2.- "Characterization of the Theta State and Transition Curves of Off-Lattice Three Dimensional Chains" A. M. Rubio, J. J. Freire, C. W. Yong, J. H. R. Clarke and M. Bishop. J. Chem. Phys. 102, 2277 (1995).
3.- "Theta State, Transition Curves and Conformational Properties of Cyclic Chains" A. M. Rubio, J. J. Freire, M. Bishop and J. H. R. Clarke. Macromolecules 28, 2240 (1995).
4.- "Monte Carlo Study of Symmetric Diblock Copolymers in Selective Solvents" L. A. Molina and J. J. Freire. Macromolecules 28, 2705 (1995).
5.- "Structure Function of Linear and Star Polymers in the Small Wave Vector Regime" M. Bishop, J. H. R. Clarke and J. J. Freire. J. Chem. Phys. 102, 5094 (1995).
6.- "Frequency-Dependent Viscosity of Linear Polymer Chains. Influence of non_Gaussian Effects" A. Rey and J. J. Freire. J. Chem. Phys. 102, 6900 (1995).
7.-"End-to-End Vector Correlation Function in Many-Chain Systems" J. J. Freire and K. Adachi. Macromolecules 28, 4747 (1995).
8.- "Conformational Properties of Ring AB Diblock Copolymers" C. H. Vlahos, N. Hadjichristidis, M. K. Kosmas, A. M. Rubio and J. J. Freire. Macromolecules 28, 6854 (1995).
9.- "Dynamics of Chains in Excluded Volume Conditions. Frequency- Dependent Viscosity of Regular Star Chains" A. Rey and J. J.Freire. J. Chem Phys. 104, 758 (1996).
10.-"Dynamic Scattering from a Homopolymer and a Diblock Copolymer Chain in Dilute and Many-Chain Solutions" L.A. Molina and J. J. Freire. J. Chem Phys. 104, 2093 (1996).
11.-"Conformational Analysis of Methyl-Phenyl-Siloxane Chains". J.J. Freire, I.F. Pierola and A. Horta. Macromolecules 29, 5143 (1996).
12.- "Conformation of A2B and A3B Miktoarm Star Copolymers in Dilute Solutions" C. Vlahos, Y. Tselikas, N. Hadjichristidis, J. Roovers, A. Rey and J. J. Freire. Macromolecules 29, 5599 (1996).
13.- "Dynamic Scattering from Mixtures of Two Polystyrene Samples in Dilute and Semidilute Solution" J. Corroto, F. Ortega, M. Vazquez and J.J. Freire. Macromolecules 29, 5948 (1996).
14.- "Monte Carlo Calculation of Second Virial Coefficient for Linear and Star Chains in a Good Solvent" A. M. Rubio and J. J. Freire. Macromolecules 29, 6946 (1996).
15.- "The Theta Condition for Linear Polymer Chains in Continous Space and Three Dimensions" C.W. Yong, J.H.R. Clarke, J. J. Freire and M. Bishop. J. Chem Phys. 105, 9666 (1996).
16.- "On the Use of a Gaussian Chain in a Monte Carlo Simulation Model for the Equilibrium Properties of Polymer Solutions" S. Jorge, J. J. Freire and A. Rey. Macromol. Theory Simul. 6, 271 (1997).
17.- "Tricritical Behavior of an Off-lattice Flexible Polymer Model: Monte Carlo Calculations of Second Virial Coefficients" A. M. Rubio and J. J. Freire. J. Chem Phys. 106, 5638 (1997).
18.- "Determination of the Potential Parameters of a Site Model from Calculations of Second Virial Coefficients of Linear and Branched Alkanes" A. Poncela, A. M. Rubio and J. J. Freire. Molec. Phys. 91, 189 (1997).
19.- "Numerical Simulation of the Scatterig Form Factor of Star Polymers" L. A. Molina, A. Rey and J. J. Freire. Comp. and Theor. Polymer Science 7, 243 (1997).
20.- "Numerical Study of Scattering from Chains Composed of Two Nonsegreegated Labeled Blocks in an Athermal Solvent: Effects of Compositional Heterogeneity" L. A. Molina and J. J. Freire. J. Chem. Phys. 109, 2904 (1998).
21.- "Intramolecular Reaction Rates of Flexible Polymers. 1. Simulation Results and the Classical Theory" M. Ortiz-Repiso, J. J. Freire and A. Rey. Macromolecules 31, 8356 (1998).
22.- "Dielectric Study of Dynamics of Subchains and Distribution of Normal Mode Relaxation Times in Dilute and Semidilute Solutions of Miscible Blockcopolymers" K. Adachi, H. Hirano and J. J. Freire. Polymer 40, 2271 (1999).
23.- "Conformational Properties of Branched Polymers: Theory and Simulations" J. J. Freire. Adv. Polym. Sci. 143, 35 (1999).
24.- "Monte Carlo Simulation of Many-Chain Star Polymer Solutions" L. A. Molina and J. J. Freire. Macromolecules 32, 499 (1999).
