TCB Publications - Search
10153. Modulation of molecular flux using a graphene nanopore capacitor. Manish Shankla and Aleksei Aksimentiev. Journal of Physical Chemistry B, 121:3724-3733, 2016.
10143. Large-conductance transmembrane porin made from DNA origami. Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser. ACS Nano, 10:8207-8214, 2016.
10142. Ion channels made from a single membrane-spanning DNA duplex. Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri, Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter, Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser. Nano Letters, 16:4665-4669, 2016.
10141. Mechanical properties of a complete microtubule revealed through molecular dynamics simulation. David B. Wells and Aleksei Aksimentiev. Biophysical Journal, 99:629-637, 2010.
10140. Microscopic perspective on the adsorption isotherm of a heterogeneous surface. Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. Journal of Physical Chemistry Letters, 2:1804-1807, 2011.
10132. End-to-end attraction of duplex DNA. Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev. Nucleic Acids Research, 40:3812-3821, 2012.
10131. Improved parametrization of Li+, Na+, K+, and Mg2+. J. Yoo and A. Aksimentiev. Journal of Physical Chemistry Letters, 3:45-50, 2012.
10130. A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment. Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev. Journal of Chemical Theory and Computation, 10:2891-2896, 2014.
10129. DNA-DNA interactions in tight supercoils are described by a small effective charge density. Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel. Physical Review Letters, 105:158101, 2010.
10128. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha. Nature Communications, 7:11045, 2016.
10127. The structure and intermolecular forces of DNA condensates. Jejoong Yoo and Aleksei Aksimentiev. Nucleic Acids Research, 44:2036-2046, 2016.
10126. Improved parameterization of amine-carboxylate and amine-phosphate interactions for molecular dynamics simulations using the CHARMM and AMBER force fields. Jejoong Yoo and Aleksei Aksimentiev. Journal of Chemical Theory and Computation, 12:430-443, 2016.
10122. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Jejoong Yoo and Aleksei Aksimentiev. Proceedings of the National Academy of Sciences, USA, 110:20099-20104, 2013.
10121. Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field. Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. ACS Nano, 9:1420-1433, 2015. PMID: 25623807.
10120. Molecular dynamics of membrane-spanning DNA channels: Conductance mechanism, electro-osmotic transport and mechanical gating. Jejoong Yoo and Aleksei Aksimentiev. Journal of Physical Chemistry Letters, 6:4680-4687, 2015.
10076. Control of nanoscale environment to improve stability of immobilized proteins on diamond surfaces. Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr, Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev, Robert J. Hamers, and Rashid Bashir. Advanced Functional Materials, 21:1040-1050, 2011.
10073. The effect of calcium on the conformation of cobalamin transporter BtuB. B. Luan, M. Caffrey, and A. Aksimentiev. PROTEINS: Structure, Function, and Bioinformatics, 78:1153-1162, 2010.
10072. Surface functionalization of thin-film diamond for highly stable and selective biological interfaces. C. Stavis, T. L. Clare, J. E. Butler, A. D. Radadia, R. Carr, H. Zeng, W. King, J. A. Carlisle, A. Aksimentiev, R. Bashir, and R.J. Hamers. Proceedings of the National Academy of Sciences, USA, 108:983-988, 2011.
10071. Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix. U. Mirsaidov, J. Comer, V. Dimitrov, A. Aksimentiev, and G. Timp. Nanotechnology, 21:395501-10, 2010.
10068. Nanopore analysis of individual RNA/antibiotic complexes. S. Wanunu, S. Bhattacharya, Y. Xie, Y. Tor, A. Aksimentiev, and M. Drndic. ACS Nano, 5:9345-9353, 2011.
10067. Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. J. Comer and A. Aksimentiev. Journal of Physical Chemistry C, 116:3376-3393, 2012.
10032. DNA attraction in mono- and divalent electrolytes. B. Luan and A. Aksimentiev. Journal of the American Chemical Society, 130:15754-15755, 2008.
10031. Self-assembly route for embedding polyoxomolybdate capsules in lipid bilayer membranes. R. Carr, I. A. Weinstock, A. Sivaprasadarao, A. Müller, and A. Aksimentiev. Nano Letters, 8:3916-3921, 2008.
10030. Strain softening in stretched DNA. B. Luan and A. Aksimentiev. Physical Review Letters, 101:118101, 2008.
10029. Electro-osmotic screening of the DNA charge in a nanopore. B. Luan and A. Aksimentiev. Physical Review E, 78:021912, 2008.
