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Comer Group Publications

*Boldface denotes author was member of the Comer Research Group when the work was done.
  1. Vergara-Jaque A, Palma-Cerda F, Lowet As, Landrau AdlC, Poblete H, Sukharev A, Comer J, Holmgren M (2019) “A Structural Model of the Inactivation Gate of Voltage Activated Potassium Channels” Biophys. J. 117, 1–11, DOI: 10.1016/j.bpj.2019.06.008
  2. Tse CH, Comer J, Chu SKS, Wang Y, Chipot C (2019) “Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane” J. Chem. Theory Comput. 15, 2913–2924, DOI: 10.1021/acs.jctc.9b00022
  3. Liu S, Comer J, van Duin ACT, van Duin DM, Liu B, Edgar JH (2019) “Predicting the Preferred Morphology of Hexagonal Boron Nitride Domain Structure on Nickel from ReaxFF-based Molecular Dynamics Simulations” Nanoscale 11, 5607–5616, DOI: 10.1039/C8NR10291K
  4. Azhagiya Singam ER, Zhang Y, Magnin G, Miranda-Carvajal I, Coates L, Thakkar R, Poblete H, Comer J (2019) “Thermodynamics of Adsorption to Graphenic Surfaces from Aqueous Solution” J. Chem. Theory Comput. 15, 1302–1316, DOI: 10.1021/acs.jctc.8b00830
  5. Poblete H, Comer J (2019) “Computational Modeling of the Adsorption of Capping Agent Biomolecules to Inorganic Nanoparticles” Photoactive Inorganic Nanoparticles, DOI: 10.1016/B978-0-12-814531-9.00002-6
  6. Preciado LM, Comer J, Núñez V, Rey-Súarez P, Pereañez J (2018) “Inhibition of a Snake Venom Metalloproteinase by the Flavonoid Myricetin” Molecules 23, 2662, DOI: 10.3390/molecules23102662
  7. Preciado LM, Pereañez J, Azhagiya Singam ER, Comer J (2018) “Interactions between Triterpenes and a P-I Type Snake Venom Metalloproteinase: Molecular Simulations and Experiments” Toxins 10, 397, DOI: 10.3390/toxins10100397
  8. Wang Y, Comer J, Chen Z, Chen J, Gumbart JC (2018) “Exploring Adsorption of Neutral Aromatic Pollutants onto Graphene Nanomaterials via Molecular Dynamics Simulations and Theoretical Linear Solvation Energy Relationships” Environ. Sci. Nano 5, 2117–2128, DOI: 10.1039/c8en00575c
  9. Camarada MB, Comer J, Poblete H, Azhagiya Singam ER, Marquez-Miranda V, Morales-Verdejo C, Gonzalez-Nilo FD (2018) “Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and PAMAM Dendrimers” Langmuir 34, 10063–10072, DOI: 10.1021/acs.langmuir.8b01809
  10. Thomas SE, Comer J, Kim MJ, Marroquin S, Murthy V, Ramani M, Hopke TG, McCall J, Choi S, DeLong RK (2018) “Comparative Functional Dynamics Studies on the Enzyme Nano-bio Interface” Int. J. Nanomedicine 2018, 4523–4536, DOI: 10.2147/IJN.S152222
  11. Marasini R, Pitchaimani A, Nguyen TDT, Comer J, Aryal S (2018) “Influence of Polyethylene Glycol Passivation on the Surface Plasmon Resonance Induced Photothermal Properties of Gold Nanorods” Nanoscale 10, 13684–13693, DOI: 10.1039/C8NR03026J
  12. Tse CH, Comer J, Wang Y, Chipot C (2018) “Link between Membrane Composition and Permeability to Drugs” J. Chem. Theory Comput. 14, 2895–2909, DOI: 10.1021/acs.jctc.8b00272
