Understanding Single Molecule Experiments

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Single molecule experiments (SME) have provided tools in high enough sensitivity and precision to manipulate, visualize and measure microscopic forces on individual molecules. Among many other SME techniques, Optical tweezers are particularly well suited to study polymer channel interactions (a nano-scale pore, biological or synthetic) and chain entropy.

The main subject of this project is polymer translocation through a pore, such as the transport of biomolecules (i.e. DNA) through large membrane channels. It is central to many biological processes such as Transduction and RNA transport through nuclear core complexes, virus infection of cell. From nanotechnological point of view, it is central to drug delivery, ultra fast DNA sequencing and lab-on-a-chip applications. SMEs are quite convenient experimental tool to reveal the physics behind these applications.

DNA pore.png

From the point of view of statistical mechanics, particularly in biological physics, understanding the thermodynamics and kinetics of biomolecules far from equilibrium is of fundamental importance.

The primary aim of this work is to understand the detailed dynamics and physics of SMEs and relavant molecular transport phenomenon via coarse grained simulations under different settings. These simulations can be used as a testing ground of related theories and experimental findings.

Currently we focus on

  • Algorithms to handle arbitrary dielectric interfaces
  • Coarse-grained modeling of a DNA chain
  • DNA chain and the channel interactions under various field conditions

Current Coworkers


Former Coworkers


In preparation.


  • video_mpeg.pngpolymer_translocation.mpg (1.48 MB)Info circle.png: A movie of driving a polyelectrolyte through a neutral channel with ESPResSo. Bead-spring polymer model contour length of 40, FENE bonds, excluded volume.