Publications

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A    
B Dorvel, G Sigalov, Q Zhao, Jeffrey Comer, Valentin Dimitrov, U Mirsaidov, Aleksei Aksimentiev, and Gregory Timp. "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore." Nucleic Acids Res 37:4170-9 (2009).
Aleksei Aksimentiev, and Robert Hołyst. "Application of the Euler characteristic to the study of homopolymer blends and copolymer melts." Polimery 46:309-322 (2001).
David B. Wells, Maxim Belkin, Jeffrey Comer, and Aleksei Aksimentiev. "Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (2012).
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Atoms-to-microns model for small solute transport through sticky nanochannels." Lab Chip 11:3766-73 (2011).
B    
Jiunn B. Heng, Aleksei Aksimentiev, C Ho, Valentin Dimitrov, T Sorsch, J Miner, W Mansfield, Klaus Schulten, and Gregory Timp. "Beyond the Gene Chip." Bell Labs Tech J 10:5-22 (2005).
C    
Christopher Maffeo, J Yoo, Jeffrey Comer, D B. Wells, B Luan, and Aleksei Aksimentiev. "Close encounters with DNA." J Phys Condens Matter 26:413101 (2014).
Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev. "A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment." Journal of Chemical Theory and Computation 10:2891-2896 (2014). PDF icon Supporting information (3.38 MB)
Jejoong Yoo, and Aleksei Aksimentiev. "Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations." J Phys Chem B 116:12946-54 (2012). PDF icon jp306598y_si_001.pdf (343.44 KB)
Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chú, David Hardy, Aruna Rajan, Amy Y. Shih, G Sigalov, Ying Yin, and Klaus Schulten. "Computer modeling in biotechnology: a partner in development." Methods Mol Biol 474:181-234 (2008).
Manish Shankla, and Aleksei Aksimentiev. "Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene." Nature Communications 5:5171 (2014).
Binquan Luan, and Aleksei Aksimentiev. "Control and reversal of the electrophoretic force on DNA in a charged nanopore." J Phys Condens Matter 22:454123 (2010).
Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr, Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev, Robert J. Hamers, and Rashid Bashir. "Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces." Adv Funct Mater 21:1040-1050 (2011).
D    
Christopher Maffeo, Jejoong Yoo, and Aleksei Aksimentiev. "De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation." Nucleic Acids Research 44:3013-3019 (2016).
Aleksei Aksimentiev. "Deciphering ionic current signatures of DNA transport through a nanopore." Nanoscale 2:468-83 (2010).
Q Zhao, G Sigalov, Valentin Dimitrov, B Dorvel, U Mirsaidov, S Sligar, Aleksei Aksimentiev, and Gregory Timp. "Detecting SNPs using a synthetic nanopore." Nano Lett 7:1680-5 (2007).
G Sigalov, Jeffrey Comer, Gregory Timp, and Aleksei Aksimentiev. "Detection of DNA sequences using an alternating electric field in a nanopore capacitor." Nano Lett 8:56-63 (2008).
Robert Hołyst, D Plewczyński, Aleksei Aksimentiev, and K Burdzy. "Diffusion on curved, periodic surfaces." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 60:302-7 (1999).
Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha. "Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation." Nature Communications 7:11045 (2016). PDF icon ncomms11045-s1.pdf (1.81 MB)
Binquan Luan, and Aleksei Aksimentiev. "DNA attraction in monovalent and divalent electrolytes." J Am Chem Soc 130:15754-5 (2008).
Winston Timp, Jeffrey Comer, and Aleksei Aksimentiev. "DNA base-calling from a nanopore using a Viterbi algorithm." Biophys J 102:L37-9 (2012).
Jeffrey Comer, and Aleksei Aksimentiev. "DNA sequence-dependent ionic currents in ultra-small solid-state nanopores." Nanoscale 18:9600-9613 (2016). PDF icon supp_triplet.pdf (98.62 KB)
Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel. "DNA-DNA interactions in tight supercoils are described by a small effective charge density." Phys Rev Lett 105:158101 (2010).
