Aleksei Aksimentiev

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Aleksei Aksimentiev

Primary Research Area

  • Biological Physics
263 Loomis Laboratory

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Biography

Professor Aksimentiev received his Ph.D in chemistry cum laude from the Institute of Physical Chemistry, Warsaw, Poland, in 1999, after completing a master's degree in particle physics at the Ivan Franko Lviv State University in his native Ukraine in 1996.

He received postdoctoral training at the Materials Science Laboratory R&D Center of Mitsui Chemicals, Tokyo, Japan, from 1999 to 2001, when he joined the Theoretical and Computational Biophysics Group at the University of Illinois as a postdoctoral research associate. He accepted the position of assistant professor of physics at Illinois in 2005

Undergraduate Research Opportunities

Several research positions are available immediately. Please e-mail to setup a meeting and discuss the possibilities.

Research Statement


Imagine assembling a few thousand marbles into a machine capable of transforming the energy of an electric field into mechanical torque at nearly 100% efficiency and lasting ten million cycles. Although marbles are not atoms, Nature has done exactly that, assembling carbon, oxygen, nitrogen, and hydrogen atoms into remarkable nanomachines. And while Nature took billions of years to transform primordial dirt into the molecular motors that power living cells, the atoms comprising present-day biomachines are no different from those found in common inorganic compounds, and they obey the same laws of physics that enable the machines's amazing properties. Understanding how the remarkable functionality of biological nanomachines comes about from the spatial arrangement of their atoms and using this knowledge to design synthetic systems that exceed in the performance of their biological counterparts is the focus of this group's research program.

Nanopore systems for single molecule detection and manipulation
Over the past years, nanopores in thin biological and synthetic membranes have emerged as a versatile new research tool for detection and manipulation of single biomolecules. In a typical setup, electric field is used to drive biomolecules through nanopores, producing electrical signals that can identify the chemical makeup of the transported molecules. Recent experimental studies have shown great potential of nanopore systems for high-throughput real-time sequencing of DNA molecules. Extensive experimental efforts are directed toward improving sequencing fidelity, which involves design and manufacturing of synthetic nanopore sensors based on graphene membranes. Computer modeling, in particular all-atom MD simulations, have become a trusted partner in the development of nanoscale biomedical sensors, allowing one to visualize and quantify the nanoscale details of interactions between biomolecules and synthetic materials. In the development of nanopore sequencing technology, this group permitted the visualization of the process of nanopore translocation and the prediction of signals that are to be used for sequencing DNA, such as ion currents. Examples of recent research projects in this area include simulations of DNA transport through graphene nanopores, engineering a biological nanopore MspA for real-time and ultra-low cost DNA sequencing and development of physical methods to slow DNA transport through solid-state nanopores.

Molecular mechanics of DNA processing machinery
DNA replication, packaging, and repair, which are among the most important cellular processes, are all facilitated and heavily regulated through DNA-protein interactions. Abnormal operations of protein motors that process information encoded in DNA are known causes of genetic and multifactorial deceases, cancer and are associated with aging. In collaborations with single-molecule experimentalists, this group develops computational models of exemplary protein-DNA systems to elucidate the molecular mechanisms of DNA processing machinery. The current research projects center around DNA replication. The demands of rapid but accurate duplication of a cell's genome require the cooperative operation of many proteins, which together form the replisome. Using available structural data, this group is building a computational model of the replisome that incorporates all essential components. Complementing DNA replication, DNA repair is crucial to survival of a biological organism. One of the most catastrophic forms of DNA damage is double-stranded DNA breakage, which is often repaired using, as a template, another DNA molecule of a similar nucleotide sequence. One of the projects in this area aims to determine the mechanism a cell uses to find such a similar-sequence template fragment on a very long DNA molecule. In eukaryotes, processing of information encoded in DNA is additionally complicated as DNA is wrapped around proteins into hierarchical structures. The projects in this area focus on mechanisms of remodeling DNA-protein structures and epigenetic regulation of such remodeling processes.

The physics of DNA assemblies
Although a biological cell utilizes a myriad of proteins to copy, express, regulate, and repair the genetic information stored in DNA, the unique physical properties of a DNA molecule underlies its biological functions. Indeed, the properties of a DNA molecule can astonish experts across disciplines. A physicist finds it surprising that DNA, which is a highly negatively charged polymer, can form a well-ordered condensate through apparent inter-DNA attractions. A biologist is astonished by the fact that the cells utilize DNA condensation to store and protect their genetic information. Binding of multivalent cations, pressure of a packing motor or spooling action of histone proteins force DNA to form compact biological structures where steric, electrostatic and structural forces give rise to unique physical phenomena. Of course, the most famous form of DNA self-assembly is hybridization, where a pair of single DNA strands carrying DNA nucleobases of complementary sequences forms a DNA duplex. Add to this a bit of computing and lots of human ingenuity and complex three-dimensional structures known as DNA origami will emerge from a disordered solution of DNA fragments. This research thrust develops precise atomic-scale and coarse-grained models of biological and synthetic DNA systems and uses such models to characterize a variety of processes in such systems. The ongoing research projects focus on the physics of DNA packaging in bacteriophage capsids, micromechanics of DNA origami and kinetics of DNA self-assembly.