  13. Carrasco-Sánchez V, Marican A, Vergara-Jaque A, Folch-Cano C, Comer J, Laurie VF (2018) “Polymeric Substances for the Removal of Ochratoxin A from Red Wine Followed by Computational Modeling of the Complexes Formed” Food Chem. 265, 159–164, DOI: 10.1016/j.foodchem.2018.05.089
  14. Comer J (2018) “Chasing a Protein's Tail: Detection of Polypeptide Translocation through Nanopores” Biophys. J. 114, 759–760, DOI: 10.1016/j.bpj.2017.12.020
  15. Vergara-Jaque A, Fong P, Comer J (2017) “Iodide Binding in Sodium-Coupled Cotransporters” J. Chem. Inf. Model. 57, 3043–3055, DOI: 10.1021/acs.jcim.7b00521
  16. Mazloom R, Jaberi-Douraki M, Comer JR, Volkova V (2017) “Potential Information Loss Due to Categorization of Minimum Inhibitory Concentration Frequency Distributions” Foodborne Pathog. Dis. 15, 44–54, DOI: 10.1089/fpd.2017.2301
  17. Ahumada M, Jacques E, Andronic C, Comer J, Poblete H, Alarcon EI (2017) “Novel Specific Peptides as Superior Surface Stabilizers for Silver Nano Structures: Role of Peptide Chain Length” J. Mater. Chem. B 5, 8925–8928, DOI: 10.1039/c7tb02349a
  18. Alarcon EI, Poblete H, Roh H, Couture J, Comer J, Kochevar IE (2017) “Rose Bengal Binding to Collagen and Tissue Photobonding” ACS Omega 2, 6646–6657, DOI: 10.1021/acsomega.7b00675
  19. Calbo J, López-Moreno A, de Juan A, Comer J, Ortí E, Pérez EM (2017) “Understanding Noncovalent Interactions of Pyrene Derivatives with Carbon Nanotubes” Chem. Eur. J. 23, 12909–12916, DOI: 10.1002/chem.201702756
  20. Comer J, Schulten K, Chipot C (2017) “Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles” J. Chem. Theory Comput. 13, 2523–2532, DOI: 10.1021/acs.jctc.7b00264
  21. Poblete H, Miranda-Carvajal I, Comer J (2017) “Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives” J. Phys. Chem. B 121, 3895–3907, DOI: 10.1021/acs.jpcb.7b01130
  22. DeLong RK, Mitchell JA, Morris RT, Comer J, Hurst MN, Ghosh K, Wanekaya A, Mudge M, Schaeffer A, Washington LL, Risor-Marhanka A, Thomas S, Marroquin S, Lekey A, Smith JJ, Garrad R, Aryal S, Abdelhakiem M, Glaspell GP (2017) “Enzyme and Cancer Cell Selectivity of Nanoparticles: Inhibition of 3-D Metastatic Phenotype and Experimental Melanoma by Zinc Oxide” J. Biomed. Nanotechnol. 13, 1–11, DOI: 10.1166/jbn.2017.2336
  23. Vergara-Jaque A, Comer J, Sepúlveda-Boza S, Santos LS, Mascayano C, Sandoval-Yáñez C (2017) “Study of Specific Interactions in Inclusion Complexes of Amine-Terminated PAMAM Dendrimer/Flavonoids by Experimental and Computational Methods” Int. J. Polym. Mater. 66, 485–494, DOI: 10.1080/00914037.2016.1252345
  24. Chipot C, Comer J (2016) “Subdiffusion in Membrane Permeation of Small Molecules” Sci. Rep. 6, 35913, DOI: 10.1038/srep35913
  25. Márquez-Miranda V, Araya-Durán I, Camarada MB, Comer J, Valencia-Gallegos JA, González-Nilo FD (2016) “Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction” Sci. Rep. 6, 29436, DOI: 10.1038/srep29436
  26. Lee C, Comer J, Herndon C, Leung N, Pavlova A, Swift R, Tung C, Rowley CN, Amaro R, Chipot C, Wang Y, Gumbart JC (2016) “Simulation-based Approaches for Determining Membrane Permeability of Small Compounds” J. Chem. Inf. Model. 56, 721–733, DOI: 10.1021/acs.jcim.6b00022
