Understanding Single Molecule Experiments

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Single-molecule experiments (SMEs) have provided tools in high enough sensitivity and precision to manipulate, visualise and measure microscopic forces on individual molecules one at a time. Among many other SME techniques optical tweezers [1] particularly suited to study polymer channel (a nano scale pores, biological or syntetic) interactions and chain entropy.

The main theme 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 gene 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 [2]. SMEs are quite convinient experimental tool to reveal Physics behind these applications.

Statistical Mechanics point of view, particularly in Biological Physics, understanding thermodynamics and kinetics of biomolecules far from equilibrium has 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 focused on

  • Algorithm to handle arbitrary dielectric boundaries
  • Coarse grained model for DNA chain
  • DNA chain and the channel interactions under various field conditions

Current Coworkers


Former Coworkers


Work in progress


Bead-Spring Polymer model contour lenght of 40, FENE bonds with excluded volume.