Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations

Recent time domain experiments have explored solvation dynamics of a probe located inside a DNA duplex, in an effort to gain information, e.g., on the dynamics of water molecules in the DNA major and minor grooves and their environment. Multiple time constants in the range of a few picoseconds to several nanoseconds were obtained. We have carried out 15 ns long atomistic molecular dynamics simulations to study the solvation dynamics of bases of a 38 base-pair long DNA duplex in an aqueous solution containing counterions. We have computed the energy-energy time correlation function (TCF) of the four individual bases (A, T, G, and C) to characterize the solvation dynamics. All the TCFs display highly nonexponential decay with time. When the trajectories are analyzed with 100 fs time resolution, the TCF of each base shows initial ultrafast decay (with tau1 approximately equal 60-80 fs) followed by two intermediate components (tau2 approximately equal 1 ps, tau3 approximately equal 20-30 ps), in near complete agreement with a recent time domain experiment on DNA solvation. Interestingly, the solvation dynamics of each of the four different nucleotide bases exhibit rather similar time scales. To explore the existence of slow relaxation at longer times reported recently in a series of experiments, we also analyzed the solvation TCFs calculated with longer time trajectories and with a larger time resolution of 1 ps. In this case, an additional slow component with a time constant of the order of 250 ps is observed. Through an analysis of partial solvation TCFs, we find that the slow decay originates mainly from the interaction of the nucleotides with the dipolar water molecules and the counterions. An interesting negative cross-correlation between water and counterions is observed, which makes an important contribution to relaxation at intermediate to longer times.     

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced "1/f noise characteristics" between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R(g)) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape.     

On Affine Equivariant Multivariate Quantiles

An extension of univariate quantiles in the multivariate set-up has been proposed and studied. The proposed approach is affine equivariant, and it is based on an adaptive transformation retransformation procedure. Behadur type linear representations of the proposed quantiles are established and consequently asymptotic distributions are also derived. As applications of these multivariate quantiles, we develop some affine equivariant quantile contour plots which can be used to study the geometry of the data cloud as well as the underlying probability distribution and to detect outliers. These quantiles can also be used to construct affine invariant versions of multivariate Q-Q plots which are useful in checking how well a given multivariate probability distribution fits the data and for comparing the distributions of two data sets. We illustrate these applications with some simulated and real data sets. We also indicate a way of extending the notion of univariate L-estimates and trimmed means in the multivariate set-up using these affine equivariant quantiles.     

Non-bioengineered silk fibroin protein 3D scaffolds for potential biotechnological and tissue engineering applications

This paper describes a new source for fabricating high-strength, non-bioengineered silk gland fibroin 3D scaffolds from Indian tropical tasar silkworm, Antheraea mylitta using SDS for dissolution. The scaffolds were fabricated by freeze drying at different prefreezing temperatures for pore size and porosity optimization. Superior mechanical properties with compressive strength in the range of 972 kPa were observed. The matrices were degraded by proteases within 28 d of incubation. Biocompatibility was assessed by feline fibroblast culture in vitro and confocal microscopy further confirmed adherence, spreading, and proliferation of primary dermal fibroblasts. Results indicate nonmulberry 3D silk gland fibroin protein as an inexpensive, high-strength, slow biodegradable, biocompatible, and alternative natural biomaterial. [Figure: see text].     

Phase diagram for a t-J bilayer: role of interlayer couplings

The phase diagram for a t-J bilayer as a function of interplanar hopping, t_⊥ and hole concentration, x is presented for a few different values of interplanar exchange, J_⊥ using variational Monte Carlo calculations. The phase diagram shows rich features, such as a coexistence of antiferromagnetism and superconductivity at underdoping, planar (d-wave) and interplanar (d_z-wave) superconducting correlations for small and large J_⊥, respectively at optimal and overdoping. Another unusual feature appears in the form of a dome shaped structure in the phase diagram where the superconducting correlations are initially assisted as interplanar hopping is enhanced for small t_⊥, while larger t_⊥ is found to be detrimental to superconductivity.     

Energy landscape, antiplasticization, and polydispersity induced crossover of heterogeneity in supercooled polydisperse liquids

Polydispersity is found to have a significant effect on the potential energy landscape; the average inherent structure energy decreases with polydispersity. Increasing polydispersity at a fixed volume fraction decreases the glass transition temperature and the fragility of glass formation analogous to the antiplasticization seen in some polymeric melts. An interesting temperature dependent crossover of heterogeneity with polydispersity is observed at low temperature due to the faster buildup of dynamic heterogeneity at lower polydispersity.     