E    
Binquan Luan, Rogan Carr, Martin Caffrey, and Aleksei Aksimentiev. "The effect of calcium on the conformation of cobalamin transporter BtuB." Proteins 78:1153-62 (2010).
Thuy Ngo, Jejoong Yoo, Q Dai, Q Zhang, C He, Aleksei Aksimentiev, and Taekjip Ha. "Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability." Nature Communications 7:10813 (2016). PDF icon ncomms10813-s1.pdf (529.11 KB)
Binquan Luan, and Aleksei Aksimentiev. "Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes." Soft Matter 6:243-246 (2010).
Maria E. Gracheva, Aleksei Aksimentiev, and Jean-Pierre Leburton. "Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor." 17:3160-3165 (2006).
Jiunn B. Heng, Aleksei Aksimentiev, C Ho, Patrick Marks, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp. "The electromechanics of DNA in a synthetic nanopore." Biophys J 90:1098-106 (2006).
Binquan Luan, and Aleksei Aksimentiev. "Electro-osmotic screening of the DNA charge in a nanopore." Phys Rev E Stat Nonlin Soft Matter Phys 78:021912 (2008).
Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev. "End-to-end attraction of duplex DNA." Nucleic Acids Res 40:3812-21 (2012). PDF icon Supporting Information (2.95 MB)
David B. Wells, Volha Abramkina, and Aleksei Aksimentiev. "Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics." J Chem Phys 127:125101 (2007).
Aleksei Aksimentiev, and Klaus Schulten. "Extending molecular modeling methodology to study insertion of membrane nanopores." Proc Natl Acad Sci U S A 101:4337-8 (2004).
G    
James Wilson, Leila Sloman, Zhiren He, and Aleksei Aksimentiev. "Graphene Nanopores for Protein Sequencing." Advanced Functional Materials 26:4830-4838 (2016).
H    
Yue-xiao Shen, Wen Si, Mustafa Erbakan, Karl Decker, Rita De Zorzi, Patrick O. Saboe, You Jung Kang, Sheereen Majd, Peter J. Butler, Thomas Walz, Aleksei Aksimentiev, Jun-li Hou, and Manish Kumar. "Highly permeable artificial water channels that self-assemble into two-dimensional arrays." Proceedings of the National Academy of Science 112:9810-9815 (2015).
Lili Sun, Marcin Tabaka, Sen Hou, Lin Li, Krzysztof Burdzy, Aleksei Aksimentiev, Christopher Maffeo, Xuzhu Zhang, and Robert Holyst. "The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study." PLoS ONE 11:e0152002 (2016). PDF icon s1file.pdf (4.91 MB)
Spencer Carson, James Wilson, Aleksei Aksimentiev, Peter R. Weigele, and Meni Wanunu. "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44:2085-2092 (2016).
I    
Aleksei Aksimentiev, and Klaus Schulten. "Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map." Biophys J 88:3745-61 (2005).
Jejoong Yoo, James Wilson, and Aleksei Aksimentiev. "Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields." Biopolymers 105:752-763 (2016). PDF icon bip22868-sup-0001-suppinfo01.pdf (921.41 KB)
Jejoong Yoo, and Aleksei Aksimentiev. "Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields." Journal of Chemical Theory and Computation 12:430-443 (2016). PDF icon ct5b00967_si_001.pdf (2.12 MB)
Jejoong Yoo, and Aleksei Aksimentiev. "Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems." The Journal of Physical Chemistry Letters 3:45-50 (2012). PDF icon jz201501a_si_001.pdf (1.69 MB)
Vadim Cherezov, Wei Liu, Jeremy P. Derrick, Binquan Luan, Aleksei Aksimentiev, Vsevolod Katritch, and Martin Caffrey. "In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin." Proteins 71:24-34 (2008).
Jejoong Yoo, and Aleksei Aksimentiev. "In situ structure and dynamics of DNA origami determined through molecular dynamics simulations." Proc Natl Acad Sci U S A 110:20099-104 (2013). PDF icon Supporting Information (4.15 MB)
Aleksei Aksimentiev, and Robert Hołyst. "Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends." Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62:6821-30 (2000).
Aleksei Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten. "Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase." Biophys J 86:1332-44 (2004).
