Difference between revisions of "Understanding Single Molecule Experiments"
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| − | Single-molecule experiments | + | <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, | ||
| − | individual molecules | ||
| − | particularly suited to study polymer channel (a nano scale | ||
| + | [[Image::DNA_pore.png| ]] | ||
| + | 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. | ||
| − | + | [[Image: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 | |
| − | |||
| − | |||
| − | Currently we | ||
| − | |||
| − | * | ||
| − | * Coarse grained | ||
* 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 | + | * 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 | ||
| − | == | + | == 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 | + | * Dr. [[Sandeep Tyagi]], Former Post-Doctoral Fellow |
== Publications == | == Publications == | ||
| − | + | ||
| + | In preparation. | ||
== Links == | == Links == | ||
| − | *{{Download|Polymer_translocation_simbio.mpg}} A movie of driving a polyelectrolyte through a neutral channel with {{ES}}. Bead-spring polymer model contour length of 40, FENE bonds, excluded volume. | + | *{{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. |
| + | |||
| + | [[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.
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
- PD Dr. Christian Holm, Project supervisor
- Dr. Marcello Sega, Post-Doctoral Fellow
- Mehmet Suzen, PhD Student
Collaborations
- Prof. Dr. Marcia Barbosa, Porto Alegre, Brazil
Former Coworkers
- Dr. Sandeep Tyagi, Former Post-Doctoral Fellow
Publications
In preparation.
Links
polymer_translocation.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.