10019. Detection of DNA sequences using an alternating electric field in a nanopore capacitor. G. Sigalov, J. Comer, G. Timp, and A. Aksimentiev. Nano Letters, 8:56-63, 2008.
10018. Stretching and unzipping nucleic acid hairpins using a synthetic nanopore. Q. Zhao, J. Comer, S. Yemenicioglu, A. Aksimentiev, and G. Timp. Nucleic Acids Research, 36:1532-1541, 2008.
10017. In meso crystal structure and computer simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin. V. Cherezov, W. Liu, J. Derrick, B. Luan, A. Aksimentiev, V. Katruc, and M. Caffrey. PROTEINS: Structure, Function, and Bioinformatics, 71:24-34, 2008.
10016. Exploring transmembrane transport through a-hemolysin with grid-steered molecular dynamics. David B. Wells, Volha Abramkina, and Aleksei Aksimentiev. Journal of Chemical Physics, 127:125101, 2007.
10015. Structure refinement of the OpcA adhesin using molecular dynamics. Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. Biophysical Journal, 93:3058-3069, 2007.
10011. Detecting SNPs using a synthetic nanopore. Q. Zhao, G. Sigalov, V. Dimitrov, B. Dorvel, U. Mirsaidov, S. Sligar, A. Aksimentiev, and G. Timp. Nano Letters, 7:1680-1685, 2007.
10009. Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor. Maria E. Gracheva, Aleksei Aksimentiev, and Jean-Pierre Leburton. Nanotechnology, 17:3160-3165, 2006.
552. 3rd generation DNA sequencing with a nanopore. Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang, Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony Ho, Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten. In Samir M. Iqbal and Rashid Bashir, editors, Nanopores: Sensing and Fundamental Biological Interactions, chapter 12, pp. 287-312. Springer, Berlin, 2011.
488. Modeling transport through synthetic nanopores. Aleksei Aksimentiev, Robert K. Brunner, Eduardo Cruz-Chu, Jeffrey Comer, and Klaus Schulten. IEEE Nanotechnology, 3:20-28, 2009.
485. Ionic current rectification through silica nanopores. Eduardo R. Cruz-Chu, Aleksei Aksimentiev, and Klaus Schulten. Journal of Physical Chemistry C, 113:1850-1862, 2009.
457. Computer modeling in biotechnology, a partner in development. Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.
414. Water-silica force field for simulating nanodevices. Eduardo R. Cruz-Chu, Aleksei Aksimentiev, and Klaus Schulten. Journal of Physical Chemistry B, 110:21497-21508, 2006.
408. The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.
407. Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor. Maria E. Gracheva, Anlin Xiong, Aleksei Aksimentiev, Klaus Schulten, Gregory Timp, and Jean-Pierre Leburton. Nanotechnology, 17:622-633, 2006.
404. The electromechanics of DNA in a synthetic nanopore. J. B. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Biophysical Journal, 90:1098-1106, 2006.
398. Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel. Jerome Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and Amit Meller. Proceedings of the National Academy of Sciences, USA, 102:12377-12382, 2005.
397. Molecular dynamics simulations of proteins in lipid bilayers. James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 15:423-431, 2005.
395. Beyond the gene chip. J. B. Heng, A. Aksimentiev, C. Ho, V. Dimitrov, T. Sorsch, J. Miner, W. Mansfield, K. Schulten, and G. Timp. Bell Labs Technical Journal, 10:5-22, 2005.
391. Stretching DNA using an electric field in a synthetic nanopore. J. B Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Nano Letters, 5:1883-1888, 2005.
387. Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map. Aleksij Aksimentiev and Klaus Schulten. Biophysical Journal, 88:3745-3761, 2005.
381. Towards understanding membrane channels. Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor, and Klaus Schulten. In Boris Martinac and Andrzej Kubalski, editors, Bacterial ion channels and their eukaryotic homologues, pp. 153-190. ASM Press, Washington, DC, 2005.
371. Microscopic kinetics of DNA translocation through synthetic nanopores. Aleksij Aksimentiev, Jiunn Benjamin Heng, Gregory Timp, and Klaus Schulten. Biophysical Journal, 87:2086-2097, 2004.
370. Sizing DNA using a nanometer-diameter pore. J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Biophysical Journal, 87:2905-2911, 2004.
358. Extending the molecular modeling methodology to study insertion of membrane nanopores. Aleksij Aksimentiev and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 101:4337-4338, 2004.
352. Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Aleksij Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten. Biophysical Journal, 86:1332-1344, 2004.
340. Large scale simulation of protein mechanics and function. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, volume 66, pp. 195-247. Elsevier Academic Press, New York, 2003.