Here, you can find, organized by topic, some representative examples of our work on Scientific Computing published in journals and specialized conferences.


Complex Networks

  • C. Muñoz-Caro,A. Niño and S. Reyes "A bibliometric approach to Systematic Mapping Studies: The case of the evolution and perspectives of community detection in complex networks", arXiv:1702.02381 [cs.SI] (2017) [arXivPDF]

  • C. Muñoz-Caro,A. Niño, S. Reyes, and M. Castillo "APINetworks Java. A Java approach to the efficient treatment of large-scale complex networks", Computer Physics Communications, 207, 549-552 (2016) [PDF]

  • A. Niño, C. Muñoz-Caro, S. Reyes, and M. Castillo "A Java API for the description of large complex networks under the object-oriented paradigm", International Journal of Complex Systems in Science, 5(1), 9-11 (2015) [PDF]

  • A. Niño, C. Muñoz-Caro, and S. Reyes "APINetworks: A general API for the treatment of complex networks in arbitrary computational environments", Computer Physics Communications, 196, 446-454 (2015) [PDF]

  • A. Niño, and C. Muñoz-Caro "Quantitative modeling of degree-degree correlation in complex networks", Physical Review E, 88, 032805 (2013) [arXiv PDF]



Parallel and distributed programming

  • J. Díaz, C. Muñoz-Caro and A. Niño, "A Survey of Parallel Programming Models and Tools in the Multi and Many-core Era", IEEE Transactions on Parallel and Distributed Systems, 23, 1369-1386 (2012) [PDF]

  • A. Niño, C. Muñoz-Caro and S. Reyes, "A Concurrent Object-Oriented Approach to the Eigenproblem Treatment in Shared Memory Multicore Environments", Lecture Notes in Computer Science, 6782, 630-642 (2011) [PDF]

  • J. Díaz, S. Reyes, R.M. Badia, A. Niño and C. Muñoz-Caro, "A General Model for the Generation and Scheduling of Parameter Sweep Experiments in Computational Grid Environments", Procedia Computer Science , 1, 565–572 (2010) [PDF]

  • S. Reyes, C. Muñoz-Caro, A. Niño, R. M. Badia and J. M. Cela, "Performance of computationally intensive parameter sweep applications on Internet-based Grids of computers: the mapping of molecular potential energy hypersurfaces", Concurrency. Computat. Pract. Exper., 19, 463-481 (2007) [PDF]



Algorithms and software development

  • M.E. Castro, J. Díaz, C. Muñoz-Caro and A. Niño, "A Uniform Object Oriented Solution to the Eigenvalue Problem for Symmetric and Hermitian Matrices", Comput. Phys. Commun., 182, 2059-2064, (2011) [PDF]

  • M.E. Castro, A. Niño and C. Muñoz-Caro, "Heuristic computation of the rovibrational G matrix in optimized molecule-fixed axes. Gmat 2.1", Comput. Phys. Commun., 181, 1471–1475 (2010) [PDF]

  • M.E. Castro, A. Niño and C. Muñoz-Caro, "Evaluation and optimal computation of angular momentum matrix elements: An information theory approach", WSEAS Transactions on Information Science and Applications, 7(2), 263-272 (2010) [PDF]

  • M.E. Castro, C. Muñoz-Caro and A. Niño, "A Metaheuristic Approach to the Optimal Definition of Molecule-fixed Axes in Rovibrational Hamiltonians", Comput. Phys. Commun., 181, 967-977 (2010) [PDF]

  • M.E. Castro, A. Niño and C. Muñoz-Caro, "Gmat. A software tool for the computation of the rovibrational G matrix", Comput. Phys. Commun., 180, 1183-1184 (2009) [PDF]

  • J. Díaz, S. Reyes, C.Muñoz-Caro and A. Niño, "MSSML: A Molecular Spectroscopic Simulations Markup Language for Rovibrational Studies", Lecture Notes in Computer Science, 5072, 997-1010 (2008) [PDF]

