Christopher Maffeo

(217) 300-1203
261 LLP

Loomis Laboratory of Physics
1110 West Green Street
Urbana, IL 61801-3080

Interesting biological functions emerge from the detailed structure and dynamics of molecules. I use molecular dynamics simulations to distill quantitative micro-biological information from the trajectories of all-atom models of DNA–protein systems. Typically I use one of a variety of equilibrium and non-equilibrium enhanced-sampling techniques, including umbrella sampling and steered molecular dynamics. Once effective interactions have been extracted in this way, they can be used to explore biomolecular dynamics on timescales inaccessible to all-atom simulations. My work has focused on DNA–DNA and DNA–protein interactions, highlighting the importance of the physical properties of DNA in determining its behavior. Please see my curriculum vitae for more information about my skills, experience and the results of my work.


  1. Christopher Maffeo, and Aleksei Aksimentiev. "MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems." Nucleic Acids Research (2020). PDF icon supplement.pdf (3.94 MB)
  2. Christopher Maffeo, Han-Yi Chou, and Aleksei Aksimentiev. "Single-molecule biophysics experiments in silico: Toward a physical model of a replisome." iScience 25:104264 (2022). PDF icon maff2022_si.pdf (1.35 MB)
  3. Christopher Maffeo, Han-Yi Chou, and Aleksei Aksimentiev. "Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations." Advanced Theory and Simulations 2:1800191 (2019).
  4. Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser, and Aleksei Aksimentiev. "A synthetic enzyme built from DNA flips 10⁷ lipids per second in biological membranes." Nature Communications 9:2426 (2018). PDF icon dna-scramblase-si.pdf (5.77 MB)
  5. Elisa Alina Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah Elisabeth Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, and Ulrich F. Keyser. "Optical voltage sensing using DNA origami." Nano Letters 18:1962-1971 (2018). PDF icon nl7b05354_si_001.pdf (2.72 MB)
  6. Eva Bertosin, Christopher M. Maffeo, Thomas Drexler, Maximilian N. Honemann, Aleksei Aksimentiev, and Hendrik Dietz. "A nanoscale reciprocating rotary mechanism with coordinated mobility control." Nature Communications 12:7138 (2021).
  7. Christopher Maffeo, and Aleksei Aksimentiev. "Molecular mechanism of DNA association with single-stranded DNA binding protein." Nucleic Acids Research 45:12125-12139 (2017).
  8. 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).
  9. 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).
  10. 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)
  11. 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)
  12. Christopher Maffeo, Swati Bhattacharya, Jejoong Yoo, David B. Wells, and Aleksei Aksimentiev. "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
  13. 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).
  14. 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)
  15. 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).
  16. Christopher Maffeo, and Aleksei Aksimentiev. "Structure, dynamics, and ion conductance of the phospholamban pentamer." Biophys J 96:4853-65 (2009).