Synthetic molecular systems
Miniature machines captivate human imagination. From a flight of a bee to a beating of a flagellum, the ability of tiny creatures to perform seemingly impossible tasks inspire us with awe. While scaling up in size human technology is relatively straightforward, scaling down the systems and mechanisms without loosing functionality, ultimately to the molecular scale, remains a major challenge. The dominance of stochastic forces over gravity and inertia, surface effects over body forces, and granularity of conventional materials render application of macroscopic engineering principles at the nanoscale obsolete. While human efforts to engineer and build nanomachines have so far produced rather modest results, biology provides outstanding examples of what can be accomplished. This research thrust focuses on the development of synthetic analogs to landmark biomolecular machines such as autonomous nanoscale walkers, selective nanochannels gated by external stimuli, and membrane-bound energy conversion systems.

Graduate Research Opportunities

Several research positions are available. Please e-mail to setup a meeting and discuss the possibilities.

Post-Doctoral Research Opportunities

We are always looking for qualified and motivated individuals. Please e-mail your CV along with a short description of your current and future research interests.

Honors

  • Dean's Award for Excellence in Research (2015)
  • Blue Waters Professorship (2014)
  • NSF CAREER Award (2010)
  • Beckman Fellow, Center for Advanced Studies (2009-2010)
  • IBM Faculty Fellow Award (2008)

Semesters Ranked Excellent Teacher by Students

SemesterCourseOutstanding
Fall 2017PHYS 211

Selected Articles in Journals

Related news

  • Research

The most powerful supercomputer in the world for academic research has established its mission for the coming year.The Texas Advanced Computing Center (TACC) announced that the National Science Foundation has approved allocations of supercomputing time on Frontera to 49 science projects for 2020-2021. Time on Frontera is awarded based on a project’s need for very large scale computing to make science and engineering discoveries, and the ability to efficiently use a supercomputer on the scale of Frontera.

“Our generous allocation of compute time on Frontera makes it possible to perform uniquely large-scale, data-driven simulations of key brain cell networks involved in memory with unprecedented biological realism,” Soltesz said.Another awardee, Caroline Riedl, research assistant professor of Physics at the University of Illinois, is part of a large international collaboration analyzing particle collision data from the Super Proton Synchrotron at CERN. Riedl was awarded 1.5 million hours to unravel the mass of hadrons and the quark structure of protons. Her work will analyze past particle physics experiments from the COMPASS experiment and explore new detectors for quantum chromodynamics research (COMPASS++/AMBER).”We were very excited to learn that our request for an LRAC allocation on TACC’s Frontera was approved,” Riedl said.

  • Research
  • Biological Physics
  • Theoretical Biological Physics
  • Biophysics

Scientists have simulated every atom of a light-harvesting structure in a photosynthetic bacterium that generates energy for the organism. The simulated organelle behaves just like its counterpart in nature, the researchers report. The work is a major step toward understanding how some biological structures convert sunlight into chemical energy, a biological innovation that is essential to life.

The researchers report their findings in the journal Cell.

The team originally was led by University of Illinois Physics Professor Klaus Schulten and the work continued after Schulten’s death in 2016. The study fulfills, in part, Schulten’s decades-long dream of discovering the mechanisms by which atomic-level interactions build and animate living systems.

  • Research
  • Theoretical Biological Physics
  • Biological Physics
  • Biophysics

While watching the production of porous membranes used for DNA sorting and sequencing, University of Illinois researchers wondered how tiny steplike defects formed during fabrication could be used to improve molecule transport. They found that the defects – formed by overlapping layers of membrane – make a big difference in how molecules move along a membrane surface. Instead of trying to fix these flaws, the team set out to use them to help direct molecules into the membrane pores.

Their findings are published in the journal Nature Nanotechnology.

Nanopore membranes have generated interest in biomedical research because they help researchers investigate individual molecules – atom by atom – by pulling them through pores for physical and chemical characterization. This technology could ultimately lead to devices that can quickly sequence DNA, RNA or proteins for personalized medicine.