  27. Comer J, Aksimentiev A (2016) “DNA Sequence-Dependent Ionic Currents in Ultra-Small Solid-State Nanopores” Nanoscale 8, 9600–9613, DOI: 10.1039/C6NR01061J
  28. Poblete H, Agarwal A, Thomas SS, Bohne C, Phospase J, Comer J, Alarcon EI (2016) “New Insights into Peptide–Silver Nanoparticle Interaction: Deciphering the Role of Cysteine and Lysine in the Peptide Sequence” Langmuir 32, 265–273, DOI: 10.1021/acs.langmuir.5b03601
  29. Comer J, Chen R, Poblete H, Vergara-Jaque A, Riviere JE (2015) “Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation” ACS Nano 9, 11761–11774, DOI: 10.1021/acsnano.5b03592
  30. Fu H, Comer J, Cai W, Chipot C (2015) “Sonoporation at Small and Large Length Scales. Effect of Cavitation Bubble Collapse on Membranes” J. Phys. Chem. Lett. 6, 413–418, DOI: 10.1021/jz502513w
  31. Poblete H, Oyarzún I, Olivero P, Comer J, Zuñiga M, Sepulveda RV, Báez-Nieto D, Leon CG, González-Nilo F, Latorre R (2015) “Molecular Determinants of Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P2) Binding to Transient Receptor Potential V1 (TRPV1) Channels” J. Biol. Chem. 290, 2086–2098, DOI: 10.1074/jbc.M114.613620

Previous Publications by Jeff Comer

  1. Comer J, Phillips JC, Schulten K, Chipot C (2014) “Multiple-Walker Strategies for Free-Energy Calculations in NAMD: Shared Adaptive Biasing Force and Walker Selection Rules” J. Chem. Theory Comput. 10, 5276–5285, DOI: 10.1021/ct500874p
  2. Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C (2015) “The Adaptive Biasing Force Method: Everything You Always Wanted to Know But Were Afraid to Ask” J. Phys. Chem. B 119, 1129–1151, DOI: 10.1021/jp506633n
  3. Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A (2014) “Close Encounters with DNA” J. Phys.: Condens. Matter 26, 413101, DOI: 10.1088/0953-8984/26/41/413101
  4. Comer J, Schulten K, Chipot C (2014) “Diffusive Models of Membrane Permeation with Explicit Orientational Freedom” J. Chem. Theory Comput. 10, 2710–2718, DOI: 10.1021/ct500209j
  5. Comer J, Schulten K, Chipot C (2014) “Calculation of Lipid-Bilayer Permeabilities Using an Average Force” J. Chem. Theory Comput. 10, 554–564, DOI: 10.1021/ct400925s
  6. Comer J, Roux B, Chipot C (2014) “Achieving Ergodic Sampling Using Replica-exchange Free-energy Calculations” Mol. Sim. 40, 218-228, DOI: 10.1080/08927022.2013.841909
  7. Carrasco-Sánchez V, Vergara-Jaque A, Zuñiga M, Comer J, John A, Nachtigall FM, Valdes O, Duran-Lara EF, Sandoval C, Santos LS (2014) “In Situ and in Silico Evaluation of Amine-and Folate-terminated Dendrimers as Nanocarriers of Anesthetics” Eur. J. Med. Chem. 73, 250–257, DOI: 10.1016/j.ejmech.2013.11.040
  8. Chaudhry JH, Comer J, Aksimentiev A, Olson LN (2014) “A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Though a Nanopore” Commun. Comput. Phys. 15, 93–125, DOI: 10.4208/cicp.101112.100413a
  9. Zoonens M, Comer J, Masscheleyn S, Pebay-Peyroula E, Chipot CJ, Miroux B, Dehez F (2013) “Dangerous Liaisons between Detergents and Membrane Proteins. The Case of Mitochondrial Uncoupling Protein 2” J. Am. Chem. Soc. 135, 15174–15182, DOI: 10.1021/ja407424v
