Rich Coals: Experiments and Modeling Using Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT).” Energy Fuels2011, 25 (6), 2559-2564. [doi]
  57. Abbott, L. J.; Colina, C. M. “Atomistic Structure Generation and Gas Adsorption Simulations of Microporous Polymer Networks.” Macromolecules2011, 44 (11), 4511-4519. [doi]
  58. McDermott, A. G.; Larsen, G. S.; Budd, P. M.; Colina, C. M.; Runt, J. “Structural Characterization of a Polymer of Intrinsic Microporosity: X-Ray Scattering with Interpretation Enhanced by Molecular Dynamics Simulations.” Macromolecules2011, 44 (1), 14-16. [doi]
  59. Larsen, G. S.; Lin, P.; Siperstein, F. R.; Colina, C. M.. “Methane Adsorption in PIM-1.” Adsorption2011, 17 (1), 21-26. [doi]
  60. Castro-Marcano, F.; Cataño-Barrera, A. M.; Colina, C. M. “Phase Behavior of Polymer Solutions from Macroscopic Properties: Application to the Perturbed Chain Statistical Associated Fluid Theory Equation of State.” Ind. Eng. Chem. Res. 2011, 50 (2), 1046-1055. [doi]
  61. Patterson, K.; Lísal, M.; Colina, C. M. “Adsorption Behavior of Model Proteins on Surfaces.” Fluid Phase Equilib.2011, 302 (1-2), 48-54. [doi]
  62. Colina, C. M.; Olivera-Fuentes, C. “Reply to ‘Comments on “Joule-Thomson Inversion Curves and Third Virial Coefficients for Pure Fluids from Molecular-Based Models” and “Predicted Inversion Curve and Third Virial Coefficient of Carbon Dioxide at High Temperatures.”’” Ind. Eng. Chem. Res.2009, 48 (14), 6904-6905. [doi]
  63. Shankar, R.; Klossner, R. R.; Weaver, J. T.; Koga, T.; van Zanten, J. H.; Krause, W. E.; Colina, C. M.; Tanaka, F.; Spontak, R. J. “Competitive Hydrogen-Bonding in Polymer Solutions with Mixed Solvents.” Soft Matter2009, 5, 304-307. [doi]
  64. Castro-Marcano, F.; Olivera-Fuentes, C. G.; Colina, C. M. “Joule-Thomson Inversion Curves and Third Virial Coefficients for Pure Fluids from Molecular-Based Models.” Ind. Eng. Chem. Res.2008, 47 (22), 8894-8905. [doi]
  65. Müller, E. A.; Colina, C. M. “Biography of Keith E. Gubbins.” J. Phys. Chem. C2007, 111 (43), 15479-15480. [doi]
  66. Hoffman, M.; Colina, C. M.; McDonald, A. G.; Arepally, G. M.; Pedersen, L.; Monroe, D. M. “Tissue Factor Around Dermal Vessels has Bound Factor VII in the Absence of Injury.” J. Thromb. Haemostasis2007, 5 (7), 1403-1408. Feature article[doi]
  67. Colina, C. M.; Venkateswarlu, D.; Duke, R.; Perera, L.; Pedersen, L. G. “What Causes the Enhancement of Activity of Factor VIIa by Tissue Factor?” J. Thromb. Haemostasis2006, 4 (12), 2726-2729. [doi]
  68. Castro-Marcano, F.; Colina, C. M.; Olivera-Fuentes, C. “Parametrization of Molecular-Based Equations of State: The PC-SAFT, SOFT-SAFT, PHSC and PSCT Models.” Pol. J. Chem.2006, 80 (1), 37-49. [abstract]
  69. Colina, C. M.; Gubbins, K. E. “Vapor-Liquid and Vapor-Liquid-Liquid Equilibria of Carbon Dioxide/n-Perfluoroalkane/n-Alkane Ternary Mixtures.” J. Phys. Chem. B2005, 109 (7), 2899-2910. [doi]
  70. Bouza, A.; Colina, C. M.; Olivera-Fuentes, C. G. “Parameterization of Molecular-Based Equations of State.” Fluid Phase Equilibr.2005, 228-229, 561-575. [doi]