Kai Tian, Karl Decker, Aleksei Aksimentiev, and Li-Qun Gu. "Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis." ACS Nano 11:1204-1213 (2017). PDF icon Supporting Information (pdf) (8.47 MB)
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. "Ion Channels Made from a Single Membrane-Spanning DNA Duplex." Nano Letters 16:4665-4669 (2016). PDF icon supporting_information.pdf (1.32 MB)
Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev. "Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field." ACS Nano 9:1420-1433 (2015). PDF icon Supporting Information (8.81 MB)
Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Ionic Current Rectification Through Silica Nanopores." J Phys Chem C Nanomater Interfaces 113:1850 (2009).
K    
Aleksei Aksimentiev, Robert Hołyst, and Krzysztof Moorthi. "Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends." Macromolecular Theory and Simulations 9:661-674 (2000).
L    
Emad Tajkhorshid, Aleksei Aksimentiev, Ilya A. Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. "Large scale simulation of protein mechanics and function." Adv Protein Chem 66:195-247 (2003).
Kerstin Göpfrich*, Chen-Yu Li*, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser. "Large-Conductance Transmembrane Porin Made from DNA Origami." ACS Nano 10:8207-8214 (2016). PDF icon supporting_information.pdf (3.19 MB)
Bala Murali Venkatesan, James Polans, Jeffrey Comer, Supriya Sridhar, David Wendell, Aleksei Aksimentiev, and Rashid Bashir. "Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore." Biomed Microdevices 13:671-82 (2011).
M    
David B. Wells, and Aleksei Aksimentiev. "Mechanical properties of a complete microtubule revealed through molecular dynamics simulation." Biophys J 99:629-37 (2010). PDF icon Supporting Information (pdf) (2.75 MB)File Atomic coordinates of the equilibrated "N" protofilament (pdb) (2.02 MB)File Atomic coordinates of the equilibrated "S" protofilament (pdb) (2.02 MB)File Atomic coordinates of the equilibrated complete microtubule (pdb) (13.16 MB)
Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev. "Mechanical Trapping of DNA in a Double-Nanopore System." Nano Letters 16:8021-8028 (2016). PDF icon Supporting Information (pdf) (2.24 MB)
Aleksei Aksimentiev, Jiunn B. Heng, Gregory Timp, and Klaus Schulten. "Microscopic Kinetics of DNA Translocation through synthetic nanopores." Biophys J 87:2086-97 (2004).
Jeffrey Comer, Valentin Dimitrov, Qian Zhao, Gregory Timp, and Aleksei Aksimentiev. "Microscopic mechanics of hairpin DNA translocation through synthetic nanopores." Biophys J 96:593-608 (2009).
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface." J Phys Chem Lett 2:1804-1807 (2011).
Christopher Maffeo, Swati Bhattacharya, Jejoong Yoo, David B. Wells, and Aleksei Aksimentiev. "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
Jeffrey Comer, David B. Wells, and Aleksei Aksimentiev. "Modeling nanopores for sequencing DNA." In DNA Nanotechnology: Methods and Protocols, edited by Giampaolo Zuccheri and Bruno Samori, 317-358. Vol. 749. Methods Mol. Biol. 749., 2011.
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev. "Modeling Pressure-Driven Transport of Proteins through a Nanochannel." IEEE Trans Nanotechnol 10:75-82 (2011).
Rogan Carr, Jeffrey Comer, and Aleksei Aksimentiev. "Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems." In Simulations in Nanobiotechnology, edited by Kilho Eom, 43-60. CRC Press, 2011.
Maxim Belkin, Shu-Han Chao, Gino Giannetti, and Aleksei Aksimentiev. "Modeling thermophoretic effects in solid-state nanopores." Journal of Computational Electronics 13:826-838 (2014).
Aleksei Aksimentiev, Robert Brunner, Eduardo Cruz-Chú, Jeffrey Comer, and Klaus Schulten. "Modeling Transport Through Synthetic Nanopores." IEEE Nanotechnol Mag 3:20-28 (2009).
Manish Shankla, and Aleksei Aksimentiev. "Modulation of Molecular Flux Using a Graphene Nanopore Capacitor." The Journal of Physical Chemistry B 121:3724-3733 (2017).