25.- "Relaxation of Flexible Chains in Dilute and Non-dilute Systems. Dynamic Monte Carlo Results for Linear and Star Chains" J. J. Freire, L. M. Molina, A. Rey and K. Adachi. Macromol. Theory Simul. 8, 321 (1999).
26.- "Determination of Potential Parameters for Alkanes" A. Lopez Rodriguez, C. Vega and J. J. Freire. J. Chem. Phys. 111, 438 (1999).
27.- "Conformational Properties of Polymer Chains in the Theta Region" A. M. Rubio, J. J. Freire, C. W. Yong and J. H. R. Clarke. J. Chem. Phys. 111, 1302 (1999).
28.- "Dynamics of Siloxane Chains Bearing Phenyl Chromophores" A. Horta, A. L. Macanita, J. J. Freire and I. F. Pierola. Polym. Int. 48, 665 (1999).
29.- "Sizes and Second Virial Coefficients of Miktoarm Star Polymers" A. M. Rubio, P. Brea, J. J. Freire and C. Vlahos. Macromolecules 33, 207 (2000).
30.- "Interaction between Two Star Chains in a Good Solvent" A. M. Rubio and J. J. Freire. Comp. and Theor. Polymer Science, 10, 89 (2000).
31.- "The Behavior of the Structure Function at Large Wavevectors for Polymers in Different Regimes" Marvin Bishop, Julian H. R. Clarke and Juan J. Freire. Macromol. Theory Simul. 9, 550 (2000).
32.- "Phase Separation of Binary Homopolymer and Ternary Homopolymer-Copolymer Mixtures through Gibbs Ensemble Simulations" A. Poncela, A. M. Rubio and J. J. Freire. J. Chem. Phys. 114, 8174 (2001).
33.- "Form Factor of an Isolated Chain with Excluded Volume" J. J. Freire, G. Alvarez and M. Bishop. Macromol. Theory Simul. 11, 11 (2002).
34.- "Dynamics of Bond Fluctuation Model Chains in Good and Theta Solvents" A. M. Rubio, M. Storey, J. F. M. Lodge and J. J. Freire. Macromol. Theory Simul. 11, 171 (2002).
35.- "Monte Carlo Simulation of Star Polymer Systems with the Bond Fluctuation Model" A. Di Cecca and J. J. Freire. Macromolecules, 35, 2851 (2002).
36.- "Simulation of Dynamic Scattering from Homopolymer and Symmetric Diblock Copolymer Solutions with the Bond Fluctuation Model" A. M. Rubio, J. F. M. Lodge and J. J. Freire. Macromolecules, 35, 5295 (2002).
37.- "Cyclization Kinetics of Nondiluted Bond Fluctuation Chains" A. M. Rubio, M. Pita and J. J. Freire. Macromolecules, 35, 5681 (2002).
38.- "Gibbs Ensemble Simulation of Symmetric Mixtures Composed by the Homopolymers AA, BB and Their Common Block Copolymer AB" A. Poncela, A. M. Rubio and J. J. Freire. J. Chem. Phys. 118, 425 (2003).
39.- "Simulation of Diffusion and Relaxations of Non-Dilute Star Chains" A. Di Cecca and J. J. Freire. Polymer 44, 2589 (2003).
40.- "Mesophase Formation in Solutions of Diblock Copolymers Simulated Using the Bond Fluctuation Model" J. J. Freire and C. McBride. Macromol. Theory Simul. 12, 237 (2003).
41.- "Block and Alternating Copolymer Chains of Styrene-Vinylmethylether and Styrene-Methylmethacrylate by Molecular Dynamics Simulation" A. Horta and J. J. Freire. Polymer 45, 1275 (2004).
42.- "Simulation Results for the Size and Intrinsic Viscosity of Several Dendrimer Molecules" J. J. Freire, E. Rodríguez and A. M. Rubio, J. Chem. Phys. 123, 154901 (2005).
43.- "Specific Interactions in Blends Containing Chitosan and Functionalized Polymers. Molecular Dynamics Simulations" C. Sandoval, C. Castro, L. Gargallo, D. Radic and J. Freire, Polymer 46, 10437 (2005).
45.- "Simulation of the Collective Dynamics Scattering of Diblock Copolymers with Heterogeneous Composition in the Semidilute Regime" E. Rodríguez and J. J. Freire, J. Non-Cryst. Solids 352, 5060 (2006).
46.- "Improved Simulation Method for the Calculation of the Intrinsic Viscosity of Some Dendrimer Molecules" E. Rodríguez, J. J. Freire, G. del Río Echenique, J.G. Hernández Cifre and J. García de la Torre, Polymer 48, 1155 (2007).
47.- "Effective Interaction Parameter in Linear/Star Polymer Blends and Comparison with that of Linear/Linear and Star/Star blends" P. E. Theodorakis, A. Avgeropoulos, J. J. Freire, M. Kosmas, and C. Vlahos, J. Chem. Phys. 126, 174904 (2007).