  10. Comer J, Dehez F, Cai W, Chipot C (2013) “Water Conduction Through a Peptide Nanotube” J. Phys. Chem. C 117, 26797–26803, DOI: 10.1021/jp4088223
  11. Vergara-Jaque A, Comer J, Monsalve L, González-Nilo FD, Sandoval C (2013) “A Computationally Efficient Methodology for Atomic-Level Characterization of Dendrimer–Drug Complexes: A Comparison of Amine- and Acetyl-Terminated PAMAM” J. Phys. Chem. B 117, 6801–6813, DOI: 10.1021/jp4000363
  12. Vilos C, Morales FA, Solar PA, Herrera NS, Gonzalez-Nilo FD, Aguayo DA, Mendoza HL, Comer J, Bravo ML, Gonzalez PA, Kato S, Cuello MA, Alonso C, Bravo EJ, Bustamante EI, Owend GI, Velasquez LA (2013) “Paclitaxel-PHBV Nanoparticles and Their Toxicity to Endometrial and Primary Ovarian Cancer Cells” Biomaterials 34, 4098–4108, DOI: 10.1016/j.biomaterials.2013.02.034
  13. Comer J, Chipot C, Gonzalez-Nilo FD (2013) “Calculating Position-dependent Diffusivity in Biased Molecular Dynamics Simulations” J. Chem. Theory Comput. 9, 876–882, DOI: 10.1021/ct300867e
  14. Comer J, Ho A, Aksimentiev A (2012) “Toward Detection of DNA-bound Proteins Using Solid-state Nanopores: Insights from Computer Simulations” Electrophoresis 33, 3466–3479, DOI: 10.1002/elps.201200164
  15. Wells D, Belkin M, Comer J, Aksimentiev A (2012) “Assessing Graphene Nanopores for Sequencing DNA” Nano Lett. 12, 4117–4123, DOI: 10.1021/nl301655d
  16. Timp W, Comer J, Aksimentiev A (2012) “DNA Base-Calling from a Nanopore Using a Viterbi Algorithm” Biophys. J. 102, L37–L39, DOI: 10.1016/j.bpj.2012.04.009
  17. Comer J, Aksimentiev A (2012) “Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics” J. Phys. Chem. C 116, 3376–3393, DOI: 10.1021/jp210641j
  18. Carr R, Comer J, Ginsberg M, Aksimentiev A (2011) “Atoms-to-microns Model for Small Solute Transport through Sticky Nanochannels” Lab Chip 11, 3766–3773, DOI: 10.1039/C1LC20697D
  19. Carr R, Comer J, Ginsberg MD, Aksimentiev A (2011) “Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface” J. Phys. Chem. Lett. 2, 1804–1807, DOI: 10.1021/jz200749d
  20. Carr R, Comer J, Aksimentiev A (2011) “Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems” Simulations in Nanobiotechnology 2, 43–60
  21. Carr R, Comer J, Ginsberg MD, Aksimentiev A (2011) “Modeling Pressure-Driven Transport of Proteins through a Nanochannel” IEEE Tran. Nanotechnol. 10, 75–82, DOI: 10.1109/TNANO.2010.2062530
  22. Venkatesan B, Polans J, Comer J, Sridhar S, Wendell D, Aksimentiev A, Bashir R (2011) “Lipid Bilayer Coated Al_2O_3 Nanopore Sensors: Towards a Hybrid Biological Solid-state Nanopore” Biomed Microdevices 13, 671–682, DOI: 10.1021/nl301655d
  23. Comer J, Wells DB, Aksimentiev A (2011) “Modeling Nanopores for Sequencing DNA” Protocols in DNA Nanotechnology 22, 317–358
  24. Comer J, Aksimentiev A (2011) “Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations” Nanopores: Sensing and Fundamental Biological Interactions 14, 335-356