Anomalous viscoelasticity near the isotropic-nematic phase transition in liquid crystals

Recent optical Kerr effect experiments have shown that orientational relaxation of nematogens shows a pronounced slow down of the response function at intermediate times and also a power law decay near the isotropic-nematic (I-N) transition. In many aspects, this behavior appears to be rather similar to the ones observed in the supercooled liquid near-glass transition. We have performed molecular dynamics simulations of model nematogens (Gay-Berne with aspect ratio 3) to explore the viscoelasticity near the I-N transition and also investigated the correlation of viscoelasticity (if any) with orientational relaxation. It is found that although the viscosity indeed undergoes a somewhat sharper than normal change near the I-N transition, it is not characterized by any divergence-like behavior (like the ones observed in the supercooled liquid). The rotational friction, on the other hand, shows a much sharper rise as the I-N transition is approached. Interestingly, the probability distribution of the amplitude of the three components of the stress tensor shows anisotropy near the I-N transition-similar anisotropy has also been seen in the deeply supercooled liquid. Frequency dependence of viscosity shows several unusual behaviors: (a) There is a weak, power law dependence on frequency [eta(')(omega) approximately omega(-alpha)] at low frequencies and (b) there is a rapid increase in the sharp peak observed in eta(')(omega) in the intermediate frequency on approach to the I-N transition density. These features can be explained from the stress-stress time correlation function. The angular velocity correlation function also exhibits a power law decay in time. The reason for this is discussed.     

Theory of the time development of the stokes shift in polar media

We present a theory for the time evolution of the Stokes shift of a polar molecule in a polar solvent. The time-dependent solute—solvent interaction is calculated in a continuum model by replacing the surrounding solvent by a frequency-dependent dielectric continuum. An expression for the time dependence of the fluorescence maximum is derived. This expression can be considered a direct generalization of the well-known Ooshika—Lippert—Mataga equation to the time domain. We also present an approximate expression for the wavelength dependence of the dynamics of the Stokes shift, and find it to be consistent with recent experimental results. We have investigated the effect of polarizability of the solute molecule and found that for many molecules this effect is not negligible.     

Glassiness of thermotropic liquid crystals across the isotropic-nematic transition

The orientational dynamics of thermotropic liquid crystals across the isotropic-nematic phase transition have traditionally been investigated at long times or low frequencies using frequency domain measurements. The situation has now changed significantly with the recent report of a series of interesting transient optical Kerr effect (OKE) experiments that probed orientational relaxation of a number of calamitic liquid crystals (which consist of rod-like molecules) directly in the time domain, over a wide time window ranging from subpicoseconds to tens of microseconds. The most intriguing revelation is that the decay of the OKE signal at short to intermediate times (from a few tens of picoseconds to several hundred nanoseconds) follows multiple temporal power laws. Another remarkable feature that has emerged from these OKE measurements is the similarity in the orientational relaxation behavior between the isotropic phase of calamitic liquid crystals near the isotropic-nematic transition and supercooled molecular liquids, notwithstanding their largely different macroscopic states. In this article, we present an overview of the understanding that has emerged from recent computational and theoretical studies of calamitic liquid crystals across the isotropic-nematic transition. Topics discussed include (a) single-particle as well as collective orientational dynamics at a short-to-intermediate time window, (b) heterogeneous dynamics in orientational degrees of freedom diagnosed by a non-Gaussian parameter, (c) fragility, and (d) temperature-dependent exploration of underlying energy landscapes as calamitic liquid crystals settle into increasingly ordered mesophases upon cooling from the high-temperature isotropic phase. A comparison of our results with those of supercooled molecular liquids reveals an array of analogous features in these two important classes of soft matter systems. We further find that the onset of growth of the orientational order in the parent nematic phase induces translational order, resulting in smectic-like layers in the potential energy minima of calamitic systems if the parent nematic phase is sandwiched between the high-temperature isotropic phase and the low-temperature smectic phase. We discuss implications of this startling observation. We also discuss recent results on the orientational dynamics of discotic liquid crystals that are found to be rather similar to those of calamitic liquid crystals.     

Infrared spectroscopy of 2-pyrrolidinone and its hydrogen bonded dimers in a cold (8 K) inert gas matrix

Matrix isolation-FTIR spectra of 2-pyrrolidinone monomer and its two hydrogen bonded dimers are recorded in N₂ matrix at 8 K temperature and in CCl₄ solution at variable temperature within the range 30-45 °C. The transient singly hydrogen bonded dimer (SHBD) is identified in the cold N₂ by comparing the matrix spectrum with that in CCl₄ solution. The spectral shifts of both amide-I and amide-A bands indicate cooperative strengthening of hydrogen bonds in doubly hydrogen bonded dimer (DHBD). Density functional theory at B3PW91/6-311++G** level of calculation is found to be in good accord to the observed spectral features.