  • M.E. Castro, C. Muñoz-Caro and A. Niño, "Accurate Numerical Computation of Rovibrational G Matrices in Molecules of Arbitrary Size", Lecture Notes in Computer Science, 5072, 1011-1025 (2008) [PDF]

  • S. Reyes, A. Niño , and C. Muñoz-Caro, "Customizing Clustering Computing for a Computational Chemistry Environment. The case of the DBO-83 nicotinic analgesic", J. Mol. Struct. (Theochem), 727, 41-48 (2005) [PDF]

  • C. Muñoz-Caro and A. Niño, "Neural modeling of torsional potential hypersurfaces in non-rigid molecules", Comput. Chem., 22(5), 355-361 (1998) [PDF]

  • A. Niño and C. Muñoz-Caro, "Enhanced procedure for the refinement of kinetic and potential functions for large-amplitude vibrations", J. Chem. Soc., Faraday Trans., 93, 2989-2990 (1997) [PDF]

  • A. Niño and C. Muñoz-Caro, "Recursive computation of hamiltonian matrix elements using harmonic oscillator eigenfunction", Comput. Chem., 19, 371-378 (1995) [PDF]

  • C. Muñoz-Caro, A. Niño and D.C. Moule, "Derivation of accurate kinetic and potential-energy functions for several simultaneous large-amplitude vibrations", J. Chem. Soc. Faraday Trans., 91, 399-403 (1995) [PDF]

  • C. Muñoz-Caro and A. Niño, "Vibrational energy levels and vibronic structure of electronic spectra in molecules with large amplitude motions", Comput. Chem., 18, 413-417 (1994) [PDF]

  • A. Niño and C. Muñoz-Caro, "Computation of kinetic constants for large range internal motions in molecules", Comput. Chem., 18, 27-32 (1994) [PDF]

  • A. Niño, C. Muñoz-Caro and D.C. Moule, "A study of quadratic+gaussian+cosine functions for the simultaneous description of intramolecular torsion and inversion", J. Mol. Struct., 318, 237-242 (1994)



Metascheduling and monitoring in computational Grids

  • S. Reyes, C. Muñoz-Caro, A. Niño, R. Sirvent and R. M. Badia, "Monitoring and Steering Grid Applications with GRID superscalar", Futur. Gener. Comp. Syst., 26, 645-653 (2010) [PDF]

  • J. Díaz, S. Reyes, A. Niño and C. Muñoz-Caro, "Derivation of Self-Scheduling Algorithms for Heterogeneous Distributed Computer Systems: Application to Internet-based Grids of Computers", Futur. Gener. Comp. Syst., 25, 617-626 (2009) [PDF]

  • J. Díaz, C. Muñoz-Caro and A. Niño, "A Fault Tolerant Adaptive Method for the Scheduling of Tasks in Dynamic Grids", The Third International Conference on Advanced Engineering Computing and Applications in Sciences, IEEE Computer Society Press. ISBN: 978-0-7695-3829-7, pp. 51-56 (2009) [PDF]

  • J. Díaz, S. Reyes, C. Muñoz-Caro and A. Niño, "A Heuristic Approach to the Allocation of Different Workloads in Computational Grid Environments", International Journal on Advances in Software, 2(1), 1-10 (2009) [PDF]

  • J. Díaz, C. Muñoz-Caro and A. Niño, "An Adaptive Approach to Task Scheduling Optimization in Dynamic Grid Environments", Proceedings of the 2009 International Conference on Grid Computing and Applications (GCA 2009). CSREA Press. ISBN: 1-60132-105-8, pp. 23-29 (2009) [PDF]

  • J. Díaz, S. Reyes, C. Muñoz-Caro and A. Niño, "A Heuristic Approach to Task Scheduling in Internet-based Grids of Computers", The Second International Conference on Advanced Engineering Computing and Applications in Sciences. IEEE Computer Society Press. ISBN: 978-0-7695-3369-8, pp. 110-116 (2008) (Awarded Best paper) [PDF]

