Decoupling phenomena in supercooled liquids: Signatures in the energy landscape

A significant deviation from the Debye model of rotational diffusion in the dynamics of orientational degrees of freedom in an equimolar mixture of ellipsoids of revolution and spheres is found to begin precisely at a temperature at which the average inherent structure energy of the system starts falling with drop in temperature. We argue that this onset temperature corresponds to the emergence of the alpha-process as a distinct mode of orientational relaxation. Equally important, we find that the coupling between the rotational and translational diffusion breaks down at a still lower temperature where a sharp change occurs in the temperature dependence of the average inherent structure energy.Comment: Submitted for publicatio

Kinetic proofreading at single molecular level: Aminoacylation of tRNA^{Ile} and the role of water as an editor

Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA^{Ile} which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case), in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i) the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8 \times 10^2).(4.33 \times 10^2) = 7.8 \times 10^4, (ii) the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA^{Ile}. The present study shows a non-michaelis type dependence of rate of reaction on tRNA^{Ile} concentration in case of valine. The editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA^{Ile} whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low

Anisotropic translational diffusion in the nematic phase: Dynamical signature of the coupling between orientational and translational order in the energy landscape

We find in a model system of thermotropic liquid crystals that the translational diffusion coefficient parallel to the director $D_{\parallel}$ first increases and then decreases as temperature drops through the nematic phase, and this reversal occurs where the smectic order parameter of the underlying inherent structures becomes significant for the first time. We argue, based on an energy landscape analysis, that the coupling between orientational and translational order can play a role in inducing the non-monotonic temperature behavior of $D_{\parallel}$. Such a view is likely to form the foundation of a theoretical framework to explain the anisotropic translation diffusion.Comment: 10 pages, 4 figure

Origin of the Sub-diffusive Behavior and Crossover From a Sub-diffusive to a Super-diffusive Dynamics Near a Biological Surface

Diffusion of a tagged particle near a constraining biological surface is examined numerically by modeling the surface-water interaction by an effective potential. The effective potential is assumed to be given by an asymmetric double well constrained by a repulsive surface towards $r=0$ and unbound at large distances. The time and space dependent probability distribution $P(r,t)$ of the underlying Smoluchowski equation is solved by using Crank-Nicholson method. The mean square displacement shows a transition from sub-diffusive (exponent $\alpha \sim$ 0.43) to a super-diffusive (exponent $\alpha \sim$ 1.75) behavior with time and ultimately to a diffusive dynamics. The decay of self intermediate scattering function ($F_{s}(k,t)$) is non-exponential in general and shows a power law behavior at the intermediate time. Such features have been observed in several recent computer simulation studies on dynamics of water in protein and micellar hydration shell. The present analysis provides a simple microscopic explanation for the transition from the sub-diffusivity and super-diffusivity. {\em The super-diffusive behavior is due to escape from the well near the surface and the sub-diffusive behavior is due to return of quasi-free molecules to form the bound state again, after the initial escape}Comment: 5 pages including 5 figures and 1 table. Submitted to PhysChemCom

A mode-coupling theory analysis of the rotation driven translational motion of aqueous polyatomic ions

In contrast to simple monatomic alkali and halide ions, complex polyatomic ions like nitrate, acetate, nitrite, chlorate etc. have not been studied in any great detail. Experiments have shown that diffusion of polyatomic ions exhibits many remarkable anomalies, notable among them is the fact that polyatomic ions with similar size show large difference in their diffusivity values. This fact has drawn relatively little interest in scientific discussions. We show here that a mode-coupling theory (MCT) can provide a physically meaningful interpretation of the anomalous diffusivity of polyatomic ions in water, by including the contribution of rotational jumps on translational friction. The two systems discussed here, namely aqueous nitrate ion and aqueous acetate ion, although have similar ionic radii exhibit largely different diffusivity values due to the differences in the rate of their rotational jump motions. We have further verified the mode-coupling theory formalism by comparing it with experimental and simulation results that agrees well with the theoretical prediction

Collective excitations in liquid DMSO : FIR spectrum, Low frequency vibrational density of states and ultrafast dipolar solvation dynamics

Valuable dynamical and structural information about neat liquid DMSO at ambient conditions can be obtained through study of low frequency vibrations in the far infrared (FIR), that is, terahertz regime. For DMSO, collective excitations as well as single molecule stretches and bends have been measured by different kinds of experiments such as OHD-RIKES and terahertz spectroscopy. In the present work we investigate the intermolecular vibrational spectrum of DMSO through three different computational techniques namely (i) the far-infra red spectrum obtained through Fourier transform of total dipole moment auto time correlation function, (ii) from Fourier transform of the translational and angular velocity time autocorrelation functions and a (iii) quenched normal mode analysis of the parent liquid at 300K. The three spectrum, although exhibit differences among each other, reveal similar features which are in good, semi-quantitative, agreement with experimental results. Study of participation ratio of the density of states obtained from normal mode analysis shows that the broad spectrum around 100 cm-1 involves collective oscillations of 300-400 molecules. Dipolar solvation dynamics exhibit ultrafast energy relaxation (dipolar solvation dynamics) with initial time correlation function around 140 fs which can be attributed to the coupling to the collective excitations. We compare properties of DMSO with those of water vis-a-vis the existence of the low frequency collective modes. Lastly, we find that the collective excitation spectrum exhibits strong temperature dependence.Comment: 24 pages,8 figure