Laboratorio de Modelado, Dinámica y Bioquímica Subcelular

Comprobante

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Generar conocimientos a través del desarrollo y aplicación de herramientas, algoritmos y modelos computacionales destinados al estudio de compuestos diversos, biomoléculas y sistemas biológicos complejos.

Líneas de Investigación

Estudiar mecanismos bioquímicos relacionados con enfermedades en células humanas y animales a nivel biofísico-computacional.
Investigar, desarrollar e innovar en propuestas farmacéuticas y biofármacos.
Emplear modelos computacionales de redes elásticas, dinámica molecular e inteligencia artificial para el estudio de mecanismos bioquímicos en células asociadas a diferentes patologías en humanos, microorganismos y animales.
Proponer bajo criterios químico biofísicos y computacionales estrategias farmacéuticas y biofarmacéuticas contra diferentes patologías.

Personal Científico

MsC. Carla Lossada

MsC. Arlene Cardozo

Lcdo. Alejandro Vivas

Contacto

Dirección

Publicaciones

Centro de Biomedicina Molecular

Lenin González-Paz, María José Alvarado, María Laura Hurtado-León, Carla Lossada, Joan Vera-Villalobos, Marcos Loroño, JL Paz, Laura N Jeffreys, F Javier Torres, Ysaias J Alvarado (2022). Comparative study of SARS-CoV-2 infection in different cell types: Biophysical-computational approach to the role of potential receptors . Computers in Biology and Medicine. Vol.142 ,105245. https://doi.org/10.1016/j.compbiomed.2022.105245.
José Luis Paz, Patricio J Espinoza-Montero, Marcos Loroño, Fernando Javier Torres, Lenin González-Paz, Edgar Márquez, Joan Vera-Villalobos, José R Mora, Fernando Moncada, Ysaias J Alvarado (2022). Propagation and Parametric Amplification in Four-Wave Mixing Processes: Intramolecular Coupling and High-Order Effects. Symmetry. Vol 14, 301. https://doi.org/10.3390/sym14020301.
Ysaias José Alvarado, Yosmari Olivarez, Carla Lossada, Joan Vera-Villalobos, José Luis Paz, Eddy Vera, Marcos Loroño, Alejandro Vivas, Fernando Javier Torres, Laura N Jeffreys, María Laura Hurtado-León, Lenin González-Paz (2022). Interaction of the New Inhibitor Paxlovid (PF-07321332) and Ivermectin With the Monomer of the Main Protease SARS-CoV-2: A Volumetric Study Based on Molecular Dynamics, Elastic Networks, Classical Thermodynamics and SPT . Computational Biology and Chemistry. Vol. 99 https://doi.org/10.1016/j.compbiolchem.2022.107692.
Ivan Mendoza, José Luis Paz, Lenin A González-Paz, Edgar A Márquez, Joan Vera-Villalobos, José R Mora, Ysaias J Alvarado, Tania Cordova-Sintjago (2022). Reaction mechanism of the gas-phase pyrolysis of N–Acetylthiourea and N, N’–diacetylthiourea: A theoretical study based in density functional theory. Computational and Theoretical Chemistry.Vol.1212 113702. https://doi.org/10.1016/j.comptc.2022.113702.
José Luis Paz, Marcos Loroño, F. Javier Torres, Lenin A. González-Paz, Edgar Marquez, José R. Mora, Ysaias J. Alvarado, Vladimiro Mujica (2022). A kinetic model for the equilibrium dynamics of absorption and scattering processes in four-wave mixing spectroscopy . AIP Advances. Vol. 12. 065322. https://doi.org/10.1063/5.0086769 .
José Luis Paz, Marcos Loroño, F. Javier Torres, Lenin A. González-Paz, Edgar Marquez, José R. Mora, Ysaias J. Alvarado, Vladimiro Mujica (2022). A kinetic model for the equilibrium dynamics of absorption and scattering processes in four-wave mixing spectroscopy . AIP Advances. Vol. 12. 065322. https://doi.org/10.1063/5.0086769 .
Lenin González-Paz, Carla Lossada, Maria Laura Hurtado-León, Francelys Fernández-Materán, José Luis Paz, Shayan Parvizi, Rafael Cardenas, Freddy Romero, Ysaias J. Alvarado (2023). Intrinsic Dynamics of the ClpXP Proteolytic Machine using Elastic Network Models. ACS OMEGA Vol.8 7302-7318. https://doi.org/10.1021/acsomega.2c04347.
