Difference between revisions of "Understanding Single Molecule Experiments"

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Single-molecule experiments [http://en.wikipedia.org/wiki/Single-molecule_experiment (SMEs)] have provided  
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<onlyinclude>[[w:Single-molecule experiment|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, [[w:Optical_tweezers|Optical tweezers]] are particularly well suited to study polymer channel interactions (a nano-scale pore, biological or synthetic) and chain entropy.</onlyinclude>
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 [http://en.wikipedia.org/wiki/Optical_tweezers]  
 
particularly suited to study polymer channel (a nano scale pores, biological or syntetic) interactions and chain entropy.
 
  
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[[Image::DNA_pore.png| ]]
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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 [[w:Transduction (genetics)|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 [[w:lab-on-a-chip|lab-on-a-chip]] applications. SMEs are quite convenient experimental tool to reveal the physics behind these applications.
  
The main theme of this project is '''polymer translocation through a pore''', such as the transport of biomolecules (i.e. DNA)
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[[Image:DNA_pore.png]]
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 [http://en.wikipedia.org/wiki/Lab-on-a-chip]. SMEs are quite convinient experimental tool to reveal Physics behind
 
these applications.
 
  
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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.
  
Statistical Mechanics point of view, particularly in Biological Physics, understanding
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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.
thermodynamics and kinetics of biomolecules far from equilibrium has fundamental importance.
 
  
 
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Currently we focus on  
The primary aim of this work is to understand the detailed dynamics and physics of SMEs
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* Algorithms to handle arbitrary dielectric interfaces
and relavant molecular transport phenomenon via coarse grained simulations under different settings. These
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* Coarse-grained modeling of a DNA chain
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
 
* DNA chain and the channel interactions under various field conditions
 
  
 
== Current Coworkers ==
 
== Current Coworkers ==
  
* PD Dr.[[Christian Holm]], Project supervisor
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* PD Dr. [[Christian Holm]], Project supervisor
 
* Dr. [[Marcello Sega]], Post-Doctoral Fellow
 
* Dr. [[Marcello Sega]], Post-Doctoral Fellow
 
* [[Mehmet Suzen]], PhD Student
 
* [[Mehmet Suzen]], PhD Student
  
== Collobarations ==
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== Collaborations ==
 
* Prof. Dr. [http://www.if.ufrgs.br/~barbosa/ Marcia Barbosa], Porto Alegre, Brazil
 
* Prof. Dr. [http://www.if.ufrgs.br/~barbosa/ Marcia Barbosa], Porto Alegre, Brazil
  
 
== Former Coworkers==
 
== Former Coworkers==
* Dr.[[Sandeep Tyagi]], Former Post-Doctoral Fellow
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* Dr. [[Sandeep Tyagi]], Former Post-Doctoral Fellow
  
 
== Publications ==
 
== Publications ==
Work in progress
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 +
In preparation.
  
 
== Links ==
 
== Links ==
*   {{Download|Polymer_translocation_simbio.mpg}} A Demonstration of Driving a polyelectrolyte through neutral channel with Espresso.
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*{{Download|Polymer_translocation_simbio.mpg|polymer_translocation.mpg|video_mpeg}}: A movie of driving a polyelectrolyte through a neutral channel with {{ES}}. Bead-spring polymer model contour length of 40, FENE bonds, excluded volume.
Bead-Spring Polymer model contour lenght of 40, FENE bonds with excluded volume.
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[[Category:Research]]

Latest revision as of 13:42, 26 September 2011


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

Collaborations

Former Coworkers

Publications

In preparation.

Links

  • 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.