Aleksei Aksimentiev

(217) 333 - 6495
263 LLP

Loomis Laboratory of Physics
1110 West Green Street
Urbana, IL

Dr. Aksimentiev has a background in soft matter physics and now deploys computational methods to investigate physical phenomena at the interface of solid-state nanodevices and biological macromolecules. In his graduate work, he applied methods of field theory to predict phase diagrams of polymer mixtures, focusing on the conformational properties of single macromolecules. Subsequently, he discovered a universal scaling of the morphological measures quantitatively characterizing the topology of the three-dimensional patterns that emerge during the process of phase transition. In the focus of his current research program are systems comprising silicon-based synthetic membranes and biomolecules— DNA, proteins, and lipids—assembled into novel silicon circuits that can act as sensors, tweezers, and scaffolds for assembly of biosynthetic complexes. His theoretical work on DNA translocation through nanopores is recognized as the first computational study of that kind. He is an expert in modeling membrane proteins and molecular motors. His pioneering work on modeling ionic transport through membrane channels is a seminal demonstration of the utility and predictive power of the molecular dynamics method, which now has many followers. Within the NIH Center for Macromolecular Modeling and Bioinformatics (UIUC), he directs development of the software solutions for computer modeling in biotechnology, which are used by many researchers worldwide. He disseminates his technical expertise through numerous self-contained study guides (tutorials) that many researchers starting out in the field of computational biological physics use as their textbooks. He integrates his research into classroom teaching through a unique interdisciplinary course Physics of Nanomachines and undergraduate Biophysical Phyiscs course. 

Select Publications

  1. 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)
  2. 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).
  3. 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)
  4. 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)
  5. Christopher Maffeo, Swati Bhattacharya, Jejoong Yoo, David B. Wells, and Aleksei Aksimentiev. "Modeling and simulation of ion channels." Chem Rev 112:6250-6284 (2012).
  6. David B. Wells, Maxim Belkin, Jeffrey Comer, and Aleksei Aksimentiev. "Assessing graphene nanopores for sequencing DNA." Nano Letters 12:4117-4123 (2012).
  7. 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)