Lenin González-Paz, Carla Lossada, Joan Vera-Villalobos, José Luis Paz, David S. Coll, Laura N. Jeffreys; Yovani Marrero-Ponce, Ysaias J. Alvarado (2023). Thermodynamic and conformational discrimination of primers for specific detection of Monkeypox virus (MpxV) by PCR: comparative analysis of primer stability and specificity with a biophysical-computational approach.Biointerface Research in Applied Chemistry vol.13, 5435. https://doi.org/10.33263/briac135.435.
Paz, José Luis; Loroño, Marcos; González-Paz, Lenin; Márquez, Edgar; Mora, Jose; Alvarado, Ysaias (2023). Stochastic nature and intramolecular coupling in optical response profiles: critical analysis through quantum models. ACS OMEGA Vol.8 (12) 10690-10712. https://doi.org/10.1021/acsomega.2c07300.
Paz, José Luis; Loroño, Marcos; González-Paz, Lenin; Márquez, Edgar; Mora, Jose; Alvarado, Ysaias (2023). Stochastic nature and intramolecular coupling in optical response profiles: critical analysis through quantum models. ACS OMEGA Vol.8 (12) 10690-10712. https://doi.org/10.1021/acsomega.2c07300 .
González-Paz, L.; Lossada, C.; Hurtado-Leon, M.L.; Vera-Villalobos, J.; Paz,J.L.; Marrero-Ponce, Y.; Martinez-Rios, F.; Alvarado, Y.J. 2024. “Biophysical analysis of potential inhibitors of SARS-CoV-2 Cell recognition and their effect on viral dynamics in different cell type: a computational prediction from in vitro experimental data”. ACS OMEGA. 9 (8) 8923-8939. DOI: 10.1021/acsomega.3c06968.
Yaranga Chávez, B.; Paz, J.L.; Gonzalez-Paz, L.A.; Alvarado, Y.J.; Santiago Contreras, J.; Loroño-González, M.A. 2024. “Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory”. Molecules.9 (29) DOI:10.3390/molecules29092064.
Paz, J.L.; Davila, C.; Loroño, M.A.; González-Paz, L.; Márquez, E.;Mora, J.R.; Alvarado, Y.J. 2024. “Analyzing coherent and incoherent optical susceptibilities in four-wave mixing: stochasticity, symmetry, and intramolecular coupling”. Results in Physics. 61, 107765. DOI: 10.1016/j.rinp.2024.107765.
Paz, J.L.; Garrido-Schaeffer, A.; Loroño, M.A.; González-Paz, L.; Márquez, E.; Mora, J.R.; Alvarado, Y.J. 2024. “Parametric Characterization of Nonlinear Optical Susceptibilities in Four-Wave Mixing: Solvent and Molecular Structure Effects”. Symmetry.16 (10) 1263. DOI: 10.3390/sym16101263.
Antequera-Zambrano, L., Parra-Sánchez, Á., González-Paz, L., Fernandez, E., & Martinez-Navarrete, G. Distribution of Genetic Determinants Associated with CRISPR-Cas Systems and Resistance to Antibiotics in the Genomes of Archaea and Bacteria. Microorganisms, 13(6), 1321, 2025. https://doi.org/10.3390/microorganisms13061321.
Reyes, L., Campos, K., Avendaño, G. D., González-Paz, L., Vivas, A., Alvarado, Y. J., & Flores, S. Seasonal footprints on ecological time series and jumps in dynamic states of protein configurations from a nonlinear forecasting method characterization. Journal of Physics: Complexity, 6(1), 01LT01, 2025. https://doi.org/10.1088/2632-072X/adbf5d. Pascal, E., González-Paz, L., & Alvarado, Y. Molecular Analysis (PCR by isothermal isolation) and Fresh Analysis to Detect the Hepatobacter penaei (NHP) Bacteria in Two Shrimp Farms in the State of Falcón, Venezuela. Recent Adv Clin Trials, 5(2), 1-7, 2025.
González-Paz, L., Lossada, C., Mora, D., Portillo, E., San-Blas, E. Effect of various physical and chemical stress conditions on the infectivity and survival of Heterorhabditis indica and Steinernema feltiae: relationship with lipid oxidative stress. Pesticide Biochemistry and Physiology, 207, 106217, 2025. https://doi.org/10.1016/j.pestbp.2024.106217.
