Understanding Single Molecule Experiments

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

• PD Dr.Christian Holm, Project supervisor
• Dr. Marcello Sega, Post-Doctoral Fellow
• Mehmet Suzen, PhD Student

Collobarations

• Prof. Dr. Marcia Barbosa, Porto Alegre, Brazil

Former Coworkers

• Dr.Sandeep Tyagi, Former Post-Doctoral Fellow

Publications

Work in progress

Links

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