Jejoong Yoo, and Aleksei Aksimentiev. "Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating." The Journal of Physical Chemistry Letters 6:4680-4687 (2015). PDF icon Supporting Information (8.97 MB)
Maxim Belkin, and Aleksei Aksimentiev. "Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores." ACS Applied Materials and Interfaces 8:12599-12608 (2016). PDF icon supporting.pdf (461.04 KB)
James Gumbart, Yi Wang, Aleksei Aksimentiev, Emad Tajkhorshid, and Klaus Schulten. "Molecular dynamics simulations of proteins in lipid bilayers." Curr Opin Struct Biol 15:423-31 (2005).
Swati Bhattacharya, Ian M. Derrington, Mikhail Pavlenok, Michael Niederweis, Jens H. Gundlach, and Aleksei Aksimentiev. "Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence." ACS Nano 6:6960-8 (2012). PDF icon Supporting Information (pdf) (2.36 MB)
Scott Michael Slone, Chen-Yu Li, Jejoong Yoo, and Aleksei Aksimentiev. "Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity." New Journal of Physics 18:055012 (2016). PDF icon supporting_information.pdf (7.84 MB)
Christopher Maffeo, and Aleksei Aksimentiev. "Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
Aleksei Aksimentiev, Robert Hołyst, and Marcin Fialkowski. "Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulation and measurements." Advances in Chemical Physics 121:141-239 (2002).
N    
Meni Wanunu, Swati Bhattacharya, Yun Xie, Yitzhak Tor, Aleksei Aksimentiev, and Marija Drndic. "Nanopore analysis of individual RNA/antibiotic complexes." ACS Nano 5:9345-53 (2011).
Jeffrey Comer, and Aleksei Aksimentiev. "Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations." In Nanopores: Sensing and Fundamental Biological Interactions, edited by Rashid Bashir and Samir Iqbal, 335-356. New York: Springer Science and Business Media, LLC, 2011.
Wei Si, and Aleksei Aksimentiev. "Nanopore Sensing of Protein Folding." ACS Nano 11, 7091-7100 (2017). PDF icon nn7b02718_si_001.pdf (12.07 MB)
Winston Timp, Utkur M. Mirsaidov, Deqiang Wang, Jeffrey Comer, Aleksei Aksimentiev, and Gregory Timp. "Nanopore Sequencing: Electrical Measurements of the Code of Life." IEEE Trans Nanotechnol 9:281-294 (2010).
Karl Decker, Martin Page, and Aleksei Aksimentiev. "Nanoscale Ion Pump Derived from a Biological Water Channel." The Journal of Physical Chemistry B 121:7899-7906 (2017). PDF icon supporting_information.pdf (8.9 MB)
O    
David B. Wells, Swati Bhattacharya, Rogan Carr, Christopher Maffeo, Anthony H. Ho, Jeffrey Comer, and Aleksei Aksimentiev. "Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores." Methods Mol Biol 870:165-86 (2012).
Jérôme Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and Amit Meller. "Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel." Proc Natl Acad Sci U S A 102:12377-82 (2005).
P    
Aleksei Aksimentiev, and Robert Hołyst. "Phase behavior of gradient copolymers." The Journal of Chemical Physics 111:2329-2339 (1999).
Mohammad Amin Alibakhshi, Justin R. Halman, James Wilson, Aleksei Aksimentiev, Kirill A. Afonin, and Meni Wanunu. "Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores." ACS Nano 11:9701-9710 (2017). PDF icon Supporting Information (12.11 MB)
Maxim Belkin, Shu-Han Chao, Magnus P. Jonsson, Cees Dekker, and Aleksei Aksimentiev. "Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA." ACS Nano 9:10598-10611 (2015). PDF icon nn5b04173_si_001.pdf (681.52 KB)
Benjamin Cressiot*, Sandra J. Greive*, Wei Si*, Tomas Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw Thomas Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A. Antson, and Meni Wanunu. "Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization." ACS Nano (2017).