Molina, L.M., Yamasqui, J.I., Aguaiza, M.E., Peralta, M.F., Cando, S.E., Guaman, A.L., Lossada, C., Paz, L.P., Alvarado, Y.J., Pérez, A., González-Paz, L. Hypothetical molecular mechanism of a novel class of bacteriocin-based antivirals for the inhibition of Respiratory Syncytial Virus (RSV). Medical Hypotheses, 194, 111529, 2025. https://doi.org/10.1016/j.mehy.2024.111529 .
Molina, L.M., Aguaiza, M.E., Yamasqui, J.I., Pinos, M.E., Yamasqui, K.M., Cardozo-Urdaneta, A., Lossada, C., Marrero-Ponce, Y., Martinez-Rios, F., Alvarado, Y.J., Pérez, A., González-Paz, L. Macromolecular interaction mechanism of the bacteriocin EntDD14 with the receptor binding domain (RBD) for the inhibition of SARS-CoV-2 and the JN.1 variant: biomedical study based on elastic networks, stochastic Markov models, and macromolecular volumetric analysis. Biophysical Chemistry, 318, 107388, 2025. https://doi.org/10.1016/j.bpc.2024.107388.
Lenin González-Paz, José Luis Paz, Marcos A Loroño-González, Julio Santiago Contreras, Carla Lossada, Alejandro Vivas, Yovani Marrero-Ponce, Felix Martinez-Rios, Patricia Rodriguez-Lugo, Yanpiero Balladores, Joan Vera-Villalobos and Ysaías. J. Alvarado. Biological Implications of the Intrinsic Deformability of Human Acetylcholinesterase Induced by Diverse Compounds: A Computational Study. Biology, 13(12), 1065, 2024. https://doi.org/10.3390/biology13121065 .
José L. Paz, Alberto Garrido-Schaeffer, Marcos A. Loroño, Lenin González-Paz, Edgar Márquez, José R. Mora and Ysaias J. Alvarado. Parametric Characterization of Nonlinear Optical Susceptibilities in Four-Wave Mixing: Solvent and Molecular Structure Effects. Symmetry. 16(10)1263, 2024. https://doi.org/10.3390/sym16101263.
José L. Paz, Alberto Garrido-Schaeffer, Marcos A. Loroño, Lenin González-Paz, Edgar Márquez, José R. Mora and Ysaias J. Alvarado. Parametric Characterization of Nonlinear Optical Susceptibilities in Four-Wave Mixing: Solvent and Molecular Structure Effects. Symmetry. 16(10)1263, 2024. https://doi.org/10.3390/sym16101263.
José L Paz, Cristhian Davila, Marcos A Loroño, Lenin González-Paz, Edgar Márquez, José R Mora, Ysaias J Alvarado. Analyzing coherent and incoherent optical susceptibilities in four-wave mixing: stochasticity, symmetry, and intramolecular coupling. Results in Physics. 61, 107765, 2024. https://doi.org/10.1016/j.rinp.2024.107765.
Breyson Yaranga Chávez, José L Paz, Lenin A Gonzalez-Paz, Ysaias J Alvarado, Julio Santiago Contreras, Marcos A Loroño-González. Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory. Molecules. 29 (9), 2064, 2024. https://doi.org/10.3390/molecules29092064.
Luis Moncayo Molina, Diana Carolina Arías Naravaez, María Verónica Pogyo Morocho, Zandra Maribel Regalado Vazquez, Aleivi Pérez, María Laura Hurtado-León, Carla Lossada, Lenin González-Paz. Interaction of Phytochemicals with Proteins Associated with Mucopolysaccharide Biosynthesis in Pseudomonas aeruginosa: a Predictive Study of Biomedical Interest. BRIAC. 14, 3, 63, 2024. https://doi.org/10.33263/BRIAC143.063.
Lenin González-Paz, Carla Lossada, María Laura Hurtado-León, Joan Vera-Villalobos, José L. Paz, Yovani Marrero-Ponce, Ysaías. J. Alvarado. Biophysical analysis of potential inhibitors of SARS-CoV-2 cell recognition and their effect on viral dynamics in different cell types: a computational prediction from in vitro experimental data. ACS Omega. 9, 8, 8923–8939, 2024. https://doi.org/10.1021/acsomega.3c06968.
Luis Moncayo Molina, Erica Paola Rojas Verdugo, María Agusta Luzuriaga Calle, Aleivi Pérez, María Laura Hurtado-León, Carla Lossada, Lenin González-Paz. Structural stability of Pseudomonas aeruginosa proteins associated with the mucoid phenotype: biomedical interest in cystic fibrosis. Biointerface Research in Applied Chemistry. 14, (3), 51, 2024. https://doi.org/10.33263/BRIAC143.051.