Biomedical subjects

Sandip Ghosal

Publications and source records attributed to Sandip Ghosal.

8 recordsLinked to original sources

PubMed2006

Electrophoresis of a polyelectrolyte through a nanopore.

A hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through a nanopore is presented. It is assumed that the speed is determined by a balance of electrical and viscous forces arising from within the pore and that classical continuum electrostatics and hydrodynamics may be considered applicable. An explicit formula for the translocation speed as a function of the pore geometry and other physical parameters is obtained and is shown to be consistent with experimental measurements on DNA translocation through nanopores in silicon membranes. Experiments also show a weak dependence of the translocation speed on polymer length that is not accounted for by the present model. It is hypothesized that this is due to secondary effects that are neglected here.

Computer Simulation↗

PubMed2006

Electroosmotic flow in a rectangular channel with variable wall zeta-potential: comparison of numerical simulation with asymptotic theory.

Electroosmotic flow in a straight micro-channel of rectangular cross-section is computed numerically for several situations where the wall zeta-potential is not constant but has a specified spatial variation. The results of the computation are compared with an earlier published asymptotic theory based on the lubrication approximation: the assumption that any axial variations take place on a long length scale compared to a characteristic channel width. The computational results are found to be in excellent agreement with the theory even when the scale of axial variations is comparable to the channel width. In the opposite limit when the wavelength of fluctuations is much shorter than the channel width, the lubrication theory fails to describe the solution either qualitatively or quantitatively. In this short wave limit the solution is well described by Ajdari's theory for electroosmotic flow between infinite parallel plates (Ajdari, A., Phys. Rev. E 1996, 53, 4996-5005.) The infinitely thin electric double layer limit is assumed in the theory as well as in the simulation.

Electrophoresis↗

PubMed2005

Mathematical model describing gradient focusing methods for trace analytes.

The problem of gradient focusing for concentrating trace analytes is considered. Variation of buffer viscosity, conductivity, and possibly also the zeta-potential results in a focusing point where the electrophoretic velocity is balanced by the electroosmotic flow (EOF) and where the sample concentrates. The axial inhomogeneity also results in an induced pressure gradient that alters the EOF profile and therefore causes Taylor dispersion. The coupled hydrodynamics and transport problem leading to the achievement of a steady state is studied in the context of the lubrication approximation: all variations in the axial direction take place over a length scale very much larger than the characteristic channel width. A single length scale sigma(m) and a single time scale tau is found to completely determine the dynamics of the evolution close to the focusing point. Using appropriate scaled variables, the time evolution of the concentration profile near equilibrium can be described by an inhomogeneous advection diffusion equation that is free of all parameters. Explicit formulas are deduced for the location of the peak centroid and its width as a function of time. A simple graphical method is proposed for optimizing the performance of the system when some tunable external parameters are available.

Journal Article↗

PubMed2004

Fluid mechanics of electroosmotic flow and its effect on band broadening in capillary electrophoresis.

Electroosmotic flow (EOF) usually accompanies electrophoretic migration of charged species in capillary electrophoresis unless special precautions are taken to suppress it. The presence of the EOF provides certain advantages in separations. It is an alternative to mechanical pumps, which are inefficient and difficult to build at small scales, for transporting reagents and analytes on microfluidic chips. The downside is that any imperfection that distorts the EOF profile reduces the separation efficiency. In this paper, the basic facts about EOF are reviewed from the perspective of fluid mechanics and its effect on separations in free solution capillary zone electrophoresis is discussed in the light of recent advances.

Electrophoresis, Capillary↗

PubMed2004

The force exerted by the membrane potential during protein import into the mitochondrial matrix.

The force exerted on a targeting sequence by the electrical potential across the inner mitochondrial membrane is calculated on the basis of continuum electrostatics. The force is found to vary from 3.0 pN to 2.2 pN (per unit elementary charge) as the radius of the inner membrane pore (assumed aqueous) is varied from 6.5 to 12 A, its measured range. In the present model, the decrease in force with increasing pore width arises from the shielding effect of water. Since the pore is not very much wider than the distance between water molecules, the full shielding effect of water may not be present; the extreme case of a purely membranous pore without water gives a force of 3.2 pN per unit charge, which should represent an upper limit. When applied to mitochondrial import experiments on the protein barnase, these results imply that forces between 11 +/- 2 pN and 13.5 +/- 2.5 pN catalyze the unfolding of barnase in those experiments. A comparison of these results with unfolding forces measured using atomic force microscopy is made.

Animals↗

PubMed2003

A simple model illustrating the role of turbulence on phytoplankton blooms.

The problem of the vertical distribution of phytoplankton is considered in the presence of gravitational settling, turbulent mixing, population growth due to cell division and a constant rate of loss due to predation and natural death. Nutrients are assumed to be plentiful so that the production rate depends only on the light available for photosynthesis. The non-linear saturation of plankton growth is modeled by allowing the attenuation rate of light to be a linear function of the plankton density. The turbulent diffusivity is assumed constant which corresponds to a mixed layer depth very much greater than the depth of light penetration (euphotic depth). It is shown that an exact analytical solution of this non-linear problem is possible for an idealized model in which the functional dependence of production on light intensity is assumed to be a step function. Non-zero solutions are shown to exist only if the parameters characterizing the system are above a certain critical curve in a two dimensional parameter space. Numerical simulations using functional forms of the production curve that resemble the measured photosynthetic response of plankton, show, that the qualitative behavior of the system is similar to that of the idealized model presented. Comparisons are made with other analytical approaches to the problem.

Computer Simulation↗

PubMed2002

Band broadening in a microcapillary with a stepwise change in the zeta-potential.

In capillary zone electrophoresis (CZE), adsorption of charged analytes to walls has been observed to cause significant band broadening. The effect is believed to be due to modification of the flow pattern and the consequent Taylor dispersion caused by the alteration of the wall charge by the adsorbed analytes. Experiments using neutral (nonadsorbing) analytes in capillaries in which the zeta-potential has been deliberately altered in a controlled way by chemically coating a segment of the capillary have been performed by Towns and Regnier (Anal. Chem. 1992, 64, 2473) in an effort to understand the mechanism of the band broadening. In this paper, the Taylor dispersion due to electroosmotic flow in such a partially coated capillary is calculated and compared to the experimental data. The theoretical predictions are found to be in excellent agreement with the data, thus supporting the hypothesis that the decreased resolution can be attributed to Taylor dispersion due to the induced pressure gradient brought about by the nonuniformity of the zeta-potential.

Journal Article↗

PubMed2002

Effect of analyte adsorption on the electroosmotic flow in microfluidic channels.

The predictability and constancy over time of the electroosmotic flow in microchannels is an important consideration in microfluidic devices. A common cause for alteration of the flow is the adsorption of analytes to channel walls, for example, during capillary electrophoresis of proteins. It is shown that certain experimental data, published by Towns and Regnier (Towns, J. K; Regnier, F. E. Anal. Chem. 1992, 64, 2473-2478.), on the anomalous elution times for proteins in capillary electrophoresis can be explained using a simple model for analyte adsorption that uses a result first reported by Anderson and Idol (Anderson, J. L.; Idol, W. K Chem. Eng. Commun. 1985, 38, 93-106.) on the electroosmotic flux in capillaries with axial variations in zeta-potential. It is suggested that it might be possible to use such a model to dynamically correct for altered elution times in capillary electrophoretic devices.

Adsorption↗