Jejoong Yoo, Chen-Yu Li, Scott Michael Slone, Christopher Maffeo, and Aleksei Aksimentiev. "A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems." In Protocols in DNA Nanotechology, edited by Giampaolo Zuccheri. 2nd ed. Methods in Molecular Biology. Humana Press, 2017.Binary Data origamitutorial.tar.gz (103.69 MB)
Jeffrey Comer, and Aleksei Aksimentiev. "Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics." J Phys Chem C Nanomater Interfaces 116:3376-3393 (2012).
Q    
Aaron John Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack Fredrick Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei Aksimentiev, and Liviu Movileanu. "Quantification of Membrane Protein-Detergent Complex Interactions." The Journal of Physical Chemistry B 121:10228-10241 (2017).
R    
Trevor Gamble, Karl Decker, Timothy S. Plett, Matthew Pevarnik, Jan-Frederik Pietschmann, Ivan Vlassiouk, Aleksei Aksimentiev, and Zuzanna S. Siwy. "Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling." The Journal of Physical Chemistry C 118:9809-9819 (2014).
Swati Bhattacharya, L Muzard, Linda Payet, Jérôme Mathé, Ulrich Bockelmann, Aleksei Aksimentiev, and Virgile Viasnoff. "Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments." The Journal of Physical Chemistry C 115:4255-4264 (2011).
Jejoong Yoo, and Aleksei Aksimentiev. "Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations." Journal of Physical Chemistry Letters 7:3812-3818 (2016). PDF icon jz6b01747_si_001.pdf (6.89 MB)
Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chú, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. "The role of molecular modeling in bionanotechnology." Phys Biol 3:S40-53 (2006).
S    
Marcin Fialkowski, Aleksei Aksimentiev, and Robert Hołyst. "Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems." Phys Rev Lett 86:240-3 (2001).
Aleksei Aksimentiev, Krzysztof Moorthi, and Robert Hołyst. "Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends." The Journal of Chemical Physics 112:6049-6062 (2000).
Laura Restrepo-Perez*, Shalini John*, Aleksei Aksimentiev, Chirlmin Joo, and Cees Dekker. "SDS-assisted protein transport through solid-state nanopores." Nanoscale 9:11685-11693 (2017). PDF icon Supporting Information (1.24 MB)
Karl Decker, Martin Page, Ashley Boyd, Irene MacAllister, Mark Ginsberg, and Aleksei Aksimentiev. "Selective Permeability of Truncated Aquaporin 1 in Silico." ACS Biomaterials Science & Engineering 3:342-348 (2017). PDF icon Supporting Information (pdf) (459.46 KB)
Maria E. Gracheva, A. Xiong, Aleksei Aksimentiev, Klaus Schulten, Gregory Timp, and Jean-Pierre Leburton. "Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor." Nanotechnology 17:622-633 (2006).
Aleksei Aksimentiev, and Robert Hołyst. "Single chain conformations in the system of symmetric and asymmetric diblock copolymers." Macromolecular Theory and Simulations 8:328-342 (1999).
Christopher Maffeo, and Aleksei Aksimentiev. "Single molecule force measurements: insights from molecular simulations. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya et al." Phys Life Rev 7:353-4; discussion 358-61 (2010).
Aleksei Aksimentiev, and Robert Hołyst. "Single-chain statistics in polymer systems." Progress in Polymer Science 24:1045-1093 (1999).
Jiunn B. Heng, Chuen Ho, Taekyung Kim, Rolf Timp, Aleksei Aksimentiev, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp. "Sizing DNA using a nanometer-diameter pore." Biophys J 87:2905-11 (2004).
Shouvik Banerjee, James Wilson, Jiwook Shim, Manish Shankla, Elise A. Corbin, Aleksei Aksimentiev, and Rashid Bashir. "Slowing DNA Transport Using Graphene–DNA Interactions." Advanced Functional Materials 25:936-946 (2015). PDF icon adfm201403719-sup-0001-s1.pdf (1.01 MB)
Stefan W. Kowalczyk, David B. Wells, Aleksei Aksimentiev, and Cees Dekker. "Slowing down DNA translocation through a nanopore in lithium chloride." Nano Lett 12:1038-44 (2012).