48.- "Polyfunctional MDI Oligomers Through Dendrimerization" M. Martinelli, M. Calderón, E. Rodríguez, J. J. Freire and M. C. Strumia, Eur. Polym. J. 43, 1978 (2007).
49.- "Monte Carlo Simulation of Star/Linear and Star/Star Blends with Chemically Identical Monomers" P. E. Theodorakis, A. Avgeropoulos, J. J. Freire, M. Kosmas and C. Vlahos, J. Phys.: Condens. Matter 19, 466111 (2007).
50.- "Intramolecular Distances and Form Factor of Cyclic Chains with Excluded Volume Interactions" A. M. Rubio, G. Álvarez and J. J. Freire, Polymer, 49, 628 (2008).
51.-"Conformational Properties and Rouse Dynamics of Different Dendrimer Molecules" J.J. Freire and A. M. Rubio, Polymer 49, 2762 (2008).
52.- "Influence of Chain Topology and Bond Potential on the Glass Transition of Polymer Chains Simulated with the Bond Fluctuation Model" J. J. Freire, J. Phys.: Condens. Matter 20, 285102 (2008).
53.- "Realistic Numerical Simulations of Dendrimer Molecules" J. J. Freire, Soft Matter 4, 2139 (2008).
54.- "Molecular Dynamics Simulation Study of Compatibility for the Polyvinylmethylether/Polystyrene Mixture" A. Ahmadi and J. J. Freire, Mol. Simul. 34, 1253 (2008).
55.- "Coarse-Grained Model for Polybenzylether Dendritic Molecules" J. J. Freire, Soft Matter 5, 1912 (2009).
56.- "A Multiscale Scheme for the Simulation of Conformational and Solution Properties of Different Dendrimer Molecules" G. del Río Echenique, R. Rodríguez Schmidt, J. J. Freire, J. G. Hernández Cifre and José García de la Torre, J. Am. Chem. Soc. 131, 8548 (2009).
57.- "Prediction of polymer mixture compatibility by Monte Carlo simulation of intermolecular binary interactions" A. Ahmadi and J. J. Freire, Polymer, 50, 3871 (2009).
58.- "Molecular dynamics simulation of miscibility in several polymer blends" A. Ahmadi and J. J. Freire, Polymer, 50, 4973 (2009).
59.- "Forcefield parameterization and molecular dynamics simulation of flexible POSSlinked (NHC) (phosphine) Ru catalytic complexes" A. Ahmadi, C. McBride, J. J. Freire, A. Kajetanowicz, J. Czaban and K. Grela, J. Phys. Chem. A, 115, 12017 (2011).
60.- "Dielectric and molecular dynamics study of the secondary relaxations of poly(styrene-co-methylmethacrylate) copolymers: Influence of the molecular architecture" M. Encinar, M.G. Prolongo, R.G. Rubio, F. Ortega, A. Ahmadi, and J.J. Freire, Eur. Phys. J. E, 34, 134 (2011).
61.- "Molecular dynamics simulations of the protonated G4 PAMAM dendrimer in an ionic liquid system" J.J. Freire,A. Ahmadi,and C. McBride, J. Phys. Chem. B, 117, 15157 (2013).
62.- "Simulation study of the G=4 PAMAM dendrimer in water at different pH condi tions" J.J. Freire, P. Efthymiopoulos and A. Ahmadi, Per. Pol. Chem. Eng., 58, 49 (2014).
63.- "Binary Interactions between Dendrimer Molecules. A Simulation Study" A. M. Rubio, C. McBride and J.J. Freire, Macromolecules, 47, 5379 (2014).
64.- "Coarse-Grained and Atomistic Simulations for the G=4 PAMAM-EDA Dendrimer " J.J. Freire, A. M. Rubio and C. McBride, Macromol. Theor. Simul., 24, 432 (2015).
65.- "Calculation of Conformational Properties and Rouse Relaxation Times of PAMAM-EDA Dendrimers under Different pH Conditions" J.J. Freire, A. M. Rubio and C. McBride, Macromol. Theor. Simul., 25, 403 (2016).
66.- "Binary Intermolecular Potential and Scattering Curves of PAMAM-EDA Dendrimers" J. J. Freire and A. M. Rubio. Macromol. Theor. Simul., 27, 1800004 (2018).
67.- "Non-Ideal Intermolecular Interactions between Charged PAMAM-EDA Dendrimers at Low Concentrations" J. J. Freire. Macromol. Theor. Simul., 29, 1800040 (2020).
68.- "Study of Segregation in Non-Dilute Solutions of Linear Diblock Copolymers and Symmetric Miktoarm (or Janus Star) Polymers Using Monte Carlo Simulations with the Bond Fluctuation Model". J.J. Freire, Polymers, 13, 2377 (2021).
69.- "Simulation of Nondilute Dendrimer Systems with the Bond Fluctuation Model". J.J. Freire, Polymers, 14, 5363 (2022).