Biomedical subjects

U Mohanty

Publications and source records attributed to U Mohanty.

15 recordsLinked to original sources

PubMed2006

Thermodynamic interpretation of the scaling of the dynamics of supercooled liquids.

The recently discovered scaling law for the relaxation times, tau(T,upsilon) = I(Tupsilon(gamma)), where T is temperature and upsilon the specific volume, is derived by a revision of the entropy model of the glass transition dynamics originally proposed by Avramov [J. Non-Cryst. Solids 262, 258 (2000)]. In this modification the entropy is calculated by an alternative route. The resulting expression for the variation of the relaxation time with T and upsilon is shown to accurately fit experimental data for several glass-forming liquids and polymers over an extended range encompassing the dynamic crossover. From this analysis, which is valid for any model in which the relaxation time is a function of the entropy, we find that the scaling exponent gamma can be identified with the Gruneisen constant.

Journal Article↗

PubMed2001

On the nature of a glassy state of matter in a hydrated protein: Relation to protein function.

Diverse biochemical and biophysical experiments indicate that all proteins, regardless of size or origin, undergo a dynamic transition near 200 K. The cause of this shift in dynamic behavior, termed a "glass transition," and its relation to protein function are important open questions. One explanation postulated for the transition is solidification of correlated motions in proteins below the transition. We verified this conjecture by showing that crambin's radius of gyration (Rg) remains constant below approximately 180 K. We show that both atom position and dynamics of protein and solvent are physically coupled, leading to a novel cooperative state. This glassy state is identified by negative slopes of the Debye-Waller (B) factor vs. temperature. It is composed of multisubstate side chains and solvent. Based on generalization of Adam-Gibbs' notion of a cooperatively rearranging region and decrease of the total entropy with temperature, we calculate the slope of the Debye-Waller factor. The results are in accord with experiment.

Crystallography, X-Ray↗

PubMed2001

Relationship between dynamical and equilibrium characteristics of glass-forming polymeric liquids.

A connection between measurable equilibrium thermodynamic quantities and a nonequilibrium property of supercooled polymeric liquids, namely, the fragility index, is proposed within the framework of a synthesis of generalized configurational entropy models. The theoretical predictions are compared with experimental data on five glass-forming polymers.

Journal Article↗

PubMed2001

On the characteristics of migration of oligomeric DNA in polyacrylamide gels and in free solution.

We review a model for the free-solution electrophoretic mobility of oligomeric double-stranded (ds) DNA. We have found that the free-solution mobility of ds DNA increases as the molecular weight of the fragment increases, up to a few hundred base pairs. This insight is combined with recent advances in the nature of counterion condensation theory of very short DNA fragments to describe quantitatively the electrophoretic mobility of oligomeric single-stranded DNA in polyacrylamide gels. The model predicts, in agreement with recent experiments, that significant anomalous migration exists with short DNA sequences, the onset of which is dependent on the size of polyacrylamide gel pores. For terminal phosphate-labeled DNA fragments, the free-solution mobility is no longer proportional to the ratio of the total effective charge and the friction coefficient. These changes in properties affect the characteristics of migration of end-labeled DNA fragments in polyacrylamide gels.

DNA↗

PubMed1996

Dressed polyions, counterion condensation, and adsorption excess in polyelectrolyte solutions.

The phenomenon of Manning-Oosawa counterion condensation is given an explicit statistical mechanical and qualitative basis via a dressed polyelectrolyte formalism in connection with the topology of the electrostatic free-energy surface and is derived explicitly in terms of the adsorption excess of ions about the polyion via the nonlinear Poisson-Boltzmann equation. The approach is closely analogous to the theory of ion binding in micelles. Our results not only elucidate a Poisson-Boltzmann analysis, which shows that a fraction of the counterions lie within a finite volume around the polyion even if the volume of the system tends towards infinity, but also provide a direct link between Manning's theta-the number of condensed counterions for each polyion site-and a statistical thermodynamic quantity, namely, the adsorption excess per monomer.

Adsorption↗

PubMed1996

Polarization of counterions in polyelectrolytes.

A theory of the polarization of counterions bound to a polyion, such as a DNA, in low and high electric field strengths is developed using statistical mechanics of inhomogeneous systems. For low fields, one finds that the polarizability p is (Zq)2rho0betaL3/(12[l + Lrho0sigma(L, b, xi, Z, I, rho0)]), where sigma = integral1 0(lambda' - lambda0) ¿dc(lambda - lambda')/dlambda¿lambda = lambda0 dlambda']), Z and L are the valence and the length of the polyion, respectively, q is the proton charge, beta = 1/kBT, T is the temperature, kB is the Boltzmann constant, I is the ionic strength, lambda = x/L and lambda0 = x0/L are scaled distances, x0 is a reference point such that the inhomogeneous counterion density at x0 is equal to rho0--the uniform density in the absence of an electric field E--and c(x) is the direct correlation function of the homogeneous counterion-polyion phase, which includes attractive and repulsive interactions. If Lsigma(L, ...) is much less than one, then the polarizability is proportional to L3. If the term Lsigma(L, ...) is much larger than one, the polarizability scales as L2. The induced dipole moment saturates and its value is the same as that of Mandel-Manning theories. The onset of the saturation, however, depends critically on the direct correlation function and hence polyelectrolyte effects. In the formalism, the polarization of the counterions is the equilibrium response to an electric field provided E is less than Esaturated. A dynamical scheme that incorporates the fact that in high fields the bound counterions conduct is discussed.

Chemical Phenomena↗

PubMed1988