  71. Walker, T. A.; Colina, C. M.; Gubbins, K. E.; Spontak, R. J. “Thermodynamics of Poly(dimethylsiloxane)/Poly(ethylmethylsiloxane) (PDMS/PEMS) Blends in the Presence of High-Pressure CO2.” Macromolecules2004, 37, 2588-2595. [doi]
  72. Colina, C. M.; Galindo, A.; Blas, F. J.; Gubbins, K. E. “Phase Behavior of Carbon Dioxide Mixtures with n-Alkanes and n-Perfluoroalkanes.” Fluid Phase Equilib.2004, 222-223, 77-85. [doi]
  73. Striolo, A.; Colina, C. M.; Gubbins, K. E.; Elvassore, N.; Lue, L. “The Depletion Attraction between Pairs of Colloid Particles in Polymer Solution.” Mol. Simul.2004, 30 (7), 437-449. [doi]
  74. Colina, C. M.; Olivera-Fuentes, C. G.; Siperstein, F. R.; Lísal, M.; Gubbins, K. E. “Thermal Properties of Supercritical Carbon Dioxide by Monte Carlo Simulations.” Mol. Simulat.2003, 29 (6-7), 405-412. [doi]
  75. Colina, C. M.; Lísal, M.; Siperstein, F. R.; Gubbins, K. E. “Accurate CO2 Joule-Thomson Inversion Curve by Molecular Simulations.” Fluid Phase Equilib.2002, 202 (2), 253-262. [doi]
  76. Colina, C. M.; Hall, C. K.; Gubbins, K. E. “Phase Behavior of PVAC-PTAN Block Copolymer in Supercritical Carbon Dioxide using SAFT.” Fluid Phase Equilib.2002, 194-197, 553-565. [doi]
  77. Colina, C. M.; Turrens, L. F.; Gubbins, K. E.; Olivera-Fuentes, C.; Vega, L. F. “Predictions of the Joule-Thomson Inversion Curve for the n-Alkane Series and Carbon Dioxide from the Soft-SAFT Equation of State.” Ind. Eng. Chem. Res.2002, 41 (5), 1069-1075. [doi]
  78. Colina, C. M.; Olivera-Fuentes, C. “Predicted Inversion Curve and Third Virial Coefficients of Carbon Dioxide at High Temperatures.” Ind. Eng. Chem. Res.2002 41 (5), 1064-1068. [doi]
  79. Castillo, M. G.; Colina, C. M.; Dubuc, J. E.; Olivera-Fuentes, C. G. “Three-Parameter Corresponding-States Correlations for Joule-Thomson Inversion Curves.” Int. J. Thermophys.1999, 20 (6), 1737-1751. [doi]
  80. Colina, C. M.; Müller, E. A. “Molecular Simulation of Joule-Thomson Inversion Curves.” Int. J. Thermophys.1999, 20 (1), 229-235. [doi]
  81. Colina, C. M.; Olivera-Fuentes, C. “Prediction of the Joule-Thomson Inversion Curve of Air from Cubic Equations of State.” Cryogenics1998, 38 (7), 721-728. [doi]
  82. Ledanois, J. M.; Müller, E. A.; Colina, C. M.; González-Mendizabal, D.; Santos, J. W.; Olivera-Fuentes, C. “Correlations for Direct Calculation of Vapor Pressures from Cubic Equations of State.” Ind. Eng. Chem. Res.1998, 37 (5), 1673-1978. [doi]
  83. Colina, C. M.; Santos, J. W.; Olivera-Fuentes, C. “Efecto de la Traslación Volumétrica en Ecuaciones de Estado Cúbicas para la Predicción de Curvas de Inversión Joule Thomson.” Información Tecnológica1998, 9 (1), 97-105.
  84. Colina, C. M.; Santos, J.; Olivera-Fuentes, C. “High-Temperature Behaviour of the Cohesion Parameter of Cubic Equations of State.” High Temp. – High Pressures1997, 29 (5), 525-532. [doi]
  85. Colina, C.; Müller, E. A. “Joule-Thomson Inversion Curves by Molecular Simulation.” Mol. Simul.1997, 19 (4), 237-246. [doi]
  86. Ledanois, J. M.; Colina, C. M.; Santos, J. W.; González-Mendizabal, D.; Olivera-Fuentes, C. “New Expressions for the Vapor Pressure of Pure Components Constructed on Characteristic Points” Ind. Eng. Chem. Res.1997, 36 (6), 2505-2508. [doi]