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Comer Group Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Calbo J, López-Moreno A, Juan Ad, 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Chipot C, Comer J (2016) “Subdiffusion in Membrane Permeation of Small Molecules” Sci. Rep. 6, 35913, DOI: 10.1038/srep35913
  12. 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
  13. 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
  14. Comer J, Aksimentiev A (2016) “DNA Sequence-Dependent Ionic Currents in Ultra-Small Solid-State Nanopores” Nanoscale 8, 9600–9613, DOI: 10.1039/C6NR01061J
  15. 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
  16. 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
  17. 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
  18. 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