  • J. Díaz, S. Reyes, A. Niño and C. Muñoz-Caro, "New Self-Scheduling Schemes for Internet-Based Grids of Computers", Proceedings of the 1st. IBERGRID, ISBN: 9788461166343, May 14-16 (2007) [PDF]

  • J. Díaz, S. Reyes, A. Niño and C. Muñoz-Caro, "A Quadratic Self-Scheduling Algorithm for Heterogeneous Distributed Computing Systems", 2006 IEEE International Conference on Cluster Computing (CLUSTER06), ISBN:1-4244-0327-8, 1-2, 683-690, (2006) [PDF]



Molecular modelling and bioactive compounds

  • N.A. Caballero, F.J. Meléndez, A.Niño and C. Muñoz-Caro, "Molecular Docking Study of the Binding of Aminopyridines within the K+ Channel", J. Mol. Model., 13, 579-586 (2007) [PDF]

  • N.A. Caballero, F.J. Meléndez, C. Muñoz-Caro and A. Niño, "Theoretical prediction of relative and absolute pKa values of aminopyridines", Biophys. Chem., 124, 155-160 (2006)

  • M. Mora, M.E. Castro, A. Niño, F. J. Melendez and C. Muñoz-Caro, "Analysis of B3LYP and MP2 conformational population distributions in trans-nicotine, acetylcholine and ABT-594", Int. J. Quantum Chem., 103, 25-33 (2005)

  • M.C. Sicilia, A. Niño, and C. Muñoz-Caro, "Mechanism of Pyridine Protonation in Water Clusters of Increasing Size", J. Phys.Chem. A, 109, 8341-8347 (2005)

  • M.C. Sicilia, A. Niño, and C. Muñoz-Caro, "Theoretical Analysis of Pyridine Protonation in Water Clusters of Increasing Size", ChemPhysChem. A, 6, 139-147 (2005)

  • M. Mora, C. Muñoz-Caro and A. Niño, "Thermodynamic conformational analysis and structural stability of the nicotinic analgesic ABT-594", J. Comp-Aid. Mol Design., 17, 713-714 (2003)

  • A. Niño, C. Muñoz-Caro R. Carbó-Dorca and X. Gironés, "Rational Modelling of the voltage-dependent K+ channel inactivation by aminopyridines", Biophys. Chem., 104(2), 417-427 (2003) [PDF]

  • C. Muñoz-Caro and A. Niño, "The nature of the receptor site for the reversible K+ channel blocking by aminopyridines", Biophys. Chem., 96, 1-14 (2002)

  • A. Niño, C. Muñoz-Caro, "Theoretical analysis of the molecular determinants responsible for the K+ channel blocking by aminopyridines", Biophys. Chem., 91, 49-60 (2001)

  • B. García, S. Ibeas, J. M. Leal, M. L. Senent, A. Niño and C. Muñoz Caro, "Theoretical and Experimental Study of the Acetohydroxamic Acid Protonation. The Solvent Effect", Chem-Eur. J., 6, 2644-2652 (2000)

  • A. Niño, C. Muñoz Caro and F. Peradejordi "Theoretical analysis of the structural and chemical reactivity properties of the schistosomicidal drug Niridazole", J. Chim. Phys., 92, 679-698 (1995)



Statistical thermodynamics

  • A. Niño, C. Muñoz-Caro, M. Mora, and S. Reyes, "Effect of the conformational kinetic energy and the rotovibrational coupling in the conformational population of bioactive compounds", J. Phys. Chem. A., 107, 10191-10198 (2003) [PDF]

  • C. Muñoz-Caro, A. Niño, J. Z. Dávalos, E. Quintanilla and J. L. Abboud, "Experimental and theoretical study of the secondary equilibrium isotope effect (SEIE) in the proton transfer between the pyridinium-d5 cation and pyridine", J. Phys. Chem. A, 107, 6160-6167 (2003)