  25. Wells DB, Bhattacharya S, Carr R, Maffeo C, Ho A, Comer J, Aksimentiev A (2011) “Optimization of the Molecular Dynamics Method for Simulations of DNA and Ion Transport through Biological Nanopores” Nanopore-based Technology: Single Molecule Characterization and DNA Sequencing
  26. Timp G, Mirsaidov U, Timp W, Wang JSaD, Dimitrov V, Scrimgeour J, Comer CLaJ, Ho HY, Zou X, Aksimentiev A, Schulten K (2011) “3rd Generation DNA Sequencing with a Nanopore” Nanopores: Sensing and Fundamental Biological Interactions 12, 287–311
  27. Mirsaidov U, Comer J, Dimitrov V, Aksimentiev A, Timp G (2010) “Slowing the Translocation of Double-Stranded DNA Using a Nanopore Smaller Than the Double Helix” Nanotechnology 21, 395501, DOI: 10.1088/0957-4484/21/39/395501
  28. Timp W, Mirsaidov U, Wang D, Comer J, Aksimentiev A, Timp G (2010) “Nanopore Sequencing: Electrical Measurements of the Code of Life” IEEE Tran. Nanotechnol. 9, 281–294, DOI: 10.1109/TNANO.2010.2044418
  29. Dorvel B, Sigalov G, Zhao Q, Comer J, Dimitrov V, Mirsaidov U, Aksimentiev A, Timp G (2009) “Analyzing the Forces Binding a Restriction Endonuclease to DNA Using a Synthetic Nanopore” Nucl. Acids Res. 37, 4170–4179, DOI: 10.1093/nar/gkp317
  30. Aksimentiev A, Brunner R, Cruz-Chu ER, Comer J, Schulten K (2009) “Modeling Transport through Synthetic Nanopores” IEEE Nanotechnol. Mag. 3, 20–28, DOI: 10.1109/MNANO.2008.931112
  31. Comer J, Dimitrov V, Zhao Q, Timp G, Aksimentiev A (2009) “Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores” Biophys. J. 96, 593–608, DOI: 10.1016/j.bpj.2008.09.023
  32. Sigalov G, Comer J, Timp G, Aksimentiev A (2008) “Detection of DNA Sequence Using an Alternating Electric Field in a Nanopore Capacitor” Nano Lett. 8, 56–63, DOI: 10.1021/nl071890k
  33. Zhao Q, Comer J, Dimitrov V, Aksimentiev A, Timp G (2008) “Stretching and Unzipping Nucleic Acid Hairpins Using a Synthetic Nanopore” Nucl. Acids Res. 36, 1532–1541, DOI: 10.1093/nar/gkm1017
  34. Aksimentiev A, Brunner R, Cohen J, Comer J, Cruz-Chu E, Hardy D, Rajan A, Shih A, Sigalov G, Yin Y, Schulten K (2008) “Computer Modeling in Biotechnology: a Partner in Development” Nanostructure Design: Methods and Protocols
  35. Farkas N, Comer J, Zhang G, Evans E, Ramsier R, Dagata J (2005) “SPM Oxidation and Parallel Writing on Zirconium Nitride Thin Films” J. Vac. Sci. Technol. A 23, 846, DOI: 10.1116/1.1864052
  36. Farkas N, Comer J, Zhang G, Evans E, Ramsier R, Dagata J (2005) “High-voltage SPM Oxidation of ZrN: Materials for Multiscale Applications” Nanotechnology 16, 262–266, DOI: 10.1088/0957-4484/16/2/014
  37. Farkas N, Comer J, Zhang G, Evans E, Ramsier R, Wight S, Dagata J (2004) “Parallel Writing on Zirconium Nitride Thin Films by Local Oxidation Nanolithography” Appl. Phys. Lett. 85, 5691, DOI: 10.1063/1.1833569
  38. Comer J, Shepard M, Henriksen P, Ramsier R (2004) “Chladni Plates Revisited” Am. J. Phys. 72, 1345, DOI: 10.1119/1.1758222
  39. Shepard M, Comer J, Young T, McNatt J, Espe M, Ramsier R, Robinson T, Nelson L (2004) “Organophosphate Adsorption on Metal Oxide Surfaces” Silanes and Other Coupling Agents, Vol. 3