Biomedical subjects

Dilip Gersappe

Publications and source records attributed to Dilip Gersappe.

5 recordsLinked to original sources

PubMed2006

Separation of DNA with different configurations on flat and nanopatterned surfaces.

We demonstrate that electrophoresis on a flat Si substrate is an effective method in separation of DNA with different configurations, e.g., linear, supercoiled, and relaxed or DNA of different length, e.g., supercoiled DNA ladder. The surface separation arises from the different number of contacts due to the conformational differences between adsorbed DNA chains. Imposing a Au nanopattern on the Si surface further improves the separation effect. The simulation of electric field on this patterned surface by the finite element method shows that Au nanodots act as local pinning points for DNA segments due to dielectrophoretic force. The results of molecular dynamics simulation showed that the conformational differences between adsorbed polymer chains were amplified on the patterned surface and enhanced separations were achieved, which are consistent with the experimental results.

Computer Simulation↗

PubMed2006

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis.

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.

Bacteriophage lambda↗

PubMed2005

Interfacial slip in sheared polymer blends.

We have developed a dynamic self-consistent field theory, without any adjustable parameters, for unentangled polymer blends under shear. Our model accounts for the interaction between polymers, and enables one to compute the evolution of the local rheology, microstructure, and the conformations of the polymer chains under shear self-consistently. We use this model to study the interfacial dynamics in sheared polymer blends and make a quantitative comparison between this model and molecular dynamics simulations. We find good agreement between the two methods.

Journal Article↗

PubMed2002

Molecular mechanisms of failure in polymer nanocomposites.

Molecular dynamics simulations of polymers reinforced with nanoscopic filler particles reveal the mechanisms by which nanofillers improve the toughness of the material. We find that the mobility of the nanofiller particle, rather than its surface area, controls its ability to dissipate energy. Our results show similarities between the toughening mechanisms observed in polymer nanocomposites and those postulated for biological structural materials such as spider silk and abalone adhesive.

Journal Article↗

PubMed2002

Modeling the dynamics of DNA electrophoresis on a flat surface.

We use molecular dynamics simulations to study the mechanism by which a flat, homogeneous surface can serve as an electrophoretic separation medium for DNA. We find that the mobility of DNA on the surface is a function of the conformation of the adsorbed DNA molecule, and that this mobility is controlled by the attraction between the DNA and the surface. Our results will provide guidelines for the fabrication of surfaces that can be used to separate DNA in a wide size range.

Adsorption↗