Utkur Mirsaidov, Jeffrey Comer, Valentin Dimitrov, Aleksei Aksimentiev, and Gregory Timp. "Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix." Nanotechnology 21:395501 (2010).
Spencer Carson, James Wilson, Aleksei Aksimentiev, and Meni Wanunu. "Smooth DNA Transport through a Narrowed Pore Geometry." Biophysical Journal 107:2381-2393 (2014).
Jehanzeb Hameed Chaudhry, Jeffrey Comer, Aleksei Aksimentiev, and Luke N. Olson. "A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore." Commun Comput Phys 15:93-125 (2014).
Binquan Luan, and Aleksei Aksimentiev. "Strain softening in stretched DNA." Phys Rev Lett 101:118101 (2008).
Maxim Belkin, Christopher Maffeo, David B. Wells, and Aleksei Aksimentiev. "Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores." ACS Nano 7:6816-24 (2013). PDF icon Supporting Information (2.8 MB)
Q Zhao, Jeffrey Comer, Valentin Dimitrov, S Yemenicioglu, Aleksei Aksimentiev, and Gregory Timp. "Stretching and unzipping nucleic acid hairpins using a synthetic nanopore." Nucleic Acids Res 36:1532-41 (2008).
Jiunn B. Heng, Aleksei Aksimentiev, Chuen Ho, Patrick Marks, Yelena V. Grinkova, S Sligar, Klaus Schulten, and Gregory Timp. "Stretching DNA using the electric field in a synthetic nanopore." Nano Lett 5:1883-8 (2005).
Jejoong Yoo, and Aleksei Aksimentiev. "The structure and intermolecular forces of DNA condensates." Nucleic Acids Research 44:2036-2046 (2016). PDF icon dnapack_supp.pdf (9.65 MB)
Christopher Maffeo, and Aleksei Aksimentiev. "Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).
Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev. "Structure refinement of the OpcA adhesin using molecular dynamics." Biophys J 93:3058-69 (2007).
Courtney J. Stavis, Tami Lasseter Clare, James E. Butler, Adarsh D. Radadia, Rogan Carr, Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev, Rashid Bashir, and Robert J. Hamers. "Surface functionalization of thin-film diamond for highly stable and selective biological interfaces." Proc Natl Acad Sci U S A 108:983-8 (2011).
Aleksei Aksimentiev, and Robert Hołyst. "Swelling and shrinking of polymer chains in homopolymer blends." Macromolecular Theory and Simulations 7:447-456 (1998).
Rogan Carr, Ira A. Weinstock, Asipu Sivaprasadarao, Achim Müller, and Aleksei Aksimentiev. "Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes." Nano Lett 8:3916-21 (2008). PDF icon Supporting Information (pdf) (8.8 MB)
T    
Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang, Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony H. Ho, Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten. "Third Generation DNA Sequencing with a Nanopore." In Nanopores: Sensing fundamental biological interactions at the single molecule level, edited by Samir M. Iqbal and Rashid Bashir, 287-311. Springer US, 2011.
Jeffrey Comer, Anthony H. Ho, and Aleksei Aksimentiev. "Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations." Electrophoresis 33:3466-79 (2012).
Emad Tajkhorshid, Jordi Cohen, Aleksei Aksimentiev, Marcos Sotomayor, and Klaus Schulten. "Toward understanding membrane channels." In Bacterial ion channels and their eukaryotic homologues, edited by Boris Martinac and Andrzej Kubalski, 153-190. Washington, DC: ASM Press, 2005.
Shu-Han Chao, Sam S. Matthews, Ryan Paxman, Aleksei Aksimentiev, Martin Gruebele, and Joshua L. Price. "Two Structural Scenarios for Protein Stabilization by PEG." J Phys Chem B 118:8388-8395 (2014).
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Swati Bhattacharya, Jejoong Yoo, and Aleksei Aksimentiev. "Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore." ACS Nano 10:4644-4651 (2016). PDF icon supporting_mspa.pdf (3.61 MB)
Eduardo Cruz-Chú, Aleksei Aksimentiev, and Klaus Schulten. "Water-silica force field for simulating nanodevices." J Phys Chem B 110:21497-508 (2006).