  • A. Niño and C. Muñoz-Caro, "Effect of large-amplitude vibrations on the thermodynamics of Malondialdehyde", J. Phys. Chem. A, 102, 1177-1180 (1998)

  • C. Muñoz-Caro, A. Niño and M. L. Senent, "Theoretical study of the effect of torsional anharmonicity on the thermodynamic properties of methanol", Chem. Phys. Letters, 273, 135-140 (1997)

  • C. Muñoz-Caro, and A. Niño, "Effect of anharmonicities on the thermodynamic properties of the water dimer", J. Phys. Chem. A, 101, 4128-4135 (1997) [PDF]

  • A. Niño and C. Muñoz-Caro, "The accurate computation of partition functions in non-rigid molecules", Comput. Chem., 21(3), 143-151 (1997) [PDF]



Spectroscopic simulations

  • M.E. Castro, C. Muñoz-Caro and A. Niño, "Analysis of the nitrile and methyl torsional vibrations of n-propyl cyanide in its S0 electronic state", Int. J. Quantum Chem., 111, 3681-3694 (2011)

  • M.E. Castro, A. Niño and C. Muñoz-Caro, "Structural and vibrational theoretical analysis of protonated formaldehyde in its X1A' ground electronic state", Theor. Chem. Acc., 119, 343-354 (2008)

  • M.L. Senent, A. Niño, C. Muñoz-Caro, Y.G. Smeyers, R. Domínguez-Gómez and J.M. Orza, "Theoretical Study of the Effect of Hydrogen-Bonding on the Stability and Vibrational Spectrum of Isolated 2,2,2-Trifluoroethanol and Its Molecular Complexes", J. Phys. Chem. A., 106, 10673- 10680 (2002)

  • D.C. Moule, W. Fraessdorf, C. Muñoz-Caro and A. Niño, "A Computer Simulation of the Ring Puckering and Oxygen Wagging Dynamics in the S0 State of Cyclobutanone", Adv. Quantum Chem., 40, 345-359 (2001) [PDF]

  • H. Liu, E.C. Lim, A. Niño, C. Muñoz-Caro, R.H. Judge and D.C. Moule, "The Torsion-Inversion-Bending Energy Levels in the S1(n,π*) Electronic State. Of Acetaldehyde. A High Resolution Study ot the Bands #7 to #21 in the Jet-Cooled Fluorescence Excitation Spectrum of Acetaldehyde", J. Mol. Spectrosc., 190, 78-90 (1998)

  • H. Liu, E.C. Lim, C. Muñoz-Caro, A. Niño, R.H. Judge and D.C. Moule, "The torsion-inversion energy levels in the S1(n,π*) electronic state of acetaldehyde from high resolution jet-cooled fluorescence excitation spectroscopy", J. Mol. Spectrosc., 175, 172-189 (1996)

  • H. Liu, E.C. Lim, C. Muñoz-Caro, A. Niño, R.H. Judge and D.C. Moule, "The T1(n,π*)-> S0 laser induced phosphorescence excitation spectrum of acetaldehyde in a supersonic free jet: Torsion and wagging potentials in the lowest triplet state.", J. Chem. Phys. , 105, 2547-2552 (1996)

  • A. Niño, C. Muñoz-Caro and D.C. Moule, "Three dimensional vibrational study of the coupling between the methyl torsion and the molecular frame in the S0 state of acetaldehyde", J. Phys. Chem, 99, 8510-8515 (1995)

  • A. Niño, C. Muñoz-Caro and D.C. Moule, "Wagging and Torsion Vibronic Structure in the T1 -> S0 electronic spectrum of acetaldehyde", J. Phys. Chem, 98, 1519-1524 (1994)

  • C. Muñoz-Caro, A. Niño and D.C. Moule, "Theoretical determination of the torsion-wagging structure of the S1 -> S0 electronic spectrum of acetaldehyde", Chem. Phys., 186, 221-231 (1994)