Publications

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2008    
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).
2010    
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).
2011    
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).
2012    
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)
2014    
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).
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)
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).
2019    
Megan Farell, Maxwell Wetherington, Manish Shankla, Inseok Chae, Shruti Subramanian, Seong H. Kim, Aleksei Aksimentiev, Joshua Robinson, and Manish Kumar. "Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features." Langmuir 35:4726-4735 (2019).
Alexander Ohmann, Kerstin Göpfrich, Himanshu Joshi, Rebecca F. Thompson, Diana Sobota, Neil A. Ranson, Aleksei Aksimentiev, and Ulrich F. Keyser. "Controlling aggregation of cholesterol-modified DNA nanostructures." Nucleic Acid Research 47:11441-11451 (2019). PDF icon si.pdf (1.74 MB)
2021    
D Winogradoff, Pin‐Yi Li, H Joshi, L Quednau, C Maffeo, and Aleksei Aksimentiev. "Chiral Systems Made from DNA." Advanced Science 8:2003113 (2021).
Diana Morzy, Roger Rubio-Sánchez, Himanshu Joshi, Aleksei Aksimentiev, Lorenzo Di Michele, and Ulrich F. Keyser. "Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures." Journal of the American Chemical Society 143:7358-7367 (2021). PDF icon si.pdf (2.68 MB)
2024    
Saman Fatima, Behzad Mehrafrooz, David G. Boggs, Noor Ali, Swapnil Singh, Megan C. Thielges, Jennifer Bridwell-Rabb, Aleksei Aksimentiev, and Lisa Olshansky. "Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein." Biochemistry (2024).